Citrus Sinensis ID: 047923

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190
Protein Sequence
SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHcccEEEEEEcccccccHHHHHHHHHHHHcHHccccEEEEEEccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccEEEEcccccccccccHHHHHHHHHccEEEEEEEccccccHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHEEEEcc
Coil and Loop (DISEMBL)
SRQNIQTFIDdqlnrgdeISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEyahivipgfyrgdpsevrsqtgsfgnsFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCdkenqlvgRESRVEIIESLLAAESKDVYILGIWGvgsigkttiaran
Flexible Loop (DISEMBL)
srqniqtfiddqlnrgdEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLlcdkenqlvgreSRVEIIESLLaaeskdvyilgiwgvgsigkttiaran
Low Complexity Region (SEG)
SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN
Disordered region (IsUnstruct)
*****************EISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYR***************************************EAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTT*****
Disordered Region (DISOPRED)
SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEER*****EKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA*
Disordered Region (DISEMBL)
SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLE***********SWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN
Disordered Region (DISPRO)
***NIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	190	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.978	0.162	0.411	1e-33
O82500	1095	Putative disease resistan	yes	no	0.963	0.167	0.416	4e-31
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.936	0.136	0.396	1e-26
Q9C5Q9	411	Protein PHLOEM PROTEIN 2-	no	no	0.726	0.335	0.361	3e-17
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.689	0.069	0.367	6e-12
Q9FHE9	354	Protein PHLOEM PROTEIN 2-	no	no	0.726	0.389	0.296	2e-11
Q9SYC9	571	Vesicle-associated protei	no	no	0.552	0.183	0.330	1e-10
Q9FHE8	392	Protein PHLOEM PROTEIN 2-	no	no	0.821	0.397	0.294	3e-10
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.710	0.083	0.291	4e-08
Q9FL92	1372	Probable WRKY transcripti	no	no	0.768	0.106	0.263	1e-06

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

 Score =  142 bits (359), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 79/192 (41%), Positives = 118/192 (61%), Gaps = 6/192 (3%)

Query: 3   QNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           + I+TF DD+ L  G  I   +  AIE    ++++FSE Y  SRWCL+ELVKI++ K  +
Sbjct: 38  KGIKTFQDDKRLEYGATIPGELCKAIEESQFAIVVFSENYATSRWCLNELVKIMECKTRF 97

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFI-- 119
              VIP FY  DPS VR+Q  SF  +F + E ++ ++ E +Q WR A  EAA+       
Sbjct: 98  KQTVIPIFYDVDPSHVRNQKESFAKAFEEHETKYKDDVEGIQRWRIALNEAANLKGSCDN 157

Query: 120 --LPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
               +++ I+++V+QI  +L ++ L   +N +VG ++ +E IESLL      V I+GIWG
Sbjct: 158 RDKTDADCIRQIVDQISSKLCKISLSYLQN-IVGIDTHLEKIESLLEIGINGVRIMGIWG 216

Query: 178 VGSIGKTTIARA 189
           +G +GKTTIARA
Sbjct: 217 MGGVGKTTIARA 228

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 =  134 bits (337), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 80/192 (41%), Positives = 110/192 (57%), Gaps = 9/192 (4%)

Query: 3   QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
           + I TF DD + R   I   +  AI    ISV++FSE Y  S WCL EL++I+K K+E  
Sbjct: 37  KGIVTFRDDHIKRSHTIGHELRAAIRESKISVVLFSENYASSSWCLDELIEIMKCKEEQG 96

Query: 63  HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP- 121
             V+P FY+ DPS++R QTG FG SF  LE    +  E+  +WR A  +AA+ +    P 
Sbjct: 97  LKVMPVFYKVDPSDIRKQTGKFGMSF--LETCCGKTEERQHNWRRALTDAANILG-DHPQ 153

Query: 122 ----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
               E+  I  +   +L++L      D  N LVG E+ +  +ESLL  ES+ V I+GIWG
Sbjct: 154 NWDNEAYKITTISKDVLEKLNATPSRDF-NDLVGMEAHIAKMESLLCLESQGVRIVGIWG 212

Query: 178 VGSIGKTTIARA 189
              +GKTTIARA
Sbjct: 213 PAGVGKTTIARA 224

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 =  119 bits (298), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 75/189 (39%), Positives = 106/189 (56%), Gaps = 11/189 (5%)

Query: 7   TFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVI 66
           TFIDD++ R   I   +  AI+   I+++IFS+ Y  S WCL+ELV+I K       +VI
Sbjct: 41  TFIDDEIERSRSIGPELLSAIKESRIAIVIFSKNYASSTWCLNELVEIHKCYTNLNQMVI 100

Query: 67  PGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSE-KLQSWRNATKEAASFMAFIL----P 121
           P F+  D SEV+ QTG FG  F   EE     SE + QSW+ A    A    + L     
Sbjct: 101 PIFFHVDASEVKKQTGEFGKVF---EETCKAKSEDEKQSWKQALAAVAVMAGYDLRKWPS 157

Query: 122 ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYIL-GIWGVGS 180
           E+ +I+E+   +L++   +   D    LVG E+ +E I+S+L  ESK+  I+ GIWG   
Sbjct: 158 EAAMIEELAEDVLRK--TMTPSDDFGDLVGIENHIEAIKSVLCLESKEARIMVGIWGQSG 215

Query: 181 IGKTTIARA 189
           IGK+TI RA
Sbjct: 216 IGKSTIGRA 224

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 = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/141 (36%), Positives = 77/141 (54%), Gaps = 3/141 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           ++ I  FID+Q  RG  +  S+   I    I+++IFSEGY  S WC+ ELVKI +Y  + 
Sbjct: 47  KEKINVFIDEQEERGKYLI-SLFDTIGESKIALVIFSEGYCESHWCMDELVKIKEYMDQN 105

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP 121
             I+IP FYR D   V+  TG FG++F  L +++    +KL  W  A        + ILP
Sbjct: 106 RLIIIPIFYRLDLDVVKDLTGKFGDNFWDLVDKYQPEPKKLHKWTEALFSVCELFSLILP 165

Query: 122 ESELI--KEVVNQILKRLAEV 140
           +   I  ++ V  I+K + +V
Sbjct: 166 KHSDISDRDFVKSIVKAVKKV 186

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.5 bits (171), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/147 (36%), Positives = 73/147 (49%), Gaps = 16/147 (10%)

Query: 44  SRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQ 103
           S +    L+ IL+++     +V P FYR  P +    + ++        ERF    E  +
Sbjct: 721 STYVPSNLLNILEHQHTEDRVVYPIFYRLSPYDFVCNSKNY--------ERFYLQDEP-K 771

Query: 104 SWRNATKEAASFMAFILP---ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIE 160
            W+ A KE      + L    ESELI E+V   LK L      DK N ++G + +VE I 
Sbjct: 772 KWQAALKEITQMPGYTLTDKSESELIDEIVRDALKVLCSA---DKVN-MIGMDMQVEEIL 827

Query: 161 SLLAAESKDVYILGIWGVGSIGKTTIA 187
           SLL  ES DV  +GIWG   IGKTTIA
Sbjct: 828 SLLCIESLDVRSIGIWGTVGIGKTTIA 854

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

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 71/145 (48%), Gaps = 7/145 (4%)

Query: 4   NIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAH 63
           NI  FID     G ++  ++   I+   ++V+IFS+ Y  S WCL EL +I     +   
Sbjct: 41  NINVFIDKDEVVGTDLV-NLFVRIQESRVAVVIFSKDYTSSEWCLDELAEIKDCINQGGL 99

Query: 64  IVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPES 123
             IP FY+  PS V    G FG++F  L+E++  + E+ Q W+ A +         L E 
Sbjct: 100 NAIPIFYKLAPSSVLELKGGFGDTFRVLKEKYKNDPERTQKWQEALESIPKLKGLRLAEK 159

Query: 124 ------ELIKEVVNQILKRLAEVLL 142
                 E + E++ +I K L ++ +
Sbjct: 160 SDRNEREFMNEMILEIQKALWQIAM 184

Arabidopsis thaliana (taxid: 3702)

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

 Score = 65.9 bits (159), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/106 (33%), Positives = 58/106 (54%), Gaps = 1/106 (0%)

Query: 3   QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
           + I  F D+   RG  ++  +   IE   ++V IFSE Y  S WCL ELVK+ +  ++  
Sbjct: 384 EKINVFTDEVELRGTNLN-YLFRRIEESRVAVAIFSERYTESCWCLDELVKMKEQMEQGK 442

Query: 63  HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNA 108
            +V+P FYR + +  +   G+FG++   LE  +    E++Q W+ A
Sbjct: 443 LVVVPVFYRLNATACKRFMGAFGDNLRNLEWEYRSEPERIQKWKEA 488

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 = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 48/163 (29%), Positives = 80/163 (49%), Gaps = 7/163 (4%)

Query: 4   NIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAH 63
           NI  FID+    G E++ ++   IE   ++++IFS  +  S  CL+EL KI + K +   
Sbjct: 42  NINVFIDENEFLGSEMA-NLLTRIEESELALVIFSVDFTRSHRCLNELAKIKERKDQGRL 100

Query: 64  IVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPES 123
           IVIP FY+  PS V+   G FG++F  LE          Q W+ A +     +   L E 
Sbjct: 101 IVIPIFYKVKPSAVKFLEGKFGDNFRALERNNRHMLPITQKWKEALESIPGSIGMPLAEQ 160

Query: 124 --ELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLA 164
                 + +N ++ ++ ++L    EN  V R + +E    L++
Sbjct: 161 SERTDNDFINSMVIKIQQLL----ENMAVRRNNEIEAQRKLVS 199

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.8 bits (138), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/158 (29%), Positives = 80/158 (50%), Gaps = 23/158 (14%)

Query: 32  ISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKL 91
           + V++ S+   F      + +K+++  +   H+V+P FY  D     S T  +G + S L
Sbjct: 74  VLVVVISDEVEFYDPWFPKFLKVIQGWQNNGHVVVPVFYGVD-----SLTRVYGWANSWL 128

Query: 92  EERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVG 151
           E      +EKL S      ++      +L +SEL++E+V  +  +L          + VG
Sbjct: 129 E------AEKLTS-----HQSKILSNNVLTDSELVEEIVRDVYGKLYPA-------ERVG 170

Query: 152 RESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA 189
             +R+  IE LL  + +D+  +GIWG+  IGKTT+A+A
Sbjct: 171 IYARLLEIEKLLYKQHRDIRSIGIWGMPGIGKTTLAKA 208

Arabidopsis thaliana (taxid: 3702)

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

 Score = 53.1 bits (126), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/182 (26%), Positives = 84/182 (46%), Gaps = 36/182 (19%)

Query: 8   FIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIP 67
           FID      D +S      +E   +SV+I       S   L +LVK+L  +K    +V+P
Sbjct: 37  FIDSD----DSLSNESQSMVERARVSVMILPGNRTVS---LDKLVKVLDCQKNKDQVVVP 89

Query: 68  GFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILPESELIK 127
             Y      VRS    + ++          +S+   S  ++ KE +        +S+L+K
Sbjct: 90  VLY-----GVRSSETEWLSAL---------DSKGFSSVHHSRKECS--------DSQLVK 127

Query: 128 EVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIA 187
           E V  + ++L  +       + +G  S++  IE ++  +  D+  +GIWG+  IGKTT+A
Sbjct: 128 ETVRDVYEKLFYM-------ERIGIYSKLLEIEKMINKQPLDIRCVGIWGMPGIGKTTLA 180

Query: 188 RA 189
           +A
Sbjct: 181 KA 182

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)

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	190
224127754	1125	tir-nbs-lrr resistance protein [Populus	0.989	0.167	0.473	1e-44
255555357	1094	leucine-rich repeat-containing protein,	0.984	0.170	0.507	2e-44
255561496	876	TMV resistance protein N, putative [Rici	0.989	0.214	0.502	3e-42
255555349	1109	leucine-rich repeat containing protein,	0.989	0.169	0.468	6e-41
224109502	1060	tir-nbs-lrr resistance protein [Populus	0.978	0.175	0.473	1e-40
255564976	944	TMV resistance protein N, putative [Rici	0.978	0.197	0.478	6e-40
224133498	1187	tir-nbs-lrr resistance protein [Populus	0.984	0.157	0.489	1e-39
317106744	947	JHS03A10.2 [Jatropha curcas]	0.984	0.197	0.479	2e-39
224127917	1470	tir-nbs-lrr resistance protein [Populus	0.978	0.126	0.465	3e-39
224145016	1254	tir-nbs-lrr resistance protein [Populus	0.989	0.149	0.487	1e-38

>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 =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 91/192 (47%), Positives = 131/192 (68%), Gaps = 4/192 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           R+ I TFID +LNRG+EIS S+  AIE   +SV++FS+ Y  S+WCL EL KIL+ KK  
Sbjct: 40  RKQISTFIDYKLNRGEEISPSLLKAIEDSKLSVVVFSDNYASSKWCLEELAKILECKKVK 99

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF--- 118
             +VIP FYR DPS VR+QTGSF ++F++ ++   E  EK+ +WR A +EAA+   +   
Sbjct: 100 GQMVIPVFYRVDPSHVRNQTGSFADAFARHDQLLKEKMEKVLNWRAAMREAANLSGWDSH 159

Query: 119 -ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
            I  ESE + ++V  IL +L +  +      L+G ++R++ +E+LL  ES+DV I+GIWG
Sbjct: 160 NIKSESEFVDDIVRDILNKLHQTSMSTHHTSLIGIDARIKKVETLLKMESQDVRIVGIWG 219

Query: 178 VGSIGKTTIARA 189
           +G IGKTTIA+A
Sbjct: 220 MGGIGKTTIAKA 231

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 =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 97/191 (50%), Positives = 129/191 (67%), Gaps = 4/191 (2%)

Query: 3   QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
           + I TFIDD L RG+EIS S+  AIE   ISV+I S+ YP S+WCL ELVKIL+  K   
Sbjct: 49  KKIPTFIDDDLERGNEISPSLLKAIEESKISVVIISQDYPSSKWCLEELVKILECMKNRG 108

Query: 63  HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF---- 118
            +VIP FYR DPS VR+QTGSF + F++ EE  + + EK+QSWR A KE A+   +    
Sbjct: 109 QMVIPVFYRVDPSHVRNQTGSFEDVFARHEESLSVSKEKVQSWRAALKEVANLSGWHSTS 168

Query: 119 ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGV 178
             PE+E +KE++  I+K+L ++        LVG ESR++ IESLL   S +V I+GIWG+
Sbjct: 169 TRPEAEAVKEIIEVIVKKLNQMSPNCYSRGLVGMESRIQEIESLLCLRSSNVRIVGIWGM 228

Query: 179 GSIGKTTIARA 189
           G +GKTT+ARA
Sbjct: 229 GGLGKTTLARA 239

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 97/193 (50%), Positives = 128/193 (66%), Gaps = 5/193 (2%)

Query: 1   SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
           +++ I TF+D ++ RG+EIS SIA AI+   +SVIIFSE Y FS+WCL EL KIL+ KK 
Sbjct: 35  NKKKIFTFMDKEIKRGEEISPSIAKAIKGSKLSVIIFSEKYAFSKWCLDELTKILECKKM 94

Query: 61  YAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF-- 118
              IVIP FYR DP  VR+Q GSF  +F+K EE   E  EK++SWR+A  EA S   +  
Sbjct: 95  NGQIVIPVFYRVDPVHVRNQRGSFACAFAKHEETLKERMEKVESWRSALNEAGSISGWNS 154

Query: 119 --ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIW 176
               PES+LI+E+V  I K+L +         LVG +SR+E IES+L  +  DV I+G+W
Sbjct: 155 LVARPESKLIEEIVKDISKKLNQTSP-SHSIGLVGIDSRLEQIESMLCLDMSDVRIIGVW 213

Query: 177 GVGSIGKTTIARA 189
           G+G IGKTT+A A
Sbjct: 214 GMGGIGKTTLAGA 226

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555349|ref|XP_002518711.1| leucine-rich repeat containing protein, putative [Ricinus communis] gi|223542092|gb|EEF43636.1| leucine-rich repeat containing protein, putative [Ricinus communis]

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 90/192 (46%), Positives = 127/192 (66%), Gaps = 4/192 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           + NI TFID++L RG+ +S S+  AIE   ISV+I SE YP+S+WCL ELVKIL+  K  
Sbjct: 48  KNNILTFIDNELVRGEALSPSLLKAIEESKISVVILSENYPYSKWCLEELVKILECMKIN 107

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF--- 118
             +VIP FY+ DPS VR+QTGSF ++F++ EE      +K++SWR A K+ A+   +   
Sbjct: 108 GQMVIPVFYKVDPSHVRNQTGSFADAFARHEESLLVTEDKVKSWRAALKDVANISGWDSR 167

Query: 119 -ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
              PESELIK+++  I ++L  +         VG ++R++ IE LL  +  DV I+GIWG
Sbjct: 168 VTSPESELIKKIIRDIWEKLNIMSSSYSPRGFVGIQTRIKQIECLLCLKLSDVRIVGIWG 227

Query: 178 VGSIGKTTIARA 189
           +G IGKTT+ARA
Sbjct: 228 MGGIGKTTLARA 239

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109502|ref|XP_002333244.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222835789|gb|EEE74224.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 90/190 (47%), Positives = 126/190 (66%), Gaps = 4/190 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           R+ I TF+D+QL RGDEIS S+   IE   +SVI+FSE Y  S+WCL EL KI + ++  
Sbjct: 66  RKQILTFVDNQLVRGDEISASLLRTIEEAKLSVIVFSENYASSKWCLEELAKIFERRRNN 125

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFIL- 120
            HIVIP FY+ DPS VR+Q GSFG++F++L ++     +K +S+ +A K+AA+   + L 
Sbjct: 126 GHIVIPVFYQVDPSNVRNQAGSFGDAFARLIKKKALTMDKEKSFTDALKDAANLSGWTLR 185

Query: 121 ---PESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
              PES+ I+++V  +LK+L  +        L G + RV  +ESLL  ES DV I+GIWG
Sbjct: 186 ESHPESQFIEKIVGDVLKKLHAMSSSHTMAGLFGIDVRVSEVESLLDMESLDVLIVGIWG 245

Query: 178 VGSIGKTTIA 187
           +G IGKTTIA
Sbjct: 246 MGGIGKTTIA 255

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 =  169 bits (427), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 91/190 (47%), Positives = 119/190 (62%), Gaps = 4/190 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           ++ I+ F+DD+L+RG+EIS ++   IE   +SVIIFSE Y FS WCL ELVKIL+ KK  
Sbjct: 41  QKQIKAFVDDKLSRGEEISAALVKVIEESMVSVIIFSENYAFSPWCLDELVKILECKKTV 100

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF--- 118
             IV+P FY  DPS+V  Q G FG +F + E+ F E  +KLQ WR A  EAA+   +   
Sbjct: 101 GQIVLPVFYHVDPSDVAEQKGGFGAAFIEHEKCFKERIDKLQKWRAALTEAANISGWSSS 160

Query: 119 -ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
            I  ES+LI+E+   ILK+L  +        LVG  SR++ IE LL  E  DV  LG+WG
Sbjct: 161 VIRSESKLIQEIAEDILKKLNHMSSSTDSKGLVGINSRIDKIELLLCVELADVRFLGLWG 220

Query: 178 VGSIGKTTIA 187
           +G  GKTT A
Sbjct: 221 MGGAGKTTTA 230

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 94/192 (48%), Positives = 125/192 (65%), Gaps = 5/192 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           R+NI TFID+ L RG+EIS S+  AIE   +SVIIFS+ Y  S+WCL EL+KIL+ +K  
Sbjct: 47  RKNILTFIDNDLRRGEEISPSLVKAIEDSMLSVIIFSQNYASSKWCLDELLKILESRKVR 106

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF--- 118
             I IP FY  DPS++R Q+GSFG+ F++L +R     E+ Q +R A  EAA+       
Sbjct: 107 GQIAIPVFYEVDPSDIRKQSGSFGDVFAQLVKRKALKMEEEQCFRAALNEAANISGHDSR 166

Query: 119 -ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
            I  ES+ I+ +V  IL +L ++      N LVG +  V  IESLL  E++DV I+GIWG
Sbjct: 167 KIESESKFIEVIVEDILNKLCKIFPVHPTN-LVGIDEHVRKIESLLDMETQDVRIVGIWG 225

Query: 178 VGSIGKTTIARA 189
           +G IGKTTIARA
Sbjct: 226 MGGIGKTTIARA 237

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106744|dbj|BAJ53239.1| JHS03A10.2 [Jatropha curcas]

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 92/192 (47%), Positives = 123/192 (64%), Gaps = 5/192 (2%)

Query: 3   QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
           + IQTFID+ L RG EIS S+  AIE   ISV I SE Y  S+WCL EL +I+K  K+  
Sbjct: 36  KKIQTFIDNNLVRGKEISSSLLKAIEESKISVPILSENYASSKWCLEELAEIIKCMKKNG 95

Query: 63  HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF---- 118
            IVIP FYR  PS+VR+QTGSF ++F++ E+    N +K+Q WR A KE A    +    
Sbjct: 96  QIVIPVFYRIRPSDVRNQTGSFHDAFARYEKSLMVNKDKVQRWRAALKEVAGLSGWDSMA 155

Query: 119 ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGV 178
           I PES LI EV+  ILK+L  +      + L+G +SR++ IE+L++ ES     +GIWG+
Sbjct: 156 IRPESTLIHEVLKDILKKLNRIFP-SYSSGLIGIDSRIKHIEALISMESSAARTVGIWGM 214

Query: 179 GSIGKTTIARAN 190
           G  GKTT+ARA 
Sbjct: 215 GGSGKTTLARAT 226

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127917|ref|XP_002329209.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222870990|gb|EEF08121.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 89/191 (46%), Positives = 122/191 (63%), Gaps = 5/191 (2%)

Query: 1   SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
            R+ I+TFIDD+L RG+EI+ ++   IE   ISVIIFS  Y  S WC+ ELVKIL+ KK 
Sbjct: 37  CRKQIKTFIDDKLERGEEITGALLRTIEESRISVIIFSRNYASSPWCVDELVKILECKKA 96

Query: 61  YAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF-- 118
           Y  IV+P FY  DPS+V  QTGSFGN+F++LE  F +  +K+  WR     AA+   +  
Sbjct: 97  YGQIVLPVFYHVDPSDVDQQTGSFGNAFAELERNFKQKMDKVPRWRADLTSAANISGWDS 156

Query: 119 --ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIW 176
               PES L++++V+ ILK+L      D +  LVG +SR+E IE+ L  +  +   +GIW
Sbjct: 157 QVTRPESSLVEQIVHHILKKLNYASSSDLKG-LVGMDSRMEQIEASLCTKLPEFCFVGIW 215

Query: 177 GVGSIGKTTIA 187
           G+G  GKTTIA
Sbjct: 216 GMGGTGKTTIA 226

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 =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 94/193 (48%), Positives = 120/193 (62%), Gaps = 5/193 (2%)

Query: 1   SRQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
            R+ I+TFIDD L RG+EI+ ++   IE   ISV+IFS+ Y  S WC+ ELVKIL+ K+ 
Sbjct: 37  CRKKIKTFIDDGLERGEEITPALLKKIEESRISVVIFSKNYASSPWCVDELVKILECKET 96

Query: 61  YAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF-- 118
              IV+P FY  DPS+V  QTGSFGN+FS+LE  F    +K+  WR     AAS   +  
Sbjct: 97  CGQIVLPVFYHVDPSDVDEQTGSFGNAFSELENIFKGKMDKVPRWRADMTYAASISGWDS 156

Query: 119 --ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIW 176
               PES+L+ EVV  I KRL       K   LVG +SR+E I  LL+    DV  +GIW
Sbjct: 157 QVTSPESKLVTEVVQTIWKRLNRASR-SKLRGLVGVDSRIEQINKLLSVVPSDVRRIGIW 215

Query: 177 GVGSIGKTTIARA 189
           G+G+IGKTTIA A
Sbjct: 216 GMGAIGKTTIAEA 228

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

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	190
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.978	0.162	0.411	1e-31
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.968	0.168	0.413	1.7e-29
TAIR|locus:2151506	1127	RPS6 "RESISTANT TO P. SYRINGAE	0.973	0.164	0.395	3.7e-29
TAIR|locus:2160472	1038	AT5G41540 [Arabidopsis thalian	0.968	0.177	0.392	6.7e-29
TAIR|locus:2151491	1123	AT5G46450 [Arabidopsis thalian	0.973	0.164	0.369	2.4e-27
TAIR|locus:2151466	1353	VICTL "VARIATION IN COMPOUND T	0.973	0.136	0.356	2.5e-27
TAIR|locus:2115870	1234	AT4G08450 [Arabidopsis thalian	0.957	0.147	0.385	4.6e-27
TAIR|locus:2162439	1008	AT5G22690 [Arabidopsis thalian	0.978	0.184	0.348	5.4e-27
TAIR|locus:2146243	900	AT5G18360 [Arabidopsis thalian	0.957	0.202	0.390	7.1e-27
TAIR|locus:2130270	1449	RPP5 "RECOGNITION OF PERONOSPO	0.973	0.127	0.383	7.4e-27

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

 Score = 360 (131.8 bits), Expect = 1.0e-31, P = 1.0e-31
 Identities = 79/192 (41%), Positives = 118/192 (61%)

Query:     3 QNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             + I+TF DD+ L  G  I   +  AIE    ++++FSE Y  SRWCL+ELVKI++ K  +
Sbjct:    38 KGIKTFQDDKRLEYGATIPGELCKAIEESQFAIVVFSENYATSRWCLNELVKIMECKTRF 97

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFI-- 119
                VIP FY  DPS VR+Q  SF  +F + E ++ ++ E +Q WR A  EAA+       
Sbjct:    98 KQTVIPIFYDVDPSHVRNQKESFAKAFEEHETKYKDDVEGIQRWRIALNEAANLKGSCDN 157

Query:   120 --LPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
                 +++ I+++V+QI  +L ++ L   +N +VG ++ +E IESLL      V I+GIWG
Sbjct:   158 RDKTDADCIRQIVDQISSKLCKISLSYLQN-IVGIDTHLEKIESLLEIGINGVRIMGIWG 216

Query:   178 VGSIGKTTIARA 189
             +G +GKTTIARA
Sbjct:   217 MGGVGKTTIARA 228

GO:0005515 "protein binding" evidence=IPI

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

 Score = 339 (124.4 bits), Expect = 1.7e-29, P = 1.7e-29
 Identities = 79/191 (41%), Positives = 109/191 (57%)

Query:     3 QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
             + I TF DD + R   I   +  AI    ISV++FSE Y  S WCL EL++I+K K+E  
Sbjct:    37 KGIVTFRDDHIKRSHTIGHELRAAIRESKISVVLFSENYASSSWCLDELIEIMKCKEEQG 96

Query:    63 HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP- 121
               V+P FY+ DPS++R QTG FG SF  LE    +  E+  +WR A  +AA+ +      
Sbjct:    97 LKVMPVFYKVDPSDIRKQTGKFGMSF--LETCCGKTEERQHNWRRALTDAANILGDHPQN 154

Query:   122 ---ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGV 178
                E+  I  +   +L++L      D  N LVG E+ +  +ESLL  ES+ V I+GIWG 
Sbjct:   155 WDNEAYKITTISKDVLEKLNATPSRDF-NDLVGMEAHIAKMESLLCLESQGVRIVGIWGP 213

Query:   179 GSIGKTTIARA 189
               +GKTTIARA
Sbjct:   214 AGVGKTTIARA 224

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:2151506 RPS6 "RESISTANT TO P. SYRINGAE 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 336 (123.3 bits), Expect = 3.7e-29, P = 3.7e-29
 Identities = 76/192 (39%), Positives = 116/192 (60%)

Query:     2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             R+ I +F D+++ R   +   + + I +  I+V++FS+ Y  S WCL+EL++I+K KKE+
Sbjct:    39 RKLIISFKDNEIERSQSLDPELKHGIRNSRIAVVVFSKTYASSSWCLNELLEIVKCKKEF 98

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP 121
               +VIP FY  DPS VR QTG FG  F K   R     EK++ W+ A  + A+ + + + 
Sbjct:    99 GQLVIPIFYNLDPSHVRKQTGDFGKIFEKTC-RNKTVDEKIR-WKEALTDVANILGYHIV 156

Query:   122 ----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
                 E+ +I+E+ N IL ++      D E+ LVG E  +  + SLL  ES++V ++GIWG
Sbjct:   157 TWDNEASMIEEIANDILGKMNISPSNDFED-LVGIEDHITKMSSLLHLESEEVRMVGIWG 215

Query:   178 VGSIGKTTIARA 189
                IGKTTIARA
Sbjct:   216 PSGIGKTTIARA 227

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

GO:0042742 "defense response to bacterium" evidence=IMP

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

 Score = 333 (122.3 bits), Expect = 6.7e-29, P = 6.7e-29
 Identities = 75/191 (39%), Positives = 111/191 (58%)

Query:     3 QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
             + I  F D ++ RG  I   +  AI    +S+++ S+ YP S WCL ELV+ILK K++  
Sbjct:    37 KGIVAFKDQEIERGQRIGPELVQAIRESRVSLVVLSKNYPSSSWCLDELVEILKCKEDQE 96

Query:    63 HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMA-FIL- 120
              IV+P FY  DPS+VR Q+G FG +F K      +  E  Q W NA  EAA+      L 
Sbjct:    97 QIVMPIFYEIDPSDVRKQSGDFGKAFGKT--CVGKTKEVKQRWTNALTEAANIGGEHSLN 154

Query:   121 --PESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGV 178
                E+E+I+++V  +  +L  +   D E ++VG ++ +  ++SLL   S +V ++GIWG 
Sbjct:   155 WTDEAEMIEKIVADVSNKLNVIPSRDFE-EMVGLDAHLRKLDSLLCLNSDEVKMIGIWGP 213

Query:   179 GSIGKTTIARA 189
               IGKTTIARA
Sbjct:   214 AGIGKTTIARA 224

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:2151491 AT5G46450 [Arabidopsis thaliana (taxid:3702)]

 Score = 319 (117.4 bits), Expect = 2.4e-27, P = 2.4e-27
 Identities = 71/192 (36%), Positives = 112/192 (58%)

Query:     2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             R++I TF D+++ R   I+  +  AI+   I+VI+FS+ Y  S WCL+EL++I++  K  
Sbjct:    38 RKSIITFKDNEMERSQSIAPELVEAIKDSRIAVIVFSKNYASSSWCLNELLEIMRCNKYL 97

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF--- 118
                VIP FY  DPS +R Q+G FG +F K  +  N+  E    W+ A  + ++ + +   
Sbjct:    98 GQQVIPVFYYLDPSHLRKQSGEFGEAFKKTCQ--NQTEEVKNQWKQALTDVSNILGYHSK 155

Query:   119 -ILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
                 E+ +I+E+ + IL +L+     D E + VG +  +E +  LL  ES +V ++GIWG
Sbjct:   156 NCNSEATMIEEISSHILGKLSLTPSNDFE-EFVGIKDHIEKVRLLLHLESDEVRMVGIWG 214

Query:   178 VGSIGKTTIARA 189
                IGKTTIARA
Sbjct:   215 TSGIGKTTIARA 226

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:2151466 VICTL "VARIATION IN COMPOUND TRIGGERED ROOT growth response-like" [Arabidopsis thaliana (taxid:3702)]

 Score = 320 (117.7 bits), Expect = 2.5e-27, P = 2.5e-27
 Identities = 68/191 (35%), Positives = 107/191 (56%)

Query:     3 QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
             +++ +F D  + R   +   +  AI    I++++FS+ Y  S WCL+EL++I+K K+E+ 
Sbjct:    34 KSVNSFRDQNMERSQSLDPMLKQAIRDSRIALVVFSKNYASSSWCLNELLEIVKCKEEFG 93

Query:    63 HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFIL-- 120
              +VIP FY  DPS VR Q G FG +F +   R N   EK+Q W  A  + A+   F    
Sbjct:    94 QMVIPIFYCLDPSHVRHQDGDFGKNFEETCGR-NTEEEKIQ-WEKALTDVANLAGFDSVT 151

Query:   121 --PESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWGV 178
                E+++I+E+ N +  +L      D     +G E  +  +  LL  E+++V ++GIWG 
Sbjct:   152 WDDEAKMIEEIANDVSGKLLSTSSTDSAENSIGIEDHIANMSVLLQLEAEEVRMVGIWGS 211

Query:   179 GSIGKTTIARA 189
               IGKTTIARA
Sbjct:   212 SGIGKTTIARA 222

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:2115870 AT4G08450 [Arabidopsis thaliana (taxid:3702)]

 Score = 317 (116.6 bits), Expect = 4.6e-27, P = 4.6e-27
 Identities = 74/192 (38%), Positives = 111/192 (57%)

Query:     2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             R+ I  F D+++ RG+ I   +  AI+   I+V++FS+ Y  S WCL+ELV+I+  K+  
Sbjct:    36 RKMIIAFKDNEIERGNSIGTELIQAIKDSRIAVVVFSKKYSSSSWCLNELVEIVNCKE-- 93

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFIL- 120
               IVIP FY  DPS+VR Q G FG SF   E   N    ++Q W  A    A+   +   
Sbjct:    94 --IVIPVFYDLDPSDVRKQEGEFGESFK--ETCKNRTDYEIQRWGQALTNVANIAGYHTR 149

Query:   121 -P--ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
              P  E++LI+E+ N +L +L ++      ++  G E  ++ +  LL  ES++V ++GIWG
Sbjct:   150 KPNNEAKLIEEITNDVLDKLMKLTPSKDFDEFFGIEDHIKELSLLLCLESEEVRMVGIWG 209

Query:   178 VGSIGKTTIARA 189
                IGKTTIARA
Sbjct:   210 PTGIGKTTIARA 221

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:2162439 AT5G22690 [Arabidopsis thaliana (taxid:3702)]

 Score = 315 (115.9 bits), Expect = 5.4e-27, P = 5.4e-27
 Identities = 67/192 (34%), Positives = 103/192 (53%)

Query:     2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             R+ I  F D+ + R   +   +  AI    I++++FS+ Y  S WCL EL++I+K K+E+
Sbjct:    35 RKLISVFKDNDIQRSQSLDPELKLAIRDSRIAIVVFSKNYAASSWCLDELLEIVKCKEEF 94

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP 121
               IVIP FY  DP  VR Q+G FG  F    +   +  +++Q WR A  + A+ + F   
Sbjct:    95 GQIVIPVFYGLDPCHVRKQSGEFGIVFENTCQ--TKTDDEIQKWRRALTDVANILGFHSS 152

Query:   122 ----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
                 E+ +++++ N +L +L      +     VG E  +  I  +L  E K V + GIWG
Sbjct:   153 NWDNEATMVEDIANDVLAKLNLTTTSNDFEGFVGIEGHIAKISLMLCLECKQVRMFGIWG 212

Query:   178 VGSIGKTTIARA 189
                IGKTTIARA
Sbjct:   213 PSGIGKTTIARA 224

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2146243 AT5G18360 [Arabidopsis thaliana (taxid:3702)]

 Score = 313 (115.2 bits), Expect = 7.1e-27, P = 7.1e-27
 Identities = 75/192 (39%), Positives = 108/192 (56%)

Query:     2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
             R+ I+TFID+ + R   IS  +  AI    I+V++ S  Y  S WCL+ELV+I    K+ 
Sbjct:    41 RKGIRTFIDNDIKRSQMISSELVRAIRESRIAVVVLSRTYASSSWCLNELVEI----KKV 96

Query:    62 AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP 121
             + +++P FY  DPS+VR +TG FG +F +  ER   + E  Q WR A    A+       
Sbjct:    97 SQMIMPVFYEVDPSDVRKRTGEFGKAFEEACER-QPDEEVKQKWREALVYIANIAGESSQ 155

Query:   122 ----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
                 E++LI ++   I   L   L  D  N LVG ++ +  ++SLL  ES +V ++GIWG
Sbjct:   156 NWDNEADLIDKIAMSISYELNSTLSRDSYN-LVGIDNHMRELDSLLCLESTEVKMVGIWG 214

Query:   178 VGSIGKTTIARA 189
                IGKTTIARA
Sbjct:   215 PAGIGKTTIARA 226

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:2130270 RPP5 "RECOGNITION OF PERONOSPORA PARASITICA 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 316 (116.3 bits), Expect = 7.4e-27, P = 7.4e-27
 Identities = 74/193 (38%), Positives = 109/193 (56%)

Query:     3 QNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA 62
             ++I TFID  + R   I+  +  AI    IS++IFS+ Y  S WCL+ELV+I K   +  
Sbjct:    38 KSINTFIDHGIERSRTIAPELISAIREARISIVIFSKNYASSTWCLNELVEIHKCFNDLG 97

Query:    63 HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEE--RFNENSEKLQSWRNATKEAASFMAFIL 120
              +VIP FY  DPSEVR QTG FG  F K  E  +  +  ++ Q W  A  + A+     L
Sbjct:    98 QMVIPVFYDVDPSEVRKQTGEFGKVFEKTCEVSKDKQPGDQKQRWVQALTDIANIAGEDL 157

Query:   121 ---P-ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIW 176
                P E+ +++++ N +  +L     C  +   VG E+ +E I+S+L  ESK+  ++GIW
Sbjct:   158 LNGPNEAHMVEKISNDVSNKLITRSKCFDD--FVGIEAHIEAIKSVLCLESKEARMVGIW 215

Query:   177 GVGSIGKTTIARA 189
             G   IGK+TI RA
Sbjct:   216 GQSGIGKSTIGRA 228

GO:0000166 "nucleotide binding" evidence=IEA;TAS

GO:0005622 "intracellular" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	190
PLN03210	1153	PLN03210, PLN03210, Resistant to P	2e-41
pfam01582	135	pfam01582, TIR, TIR domain	7e-21
smart00255	140	smart00255, TIR, Toll - interleukin 1 - resistance	7e-20
PLN03194	187	PLN03194, PLN03194, putative disease resistance pr	2e-08
pfam13676	102	pfam13676, TIR_2, TIR domain	4e-04

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

 Score =  148 bits (374), Expect = 2e-41
 Identities = 72/192 (37%), Positives = 112/192 (58%), Gaps = 7/192 (3%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
           R+ I  F D+++ R   +   +  AI    I+V++FS+ Y  S WCL+EL++I++ K+E 
Sbjct: 38  RKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEEL 97

Query: 62  AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP 121
             +VIP FY  DPS VR QTG FG +F K  +   E+ +    W+ A  + A+ + +   
Sbjct: 98  GQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKTEDEKIQ--WKQALTDVANILGYHSQ 155

Query: 122 ----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKDVYILGIWG 177
               E+++I+E+ N +L +L      D E+  VG E  +  + SLL  ES++V ++GIWG
Sbjct: 156 NWPNEAKMIEEIANDVLGKLNLTPSNDFED-FVGIEDHIAKMSSLLHLESEEVRMVGIWG 214

Query: 178 VGSIGKTTIARA 189
              IGKTTIARA
Sbjct: 215 SSGIGKTTIARA 226

syringae 6; Provisional. Length = 1153

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

 Score = 83.5 bits (207), Expect = 7e-21
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 3/110 (2%)

Query: 2   RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
            + I+  IDD     G+ I E++  AIE    +++IFS  Y  S WCL ELV+I+K   E
Sbjct: 24  EKGIKLCIDDRDELPGESILENLFEAIEKSRRAIVIFSSNYASSEWCLDELVEIVKCALE 83

Query: 61  --YAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNA 108
                +++P FY+ DPS+VR Q+G FG +F K  +   +  +K++ W+ A
Sbjct: 84  GGGKKVILPIFYKVDPSDVRPQSGKFGKAFLKTLKWSGDKEDKIRFWKKA 133

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 = 80.8 bits (200), Expect = 7e-20
 Identities = 43/114 (37%), Positives = 53/114 (46%), Gaps = 3/114 (2%)

Query: 2   RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEY 61
              +  FIDD    G    E I  AIE   I++++ S  Y  S WCL ELV  L+   E 
Sbjct: 28  GYGLCVFIDDFE-PGGGDLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAALENALEE 86

Query: 62  -AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAAS 114
               VIP FY   PS+VR Q G F   F K   ++ E  EK Q W+ A     S
Sbjct: 87  GGLRVIPIFYEVIPSDVRKQPGKFRKVFKKNYLKWPE-DEKEQFWKKALYAVPS 139

Length = 140

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 5/79 (6%)

Query: 1   SRQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKK 59
           SR N++ F+D++ +  GD++ + I  AI +  + V +FS  Y  S +CLHEL  I++ KK
Sbjct: 51  SRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELALIMESKK 110

Query: 60  EYAHIVIPGFYRGDPSEVR 78
                VIP F    PS++R
Sbjct: 111 R----VIPIFCDVKPSQLR 125

Length = 187

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

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 2  RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHEL 51
             I+ ++D  +  G++  + I  A+ S  + +++ S  Y  S WC  E 
Sbjct: 22 AAGIRVWLDWDIPPGEDWRDEIEEALRSADVVLVLLSPAYLASPWCRAEW 71

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	190
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	99.84
smart00255	140	TIR Toll - interleukin 1 - resistance.	99.69
PF13676	102	TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_	99.19
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.59
PTZ00202	550	tuzin; Provisional	97.75
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.6
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.45
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.42
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.33
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.1
KOG2028	554	consensus ATPase related to the helicase subunit o	97.02
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	96.96
PRK15455	644	PrkA family serine protein kinase; Provisional	96.78
PRK10416	318	signal recognition particle-docking protein FtsY;	96.77
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.74
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	96.74
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	96.74
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.74
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.72
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.69
KOG3678	832	consensus SARM protein (with sterile alpha and arm	96.66
PRK05439	311	pantothenate kinase; Provisional	96.63
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.58
CHL00095	821	clpC Clp protease ATP binding subunit	96.57
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.56
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.55
PRK13341	725	recombination factor protein RarA/unknown domain f	96.51
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.49
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.47
PRK10865	857	protein disaggregation chaperone; Provisional	96.45
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.42
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.4
PRK03992	389	proteasome-activating nucleotidase; Provisional	96.39
PHA02544	316	44 clamp loader, small subunit; Provisional	96.38
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.28
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.27
PLN02318	656	phosphoribulokinase/uridine kinase	96.25
PRK09435	332	membrane ATPase/protein kinase; Provisional	96.23
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.17
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	96.16
PRK14974	336	cell division protein FtsY; Provisional	96.15
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.13
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.13
CHL00181	287	cbbX CbbX; Provisional	96.07
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.0
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.8
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	95.75
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	95.66
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.62
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.6
PRK08099	399	bifunctional DNA-binding transcriptional repressor	95.59
PLN02200	234	adenylate kinase family protein	95.57
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.55
PLN02348	395	phosphoribulokinase	95.5
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.49
PF08937	130	DUF1863: MTH538 TIR-like domain (DUF1863); InterPr	95.46
PLN02796	347	D-glycerate 3-kinase	95.45
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	95.42
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	95.37
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.36
PRK09376	416	rho transcription termination factor Rho; Provisio	95.36
PRK06620	214	hypothetical protein; Validated	95.35
TIGR00959	428	ffh signal recognition particle protein. This mode	95.29
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.28
PRK09087	226	hypothetical protein; Validated	95.26
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.25
PRK10865	857	protein disaggregation chaperone; Provisional	95.25
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.21
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.21
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.08
CHL00176	638	ftsH cell division protein; Validated	95.08
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	95.07
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.05
PLN03046	460	D-glycerate 3-kinase; Provisional	94.94
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	94.87
PRK09183	259	transposase/IS protein; Provisional	94.86
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.83
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.83
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	94.8
PRK08084	235	DNA replication initiation factor; Provisional	94.79
COG1123	539	ATPase components of various ABC-type transport sy	94.76
PRK10867	433	signal recognition particle protein; Provisional	94.74
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.72
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	94.62
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	94.61
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	94.58
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	94.56
PRK06526	254	transposase; Provisional	94.52
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	94.52
PLN02165	334	adenylate isopentenyltransferase	94.5
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	94.5
PRK14248	268	phosphate ABC transporter ATP-binding protein; Pro	94.48
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.42
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.41
PRK08727	233	hypothetical protein; Validated	94.38
PRK12289	352	GTPase RsgA; Reviewed	94.29
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	94.24
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.23
PRK12377	248	putative replication protein; Provisional	94.2
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	94.18
PRK09473	330	oppD oligopeptide transporter ATP-binding componen	94.14
PRK11308	327	dppF dipeptide transporter ATP-binding subunit; Pr	94.14
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	94.14
PRK13546	264	teichoic acids export protein ATP-binding subunit;	94.13
PRK07952	244	DNA replication protein DnaC; Validated	94.12
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	94.11
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	94.11
PRK14265	274	phosphate ABC transporter ATP-binding protein; Pro	94.06
PRK09112	351	DNA polymerase III subunit delta'; Validated	94.06
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	94.04
PRK14236	272	phosphate transporter ATP-binding protein; Provisi	94.01
PRK10536	262	hypothetical protein; Provisional	94.01
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.0
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.99
PRK14489	366	putative bifunctional molybdopterin-guanine dinucl	93.98
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	93.98
COG0714	329	MoxR-like ATPases [General function prediction onl	93.95
PRK14271	276	phosphate ABC transporter ATP-binding protein; Pro	93.92
PRK14237	267	phosphate transporter ATP-binding protein; Provisi	93.88
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	93.86
) 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	93.83
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.82
PRK15079	331	oligopeptide ABC transporter ATP-binding protein O	93.75
cd03291	282	ABCC_CFTR1 The CFTR subfamily domain 1. The cystic	93.7
PRK14275	286	phosphate ABC transporter ATP-binding protein; Pro	93.68
PRK07471	365	DNA polymerase III subunit delta'; Validated	93.68
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	93.67
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	93.64
PF13245	76	AAA_19: Part of AAA domain	93.63
PRK14252	265	phosphate ABC transporter ATP-binding protein; Pro	93.63
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	93.61
KOG1969	877	consensus DNA replication checkpoint protein CHL12	93.61
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	93.58
PRK04220	301	2-phosphoglycerate kinase; Provisional	93.58
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.56
TIGR03156	351	GTP_HflX GTP-binding protein HflX. This protein fa	93.55
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.45
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.36
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	93.33
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.32
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	93.31
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	93.28
PRK05642	234	DNA replication initiation factor; Validated	93.24
PRK14264	305	phosphate ABC transporter ATP-binding protein; Pro	93.22
PRK14254	285	phosphate ABC transporter ATP-binding protein; Pro	93.21
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.21
PRK13631	320	cbiO cobalt transporter ATP-binding subunit; Provi	93.18
KOG0062	582	consensus ATPase component of ABC transporters wit	93.17
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	93.12
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	93.12
COG1072	283	CoaA Panthothenate kinase [Coenzyme metabolism]	93.11
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	93.08
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	93.06
PRK13409	590	putative ATPase RIL; Provisional	93.04
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	92.98
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.97
CHL00095	821	clpC Clp protease ATP binding subunit	92.95
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	92.94
PRK10261	623	glutathione transporter ATP-binding protein; Provi	92.92
PLN02199	303	shikimate kinase	92.91
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	92.83
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	92.82
PRK12422	445	chromosomal replication initiation protein; Provis	92.81
PRK08116	268	hypothetical protein; Validated	92.81
cd03288	257	ABCC_SUR2 The SUR domain 2. The sulfonylurea recep	92.8
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	92.78
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	92.76
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	92.76
PRK13409	590	putative ATPase RIL; Provisional	92.76
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	92.75
PRK06921	266	hypothetical protein; Provisional	92.75
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	92.74
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	92.73
PRK10982	491	galactose/methyl galaxtoside transporter ATP-bindi	92.71
PRK06835	329	DNA replication protein DnaC; Validated	92.67
PRK13765	637	ATP-dependent protease Lon; Provisional	92.63
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	92.6
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.58
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.57
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	92.55
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	92.53
PRK13536	340	nodulation factor exporter subunit NodI; Provision	92.52
PHA02244	383	ATPase-like protein	92.48
PRK10261	623	glutathione transporter ATP-binding protein; Provi	92.47
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	92.47
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.46
PRK00149	450	dnaA chromosomal replication initiation protein; R	92.44
PRK11819	556	putative ABC transporter ATP-binding protein; Revi	92.37
PRK10762	501	D-ribose transporter ATP binding protein; Provisio	92.36
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	92.26
TIGR03719	552	ABC_ABC_ChvD ATP-binding cassette protein, ChvD fa	92.25
PRK15064	530	ABC transporter ATP-binding protein; Provisional	92.25
PLN03073	718	ABC transporter F family; Provisional	92.23
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	92.2
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.2
TIGR00767	415	rho transcription termination factor Rho. Members	92.17
PRK10070	400	glycine betaine transporter ATP-binding subunit; P	92.12
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	92.11
PRK11288	501	araG L-arabinose transporter ATP-binding protein;	92.11
PRK13477	512	bifunctional pantoate ligase/cytidylate kinase; Pr	92.08
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	92.08
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	92.03
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.01
PRK00098	298	GTPase RsgA; Reviewed	92.01
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	92.01
PRK09866	741	hypothetical protein; Provisional	92.0
PRK10636	638	putative ABC transporter ATP-binding protein; Prov	92.0
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	91.95
PRK12337	475	2-phosphoglycerate kinase; Provisional	91.95
PRK08181	269	transposase; Validated	91.92
PRK10938	490	putative molybdenum transport ATP-binding protein	91.9
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	91.9
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	91.86
TIGR02633	500	xylG D-xylose ABC transporter, ATP-binding protein	91.86
PRK11147	635	ABC transporter ATPase component; Reviewed	91.83
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	91.82
PTZ00035	337	Rad51 protein; Provisional	91.82
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	91.81
PF11868	192	DUF3388: Protein of unknown function (DUF3388); In	91.8
TIGR00665	434	DnaB replicative DNA helicase. This model describe	91.73
PRK08840	464	replicative DNA helicase; Provisional	91.72
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	91.71
TIGR02236	310	recomb_radA DNA repair and recombination protein R	91.69
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	91.68
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	91.63
COG4240	300	Predicted kinase [General function prediction only	91.59
PRK06851	367	hypothetical protein; Provisional	91.57
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	91.54
PRK13851	344	type IV secretion system protein VirB11; Provision	91.53
cd00983	325	recA RecA is a bacterial enzyme which has roles in	91.48
PRK08760	476	replicative DNA helicase; Provisional	91.47
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	91.47
COG4172	534	ABC-type uncharacterized transport system, duplica	91.47
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	91.45
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	91.4
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	91.36
PLN03073	718	ABC transporter F family; Provisional	91.34
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	91.32
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	91.32
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	91.29
CHL00195	489	ycf46 Ycf46; Provisional	91.25
PRK12288	347	GTPase RsgA; Reviewed	91.24
TIGR03415	382	ABC_choXWV_ATP choline ABC transporter, ATP-bindin	91.24
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	91.22
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	91.2
PRK14088	440	dnaA chromosomal replication initiation protein; P	91.19
PRK05022	509	anaerobic nitric oxide reductase transcription reg	91.19
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	91.17
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	91.12
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	91.08
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	91.05
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	91.04
PRK05973	237	replicative DNA helicase; Provisional	91.02
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	91.0
COG1484	254	DnaC DNA replication protein [DNA replication, rec	90.91
PHA02624	647	large T antigen; Provisional	90.88
COG0488	530	Uup ATPase components of ABC transporters with dup	90.87
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	90.86
PRK15494	339	era GTPase Era; Provisional	90.78
PRK11823	446	DNA repair protein RadA; Provisional	90.73
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	90.72
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	90.7
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	90.7
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	90.69
PRK09354	349	recA recombinase A; Provisional	90.68
KOG1547	336	consensus Septin CDC10 and related P-loop GTPases	90.66
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	90.62
TIGR03453	387	partition_RepA plasmid partitioning protein RepA.	90.62
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	90.6
PRK08006	471	replicative DNA helicase; Provisional	90.58
PRK04301	317	radA DNA repair and recombination protein RadA; Va	90.54
PRK08939	306	primosomal protein DnaI; Reviewed	90.44
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	90.34
TIGR01842	544	type_I_sec_PrtD type I secretion system ABC transp	90.33
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	90.3
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	90.29
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	90.26
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	90.25
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	90.25
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	90.19
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	90.19
TIGR01663	526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	90.13
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	90.1
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	89.95
PRK10522	547	multidrug transporter membrane component/ATP-bindi	89.94
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	89.91
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	89.86
PRK13869	405	plasmid-partitioning protein RepA; Provisional	89.86
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	89.85
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	89.82
PRK00652	325	lpxK tetraacyldisaccharide 4'-kinase; Reviewed	89.81
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	89.81
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	89.77
PRK08506	472	replicative DNA helicase; Provisional	89.72
PTZ00322	664	6-phosphofructo-2-kinase/fructose-2,6-biphosphatas	89.71
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	89.71
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	89.64
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	89.64
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	89.61
PRK11670	369	antiporter inner membrane protein; Provisional	89.58
PRK14087	450	dnaA chromosomal replication initiation protein; P	89.55
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	89.55
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	89.53
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	89.48
PRK09563	287	rbgA GTPase YlqF; Reviewed	89.42
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	89.39
KOG1805	1100	consensus DNA replication helicase [Replication, r	89.31
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	89.3
PRK03003	472	GTP-binding protein Der; Reviewed	89.28
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	89.28
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.25
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	89.23
PRK01889	356	GTPase RsgA; Reviewed	89.05
PHA02542	473	41 41 helicase; Provisional	89.0
PRK05748	448	replicative DNA helicase; Provisional	89.0
PRK09165	497	replicative DNA helicase; Provisional	88.91
PRK15424	538	propionate catabolism operon regulatory protein Pr	88.8
PHA02519	387	plasmid partition protein SopA; Reviewed	88.78
PRK13833	323	conjugal transfer protein TrbB; Provisional	88.76
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	88.74
smart00350	509	MCM minichromosome maintenance proteins.	88.7
PF01057	271	Parvo_NS1: Parvovirus non-structural protein NS1;	88.61
PRK13705	388	plasmid-partitioning protein SopA; Provisional	88.6
TIGR00954	659	3a01203 Peroxysomal Fatty Acyl CoA Transporter (FA	88.56
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	88.55
PRK06904	472	replicative DNA helicase; Validated	88.55
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	88.49
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	88.47
TIGR01194	555	cyc_pep_trnsptr cyclic peptide transporter. This m	88.44
PRK11860	661	bifunctional 3-phosphoshikimate 1-carboxyvinyltran	88.36
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	88.36
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	88.36
PLN03211	659	ABC transporter G-25; Provisional	88.21
PRK12608	380	transcription termination factor Rho; Provisional	88.06
COG2074	299	2-phosphoglycerate kinase [Carbohydrate transport	88.04
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	88.02
KOG0736	953	consensus Peroxisome assembly factor 2 containing	88.02
PRK15115	444	response regulator GlrR; Provisional	87.79
TIGR03029	274	EpsG chain length determinant protein tyrosine kin	87.73
PRK07004	460	replicative DNA helicase; Provisional	87.7
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	87.68
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	87.63
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	87.63
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	87.59
PRK12299	335	obgE GTPase CgtA; Reviewed	87.52
PRK05636	505	replicative DNA helicase; Provisional	87.52
TIGR00993	763	3a0901s04IAP86 chloroplast protein import componen	87.44
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	87.35
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	87.17
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	87.11
PRK12298	390	obgE GTPase CgtA; Reviewed	86.97
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	86.87
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	86.79
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	86.78
PF08357	150	SEFIR: SEFIR domain; InterPro: IPR013568 This doma	86.73
PRK05595	444	replicative DNA helicase; Provisional	86.59
KOG4181	491	consensus Uncharacterized conserved protein [Funct	86.4
PRK13764	602	ATPase; Provisional	86.39
KOG2702	323	consensus Predicted panthothenate kinase/uridine k	86.37
KOG0780	483	consensus Signal recognition particle, subunit Srp	86.36
PRK00093	435	GTP-binding protein Der; Reviewed	86.08
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	86.02
PRK09862	506	putative ATP-dependent protease; Provisional	85.75
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	85.62
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	85.49
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	85.43
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	85.42
COG4175	386	ProV ABC-type proline/glycine betaine transport sy	85.34
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	85.28
TIGR03597	360	GTPase_YqeH ribosome biogenesis GTPase YqeH. This	85.15
COG4987	573	CydC ABC-type transport system involved in cytochr	85.07
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	85.02
COG1162	301	Predicted GTPases [General function prediction onl	84.98
PLN02772	398	guanylate kinase	84.9
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	84.75
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	84.57
COG5192	1077	BMS1 GTP-binding protein required for 40S ribosome	84.53
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	84.51
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	84.48
PLN03140	1470	ABC transporter G family member; Provisional	84.38
COG1084	346	Predicted GTPase [General function prediction only	84.3
COG0606	490	Predicted ATPase with chaperone activity [Posttran	84.18
PTZ00265	1466	multidrug resistance protein (mdr1); Provisional	83.98
COG1855	604	ATPase (PilT family) [General function prediction	83.89
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	83.82
TIGR02533	486	type_II_gspE general secretory pathway protein E.	83.48
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	83.44
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	83.41
TIGR00956	1394	3a01205 Pleiotropic Drug Resistance (PDR) Family p	83.24
TIGR00955	617	3a01204 The Eye Pigment Precursor Transporter (EPP	83.2
PLN03232	1495	ABC transporter C family member; Provisional	82.94
PRK07773	886	replicative DNA helicase; Validated	82.8
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	82.57
COG4586	325	ABC-type uncharacterized transport system, ATPase	82.56
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	82.46
PRK08149	428	ATP synthase SpaL; Validated	82.43
COG1341	398	Predicted GTPase or GTP-binding protein [General f	82.3
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	82.3
PRK06321	472	replicative DNA helicase; Provisional	81.64
TIGR01271	1490	CFTR_protein cystic fibrosis transmembrane conduct	81.52
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	81.31
PRK05922	434	type III secretion system ATPase; Validated	81.3
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	81.29
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	81.27
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	81.21
TIGR00956	1394	3a01205 Pleiotropic Drug Resistance (PDR) Family p	81.18
PLN03130	1622	ABC transporter C family member; Provisional	81.18
PRK09519	790	recA DNA recombination protein RecA; Reviewed	81.17
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	81.13
CHL00189	742	infB translation initiation factor 2; Provisional	81.05
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	81.03
PTZ00265	1466	multidrug resistance protein (mdr1); Provisional	81.01
PRK13796	365	GTPase YqeH; Provisional	80.98
PLN03140	1470	ABC transporter G family member; Provisional	80.96
PTZ00243	1560	ABC transporter; Provisional	80.95
PRK12297	424	obgE GTPase CgtA; Reviewed	80.85
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	80.72
PHA03132	580	thymidine kinase; Provisional	80.65
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	80.52
KOG0927	614	consensus Predicted transporter (ABC superfamily)	80.31
PRK14086	617	dnaA chromosomal replication initiation protein; P	80.26
PRK12296	500	obgE GTPase CgtA; Reviewed	80.22
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	80.19
TIGR01257	2272	rim_protein retinal-specific rim ABC transporter.	80.12

>PLN03210 Resistant to P

Probab=100.00  E-value=3e-55  Score=408.07  Aligned_cols=186  Identities=37%  Similarity=0.674  Sum_probs=175.5

Q ss_pred             CCCeeEEEeCCCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCccccccC
Q 047923            2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQT   81 (190)
Q Consensus         2 ~~gi~~f~d~~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~Vr~q~   81 (190)
                      ++||+||+|+++++|+.|++++++||++|+++|||||++||+|+||||||++|++|+++.+++|+||||+|+|+|||+|+
T Consensus        38 ~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~  117 (1153)
T PLN03210         38 RKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQT  117 (1153)
T ss_pred             HCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhcc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhhHHHHHHHhhhhhhHHHHhHHHHHHHhhccccccCc----hhhhHHHHHHHHHhhhhhhhhccccccccccchhHH
Q 047923           82 GSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP----ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVE  157 (190)
Q Consensus        82 g~~~~~f~~~~~~~~~~~e~v~kWr~AL~ev~~~~g~~~~----e~~~i~~iv~~v~~~l~~~~~~~~~~~~vG~d~~~~  157 (190)
                      |.|+++|.++....  ..+++++||+||+++++++|+++.    |+++|++|+++|++++...++ .+..++||++.+++
T Consensus       118 g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~~~~E~~~i~~Iv~~v~~~l~~~~~-~~~~~~vG~~~~l~  194 (1153)
T PLN03210        118 GDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQNWPNEAKMIEEIANDVLGKLNLTPS-NDFEDFVGIEDHIA  194 (1153)
T ss_pred             chHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCCCCCHHHHHHHHHHHHHHhhccccC-cccccccchHHHHH
Confidence            99999999987654  345799999999999999999875    999999999999999988776 78889999999999


Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++.++|..++++++++|||||||+||||||+++
T Consensus       195 ~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l  227 (1153)
T PLN03210        195 KMSSLLHLESEEVRMVGIWGSSGIGKTTIARAL  227 (1153)
T ss_pred             HHHHHHccccCceEEEEEEcCCCCchHHHHHHH
Confidence            999999888888999999999999999999864

syringae 6; Provisional

>PLN03194 putative disease resistance protein; Provisional

Probab=100.00  E-value=1e-39  Score=242.68  Aligned_cols=122  Identities=31%  Similarity=0.506  Sum_probs=110.6

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCcccccc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQ   80 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~Vr~q   80 (190)
                      ++||+||+|+ ++++|+.|.+.|.+||++|+++|||||++|++|+|||+||++|++|+    ..|+||||+|+|+|||+|
T Consensus        52 ~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~~I~e~~----~~ViPIFY~VdPsdVr~q  127 (187)
T PLN03194         52 RLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELALIMESK----KRVIPIFCDVKPSQLRVV  127 (187)
T ss_pred             HCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHHHHHHcC----CEEEEEEecCCHHHhhcc
Confidence            5799999999 89999999999999999999999999999999999999999999975    479999999999999997


Q ss_pred             -CCchhhHHHHHHHhhhhhhHHHHhHHHHHHHhhccccccCc-----hhhhHHHHHHHHHhhhhhh
Q 047923           81 -TGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP-----ESELIKEVVNQILKRLAEV  140 (190)
Q Consensus        81 -~g~~~~~f~~~~~~~~~~~e~v~kWr~AL~ev~~~~g~~~~-----e~~~i~~iv~~v~~~l~~~  140 (190)
                       .+.             .+.+++++||.||.++++++|+++.     |+++|+.|+++|.++|-..
T Consensus       128 ~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~~~~~~e~e~i~~iv~~v~k~l~~~  180 (187)
T PLN03194        128 DNGT-------------CPDEEIRRFNWALEEAKYTVGLTFDSLKGNWSEVVTMASDAVIKNLIEL  180 (187)
T ss_pred             ccCC-------------CCHHHHHHHHHHHHHHhccccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence             432             1246899999999999999998764     8999999999999987544

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

Probab=99.84  E-value=3.8e-22  Score=145.42  Aligned_cols=108  Identities=26%  Similarity=0.463  Sum_probs=93.8

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCC--eeEEeEEeecCCcccc-
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYA--HIVIPGFYRGDPSEVR-   78 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~--~~v~PvFy~v~ps~Vr-   78 (190)
                      .|+++|+++ |+.+|..+.+++.++|++|+++|+|||++|++|.||+.||..++++....+  ..|+|+||+|.+++++ 
T Consensus        27 ~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~~~~~~~~~~~~Il~v~~~v~~~~~~~  106 (141)
T PF01582_consen   27 YGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEALERLLEEGRDKLILPVFYDVSPSDVRP  106 (141)
T ss_dssp             STS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHHHHHHCSTCTTEEEEESSSS-CHHCHT
T ss_pred             CCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhhhhccccccccceeeEeccCChhhcCh
Confidence            399999999 999999999999999999999999999999999999999999999986644  8999999999999999 


Q ss_pred             ccCCchhhHHHHHHHhhhhh--hHHHHhHHHHHH
Q 047923           79 SQTGSFGNSFSKLEERFNEN--SEKLQSWRNATK  110 (190)
Q Consensus        79 ~q~g~~~~~f~~~~~~~~~~--~e~v~kWr~AL~  110 (190)
                      .+.+.|...|..+......+  .++...|+.++.
T Consensus       107 ~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~  140 (141)
T PF01582_consen  107 DQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY  140 (141)
T ss_dssp             HHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred             hhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence            68888888887776655543  467899998764

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=99.69  E-value=2.6e-16  Score=113.97  Aligned_cols=110  Identities=34%  Similarity=0.540  Sum_probs=90.1

Q ss_pred             CCCeeEEEeCCCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhc-CCeeEEeEEeecCCcccccc
Q 047923            2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE-YAHIVIPGFYRGDPSEVRSQ   80 (190)
Q Consensus         2 ~~gi~~f~d~~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~-~~~~v~PvFy~v~ps~Vr~q   80 (190)
                      ..|+.+|.|+....+.... +|.++|++|+..|+|+|++|..|.||..|+..+..+... ....||||+|+..|+++..+
T Consensus        28 ~~~~~v~~d~~~~~~~~~~-~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a~~~~~~~~~~~iIPI~~~~~~~~~~~~  106 (140)
T smart00255       28 GYGLCVFIDDFEPGGGDLE-EIDEAIEKSRIAIVVLSPNYAESEWCLDELVAALENALEEGGLRVIPIFYEVIPSDVRKQ  106 (140)
T ss_pred             cCCcEEEecCcccccchHH-HHHHHHHHCcEEEEEECcccccChhHHHHHHHHHHHHHHcCCCeEEEEEEecChHHHHhc
Confidence            4589999998544444443 999999999999999999999999999999999987754 56799999999999999999


Q ss_pred             CCchhhHHHHHHHhhhhhhHHHHhHHHHHHHhh
Q 047923           81 TGSFGNSFSKLEERFNENSEKLQSWRNATKEAA  113 (190)
Q Consensus        81 ~g~~~~~f~~~~~~~~~~~e~v~kWr~AL~ev~  113 (190)
                      .+.+...+..+.....++..+ ..|+.++..+.
T Consensus       107 ~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~  138 (140)
T smart00255      107 PGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVP  138 (140)
T ss_pred             ccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhc
Confidence            999998887775555554433 68999887665

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

Probab=99.19  E-value=3e-12  Score=87.86  Aligned_cols=70  Identities=31%  Similarity=0.521  Sum_probs=56.4

Q ss_pred             CCCeeEEEeCCCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCccc
Q 047923            2 RQNIQTFIDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEV   77 (190)
Q Consensus         2 ~~gi~~f~d~~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~V   77 (190)
                      ++|+++|+|.++.+|+++.+.+.++|++|+..|+++|++|..|.||..|+....+    .+..|+||.  +++.++
T Consensus        22 ~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~----~~~~iipv~--~~~~~~   91 (102)
T PF13676_consen   22 SAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK----RGKPIIPVR--LDPCEL   91 (102)
T ss_dssp             HTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC----TSESEEEEE--CSGGGS
T ss_pred             hcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH----CCCEEEEEE--ECCcCC
Confidence            4799999999889999999999999999999999999999999999999888733    456899996  555544

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.59  E-value=2.8e-08  Score=91.22  Aligned_cols=39  Identities=41%  Similarity=0.624  Sum_probs=35.2

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ||.+..++.+.+.|..+.+  .++||+||||+||||||+.+
T Consensus       161 VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi  199 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQI  199 (889)
T ss_pred             ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHH
Confidence            9999999999999877644  99999999999999999864

>PTZ00202 tuzin; Provisional

Probab=97.75  E-value=5.1e-05  Score=64.64  Aligned_cols=46  Identities=22%  Similarity=0.288  Sum_probs=38.0

Q ss_pred             cccccccccchhHHHHHHHhhhcCCC-eEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKD-VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~-~~vi~i~G~gGiGKTTla~~  189 (190)
                      .....++||+.++..+...|...+.. .+++.|.|++|.|||||++.
T Consensus       259 a~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~  305 (550)
T PTZ00202        259 AVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRS  305 (550)
T ss_pred             CCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHH
Confidence            34578999999999999998754333 56999999999999999764

>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=97.60  E-value=7.6e-05  Score=58.14  Aligned_cols=45  Identities=24%  Similarity=0.397  Sum_probs=31.0

Q ss_pred             ccccccccchhHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++++|.+.-+..+.-++..   ..+.+.-+=+||.+|.||||||..
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~I   69 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARI   69 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHH
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHH
Confidence            347899999888877655543   234477888999999999999974

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.45  E-value=9e-05  Score=61.17  Aligned_cols=46  Identities=22%  Similarity=0.367  Sum_probs=35.8

Q ss_pred             ccccccccchhHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|++..++.+..++..   .....+.+-++|.+|+||||||+++
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~i   71 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANII   71 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHH
Confidence            346799999999999877753   2223556779999999999999863

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.42  E-value=0.00011  Score=61.98  Aligned_cols=47  Identities=23%  Similarity=0.232  Sum_probs=36.7

Q ss_pred             cccccccccchhHHHHHHHhhhc--CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE--SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~--~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+..++||+.+++++...|...  ......+-|+|.+|+||||+++.+
T Consensus        27 ~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v   75 (394)
T PRK00411         27 YVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKV   75 (394)
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHH
Confidence            45678999999999999888542  223344669999999999999853

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.33  E-value=0.00016  Score=60.13  Aligned_cols=43  Identities=19%  Similarity=0.257  Sum_probs=36.3

Q ss_pred             cccccchhHHHHHHHhhhc----CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAE----SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~----~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++|++..++++.+.+...    ....++++++|.+|.||||||+++
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~L   98 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECL   98 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHH
Confidence            7999999999999888652    234689999999999999999864

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

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

Probab=97.10  E-value=0.00015  Score=60.66  Aligned_cols=42  Identities=26%  Similarity=0.474  Sum_probs=27.1

Q ss_pred             ccccccchhH---HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRV---EIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~---~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++||.+.-+   ..+..++.  +..+..+-+||.+|+||||||+.+
T Consensus        24 de~vGQ~HLlg~~~~lrr~v~--~~~l~SmIl~GPPG~GKTTlA~li   68 (436)
T COG2256          24 DEVVGQEHLLGEGKPLRRAVE--AGHLHSMILWGPPGTGKTTLARLI   68 (436)
T ss_pred             HHhcChHhhhCCCchHHHHHh--cCCCceeEEECCCCCCHHHHHHHH
Confidence            4566665433   12223332  345777889999999999999853

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

Probab=97.02  E-value=0.00024  Score=59.03  Aligned_cols=42  Identities=33%  Similarity=0.531  Sum_probs=27.9

Q ss_pred             ccccccchhHHH---HHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEI---IESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~---~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++||.+.-+-+   +.+++  +.+.+..+-+||.+|.||||||+.+
T Consensus       138 ~dyvGQ~hlv~q~gllrs~i--eq~~ipSmIlWGppG~GKTtlArli  182 (554)
T KOG2028|consen  138 DDYVGQSHLVGQDGLLRSLI--EQNRIPSMILWGPPGTGKTTLARLI  182 (554)
T ss_pred             HHhcchhhhcCcchHHHHHH--HcCCCCceEEecCCCCchHHHHHHH
Confidence            456666543322   22222  3356888899999999999999853

>cd01858 NGP_1 NGP-1

Probab=96.96  E-value=0.014  Score=42.69  Aligned_cols=50  Identities=14%  Similarity=0.167  Sum_probs=28.9

Q ss_pred             HHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCC
Q 047923           23 IAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDP   74 (190)
Q Consensus        23 l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~p   74 (190)
                      +.++++++++.+.|..-....+.. -.++.+.+... ..+..++-|+=++|-
T Consensus         2 ~~~~l~~aD~il~VvD~~~p~~~~-~~~i~~~l~~~-~~~~p~ilVlNKiDl   51 (157)
T cd01858           2 LYKVIDSSDVVIQVLDARDPMGTR-CKHVEEYLKKE-KPHKHLIFVLNKCDL   51 (157)
T ss_pred             hhHhhhhCCEEEEEEECCCCcccc-CHHHHHHHHhc-cCCCCEEEEEEchhc
Confidence            568999999999999865543221 12344444321 223456666656553

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.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.78  E-value=0.0011  Score=58.29  Aligned_cols=44  Identities=25%  Similarity=0.269  Sum_probs=36.4

Q ss_pred             ccccccchhHHHHHHHhhh----cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA----ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~----~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|++..++.+.+.|..    -...-+++-++|.+|+||||||+.+
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~l  123 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERL  123 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHH
Confidence            4689999999999888732    2345689999999999999999864

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.77  E-value=0.0063  Score=50.17  Aligned_cols=21  Identities=29%  Similarity=0.504  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+++++|.+|.||||++..
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~k  133 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGK  133 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHH
Confidence            367999999999999999864

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.74  E-value=0.0048  Score=49.73  Aligned_cols=20  Identities=30%  Similarity=0.400  Sum_probs=17.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhc
Q 047923          169 DVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.+++.++|.+|+||||++.
T Consensus        71 ~~~vi~l~G~~G~GKTTt~a   90 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIA   90 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHH
Confidence            46899999999999999875

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=96.74  E-value=0.0016  Score=58.33  Aligned_cols=43  Identities=26%  Similarity=0.344  Sum_probs=33.6

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+++|.+..+..+.+.+..  .....+.|+|.+|.||||||+.
T Consensus       152 ~~~~iiGqs~~~~~l~~~ia~--~~~~~vlL~Gp~GtGKTTLAr~  194 (615)
T TIGR02903       152 AFSEIVGQERAIKALLAKVAS--PFPQHIILYGPPGVGKTTAARL  194 (615)
T ss_pred             cHHhceeCcHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHH
Confidence            346789999988887766543  2345689999999999999985

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.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=96.74  E-value=0.0011  Score=55.56  Aligned_cols=45  Identities=20%  Similarity=0.231  Sum_probs=33.6

Q ss_pred             cccccccchhHHHHHHHhhhc--C---------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE--S---------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~--~---------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++.|++..++.+.+.+...  .         ..-+-+-++|.+|+||||||+++
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakai  176 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAV  176 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHH
Confidence            356889999999998776421  1         11345778999999999999864

Many proteins may score above the trusted cutoff because an internal

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.74  E-value=0.009  Score=51.32  Aligned_cols=20  Identities=30%  Similarity=0.285  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++-++|.+|+||||+|..
T Consensus        95 p~vI~lvG~~GsGKTTtaak  114 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAK  114 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            57889999999999999864

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.72  E-value=0.0047  Score=50.21  Aligned_cols=21  Identities=43%  Similarity=0.569  Sum_probs=18.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+|||.|-.|.||||+|+.
T Consensus        61 ~p~IIGIaG~~GSGKSTlar~   81 (290)
T TIGR00554        61 IPYIISIAGSVAVGKSTTARI   81 (290)
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            467999999999999999974

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.

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

Probab=96.69  E-value=0.0041  Score=55.71  Aligned_cols=44  Identities=30%  Similarity=0.333  Sum_probs=36.0

Q ss_pred             ccccccchhHHHHHHHhhhc--CC--CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE--SK--DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~--~~--~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+..|.+.-++.+.+.|.-.  .+  +-.++.++|.+|+|||.|++.|
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSI  370 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSI  370 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHH
Confidence            46789999999999988642  22  3579999999999999999864

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

Probab=96.66  E-value=0.0036  Score=53.61  Aligned_cols=64  Identities=20%  Similarity=0.336  Sum_probs=50.4

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcC--------chhhHHHHHHHHHhhhcCCeeEEeEEee
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPF--------SRWCLHELVKILKYKKEYAHIVIPGFYR   71 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~--------S~wcl~El~~i~~~~~~~~~~v~PvFy~   71 (190)
                      +|+++|||- ++..|+ +.+.|++.|...+-+|.|++||-..        -.|--.||...++|.    ..|+|||..
T Consensus       638 ~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~nCeDWVHKEl~~Afe~~----KNIiPI~D~  710 (832)
T KOG3678|consen  638 RGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDNCEDWVHKELKCAFEHQ----KNIIPIFDT  710 (832)
T ss_pred             cCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccccHHHHHHHHHHHHHHhc----CCeeeeecc
Confidence            699999998 888886 4578999999999999999998432        345555666666655    679999854

>PRK05439 pantothenate kinase; Provisional

Probab=96.63  E-value=0.0066  Score=49.84  Aligned_cols=21  Identities=43%  Similarity=0.632  Sum_probs=19.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-+|||-|-+|+||||+|+.
T Consensus        85 ~~~iIgIaG~~gsGKSTla~~  105 (311)
T PRK05439         85 VPFIIGIAGSVAVGKSTTARL  105 (311)
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            478999999999999999975

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

Probab=96.58  E-value=0.0022  Score=55.05  Aligned_cols=40  Identities=30%  Similarity=0.297  Sum_probs=30.8

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++++.+...+.+...|...    ..+-++|++|+||||+|+.+
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~l  214 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRL  214 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHH
Confidence            45777778888887777643    34667999999999999853

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.57  E-value=0.0028  Score=58.63  Aligned_cols=41  Identities=27%  Similarity=0.415  Sum_probs=32.8

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++||+..++.+.+.|....  ..-+-++|.+|+|||++|+.
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~--~~n~lL~G~pGvGKTal~~~  219 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT--KNNPILIGEPGVGKTAIAEG  219 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc--cCCeEEECCCCCCHHHHHHH
Confidence            458999999999999987542  12234899999999999975

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

Probab=96.56  E-value=0.0027  Score=57.98  Aligned_cols=42  Identities=29%  Similarity=0.338  Sum_probs=32.9

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.++||+..++.+...|....  ..-+-++|.+|+||||+|+.+
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~--~~n~lL~G~pG~GKT~l~~~l  223 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRK--KNNPLLVGEPGVGKTAIAEGL  223 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHH
Confidence            468999999999988876542  223458999999999999753

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

Probab=96.55  E-value=0.0093  Score=54.88  Aligned_cols=44  Identities=25%  Similarity=0.262  Sum_probs=35.4

Q ss_pred             ccccccchhHHHHHHHhhhc----CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE----SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~----~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+.+|.+.-++.+.++|...    ...-.++.++|.+|+||||+|+.+
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~i  369 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSI  369 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHH
Confidence            46899999999998887642    224568999999999999999853

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

Probab=96.51  E-value=0.0019  Score=58.76  Aligned_cols=43  Identities=28%  Similarity=0.434  Sum_probs=30.7

Q ss_pred             cccccccchhHH---HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVE---IIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~---~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++++|.+.-+.   .+..++..  +....+-+||.+|+||||||+++
T Consensus        27 ldd~vGQe~ii~~~~~L~~~i~~--~~~~slLL~GPpGtGKTTLA~aI   72 (725)
T PRK13341         27 LEEFVGQDHILGEGRLLRRAIKA--DRVGSLILYGPPGVGKTTLARII   72 (725)
T ss_pred             HHHhcCcHHHhhhhHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHH
Confidence            356889887664   34444443  34556779999999999999864

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.49  E-value=0.0032  Score=58.39  Aligned_cols=41  Identities=17%  Similarity=0.328  Sum_probs=32.3

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++||+..++.+...|....  ..-+-++|-+|+||||||+.
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~--~~n~lLvG~pGvGKTal~~~  227 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRR--QNNPILTGEAGVGKTAVVEG  227 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCC--cCceeEECCCCCCHHHHHHH
Confidence            568999999999988776542  22344899999999999975

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

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

Probab=96.47  E-value=0.0025  Score=51.38  Aligned_cols=45  Identities=22%  Similarity=0.402  Sum_probs=33.4

Q ss_pred             ccccccccchhHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+++|.+.-++.+.=.+..   ..+.+--+=++|.+|.||||||.-
T Consensus        24 ~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~I   71 (332)
T COG2255          24 TLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHI   71 (332)
T ss_pred             cHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHH
Confidence            346899999888877655543   223366677899999999999964

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.45  E-value=0.0044  Score=57.60  Aligned_cols=41  Identities=20%  Similarity=0.330  Sum_probs=32.5

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++||+..++.+...|....  ..-+-++|-+|+||||||+.
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~--~~n~lL~G~pGvGKT~l~~~  218 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEG  218 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCC--cCceEEECCCCCCHHHHHHH
Confidence            468999999999998886542  22344889999999999975

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

Probab=96.42  E-value=0.0026  Score=50.64  Aligned_cols=20  Identities=35%  Similarity=0.272  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.|+|.+|+|||||++.
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~   62 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRN   62 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHH
Confidence            44788999999999999985

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.40  E-value=0.0037  Score=57.70  Aligned_cols=47  Identities=26%  Similarity=0.254  Sum_probs=37.5

Q ss_pred             cccccccccchhHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++.+.|||.++++|...|..   ++..-.++=|+|.+|.|||++++.|
T Consensus       752 YVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~V  801 (1164)
T PTZ00112        752 VVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSV  801 (1164)
T ss_pred             cCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHH
Confidence            4567899999999999888764   2222457779999999999998754

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=96.39  E-value=0.0024  Score=54.02  Aligned_cols=44  Identities=18%  Similarity=0.252  Sum_probs=33.0

Q ss_pred             ccccccchhHHHHHHHhhhc--C---------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE--S---------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~--~---------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|++..++++.+.+...  .         ...+-+-++|.+|.|||+||+++
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkai  185 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAV  185 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHH
Confidence            46789999999998866421  0         12345778999999999999874

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.38  E-value=0.0018  Score=52.93  Aligned_cols=46  Identities=20%  Similarity=0.111  Sum_probs=35.3

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+...+.+..++..+. --.++=++|.+|+||||+|+++
T Consensus        18 ~~~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l   63 (316)
T PHA02544         18 STIDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKAL   63 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHH
Confidence            344678999999998888886431 2356667999999999999863

>TIGR00763 lon ATP-dependent protease La

Probab=96.28  E-value=0.016  Score=53.40  Aligned_cols=44  Identities=25%  Similarity=0.270  Sum_probs=33.4

Q ss_pred             ccccccchhHHHHHHHhhhc----CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE----SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~----~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.+.-++.+.+++...    ...-.++-++|.+|+||||+|+++
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~i  367 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSI  367 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHH
Confidence            45789998888888766421    223457889999999999999864

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.27  E-value=0.0044  Score=48.27  Aligned_cols=21  Identities=19%  Similarity=0.447  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+.+-|+|-.|+|||+||+++
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai   62 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQAL   62 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            456789999999999999863

>PLN02318 phosphoribulokinase/uridine kinase

Probab=96.25  E-value=0.0045  Score=54.88  Aligned_cols=31  Identities=26%  Similarity=0.428  Sum_probs=24.5

Q ss_pred             HHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          160 ESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       160 ~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++....+++.+|||.|..|.||||||+.+
T Consensus        55 ~qlL~~~~~~riIIGIaGpSGSGKTTLAk~L   85 (656)
T PLN02318         55 CQLLAQKNDGIILVGVAGPSGAGKTVFTEKV   85 (656)
T ss_pred             HHHHHhcCCCeEEEEEECCCCCcHHHHHHHH
Confidence            3445445556899999999999999999864

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=96.23  E-value=0.0082  Score=49.74  Aligned_cols=33  Identities=27%  Similarity=0.412  Sum_probs=24.1

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.+.+.....+..+|||.|.+|.|||||+..
T Consensus        43 ~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~   75 (332)
T PRK09435         43 QELLDALLPHTGNALRIGITGVPGVGKSTFIEA   75 (332)
T ss_pred             HHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHH
Confidence            344444433334578999999999999999864

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.17  E-value=0.017  Score=48.97  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++++++|.+|+||||++..
T Consensus       241 ~~vI~LVGptGvGKTTTiaK  260 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAK  260 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHH
Confidence            57899999999999999864

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=96.16  E-value=0.072  Score=38.24  Aligned_cols=52  Identities=17%  Similarity=0.077  Sum_probs=32.6

Q ss_pred             hHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecC
Q 047923           20 SESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGD   73 (190)
Q Consensus        20 ~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~   73 (190)
                      .-++.++|+.+++.+.|+.-....+.+.. ++...+.... .+..++-|+=+.|
T Consensus         2 ~~~~~~~i~~aD~vl~ViD~~~p~~~~~~-~l~~~l~~~~-~~k~~iivlNK~D   53 (141)
T cd01857           2 WRQLWRVVERSDIVVQIVDARNPLLFRPP-DLERYVKEVD-PRKKNILLLNKAD   53 (141)
T ss_pred             HHHHHHHHhhCCEEEEEEEccCCcccCCH-HHHHHHHhcc-CCCcEEEEEechh
Confidence            35678999999999999987766655522 4444444221 2345555555544

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.15  E-value=0.02  Score=47.54  Aligned_cols=19  Identities=32%  Similarity=0.372  Sum_probs=16.8

Q ss_pred             eEEEEEEcCCCCcHHHHhc
Q 047923          170 VYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~  188 (190)
                      ..++.++|++|+||||++.
T Consensus       140 ~~vi~~~G~~GvGKTTtia  158 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIA  158 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHH
Confidence            5799999999999999654

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.13  E-value=0.03  Score=47.99  Aligned_cols=20  Identities=25%  Similarity=0.302  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.++|.+|+||||+|..
T Consensus       100 ~~vi~lvG~~GvGKTTtaaK  119 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTK  119 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            57999999999999998754

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.13  E-value=0.008  Score=55.88  Aligned_cols=41  Identities=20%  Similarity=0.340  Sum_probs=32.3

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++||+..++.+...|....  -.-+-++|-+|+|||+||+.
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~--~~n~lL~G~pGvGKT~l~~~  213 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRT--KNNPVLIGEPGVGKTAIVEG  213 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHH
Confidence            458999999999998886542  22234799999999999975

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.

>CHL00181 cbbX CbbX; Provisional

Probab=96.07  E-value=0.0065  Score=49.35  Aligned_cols=19  Identities=32%  Similarity=0.314  Sum_probs=16.4

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      .+-++|.+|.||||+|+++
T Consensus        61 ~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            3668999999999999864

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.00  E-value=0.0063  Score=52.72  Aligned_cols=46  Identities=20%  Similarity=0.212  Sum_probs=34.9

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+.-+..+..++..+. --..+=++|..|+||||+|+.+
T Consensus        15 ~~f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriL   60 (484)
T PRK14956         15 QFFRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARIL   60 (484)
T ss_pred             CCHHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHH
Confidence            344679999988888888776542 1235679999999999999853

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.80  E-value=0.0087  Score=48.52  Aligned_cols=18  Identities=33%  Similarity=0.346  Sum_probs=15.5

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -+-++|.+|.||||+|++
T Consensus        60 ~vll~G~pGTGKT~lA~~   77 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALR   77 (284)
T ss_pred             eEEEEcCCCCCHHHHHHH
Confidence            466899999999999964

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=95.75  E-value=0.0091  Score=53.55  Aligned_cols=47  Identities=26%  Similarity=0.330  Sum_probs=37.5

Q ss_pred             cccccccccchhHHHHHHHhhhcC---CCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAES---KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~---~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++++..++....   ...+++.|+|..|.||||+++.+
T Consensus        81 ~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~l  130 (637)
T TIGR00602        81 ETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKIL  130 (637)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHH
Confidence            344679999999999998887532   23578999999999999998753

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

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

Probab=95.66  E-value=0.01  Score=51.03  Aligned_cols=44  Identities=23%  Similarity=0.277  Sum_probs=32.3

Q ss_pred             ccccccchhHHHHHHHhhhc--C---------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE--S---------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~--~---------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++-|.+..++++.+.+...  +         ..-+-+-++|.+|.|||+||+++
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraI  237 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAV  237 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHH
Confidence            45678999888888766421  1         12345668999999999999874

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.62  E-value=0.026  Score=48.40  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=17.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+++.++|.+|+||||++..
T Consensus       221 ~~~i~~vGptGvGKTTt~~k  240 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAK  240 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            35899999999999998753

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.60  E-value=0.0059  Score=48.75  Aligned_cols=22  Identities=36%  Similarity=0.330  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...-+-++|.+|.||||+|+++
T Consensus        41 ~~~~vll~GppGtGKTtlA~~i   62 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARIL   62 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHH
Confidence            3556778999999999999863

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.

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

Probab=95.59  E-value=0.0061  Score=51.80  Aligned_cols=23  Identities=30%  Similarity=0.224  Sum_probs=20.0

Q ss_pred             CCeEEEEEEcCCCCcHHHHhccC
Q 047923          168 KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-++.|+|.|..|.||||||+++
T Consensus       217 ~~~~~IvI~G~~gsGKTTL~~~L  239 (399)
T PRK08099        217 FFVRTVAILGGESSGKSTLVNKL  239 (399)
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHH
Confidence            34889999999999999999763

>PLN02200 adenylate kinase family protein

Probab=95.57  E-value=0.0076  Score=47.49  Aligned_cols=20  Identities=25%  Similarity=0.224  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++.|.|++|.||||+|+.
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~   62 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEK   62 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHH
Confidence            56889999999999999874

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.55  E-value=0.054  Score=46.32  Aligned_cols=20  Identities=25%  Similarity=0.127  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.++|.+|+||||+|..
T Consensus       223 ~~vi~lvGptGvGKTTtaaK  242 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAK  242 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46899999999999999864

>PLN02348 phosphoribulokinase

Probab=95.50  E-value=0.014  Score=49.36  Aligned_cols=24  Identities=21%  Similarity=0.338  Sum_probs=20.7

Q ss_pred             CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          167 SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       167 ~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+...+|||-|-.|.||||+|+.+
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L   69 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRL   69 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHH
Confidence            345789999999999999999853

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

Probab=95.49  E-value=0.014  Score=53.42  Aligned_cols=41  Identities=32%  Similarity=0.413  Sum_probs=32.4

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++||+..++.+.+.|..... - -+-++|-+|+|||+||+.
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~-~-n~LLvGppGvGKT~lae~  226 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRK-N-NPLLVGESGVGKTAIAEG  226 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCC-C-CeEEECCCCCCHHHHHHH
Confidence            4589999999999998876422 1 123799999999999985

>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=95.46  E-value=0.026  Score=40.24  Aligned_cols=50  Identities=18%  Similarity=0.303  Sum_probs=34.7

Q ss_pred             CcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeE
Q 047923           15 RGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPG   68 (190)
Q Consensus        15 ~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~Pv   68 (190)
                      ..+.|...|.++|.+|.+.||+.|++-..|+|+--|+...++    .+..|+-|
T Consensus        56 ~~~~ik~~I~~~i~~s~~~IVLig~~T~~s~wV~~EI~~A~~----~~~~Ii~V  105 (130)
T PF08937_consen   56 SSEYIKRKIRERIKNSSVTIVLIGPNTAKSKWVNWEIEYALK----KGKPIIGV  105 (130)
T ss_dssp             TTTTHHHHHHHHHHTEEEEEEE--TT----HHHHHHHHHHTT----T---EEEE
T ss_pred             hHHHHHHHHHHHHhcCCEEEEEeCCCcccCcHHHHHHHHHHH----CCCCEEEE
Confidence            445788899999999999999999999999999999998776    33455555

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.

>PLN02796 D-glycerate 3-kinase

Probab=95.45  E-value=0.0079  Score=49.98  Aligned_cols=22  Identities=32%  Similarity=0.329  Sum_probs=19.1

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-++||.|..|.||||||+.+
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L  120 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFAL  120 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHH
Confidence            3578999999999999999753

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

Probab=95.42  E-value=0.012  Score=52.85  Aligned_cols=44  Identities=32%  Similarity=0.316  Sum_probs=36.2

Q ss_pred             ccccccchhHHHHHHHhhh----cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA----ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~----~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++..|++.-++.+.+.+.-    ++.+-.++..+|.+|+|||.+|+.|
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSI  458 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSI  458 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHH
Confidence            4668999999999988763    3345689999999999999999864

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

Probab=95.37  E-value=0.015  Score=49.43  Aligned_cols=44  Identities=18%  Similarity=0.201  Sum_probs=32.7

Q ss_pred             ccccccchhHHHHHHHhhh--c---------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA--E---------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~--~---------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++++.+.+..  .         -..-+-+-++|.+|.|||+||+++
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkal  199 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAV  199 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHH
Confidence            5678999888888776542  1         112456779999999999999864

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.36  E-value=0.015  Score=51.94  Aligned_cols=46  Identities=26%  Similarity=0.343  Sum_probs=35.7

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+.+..+. -..-+=++|..|+||||+|+.+
T Consensus        21 ~~f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~l   66 (598)
T PRK09111         21 QTFDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARIL   66 (598)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHH
Confidence            345689999999999988886542 1335668999999999999853

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=95.36  E-value=0.0072  Score=51.07  Aligned_cols=20  Identities=20%  Similarity=-0.044  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-.+|+|.+|+||||||+.|
T Consensus       170 QR~lIvgppGvGKTTLaK~I  189 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNI  189 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHH
Confidence            34678999999999999864

>PRK06620 hypothetical protein; Validated

Probab=95.35  E-value=0.0087  Score=46.51  Aligned_cols=19  Identities=37%  Similarity=0.455  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +.+-|||..|+|||+|+++
T Consensus        45 ~~l~l~Gp~G~GKThLl~a   63 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKI   63 (214)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            5688999999999999985

>TIGR00959 ffh signal recognition particle protein

Probab=95.29  E-value=0.072  Score=45.75  Aligned_cols=19  Identities=26%  Similarity=0.307  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCCcHHHHhc
Q 047923          170 VYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~  188 (190)
                      ..++-++|.+|+||||+|.
T Consensus        99 p~vi~~vG~~GsGKTTtaa  117 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCG  117 (428)
T ss_pred             CEEEEEECCCCCcHHHHHH
Confidence            5689999999999999964

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.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.28  E-value=0.016  Score=50.70  Aligned_cols=46  Identities=24%  Similarity=0.236  Sum_probs=34.5

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+.-+..+...+..+. -...+=++|..|+||||+|+.+
T Consensus        18 ~~f~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~Aril   63 (507)
T PRK06645         18 SNFAELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARII   63 (507)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHH
Confidence            344679999998888877665432 1345678999999999999853

>PRK09087 hypothetical protein; Validated

Probab=95.26  E-value=0.019  Score=44.97  Aligned_cols=20  Identities=25%  Similarity=0.218  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+.+.|||..|+|||+|+++
T Consensus        44 ~~~l~l~G~~GsGKThLl~~   63 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASI   63 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            45689999999999999985

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.25  E-value=0.015  Score=53.23  Aligned_cols=45  Identities=20%  Similarity=0.220  Sum_probs=33.2

Q ss_pred             cccccccchhHHHHHHHhhhc--------C---CCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE--------S---KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~--------~---~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++.|.+..++.+.+++...        .   ..-+-+-++|.+|.||||||+++
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~larai  232 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAV  232 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHH
Confidence            356889999888887776421        1   12345779999999999999864

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.25  E-value=0.023  Score=52.88  Aligned_cols=45  Identities=18%  Similarity=0.361  Sum_probs=34.5

Q ss_pred             cccccccchhHHHHHHHhhhc------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-++.+...+...      .+. ...+-++|..|+||||||+++
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aL  618 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKAL  618 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHH
Confidence            457889999988887776532      121 457889999999999999864

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

Probab=95.21  E-value=0.027  Score=50.03  Aligned_cols=43  Identities=21%  Similarity=0.229  Sum_probs=28.1

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-+.+-.+.+.++.......-.+|-+.|+.|.||||+|+++
T Consensus       370 ~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~L  412 (568)
T PRK05537        370 EWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKAL  412 (568)
T ss_pred             hhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHH
Confidence            3445554444444444333334457889999999999999864

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.21  E-value=0.011  Score=47.89  Aligned_cols=20  Identities=25%  Similarity=0.310  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -++++++|.+|+||||++..
T Consensus       194 ~~vi~~vGptGvGKTTt~~k  213 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAK  213 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46999999999999999864

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.08  E-value=0.026  Score=45.87  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=19.0

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ++.+++|.|.+|.|||||...
T Consensus       103 ~~~~v~l~G~pGsGKTTLl~~  123 (290)
T PRK10463        103 KQLVLNLVSSPGSGKTTLLTE  123 (290)
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            589999999999999999853

>CHL00176 ftsH cell division protein; Validated

Probab=95.08  E-value=0.014  Score=52.55  Aligned_cols=45  Identities=24%  Similarity=0.161  Sum_probs=32.0

Q ss_pred             cccccccchhHHHHHHHhhhcC----------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAES----------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~----------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++.|.+..++++.+++..-.          ..-+-+-++|.+|.|||+||+++
T Consensus       182 f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAral  236 (638)
T CHL00176        182 FRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAI  236 (638)
T ss_pred             HHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHH
Confidence            3568899888887776653211          11335778999999999999974

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=95.07  E-value=0.021  Score=46.81  Aligned_cols=22  Identities=23%  Similarity=0.348  Sum_probs=18.8

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-..|.+.||.|.||||+|+.+
T Consensus       132 ~~~~I~l~G~~GsGKStvg~~L  153 (309)
T PRK08154        132 RRRRIALIGLRGAGKSTLGRML  153 (309)
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            3567999999999999999853

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.05  E-value=0.017  Score=50.41  Aligned_cols=45  Identities=20%  Similarity=0.146  Sum_probs=30.4

Q ss_pred             cccccccchhHHHHHHHhhh----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAA----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++.|.+..++++.+++..          +...-+-+-++|.+|.|||+||+++
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~al  108 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAV  108 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHH
Confidence            35678888777766655431          0111234668999999999999864

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.

>PLN03046 D-glycerate 3-kinase; Provisional

Probab=94.94  E-value=0.014  Score=49.81  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=18.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      --+|||.|..|.|||||++.+
T Consensus       212 PlIIGIsG~qGSGKSTLa~~L  232 (460)
T PLN03046        212 PLVIGFSAPQGCGKTTLVFAL  232 (460)
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            569999999999999999753

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

Probab=94.87  E-value=0.03  Score=45.54  Aligned_cols=32  Identities=25%  Similarity=0.382  Sum_probs=24.7

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .++...+........+|||-|.||.||+||.-
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~   69 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIE   69 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHH
Confidence            44555555555568899999999999999964

>PRK09183 transposase/IS protein; Provisional

Probab=94.86  E-value=0.014  Score=46.61  Aligned_cols=20  Identities=30%  Similarity=0.318  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+.|+|..|+|||+||.++
T Consensus       103 ~~v~l~Gp~GtGKThLa~al  122 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIAL  122 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHH
Confidence            45779999999999999863

>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=94.83  E-value=0.035  Score=46.23  Aligned_cols=43  Identities=21%  Similarity=0.319  Sum_probs=36.4

Q ss_pred             ccccccchhHHHHHHHhhhcC----CCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAES----KDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~----~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|++..++.+.+.+....    ..-+++=+.|..|.||||||..
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~  107 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAEL  107 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHH
Confidence            479999999999999887532    2378999999999999999975

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.83  E-value=0.028  Score=49.55  Aligned_cols=43  Identities=23%  Similarity=0.413  Sum_probs=32.0

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++++|.+..++.+...+.... ... +=|+|-.|+||||+|+++
T Consensus        64 f~~iiGqs~~i~~l~~al~~~~-~~~-vLi~Ge~GtGKt~lAr~i  106 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCGPN-PQH-VIIYGPPGVGKTAAARLV  106 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhCCC-Cce-EEEECCCCCCHHHHHHHH
Confidence            3579999988888876654322 233 458999999999999863

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=94.80  E-value=0.024  Score=49.67  Aligned_cols=44  Identities=27%  Similarity=0.294  Sum_probs=31.6

Q ss_pred             ccccccchhHHHHHHHhhhc-----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE-----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~-----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++.+.+.+...           -...+-+-++|.+|.|||++|+++
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAl  236 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAV  236 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHH
Confidence            56778998888887765321           112344678999999999999874

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=94.79  E-value=0.015  Score=45.75  Aligned_cols=20  Identities=15%  Similarity=0.375  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+.+-|||..|+|||+|+++
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a   64 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHA   64 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            45788999999999999975

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

Probab=94.76  E-value=0.016  Score=50.72  Aligned_cols=20  Identities=40%  Similarity=0.519  Sum_probs=18.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++||+|-.|.||||||+.+
T Consensus       318 E~lglVGeSGsGKSTlar~i  337 (539)
T COG1123         318 ETLGLVGESGSGKSTLARIL  337 (539)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999864

>PRK10867 signal recognition particle protein; Provisional

Probab=94.74  E-value=0.19  Score=43.25  Aligned_cols=19  Identities=32%  Similarity=0.373  Sum_probs=16.6

Q ss_pred             eEEEEEEcCCCCcHHHHhc
Q 047923          170 VYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~  188 (190)
                      -.++-++|.+|+||||+|.
T Consensus       100 p~vI~~vG~~GsGKTTtaa  118 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAG  118 (433)
T ss_pred             CEEEEEECCCCCcHHHHHH
Confidence            5789999999999999664

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

Probab=94.72  E-value=0.036  Score=46.58  Aligned_cols=47  Identities=23%  Similarity=0.272  Sum_probs=35.0

Q ss_pred             cccccccccchhHHHHHHHhhhc-CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE-SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~-~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+..+.+||++.+++...|..- .+. -.-+-|+|-.|.|||+.++.|
T Consensus        14 ~iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v   62 (366)
T COG1474          14 YIPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFV   62 (366)
T ss_pred             CCcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHH
Confidence            44556999999999998887642 111 222788999999999998753

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

Probab=94.62  E-value=0.06  Score=49.33  Aligned_cols=44  Identities=18%  Similarity=0.305  Sum_probs=33.8

Q ss_pred             ccccccchhHHHHHHHhhhc------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+.-++.+.+.+...      .+. ..++-++|..|+|||+||+++
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~l  504 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQL  504 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHH
Confidence            56889999889888776632      112 446779999999999999864

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

Probab=94.61  E-value=0.027  Score=44.59  Aligned_cols=47  Identities=19%  Similarity=0.322  Sum_probs=33.0

Q ss_pred             cccccccccchhHHHHHHHhhh--cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAA--ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~--~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++++|.|..++.+.+-...  ......-+=+||..|.|||+|++++
T Consensus        24 ~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkal   72 (249)
T PF05673_consen   24 IRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKAL   72 (249)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHH
Confidence            3446799999999988653321  1112444557999999999999864

>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=94.58  E-value=0.02  Score=44.91  Aligned_cols=21  Identities=33%  Similarity=0.355  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||++.+
T Consensus        47 Ge~~~i~G~NGsGKSTLl~~i   67 (236)
T cd03267          47 GEIVGFIGPNGAGKTTTLKIL   67 (236)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            358999999999999999853

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.

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

Probab=94.56  E-value=0.022  Score=44.36  Aligned_cols=21  Identities=29%  Similarity=0.359  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||++.+
T Consensus        48 Ge~~~i~G~nGsGKSTLl~~l   68 (224)
T cd03220          48 GERIGLIGRNGAGKSTLLRLL   68 (224)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999999853

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.

>PRK06526 transposase; Provisional

Probab=94.52  E-value=0.018  Score=45.97  Aligned_cols=20  Identities=25%  Similarity=0.145  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|.+|.|||+||.++
T Consensus        99 ~nlll~Gp~GtGKThLa~al  118 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGL  118 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHH
Confidence            45789999999999999863

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=94.52  E-value=0.021  Score=45.83  Aligned_cols=21  Identities=24%  Similarity=0.267  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||++.+
T Consensus        50 Ge~~~I~G~nGsGKSTLl~~i   70 (271)
T PRK14238         50 NEVTAIIGPSGCGKSTYIKTL   70 (271)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            358999999999999999853

>PLN02165 adenylate isopentenyltransferase

Probab=94.50  E-value=0.021  Score=47.31  Aligned_cols=20  Identities=20%  Similarity=0.277  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.|+|+.|.||||||..
T Consensus        43 g~iivIiGPTGSGKStLA~~   62 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVD   62 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            45899999999999999974

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

Probab=94.50  E-value=0.021  Score=48.00  Aligned_cols=21  Identities=38%  Similarity=0.578  Sum_probs=19.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -+.++|||.+|.|||.+|+++
T Consensus       148 PlgllL~GPPGcGKTllArai  168 (413)
T PLN00020        148 PLILGIWGGKGQGKSFQCELV  168 (413)
T ss_pred             CeEEEeeCCCCCCHHHHHHHH
Confidence            689999999999999999864

>PRK14248 phosphate ABC transporter ATP-binding protein; Provisional

Probab=94.48  E-value=0.022  Score=45.61  Aligned_cols=21  Identities=24%  Similarity=0.322  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus        47 Ge~~~i~G~nGsGKSTLl~~l   67 (268)
T PRK14248         47 HAVTALIGPSGCGKSTFLRSI   67 (268)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999998753

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

Probab=94.42  E-value=0.04  Score=47.05  Aligned_cols=20  Identities=25%  Similarity=0.207  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|..|+||||||+++
T Consensus       109 ~~iLl~Gp~GtGKT~lAr~l  128 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQTL  128 (412)
T ss_pred             ceEEEEcCCCCCHHHHHHHH
Confidence            45778999999999999863

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.41  E-value=0.074  Score=45.10  Aligned_cols=20  Identities=25%  Similarity=0.283  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+++.++|..|+||||.+..
T Consensus       174 ~~vi~lvGptGvGKTTT~aK  193 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAK  193 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46899999999999998753

>PRK08727 hypothetical protein; Validated

Probab=94.38  E-value=0.053  Score=42.57  Aligned_cols=20  Identities=35%  Similarity=0.242  Sum_probs=17.5

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-|+|..|.|||+|++++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~   61 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALAL   61 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45899999999999999863

>PRK12289 GTPase RsgA; Reviewed

Probab=94.29  E-value=0.28  Score=41.12  Aligned_cols=30  Identities=13%  Similarity=0.395  Sum_probs=20.7

Q ss_pred             HhhcccceEEEecCCCc-CchhhHHHHHHHH
Q 047923           26 AIESPAISVIIFSEGYP-FSRWCLHELVKIL   55 (190)
Q Consensus        26 ai~~s~~~ivv~S~~y~-~S~wcl~El~~i~   55 (190)
                      ++.+++..++|++-.=. .+.|-++++....
T Consensus        86 ~~aNvD~vLlV~d~~~p~~~~~~LdR~L~~a  116 (352)
T PRK12289         86 PVANADQILLVFALAEPPLDPWQLSRFLVKA  116 (352)
T ss_pred             hhhcCCEEEEEEECCCCCCCHHHHHHHHHHH
Confidence            58889999999996523 2566667665544

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

Probab=94.24  E-value=0.026  Score=45.21  Aligned_cols=21  Identities=33%  Similarity=0.397  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|..|.|||||.+.+
T Consensus        50 Ge~~~l~G~nGsGKSTLl~~L   70 (269)
T cd03294          50 GEIFVIMGLSGSGKSTLLRCI   70 (269)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            458999999999999998753

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.

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

Probab=94.23  E-value=0.026  Score=46.52  Aligned_cols=20  Identities=25%  Similarity=0.395  Sum_probs=18.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      |+|=++|.+|.|||+|+|++
T Consensus       178 RliLlhGPPGTGKTSLCKaL  197 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTSLCKAL  197 (423)
T ss_pred             eEEEEeCCCCCChhHHHHHH
Confidence            78889999999999999863

>PRK12377 putative replication protein; Provisional

Probab=94.20  E-value=0.037  Score=44.03  Aligned_cols=21  Identities=24%  Similarity=0.145  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+-++|-.|+|||+||.++
T Consensus       101 ~~~l~l~G~~GtGKThLa~AI  121 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAI  121 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            356889999999999999864

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

Probab=94.18  E-value=0.03  Score=44.22  Aligned_cols=43  Identities=28%  Similarity=0.253  Sum_probs=30.7

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..-.++||-+.-++.+.-....  .++.-+-|-||+|+||||-+.
T Consensus        24 ~~l~dIVGNe~tv~rl~via~~--gnmP~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   24 SVLQDIVGNEDTVERLSVIAKE--GNMPNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             hHHHHhhCCHHHHHHHHHHHHc--CCCCceEeeCCCCCchhhHHH
Confidence            3446789988777666543333  247778899999999999654

>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional

Probab=94.14  E-value=0.026  Score=46.80  Aligned_cols=21  Identities=38%  Similarity=0.294  Sum_probs=18.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|-.|.|||||++++
T Consensus        42 Ge~~~ivG~sGsGKSTL~~~l   62 (330)
T PRK09473         42 GETLGIVGESGSGKSQTAFAL   62 (330)
T ss_pred             CCEEEEECCCCchHHHHHHHH
Confidence            457999999999999999864

>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional

Probab=94.14  E-value=0.028  Score=46.55  Aligned_cols=20  Identities=35%  Similarity=0.438  Sum_probs=17.9

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|-.|.|||||++.+
T Consensus        42 e~~~IvG~sGsGKSTLl~~l   61 (327)
T PRK11308         42 KTLAVVGESGCGKSTLARLL   61 (327)
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            57999999999999999864

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=94.14  E-value=0.027  Score=48.37  Aligned_cols=20  Identities=40%  Similarity=0.614  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++|+.|..|+||||+++.
T Consensus       367 gEvigilGpNgiGKTTFvk~  386 (591)
T COG1245         367 GEVIGILGPNGIGKTTFVKL  386 (591)
T ss_pred             ceEEEEECCCCcchHHHHHH
Confidence            46999999999999999975

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=94.13  E-value=0.031  Score=44.84  Aligned_cols=21  Identities=24%  Similarity=0.472  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus        50 Ge~~~liG~NGsGKSTLlk~L   70 (264)
T PRK13546         50 GDVIGLVGINGSGKSTLSNII   70 (264)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357899999999999999853

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.12  E-value=0.05  Score=43.17  Aligned_cols=21  Identities=24%  Similarity=0.186  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+-++|-+|.|||+||.++
T Consensus        99 ~~~~~l~G~~GtGKThLa~ai  119 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAI  119 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            446789999999999999864

>cd01878 HflX HflX subfamily

Probab=94.11  E-value=0.029  Score=42.71  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=18.9

Q ss_pred             CCeEEEEEEcCCCCcHHHHhcc
Q 047923          168 KDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +....++|.|.+|+|||||.+.
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~   60 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNA   60 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHH
Confidence            4567899999999999999864

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.

>cd01856 YlqF YlqF

Probab=94.11  E-value=0.66  Score=34.37  Aligned_cols=28  Identities=11%  Similarity=0.141  Sum_probs=22.6

Q ss_pred             cchHHHHHHhhcccceEEEecCCCcCch
Q 047923           18 EISESIAYAIESPAISVIIFSEGYPFSR   45 (190)
Q Consensus        18 ~~~~~l~~ai~~s~~~ivv~S~~y~~S~   45 (190)
                      .+..++.++++++++.+.|+..+...+.
T Consensus         8 ~~~~~~~~~i~~aD~il~v~D~~~~~~~   35 (171)
T cd01856           8 KALRQIKEKLKLVDLVIEVRDARIPLSS   35 (171)
T ss_pred             HHHHHHHHHHhhCCEEEEEeeccCccCc
Confidence            4567899999999999999987765443

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.

>PRK14265 phosphate ABC transporter ATP-binding protein; Provisional

Probab=94.06  E-value=0.032  Score=44.88  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||++.+
T Consensus        46 Ge~~~IiG~nGsGKSTLl~~l   66 (274)
T PRK14265         46 KKIIAFIGPSGCGKSTLLRCF   66 (274)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999999853

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=94.06  E-value=0.059  Score=45.08  Aligned_cols=45  Identities=22%  Similarity=0.213  Sum_probs=34.4

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .....++|.+.-.+.+...+..+. --..+=|.|..|+||||+|..
T Consensus        20 ~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~   64 (351)
T PRK09112         20 SENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFH   64 (351)
T ss_pred             CchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHH
Confidence            445679999988888888776542 123567899999999999975

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=94.04  E-value=0.031  Score=44.75  Aligned_cols=21  Identities=24%  Similarity=0.291  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|-.|.|||||.+.+
T Consensus        45 Ge~~~i~G~nGsGKSTLl~~l   65 (267)
T PRK14235         45 KTVTAFIGPSGCGKSTFLRCL   65 (267)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357899999999999999853

>PRK14236 phosphate transporter ATP-binding protein; Provisional

Probab=94.01  E-value=0.031  Score=44.86  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|-.|.|||||++.+
T Consensus        51 Ge~~~I~G~nGsGKSTLl~~l   71 (272)
T PRK14236         51 NRVTAFIGPSGCGKSTLLRCF   71 (272)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            358999999999999999853

>PRK10536 hypothetical protein; Provisional

Probab=94.01  E-value=0.074  Score=42.52  Aligned_cols=39  Identities=18%  Similarity=0.169  Sum_probs=28.8

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.++......+..+|..    ..++-+.|..|.|||+||.+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~----~~lV~i~G~aGTGKT~La~a   93 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES----KQLIFATGEAGCGKTWISAA   93 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc----CCeEEEECCCCCCHHHHHHH
Confidence            4456676666666666643    23788999999999999975

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.00  E-value=0.029  Score=47.25  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.++|..|+||||++..
T Consensus       137 g~ii~lvGptGvGKTTtiak  156 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAK  156 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            46899999999999999864

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.99  E-value=0.1  Score=44.18  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-+++.++|..|+||||++..
T Consensus       205 ~~~ii~lvGptGvGKTTt~ak  225 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVK  225 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            367999999999999999754

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

Probab=93.98  E-value=0.048  Score=45.85  Aligned_cols=21  Identities=33%  Similarity=0.490  Sum_probs=18.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++++|.|..|.|||||...
T Consensus       204 ~~~~~~~~g~~~~GKtt~~~~  224 (366)
T PRK14489        204 APPLLGVVGYSGTGKTTLLEK  224 (366)
T ss_pred             CccEEEEecCCCCCHHHHHHH
Confidence            477999999999999999764

>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=93.98  E-value=0.032  Score=43.30  Aligned_cols=22  Identities=18%  Similarity=0.181  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-.+++|.|-.|.|||||++.+
T Consensus        39 ~Ge~~~i~G~nGsGKSTLl~~l   60 (226)
T cd03248          39 PGEVTALVGPSGSGKSTVVALL   60 (226)
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            3457999999999999999853

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.

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

Probab=93.95  E-value=0.061  Score=44.40  Aligned_cols=41  Identities=34%  Similarity=0.362  Sum_probs=27.7

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.....+...+..+.    -+=+.|.+|+|||+||+.+
T Consensus        23 ~~~~~g~~~~~~~~l~a~~~~~----~vll~G~PG~gKT~la~~l   63 (329)
T COG0714          23 EKVVVGDEEVIELALLALLAGG----HVLLEGPPGVGKTLLARAL   63 (329)
T ss_pred             CCeeeccHHHHHHHHHHHHcCC----CEEEECCCCccHHHHHHHH
Confidence            3448887766666554443331    2457799999999999863

>PRK14271 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.92  E-value=0.033  Score=44.85  Aligned_cols=21  Identities=29%  Similarity=0.303  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||++.+
T Consensus        47 Ge~~~I~G~nGsGKSTLl~~l   67 (276)
T PRK14271         47 RAVTSLMGPTGSGKTTFLRTL   67 (276)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            457999999999999999853

>PRK14237 phosphate transporter ATP-binding protein; Provisional

Probab=93.88  E-value=0.034  Score=44.48  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|-.|.|||||.+.+
T Consensus        46 Ge~~~I~G~nGsGKSTLl~~l   66 (267)
T PRK14237         46 NKITALIGPSGSGKSTYLRSL   66 (267)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999999853

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=93.86  E-value=0.03  Score=46.60  Aligned_cols=20  Identities=25%  Similarity=0.310  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-|+|.+|+||||+++++
T Consensus        41 ~~i~I~G~~GtGKT~l~~~~   60 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTKYV   60 (365)
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            34778999999999999853

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.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=93.83  E-value=0.09  Score=37.40  Aligned_cols=43  Identities=21%  Similarity=0.417  Sum_probs=31.3

Q ss_pred             ccccccchhHHHHHHHhhh-----cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAA-----ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|..--.+.+.+.+..     ..++--|+...|-.|+|||.+|+.
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~l   72 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRL   72 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHH
Confidence            3577777666666555542     234578999999999999998875

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

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.82  E-value=0.098  Score=48.81  Aligned_cols=45  Identities=22%  Similarity=0.385  Sum_probs=34.9

Q ss_pred             cccccccchhHHHHHHHhhhc------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-++.+...+...      .+. ...+-+.|..|+|||++|+++
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~L  615 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKAL  615 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHH
Confidence            356899999999998877642      111 456779999999999999864

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.

>PRK15079 oligopeptide ABC transporter ATP-binding protein OppF; Provisional

Probab=93.75  E-value=0.036  Score=45.94  Aligned_cols=21  Identities=43%  Similarity=0.484  Sum_probs=18.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|+|-.|.|||||++.+
T Consensus        47 Ge~~~lvG~sGsGKSTLlk~i   67 (331)
T PRK15079         47 GETLGVVGESGCGKSTFARAI   67 (331)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            458999999999999999864

>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1

Probab=93.70  E-value=0.038  Score=44.75  Aligned_cols=21  Identities=29%  Similarity=0.229  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|-.|.|||||++.+
T Consensus        63 Ge~~~liG~NGsGKSTLl~~I   83 (282)
T cd03291          63 GEMLAITGSTGSGKTSLLMLI   83 (282)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999999853

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.

>PRK14275 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.68  E-value=0.041  Score=44.54  Aligned_cols=20  Identities=40%  Similarity=0.579  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus        66 e~~~l~G~nGsGKSTLl~~L   85 (286)
T PRK14275         66 YVTAIIGPSGCGKSTFLRAI   85 (286)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            58999999999999998753

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=93.68  E-value=0.063  Score=45.16  Aligned_cols=45  Identities=20%  Similarity=0.141  Sum_probs=33.9

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+++|.+.-.+.+.+.+..+. --.-+=++|..|+||||+|.+
T Consensus        16 ~~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~   60 (365)
T PRK07471         16 RETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYR   60 (365)
T ss_pred             CchhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHH
Confidence            344679999988888887776542 123466899999999999975

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=93.67  E-value=0.069  Score=48.64  Aligned_cols=46  Identities=17%  Similarity=0.278  Sum_probs=34.9

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+.-++.+...+..+. -....=++|..|+||||+|+.+
T Consensus        15 ~~f~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriL   60 (725)
T PRK07133         15 KTFDDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIF   60 (725)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHH
Confidence            344679999998888888886542 1344558999999999999853

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=93.64  E-value=0.038  Score=45.71  Aligned_cols=20  Identities=35%  Similarity=0.451  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+.|.|..|.|||||++.
T Consensus       162 ~~~~~~~G~~~~gkstl~~~  181 (325)
T TIGR01526       162 VKTVAILGGESTGKSTLVNK  181 (325)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45789999999999999985

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.

>PF13245 AAA_19: Part of AAA domain

Probab=93.63  E-value=0.039  Score=35.59  Aligned_cols=17  Identities=29%  Similarity=0.292  Sum_probs=13.3

Q ss_pred             EEEEEEcCCCCcHHHHh
Q 047923          171 YILGIWGVGSIGKTTIA  187 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla  187 (190)
                      +++-|.|.+|.||||++
T Consensus        11 ~~~vv~g~pGtGKT~~~   27 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTL   27 (76)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35667899999999554

>PRK14252 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.63  E-value=0.04  Score=43.96  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .=.+++|.|..|.|||||.+.+
T Consensus        41 ~Ge~~~i~G~nGsGKSTLl~~l   62 (265)
T PRK14252         41 EKQVTALIGPSGCGKSTFLRCF   62 (265)
T ss_pred             CCcEEEEECCCCCCHHHHHHHH
Confidence            3457999999999999998753

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

Probab=93.61  E-value=0.12  Score=47.60  Aligned_cols=44  Identities=16%  Similarity=0.227  Sum_probs=33.9

Q ss_pred             ccccccchhHHHHHHHhhhc------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+.-++.+.+.+...      .++ ...+-++|..|+|||+||+++
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~L  508 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQL  508 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHH
Confidence            46889999999988877632      122 456778999999999999863

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

Probab=93.61  E-value=0.034  Score=50.24  Aligned_cols=20  Identities=40%  Similarity=0.479  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+++-++|.+|+||||||..
T Consensus       326 kKilLL~GppGlGKTTLAHV  345 (877)
T KOG1969|consen  326 KKILLLCGPPGLGKTTLAHV  345 (877)
T ss_pred             cceEEeecCCCCChhHHHHH
Confidence            67888999999999999964

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=93.58  E-value=0.38  Score=41.10  Aligned_cols=40  Identities=25%  Similarity=0.228  Sum_probs=27.0

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..|.......+.+++. +-..-.++-|-|.+|+||||+|-.
T Consensus       174 ~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~GKT~~al~  213 (421)
T TIGR03600       174 LTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMGKTTLALN  213 (421)
T ss_pred             CcceeCCChhHHHHhc-CCCCCceEEEEeCCCCCHHHHHHH
Confidence            4566666666666654 222244677889999999999853

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.

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=93.58  E-value=0.041  Score=44.96  Aligned_cols=20  Identities=35%  Similarity=0.388  Sum_probs=17.4

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      -++.|.|..|+||||+|+.+
T Consensus        93 ~iIlI~G~sgsGKStlA~~L  112 (301)
T PRK04220         93 IIILIGGASGVGTSTIAFEL  112 (301)
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            47889999999999999753

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.56  E-value=0.039  Score=48.03  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++++|..|+||||++..
T Consensus       256 g~Vi~LvGpnGvGKTTTiaK  275 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAK  275 (484)
T ss_pred             CcEEEEECCCCccHHHHHHH
Confidence            36999999999999998764

>TIGR03156 GTP_HflX GTP-binding protein HflX

Probab=93.55  E-value=0.16  Score=42.48  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=18.0

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +...++|+|.+++|||||-.+
T Consensus       188 ~~~~ValvG~~NvGKSSLln~  208 (351)
T TIGR03156       188 DVPTVALVGYTNAGKSTLFNA  208 (351)
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            456799999999999999764

This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.45  E-value=0.076  Score=48.68  Aligned_cols=44  Identities=18%  Similarity=0.169  Sum_probs=30.7

Q ss_pred             ccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+.-++.+.+.+..           +-..-+-+-++|.+|.|||+||+++
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakal  507 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAV  507 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHH
Confidence            4567888887777665542           1111344678999999999999874

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.36  E-value=0.042  Score=48.31  Aligned_cols=20  Identities=25%  Similarity=0.252  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|.+|+||||++..
T Consensus       350 G~vIaLVGPtGvGKTTtaak  369 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAK  369 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            47999999999999999864

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.33  E-value=0.046  Score=46.79  Aligned_cols=20  Identities=25%  Similarity=0.307  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++++|..|+||||+...
T Consensus       191 g~vi~lvGpnG~GKTTtlak  210 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAK  210 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            47899999999999999863

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.32  E-value=0.053  Score=44.32  Aligned_cols=19  Identities=37%  Similarity=0.293  Sum_probs=16.2

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      .+-|.|..|.||||+++++
T Consensus       134 ~ilI~G~tGSGKTTll~al  152 (299)
T TIGR02782       134 NILVVGGTGSGKTTLANAL  152 (299)
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4569999999999999763

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=93.31  E-value=0.064  Score=47.31  Aligned_cols=45  Identities=20%  Similarity=0.324  Sum_probs=34.6

Q ss_pred             ccccccccchhHHHHHHHhhhcCC-CeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAESK-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....++|....++++.+.+..-.. +.. |-|+|-.|.|||++|+++
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~~~~p-vli~Ge~GtGK~~lA~~i  239 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVARSNST-VLLRGESGTGKELIAKAI  239 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhCcCCC-EEEECCCCccHHHHHHHH
Confidence            346789999999999887765322 333 449999999999999864

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.

>cd01854 YjeQ_engC YjeQ/EngC

Probab=93.28  E-value=0.074  Score=43.18  Aligned_cols=19  Identities=26%  Similarity=0.345  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++++.|..|+|||||.+.
T Consensus       162 k~~~~~G~sg~GKSTlin~  180 (287)
T cd01854         162 KTSVLVGQSGVGKSTLINA  180 (287)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            5789999999999999864

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=93.24  E-value=0.047  Score=42.95  Aligned_cols=19  Identities=21%  Similarity=0.723  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +.+-|||-.|+|||.|+++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a   64 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQA   64 (234)
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            5678999999999999986

>PRK14264 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.22  E-value=0.051  Score=44.44  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|..|.|||||.+.+
T Consensus        71 Ge~~~IvG~nGsGKSTLl~~L   91 (305)
T PRK14264         71 KSVTALIGPSGCGKSTFLRCL   91 (305)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            458999999999999999753

>PRK14254 phosphate ABC transporter ATP-binding protein; Provisional

Probab=93.21  E-value=0.051  Score=44.00  Aligned_cols=21  Identities=24%  Similarity=0.313  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|-.|.|||||.+.+
T Consensus        65 Ge~~~I~G~nGsGKSTLl~~l   85 (285)
T PRK14254         65 NQVTAMIGPSGCGKSTFLRCI   85 (285)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999998753

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.21  E-value=0.067  Score=43.85  Aligned_cols=20  Identities=30%  Similarity=0.190  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..+.|.|-.|.|||||+++
T Consensus       144 ~~~ili~G~tGsGKTTll~a  163 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKS  163 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            46789999999999999875

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.

>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=93.18  E-value=0.052  Score=44.78  Aligned_cols=21  Identities=29%  Similarity=0.203  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|-.|.|||||.+.+
T Consensus        52 Ge~~~I~G~nGsGKSTLl~~L   72 (320)
T PRK13631         52 NKIYFIIGNSGSGKSTLVTHF   72 (320)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999998753

>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=93.17  E-value=0.036  Score=48.13  Aligned_cols=20  Identities=40%  Similarity=0.529  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      |--|+||..|+|||||-+++
T Consensus       107 rRYGLvGrNG~GKsTLLRai  126 (582)
T KOG0062|consen  107 RRYGLVGRNGIGKSTLLRAI  126 (582)
T ss_pred             cccceeCCCCCcHHHHHHHH
Confidence            55799999999999998874

>cd01855 YqeH YqeH

Probab=93.12  E-value=0.076  Score=40.08  Aligned_cols=30  Identities=13%  Similarity=-0.106  Sum_probs=21.8

Q ss_pred             ccchHHHHHHhhcccceEEEecCCCcCchh
Q 047923           17 DEISESIAYAIESPAISVIIFSEGYPFSRW   46 (190)
Q Consensus        17 ~~~~~~l~~ai~~s~~~ivv~S~~y~~S~w   46 (190)
                      +.|...+...++.+++.+.|+.-.-....|
T Consensus        22 ~~~~~~l~~~~~~ad~il~VvD~~~~~~~~   51 (190)
T cd01855          22 DFILNLLSSISPKKALVVHVVDIFDFPGSL   51 (190)
T ss_pred             HHHHHHHHhcccCCcEEEEEEECccCCCcc
Confidence            344566777889999999999976554444

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.

>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=93.12  E-value=0.11  Score=38.68  Aligned_cols=31  Identities=23%  Similarity=0.388  Sum_probs=23.2

Q ss_pred             hhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          154 SRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       154 ~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++++.++|..     +++.+.|..|+|||||..+
T Consensus        24 ~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~   54 (161)
T PF03193_consen   24 EGIEELKELLKG-----KTSVLLGQSGVGKSSLINA   54 (161)
T ss_dssp             TTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHH
T ss_pred             cCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHH
Confidence            345666666643     4788899999999999864

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.

>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]

Probab=93.11  E-value=0.09  Score=42.27  Aligned_cols=34  Identities=29%  Similarity=0.495  Sum_probs=23.9

Q ss_pred             HHHHHHHhhhcCC-CeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESK-DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~-~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+...|..... ..-+|||.|-.|+||+|+|+.
T Consensus        67 ~~~~~~~l~~~~~~~pfIIgiaGsvavGKST~ar~  101 (283)
T COG1072          67 FAELLRFLGTNNQQRPFIIGIAGSVAVGKSTTARI  101 (283)
T ss_pred             HHHHHHHhccCCCCCCEEEEeccCccccHHHHHHH
Confidence            3344444443333 367999999999999999974

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

Probab=93.08  E-value=0.047  Score=41.13  Aligned_cols=20  Identities=35%  Similarity=0.313  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|..|+|||.||.++
T Consensus        48 ~~l~l~G~~G~GKThLa~ai   67 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAI   67 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHH
T ss_pred             eEEEEEhhHhHHHHHHHHHH
Confidence            45889999999999999753

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.

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

Probab=93.06  E-value=0.067  Score=45.68  Aligned_cols=20  Identities=25%  Similarity=0.207  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-++|..|+|||+||+++
T Consensus       117 ~~iLL~GP~GsGKT~lAraL  136 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTL  136 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHH
Confidence            35778999999999999864

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.

>PRK13409 putative ATPase RIL; Provisional

Probab=93.04  E-value=0.056  Score=48.31  Aligned_cols=21  Identities=38%  Similarity=0.460  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.++||+|..|.|||||.+.+
T Consensus        99 Gev~gLvG~NGaGKSTLlkiL  119 (590)
T PRK13409         99 GKVTGILGPNGIGKTTAVKIL  119 (590)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            468999999999999998753

>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=92.98  E-value=0.095  Score=44.01  Aligned_cols=46  Identities=26%  Similarity=0.221  Sum_probs=29.2

Q ss_pred             cccccccccchhHHHH---HHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEII---ESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~---~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.++||...-.+..   .+++....=.=+.+=|.|.+|.|||+||-+
T Consensus        21 ~~~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~   69 (398)
T PF06068_consen   21 YIADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMA   69 (398)
T ss_dssp             SEETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHH
T ss_pred             eccccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHH
Confidence            4567899998766665   344443321235666999999999999964

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.

>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=92.97  E-value=0.065  Score=42.81  Aligned_cols=37  Identities=30%  Similarity=0.203  Sum_probs=25.9

Q ss_pred             chhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          153 ESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       153 d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+.+.++|......-..+-|.|..|.||||++++
T Consensus       110 ~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~a  146 (270)
T PF00437_consen  110 GSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNA  146 (270)
T ss_dssp             HHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHH
T ss_pred             hhhHHHHHHHHhhccccceEEEEECCCccccchHHHH
Confidence            3344556666654322356788999999999999875

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 ....

>CHL00095 clpC Clp protease ATP binding subunit

Probab=92.95  E-value=0.18  Score=46.97  Aligned_cols=44  Identities=16%  Similarity=0.329  Sum_probs=33.1

Q ss_pred             ccccccchhHHHHHHHhhhc------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+.-++.+...+...      .+. ...+-++|..|+|||+||+++
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~L  559 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKAL  559 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHH
Confidence            57889999999987766531      111 445668999999999999863

>cd01859 MJ1464 MJ1464

Probab=92.94  E-value=0.14  Score=37.22  Aligned_cols=38  Identities=26%  Similarity=0.418  Sum_probs=24.7

Q ss_pred             ccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          151 GRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       151 G~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      |.+.-.+.+.+.+.......+ +.++|.+|+|||||...
T Consensus        83 gi~~L~~~l~~~~~~~~~~~~-~~~ig~~~~Gkssl~~~  120 (156)
T cd01859          83 GTKILRRTIKELAKIDGKEGK-VGVVGYPNVGKSSIINA  120 (156)
T ss_pred             cHHHHHHHHHHHHhhcCCCcE-EEEECCCCCCHHHHHHH
Confidence            555555555555543322344 48999999999999754

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.

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=92.92  E-value=0.055  Score=48.66  Aligned_cols=21  Identities=33%  Similarity=0.213  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|..|.|||||++++
T Consensus        42 Ge~~~lvG~nGsGKSTLl~~l   62 (623)
T PRK10261         42 GETLAIVGESGSGKSVTALAL   62 (623)
T ss_pred             CCEEEEECCCCChHHHHHHHH
Confidence            357999999999999999864

>PLN02199 shikimate kinase

Probab=92.91  E-value=0.054  Score=44.15  Aligned_cols=19  Identities=26%  Similarity=0.328  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +.|.++||.|.||||+++.
T Consensus       103 ~~I~LIG~~GSGKSTVgr~  121 (303)
T PLN02199        103 RSMYLVGMMGSGKTTVGKL  121 (303)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3578999999999999975

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.83  E-value=0.56  Score=38.55  Aligned_cols=44  Identities=20%  Similarity=0.273  Sum_probs=32.5

Q ss_pred             ccccccchhHHHHHHHhhh----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++-|.|.-++.+.+..-.          .....+-|-++|.+|.||+.||++|
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAV  186 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAV  186 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHH
Confidence            3556999888888764221          1223777888999999999999986

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=92.82  E-value=0.062  Score=48.98  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|-.|.|||||+|.+
T Consensus       500 e~vaIvG~SGsGKSTL~KLL  519 (709)
T COG2274         500 EKVAIVGRSGSGKSTLLKLL  519 (709)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            56999999999999999853

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=92.81  E-value=0.056  Score=46.67  Aligned_cols=20  Identities=25%  Similarity=0.360  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-|||..|+|||+|++++
T Consensus       142 npl~L~G~~G~GKTHLl~Ai  161 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAA  161 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHH
Confidence            45779999999999999864

>PRK08116 hypothetical protein; Validated

Probab=92.81  E-value=0.058  Score=43.39  Aligned_cols=19  Identities=37%  Similarity=0.473  Sum_probs=16.6

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      -+-+||-.|.|||.||.++
T Consensus       116 gl~l~G~~GtGKThLa~ai  134 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACI  134 (268)
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4779999999999999864

>cd03288 ABCC_SUR2 The SUR domain 2

Probab=92.80  E-value=0.064  Score=42.63  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|-.|.|||||.+.+
T Consensus        48 e~~~i~G~nGsGKSTLl~~l   67 (257)
T cd03288          48 QKVGICGRTGSGKSSLSLAF   67 (257)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57999999999999999853

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=92.78  E-value=0.1  Score=44.30  Aligned_cols=21  Identities=33%  Similarity=0.300  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+-|+|..|.|||+|++++
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai  156 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAI  156 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHH
Confidence            345789999999999999864

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).

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=92.76  E-value=0.067  Score=46.84  Aligned_cols=21  Identities=29%  Similarity=0.340  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus       289 Ge~~~l~G~NGsGKSTLlk~i  309 (510)
T PRK09700        289 GEILGFAGLVGSGRTELMNCL  309 (510)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            358899999999999999854

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

Probab=92.76  E-value=0.18  Score=42.25  Aligned_cols=46  Identities=26%  Similarity=0.206  Sum_probs=32.9

Q ss_pred             cccccccccchhHHH---HHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEI---IESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~---~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++||...-.+.   +.++...+.-.-+-|=|.|.+|.|||+||-.
T Consensus        36 ~~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~g   84 (450)
T COG1224          36 FIGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMG   84 (450)
T ss_pred             EcCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHH
Confidence            355789998866554   3556655433356777899999999999953

>PRK13409 putative ATPase RIL; Provisional

Probab=92.76  E-value=0.062  Score=48.05  Aligned_cols=20  Identities=45%  Similarity=0.625  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||++.+
T Consensus       366 eiv~l~G~NGsGKSTLlk~L  385 (590)
T PRK13409        366 EVIGIVGPNGIGKTTFAKLL  385 (590)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            47999999999999999853

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.75  E-value=0.17  Score=42.80  Aligned_cols=65  Identities=18%  Similarity=0.265  Sum_probs=38.0

Q ss_pred             hhhhHHHHHHHHHhhhhhhhhccccccccccchhHHHHHHHhhhc----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          122 ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAE----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       122 e~~~i~~iv~~v~~~l~~~~~~~~~~~~vG~d~~~~~~~~~l~~~----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +..+++.+-.+|.+.-+.    ..=+++.|...-++-+.+.....          ....+-+-.+|.+|.|||-|||+|
T Consensus       191 d~~Lve~lerdIl~~np~----ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAv  265 (491)
T KOG0738|consen  191 DADLVEALERDILQRNPN----IKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAV  265 (491)
T ss_pred             hHHHHHHHHHHHhccCCC----cChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHH
Confidence            445555555555433211    12245677776655554432211          112566678899999999999985

>PRK06921 hypothetical protein; Provisional

Probab=92.75  E-value=0.059  Score=43.29  Aligned_cols=21  Identities=24%  Similarity=0.289  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.-+-++|-.|+|||+||.++
T Consensus       117 ~~~l~l~G~~G~GKThLa~ai  137 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAA  137 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHH
Confidence            456789999999999999864

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=92.74  E-value=0.064  Score=46.92  Aligned_cols=20  Identities=35%  Similarity=0.511  Sum_probs=17.9

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       289 e~~~l~G~NGsGKSTLlk~i  308 (506)
T PRK13549        289 EILGIAGLVGAGRTELVQCL  308 (506)
T ss_pred             cEEEEeCCCCCCHHHHHHHH
Confidence            58999999999999999864

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=92.73  E-value=0.067  Score=46.86  Aligned_cols=20  Identities=40%  Similarity=0.539  Sum_probs=18.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       290 e~~~l~G~NGsGKSTLl~~i  309 (510)
T PRK15439        290 EILGLAGVVGAGRTELAETL  309 (510)
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999864

>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional

Probab=92.71  E-value=0.067  Score=46.60  Aligned_cols=20  Identities=35%  Similarity=0.388  Sum_probs=17.9

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       275 e~~~l~G~nGsGKSTLl~~l  294 (491)
T PRK10982        275 EILGIAGLVGAKRTDIVETL  294 (491)
T ss_pred             cEEEEecCCCCCHHHHHHHH
Confidence            58999999999999998864

>PRK06835 DNA replication protein DnaC; Validated

Probab=92.67  E-value=0.061  Score=44.59  Aligned_cols=20  Identities=25%  Similarity=0.240  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|-.|+|||.||.++
T Consensus       184 ~~Lll~G~~GtGKThLa~aI  203 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCI  203 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHH
Confidence            56889999999999999864

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=92.63  E-value=0.11  Score=46.74  Aligned_cols=40  Identities=28%  Similarity=0.427  Sum_probs=31.3

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.++|.+.-++.+...+...    +.+-++|-+|.||||+|+++
T Consensus        31 ~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l   70 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAM   70 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHH
Confidence            46889888888777666544    35778999999999999863

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=92.60  E-value=0.072  Score=42.08  Aligned_cols=20  Identities=30%  Similarity=0.396  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =..+||+|..|.|||||-|.
T Consensus        53 Ge~vGiiG~NGaGKSTLlkl   72 (249)
T COG1134          53 GERVGIIGHNGAGKSTLLKL   72 (249)
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            34699999999999999874

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

Probab=92.58  E-value=0.13  Score=47.21  Aligned_cols=38  Identities=24%  Similarity=0.496  Sum_probs=29.7

Q ss_pred             ccccccchhHHHHHHHhhhcC--CCeEEEEEEcCCCCcHHHHhc
Q 047923          147 NQLVGRESRVEIIESLLAAES--KDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~--~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .-++|||.+.+.+.+.|....  |.+    ++|-+|+|||+++.
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~KNNPv----LiGEpGVGKTAIvE  209 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTKNNPV----LVGEPGVGKTAIVE  209 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCCCCCe----EecCCCCCHHHHHH
Confidence            347899999999999887532  324    34999999999875

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.57  E-value=0.19  Score=46.88  Aligned_cols=45  Identities=20%  Similarity=0.355  Sum_probs=34.6

Q ss_pred             cccccccchhHHHHHHHhhhc------CC-CeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE------SK-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~------~~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-++.+.+.+...      .+ ...++-++|..|+|||.||+++
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~L  616 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALAL  616 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHH
Confidence            357899999999998776431      11 2557889999999999999863

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=92.55  E-value=0.12  Score=45.58  Aligned_cols=43  Identities=30%  Similarity=0.336  Sum_probs=32.3

Q ss_pred             ccccccchhHHHHHHHhhhc---CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRESRVEIIESLLAAE---SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~---~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++.--...++++..||...   ....+++-+.|.+|.||||..+.
T Consensus        19 ~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~   64 (519)
T PF03215_consen   19 DELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKV   64 (519)
T ss_pred             HHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHH
Confidence            34555566788888888752   22367999999999999999875

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=92.53  E-value=0.069  Score=46.88  Aligned_cols=20  Identities=25%  Similarity=0.227  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =..++|+|..|.|||||++.
T Consensus       361 G~~vaIvG~SGsGKSTLl~l  380 (529)
T TIGR02868       361 GERVAILGPSGSGKSTLLML  380 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999985

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.

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=92.52  E-value=0.072  Score=44.33  Aligned_cols=20  Identities=40%  Similarity=0.544  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.++||.|..|.|||||.+.
T Consensus        67 Gei~gLlGpNGaGKSTLl~~   86 (340)
T PRK13536         67 GECFGLLGPNGAGKSTIARM   86 (340)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            46899999999999999875

>PHA02244 ATPase-like protein

Probab=92.48  E-value=0.1  Score=43.86  Aligned_cols=18  Identities=28%  Similarity=0.226  Sum_probs=15.3

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +-|+|..|+|||+||+++
T Consensus       122 VLL~GppGtGKTtLA~aL  139 (383)
T PHA02244        122 VFLKGGAGSGKNHIAEQI  139 (383)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            446899999999999864

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=92.47  E-value=0.07  Score=47.97  Aligned_cols=20  Identities=35%  Similarity=0.381  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|-.|.|||||++.+
T Consensus       351 e~~~lvG~nGsGKSTLlk~i  370 (623)
T PRK10261        351 ETLSLVGESGSGKSTTGRAL  370 (623)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999863

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=92.47  E-value=0.075  Score=46.75  Aligned_cols=20  Identities=35%  Similarity=0.370  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       313 e~~~i~G~nGsGKSTLlk~l  332 (529)
T PRK15134        313 ETLGLVGESGSGKSTTGLAL  332 (529)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57999999999999999853

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.46  E-value=0.12  Score=43.58  Aligned_cols=33  Identities=24%  Similarity=0.239  Sum_probs=23.6

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++.++|..+-..-.++-|.|-+|+|||||+.+
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq  101 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQ  101 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHH
Confidence            344455654333456889999999999999864

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=92.44  E-value=0.12  Score=44.66  Aligned_cols=21  Identities=33%  Similarity=0.300  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-+-|+|..|.|||+|++++
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai  168 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAI  168 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            456789999999999999864

>PRK11819 putative ABC transporter ATP-binding protein; Reviewed

Probab=92.37  E-value=0.079  Score=46.95  Aligned_cols=20  Identities=35%  Similarity=0.483  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       351 e~~~l~G~NGsGKSTLl~~i  370 (556)
T PRK11819        351 GIVGIIGPNGAGKSTLFKMI  370 (556)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57999999999999998853

>PRK10762 D-ribose transporter ATP binding protein; Provisional

Probab=92.36  E-value=0.077  Score=46.36  Aligned_cols=20  Identities=30%  Similarity=0.497  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       279 e~~~liG~NGsGKSTLl~~l  298 (501)
T PRK10762        279 EILGVSGLMGAGRTELMKVL  298 (501)
T ss_pred             cEEEEecCCCCCHHHHHHHH
Confidence            48999999999999998853

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=92.26  E-value=0.27  Score=42.48  Aligned_cols=18  Identities=28%  Similarity=0.388  Sum_probs=15.9

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      .++|+|.+++|||||..+
T Consensus       217 kV~ivG~~nvGKSSLln~  234 (449)
T PRK05291        217 KVVIAGRPNVGKSSLLNA  234 (449)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            578999999999999764

>TIGR03719 ABC_ABC_ChvD ATP-binding cassette protein, ChvD family

Probab=92.25  E-value=0.086  Score=46.67  Aligned_cols=20  Identities=35%  Similarity=0.501  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       349 e~~~l~G~NGsGKSTLl~~l  368 (552)
T TIGR03719       349 GIVGVIGPNGAGKSTLFRMI  368 (552)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999853

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.

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=92.25  E-value=0.083  Score=46.48  Aligned_cols=20  Identities=40%  Similarity=0.483  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       346 e~~~l~G~NGsGKSTLl~~i  365 (530)
T PRK15064        346 ERLAIIGENGVGKTTLLRTL  365 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            58999999999999999853

>PLN03073 ABC transporter F family; Provisional

Probab=92.23  E-value=0.085  Score=48.28  Aligned_cols=21  Identities=33%  Similarity=0.306  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =..+||+|-.|.|||||.+.+
T Consensus       203 Ge~~gLvG~NGsGKSTLLr~l  223 (718)
T PLN03073        203 GRHYGLVGRNGTGKTTFLRYM  223 (718)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357999999999999998864

>TIGR02012 tigrfam_recA protein RecA

Probab=92.20  E-value=0.19  Score=41.58  Aligned_cols=30  Identities=33%  Similarity=0.386  Sum_probs=21.8

Q ss_pred             HHHHhh-hcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          159 IESLLA-AESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       159 ~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +..+|. .+=..-+++-|+|.+|.||||||-
T Consensus        43 LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL   73 (321)
T TIGR02012        43 LDLALGVGGLPRGRIIEIYGPESSGKTTLAL   73 (321)
T ss_pred             HHHHhcCCCCcCCeEEEEECCCCCCHHHHHH
Confidence            335554 332346788899999999999985

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.

>TIGR00416 sms DNA repair protein RadA

Probab=92.20  E-value=0.13  Score=44.48  Aligned_cols=35  Identities=20%  Similarity=0.175  Sum_probs=25.3

Q ss_pred             hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++..+|..+-..-.++-|.|-+|+|||||+..
T Consensus        79 Gi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq  113 (454)
T TIGR00416        79 GFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQ  113 (454)
T ss_pred             CcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHH
Confidence            34555566654434456888999999999999864

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)).

>TIGR00767 rho transcription termination factor Rho

Probab=92.17  E-value=0.079  Score=45.03  Aligned_cols=20  Identities=20%  Similarity=-0.046  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|.+|.|||||++.+
T Consensus       169 q~~~IvG~~g~GKTtL~~~i  188 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKI  188 (415)
T ss_pred             CEEEEECCCCCChhHHHHHH
Confidence            45789999999999999853

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

>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional

Probab=92.12  E-value=0.079  Score=45.13  Aligned_cols=21  Identities=33%  Similarity=0.382  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus        54 Gei~~LvG~NGsGKSTLLr~I   74 (400)
T PRK10070         54 GEIFVIMGLSGSGKSTMVRLL   74 (400)
T ss_pred             CCEEEEECCCCchHHHHHHHH
Confidence            357999999999999998853

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.11  E-value=0.093  Score=43.48  Aligned_cols=20  Identities=25%  Similarity=0.317  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+++
T Consensus       109 e~v~IvG~~GsGKSTLl~~L  128 (329)
T PRK14257        109 KVTAFIGPSGCGKSTFLRNL  128 (329)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57999999999999999864

>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional

Probab=92.11  E-value=0.089  Score=45.96  Aligned_cols=20  Identities=20%  Similarity=0.536  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       280 e~~~iiG~NGsGKSTLlk~l  299 (501)
T PRK11288        280 EIVGLFGLVGAGRSELMKLL  299 (501)
T ss_pred             cEEEEEcCCCCCHHHHHHHH
Confidence            58999999999999998853

>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional

Probab=92.08  E-value=0.085  Score=46.27  Aligned_cols=21  Identities=38%  Similarity=0.458  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+|+|-|..|.||||+|+.+
T Consensus       284 ~~ii~i~G~sgsGKst~a~~l  304 (512)
T PRK13477        284 QPIIAIDGPAGAGKSTVTRAV  304 (512)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            357899999999999999863

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=92.08  E-value=0.43  Score=41.24  Aligned_cols=18  Identities=33%  Similarity=0.536  Sum_probs=15.7

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -+.|+|.+|+|||||..+
T Consensus       205 kVvIvG~~nvGKSSLiN~  222 (442)
T TIGR00450       205 KLAIVGSPNVGKSSLLNA  222 (442)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            467999999999999864

TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer.

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=92.03  E-value=0.087  Score=46.23  Aligned_cols=20  Identities=40%  Similarity=0.596  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus       311 e~~~l~G~NGsGKSTLl~~l  330 (520)
T TIGR03269       311 EIFGIVGTSGAGKTTLSKII  330 (520)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            47899999999999999853

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.01  E-value=0.11  Score=32.14  Aligned_cols=18  Identities=33%  Similarity=0.357  Sum_probs=15.8

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      +..|.|-.|.|||||..+
T Consensus        25 ~tli~G~nGsGKSTllDA   42 (62)
T PF13555_consen   25 VTLITGPNGSGKSTLLDA   42 (62)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            678999999999999765

>PRK00098 GTPase RsgA; Reviewed

Probab=92.01  E-value=0.092  Score=42.86  Aligned_cols=19  Identities=26%  Similarity=0.400  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++++|..|+|||||.++
T Consensus       165 k~~~~~G~sgvGKStlin~  183 (298)
T PRK00098        165 KVTVLAGQSGVGKSTLLNA  183 (298)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4788999999999999764

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

Probab=92.01  E-value=0.083  Score=44.08  Aligned_cols=43  Identities=19%  Similarity=0.285  Sum_probs=29.7

Q ss_pred             cccccchhHHHHHHHhhhc--C---------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAE--S---------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~--~---------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++=|.+.+.+++.+-....  +         +.-.=+=+||.+|.|||-|||+|
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAV  205 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAV  205 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHH
Confidence            3447888888887765431  1         11233447999999999999986

>PRK09866 hypothetical protein; Provisional

Probab=92.00  E-value=0.15  Score=45.86  Aligned_cols=38  Identities=26%  Similarity=0.265  Sum_probs=27.8

Q ss_pred             chhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          153 ESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       153 d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++.+.+.|..-.....+++|+|..|.|||||.+++
T Consensus        52 ~~ri~~L~~~L~Kv~~~~~~valvG~sgaGKSTLiNaL   89 (741)
T PRK09866         52 AERHAMLNNELRKISRLEMVLAIVGTMKAGKSTTINAI   89 (741)
T ss_pred             HHHHHHHHHHHHHHhccceEEEEECCCCCCHHHHHHHH
Confidence            44566666666543334588999999999999998763

>PRK10636 putative ABC transporter ATP-binding protein; Provisional

Probab=92.00  E-value=0.093  Score=47.38  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|+|..|.|||||.+.+
T Consensus       338 Ge~~~l~G~NGsGKSTLlk~l  358 (638)
T PRK10636        338 GSRIGLLGRNGAGKSTLIKLL  358 (638)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            358999999999999998853

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=91.95  E-value=0.085  Score=45.91  Aligned_cols=20  Identities=45%  Similarity=0.544  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+||+|..|.|||||||.+
T Consensus       363 ~~lgIIGPSgSGKSTLaR~l  382 (580)
T COG4618         363 EALGIIGPSGSGKSTLARLL  382 (580)
T ss_pred             ceEEEECCCCccHHHHHHHH
Confidence            57899999999999999863

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=91.95  E-value=0.098  Score=45.22  Aligned_cols=21  Identities=33%  Similarity=0.409  Sum_probs=18.6

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.++-+.|.+|+||||+|..
T Consensus       254 ~p~vil~~G~~G~GKSt~a~~  274 (475)
T PRK12337        254 RPLHVLIGGVSGVGKSVLASA  274 (475)
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            368899999999999999975

>PRK08181 transposase; Validated

Probab=91.92  E-value=0.082  Score=42.58  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|.+|.|||.||.++
T Consensus       107 ~nlll~Gp~GtGKTHLa~Ai  126 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAI  126 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHH
Confidence            34789999999999999864

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=91.90  E-value=0.097  Score=45.55  Aligned_cols=20  Identities=25%  Similarity=0.182  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|-.|.|||||.+.+
T Consensus       287 e~~~i~G~NGsGKSTLl~~l  306 (490)
T PRK10938        287 EHWQIVGPNGAGKSTLLSLI  306 (490)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            47899999999999998853

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=91.90  E-value=0.13  Score=42.42  Aligned_cols=35  Identities=23%  Similarity=0.283  Sum_probs=25.8

Q ss_pred             hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      -...+..+|..+-..-.++-|+|-+|.||||||..
T Consensus        81 g~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~  115 (316)
T TIGR02239        81 GSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHT  115 (316)
T ss_pred             CCHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHH
Confidence            34455566655444578899999999999999863

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).

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=91.86  E-value=0.19  Score=36.60  Aligned_cols=20  Identities=25%  Similarity=0.552  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++++|.+|+||+||..+
T Consensus       100 ~~~~~~~G~~~~GKstlin~  119 (155)
T cd01849         100 SITVGVIGYPNVGKSSVINA  119 (155)
T ss_pred             CcEEEEEccCCCCHHHHHHH
Confidence            45688999999999998754

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.

>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein

Probab=91.86  E-value=0.1  Score=45.61  Aligned_cols=21  Identities=33%  Similarity=0.450  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|..|.|||||.+.+
T Consensus       286 Ge~~~l~G~NGsGKSTLl~~l  306 (500)
T TIGR02633       286 GEILGVAGLVGAGRTELVQAL  306 (500)
T ss_pred             CcEEEEeCCCCCCHHHHHHHH
Confidence            358999999999999998753

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).

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=91.83  E-value=0.098  Score=47.16  Aligned_cols=20  Identities=25%  Similarity=0.328  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       346 e~~~l~G~NGsGKSTLlk~l  365 (635)
T PRK11147        346 DKIALIGPNGCGKTTLLKLM  365 (635)
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            47999999999999998853

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=91.82  E-value=0.13  Score=42.32  Aligned_cols=20  Identities=25%  Similarity=0.461  Sum_probs=17.0

Q ss_pred             CeEEEEEEc-CCCCcHHHHhc
Q 047923          169 DVYILGIWG-VGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G-~gGiGKTTla~  188 (190)
                      ..++|+++| -||+||||+|-
T Consensus        92 ~~~vIav~~~KGGvGkTT~a~  112 (322)
T TIGR03815        92 RGVVVAVIGGRGGAGASTLAA  112 (322)
T ss_pred             CceEEEEEcCCCCCcHHHHHH
Confidence            368999995 79999999985

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.

>PTZ00035 Rad51 protein; Provisional

Probab=91.82  E-value=0.15  Score=42.37  Aligned_cols=33  Identities=21%  Similarity=0.303  Sum_probs=24.6

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.++|..+-..-.++-|+|-.|.|||||+..
T Consensus       105 ~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~  137 (337)
T PTZ00035        105 TQLDKLLGGGIETGSITELFGEFRTGKTQLCHT  137 (337)
T ss_pred             HHHHHHhCCCCCCCeEEEEECCCCCchhHHHHH
Confidence            445566654434467899999999999999863

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=91.81  E-value=0.085  Score=43.61  Aligned_cols=31  Identities=19%  Similarity=0.105  Sum_probs=21.3

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+...|..+    +-|-|.|.+|.||||+|+++
T Consensus        54 ~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~l   84 (327)
T TIGR01650        54 TKAICAGFAYD----RRVMVQGYHGTGKSTHIEQI   84 (327)
T ss_pred             HHHHHHHHhcC----CcEEEEeCCCChHHHHHHHH
Confidence            34444445332    24778999999999999853

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.

>PF11868 DUF3388: Protein of unknown function (DUF3388); InterPro: IPR024514 This domain is found in a family of bacterial proteins that are functionally uncharacterised

Probab=91.80  E-value=0.15  Score=37.70  Aligned_cols=27  Identities=26%  Similarity=0.485  Sum_probs=19.6

Q ss_pred             HHHHhhhcCCCeEEEEEEcCCCCcHHHHh
Q 047923          159 IESLLAAESKDVYILGIWGVGSIGKTTIA  187 (190)
Q Consensus       159 ~~~~l~~~~~~~~vi~i~G~gGiGKTTla  187 (190)
                      +.+++..  ++-.+|||.||+-+|||--+
T Consensus        45 maEl~K~--~Gh~lIGiRGmPRVGKTEsi   71 (192)
T PF11868_consen   45 MAELFKE--EGHKLIGIRGMPRVGKTESI   71 (192)
T ss_pred             HHHHHHh--cCceEEeecCCCccCchhHH
Confidence            3344443  35789999999999999643

Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.

>TIGR00665 DnaB replicative DNA helicase

Probab=91.73  E-value=0.73  Score=39.52  Aligned_cols=40  Identities=18%  Similarity=0.192  Sum_probs=26.2

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..|.......+.+++. +-..-.++-|-|.+|+||||+|..
T Consensus       175 ~~gi~tG~~~LD~~~~-G~~~G~l~vi~g~pg~GKT~~~l~  214 (434)
T TIGR00665       175 ITGVPTGFTDLDKLTS-GLQPSDLIILAARPSMGKTAFALN  214 (434)
T ss_pred             CCcccCCchhhHhhcC-CCCCCeEEEEEeCCCCChHHHHHH
Confidence            4455555555655553 222345777889999999999853

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.

>PRK08840 replicative DNA helicase; Provisional

Probab=91.72  E-value=1  Score=39.21  Aligned_cols=39  Identities=21%  Similarity=0.203  Sum_probs=24.5

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|...-...+.+++.. -..-.++-|-|.+|+||||+|-
T Consensus       197 ~~gi~TG~~~LD~~~~G-~~~g~LiviaarPg~GKTafal  235 (464)
T PRK08840        197 VTGVDTGFTDLNKKTAG-LQGSDLIIVAARPSMGKTTFAM  235 (464)
T ss_pred             CCCcCCCcHHHHHhhcC-CCCCceEEEEeCCCCchHHHHH
Confidence            45666555555554421 1123456677999999999973

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=91.71  E-value=0.096  Score=43.49  Aligned_cols=20  Identities=40%  Similarity=0.257  Sum_probs=17.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..|-|.|..|.||||+.++
T Consensus       160 ~~nili~G~tgSGKTTll~a  179 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFTNA  179 (332)
T ss_pred             CCcEEEECCCCCCHHHHHHH
Confidence            34588999999999999875

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=91.69  E-value=0.22  Score=40.68  Aligned_cols=32  Identities=25%  Similarity=0.322  Sum_probs=22.6

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+|..+-..-.++-|+|.+|.||||||-.
T Consensus        83 ~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~  114 (310)
T TIGR02236        83 ELDELLGGGIETQAITEVFGEFGSGKTQICHQ  114 (310)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHH
Confidence            34455553323357888999999999999853

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=91.68  E-value=0.17  Score=41.61  Aligned_cols=32  Identities=19%  Similarity=0.387  Sum_probs=23.4

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..+.++|..+-..-++.=|+|.+|.||||||-
T Consensus        83 ~~LD~lLgGGi~~G~iteI~G~~GsGKTql~l  114 (313)
T TIGR02238        83 QALDGILGGGIESMSITEVFGEFRCGKTQLSH  114 (313)
T ss_pred             HHHHHHhCCCCcCCeEEEEECCCCCCcCHHHH
Confidence            34445665443446788899999999999985

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=91.63  E-value=0.12  Score=42.71  Aligned_cols=20  Identities=30%  Similarity=0.227  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-|.|..|.||||+++++
T Consensus       149 ~~ilI~G~tGSGKTTll~aL  168 (319)
T PRK13894        149 RNILVIGGTGSGKTTLVNAI  168 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45778899999999998753

>COG4240 Predicted kinase [General function prediction only]

Probab=91.59  E-value=0.098  Score=41.18  Aligned_cols=21  Identities=33%  Similarity=0.466  Sum_probs=18.3

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .--++||.|.-|.|||||+-+
T Consensus        49 rPli~gisGpQGSGKStls~~   69 (300)
T COG4240          49 RPLIVGISGPQGSGKSTLSAL   69 (300)
T ss_pred             CceEEEeecCCCCchhhHHHH
Confidence            356899999999999999864

>PRK06851 hypothetical protein; Provisional

Probab=91.57  E-value=0.49  Score=39.84  Aligned_cols=21  Identities=19%  Similarity=0.098  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -+++-|-|.+|+|||||++.+
T Consensus       214 ~~~~~i~G~pG~GKstl~~~i  234 (367)
T PRK06851        214 KNRYFLKGRPGTGKSTMLKKI  234 (367)
T ss_pred             ceEEEEeCCCCCcHHHHHHHH
Confidence            467889999999999998753

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

Probab=91.54  E-value=0.1  Score=42.86  Aligned_cols=20  Identities=40%  Similarity=0.401  Sum_probs=18.1

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|||.+|.|||-||++|
T Consensus       167 kg~ll~GppGtGKTlla~~V  186 (388)
T KOG0651|consen  167 KGLLLYGPPGTGKTLLARAV  186 (388)
T ss_pred             ceeEEeCCCCCchhHHHHHH
Confidence            57899999999999999875

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=91.53  E-value=0.12  Score=43.19  Aligned_cols=21  Identities=24%  Similarity=0.297  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..+-|.|-.|.||||+++++
T Consensus       162 ~~nilI~G~tGSGKTTll~aL  182 (344)
T PRK13851        162 RLTMLLCGPTGSGKTTMSKTL  182 (344)
T ss_pred             CCeEEEECCCCccHHHHHHHH
Confidence            345889999999999999863

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=91.48  E-value=0.24  Score=40.95  Aligned_cols=31  Identities=32%  Similarity=0.379  Sum_probs=22.0

Q ss_pred             HHHHhh-hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          159 IESLLA-AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       159 ~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..+|. .+=..-+++=|+|.+|.||||||-.
T Consensus        43 LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~   74 (325)
T cd00983          43 LDIALGIGGYPKGRIIEIYGPESSGKTTLALH   74 (325)
T ss_pred             HHHHhcCCCccCCeEEEEECCCCCCHHHHHHH
Confidence            345555 3323356788999999999999853

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK08760 replicative DNA helicase; Provisional

Probab=91.47  E-value=1  Score=39.33  Aligned_cols=39  Identities=18%  Similarity=0.205  Sum_probs=25.6

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       209 ~~Gi~TG~~~LD~~t~-G~~~G~LivIaarPg~GKTafal  247 (476)
T PRK08760        209 ITGLPTGYNDFDAMTA-GLQPTDLIILAARPAMGKTTFAL  247 (476)
T ss_pred             CCcccCCcHHHHHHhc-CCCCCceEEEEeCCCCChhHHHH
Confidence            4455555666655442 21224567788999999999985

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=91.47  E-value=0.1  Score=44.68  Aligned_cols=20  Identities=35%  Similarity=0.353  Sum_probs=16.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+-++|.+|+||||||+++
T Consensus        48 ~~ILLiGppG~GKT~lAraL   67 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIARRL   67 (441)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            34668999999999999864

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.

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=91.47  E-value=0.087  Score=44.81  Aligned_cols=20  Identities=35%  Similarity=0.443  Sum_probs=17.9

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+||+|-.|.|||||++++
T Consensus       314 qTlGlVGESGSGKsTlG~al  333 (534)
T COG4172         314 QTLGLVGESGSGKSTLGLAL  333 (534)
T ss_pred             CeEEEEecCCCCcchHHHHH
Confidence            57999999999999999863

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=91.45  E-value=0.21  Score=40.23  Aligned_cols=30  Identities=10%  Similarity=0.176  Sum_probs=23.2

Q ss_pred             cchHHHHHHhhcccceEEEecCCCcCchhh
Q 047923           18 EISESIAYAIESPAISVIIFSEGYPFSRWC   47 (190)
Q Consensus        18 ~~~~~l~~ai~~s~~~ivv~S~~y~~S~wc   47 (190)
                      ....++.++++++++.+.|+.-....+..+
T Consensus        10 k~~~~~~~~l~~aDvVl~V~Dar~p~~~~~   39 (276)
T TIGR03596        10 KARREIKEKLKLVDVVIEVLDARIPLSSRN   39 (276)
T ss_pred             HHHHHHHHHHhhCCEEEEEEeCCCCCCCCC
Confidence            345788999999999999998765555444

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.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=91.40  E-value=0.12  Score=45.58  Aligned_cols=21  Identities=33%  Similarity=0.477  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|..|.|||||.+.+
T Consensus        50 GEivgIiGpNGSGKSTLLkiL   70 (549)
T PRK13545         50 GEIVGIIGLNGSGKSTLSNLI   70 (549)
T ss_pred             CCEEEEEcCCCCCHHHHHHHH
Confidence            358999999999999999853

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=91.36  E-value=0.28  Score=39.32  Aligned_cols=36  Identities=31%  Similarity=0.325  Sum_probs=23.4

Q ss_pred             ccch-hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          151 GRES-RVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       151 G~d~-~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      |... ..+.+..++...   -.++.|.|..|.||||+.++
T Consensus        63 g~~~~~~~~l~~~~~~~---~GlilisG~tGSGKTT~l~a   99 (264)
T cd01129          63 GLKPENLEIFRKLLEKP---HGIILVTGPTGSGKTTTLYS   99 (264)
T ss_pred             CCCHHHHHHHHHHHhcC---CCEEEEECCCCCcHHHHHHH
Confidence            4443 333444444322   34688999999999999874

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.

>PLN03073 ABC transporter F family; Provisional

Probab=91.34  E-value=0.12  Score=47.38  Aligned_cols=20  Identities=30%  Similarity=0.398  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+.+
T Consensus       536 e~i~LvG~NGsGKSTLLk~L  555 (718)
T PLN03073        536 SRIAMVGPNGIGKSTILKLI  555 (718)
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            47999999999999998853

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.32  E-value=0.39  Score=38.74  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+.++|-+|.||||+++.
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~   94 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAK   94 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            46899999999999998864

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=91.32  E-value=0.11  Score=46.05  Aligned_cols=20  Identities=30%  Similarity=0.330  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|..|.|||||++.+
T Consensus       370 ~~~aIvG~sGsGKSTLl~ll  389 (582)
T PRK11176        370 KTVALVGRSGSGKSTIANLL  389 (582)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            56899999999999999853

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=91.29  E-value=0.17  Score=46.09  Aligned_cols=44  Identities=23%  Similarity=0.268  Sum_probs=32.9

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....++.+.+.+..-...-.-|=|.|-.|.|||++|+++
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~i  419 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAI  419 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHH
Confidence            46999998888887766542222234568899999999999864

>CHL00195 ycf46 Ycf46; Provisional

Probab=91.25  E-value=0.21  Score=43.70  Aligned_cols=44  Identities=16%  Similarity=0.132  Sum_probs=28.2

Q ss_pred             ccccccchhHHHHHHHhh---h-----cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLA---A-----ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~---~-----~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++-|.+.-++.+.+...   .     +-..-+-+=++|.+|.|||.+|+++
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkai  279 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAI  279 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHH
Confidence            456687766665544211   1     1112345668999999999999874

>PRK12288 GTPase RsgA; Reviewed

Probab=91.24  E-value=0.2  Score=41.81  Aligned_cols=30  Identities=27%  Similarity=0.352  Sum_probs=21.0

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++++.++|..     .++.++|..|+|||||..++
T Consensus       196 ideL~~~L~~-----ki~~~vG~sgVGKSTLiN~L  225 (347)
T PRK12288        196 LEELEAALTG-----RISIFVGQSGVGKSSLINAL  225 (347)
T ss_pred             HHHHHHHHhh-----CCEEEECCCCCCHHHHHHHh
Confidence            4455555542     24679999999999998653

>TIGR03415 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein

Probab=91.24  E-value=0.12  Score=43.76  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus        50 Gei~~I~G~nGsGKSTLlr~L   70 (382)
T TIGR03415        50 GEICVLMGLSGSGKSSLLRAV   70 (382)
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            357999999999999999853

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=91.22  E-value=0.27  Score=39.63  Aligned_cols=21  Identities=33%  Similarity=0.219  Sum_probs=18.6

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..-++|+|..|.|||||.+.
T Consensus       110 ~~~~~~i~g~~g~GKttl~~~  130 (270)
T TIGR02858       110 RVLNTLIISPPQCGKTTLLRD  130 (270)
T ss_pred             CeeEEEEEcCCCCCHHHHHHH
Confidence            467899999999999999875

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.

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

Probab=91.20  E-value=0.11  Score=44.44  Aligned_cols=20  Identities=35%  Similarity=0.353  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-++|..|+||||||+++
T Consensus        51 ~~ILliGp~G~GKT~LAr~L   70 (443)
T PRK05201         51 KNILMIGPTGVGKTEIARRL   70 (443)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            34678999999999999863

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=91.19  E-value=0.11  Score=44.81  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-+-|||-.|.|||+|++++
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai  150 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSI  150 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHH
Confidence            345889999999999999864

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=91.19  E-value=0.18  Score=44.20  Aligned_cols=46  Identities=22%  Similarity=0.350  Sum_probs=34.9

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....++|....++.+.+.+..-...-.-|=|.|-.|.|||++|+++
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~i  230 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAI  230 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHH
Confidence            3457999999999888877653322234558999999999999864

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=91.17  E-value=0.26  Score=36.86  Aligned_cols=20  Identities=20%  Similarity=0.532  Sum_probs=16.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.++++|++++||+||-.+
T Consensus       117 ~~~~~~vG~pnvGKSslin~  136 (172)
T cd04178         117 SITVGVVGFPNVGKSSLINS  136 (172)
T ss_pred             CcEEEEEcCCCCCHHHHHHH
Confidence            34688999999999999754

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

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=91.12  E-value=0.12  Score=46.89  Aligned_cols=19  Identities=32%  Similarity=0.435  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       480 e~vaIvG~sGsGKSTLlkl  498 (686)
T TIGR03797       480 EFVAIVGPSGSGKSTLLRL  498 (686)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999985

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=91.08  E-value=0.48  Score=40.97  Aligned_cols=59  Identities=25%  Similarity=0.318  Sum_probs=43.5

Q ss_pred             HHHHHHHHhhhhhhhhccccccccccchhHHHHHHHhhh--cCCCeEEEEEEcCCCCcHHHHhc
Q 047923          127 KEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAA--ESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       127 ~~iv~~v~~~l~~~~~~~~~~~~vG~d~~~~~~~~~l~~--~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +++..+....+..+   ..+..++||+.++..+.+++..  +.+.-..+-+.|.+|.|||.+-.
T Consensus       133 ke~~~~~~~~l~~t---~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~  193 (529)
T KOG2227|consen  133 KEISEQRSESLLNT---APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLS  193 (529)
T ss_pred             HHHHHHHHHHHHhc---CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHH
Confidence            33444445455444   4567899999999999999875  34457778889999999998753

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=91.05  E-value=0.13  Score=45.55  Aligned_cols=19  Identities=26%  Similarity=0.352  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       356 e~vaiVG~sGsGKSTl~~L  374 (567)
T COG1132         356 EKVAIVGPSGSGKSTLIKL  374 (567)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5688999999999999975

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

Probab=91.04  E-value=0.2  Score=40.97  Aligned_cols=42  Identities=26%  Similarity=0.339  Sum_probs=34.0

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+++|.+.-+..+.+-+..  ......-.||.+|.|||+-|.+
T Consensus        35 ~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStala   76 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALA   76 (346)
T ss_pred             HHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHH
Confidence            45788999888888777655  3577788999999999998864

>PRK05973 replicative DNA helicase; Provisional

Probab=91.02  E-value=0.16  Score=40.13  Aligned_cols=20  Identities=15%  Similarity=0.004  Sum_probs=16.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++-|.|.+|.||||+|-.
T Consensus        64 Gsl~LIaG~PG~GKT~lalq   83 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLE   83 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHH
Confidence            45677899999999999853

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=91.00  E-value=0.13  Score=46.81  Aligned_cols=20  Identities=30%  Similarity=0.330  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|..|.|||||++.+
T Consensus       501 ~~vaIvG~SGsGKSTLlklL  520 (708)
T TIGR01193       501 SKTTIVGMSGSGKSTLAKLL  520 (708)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999853

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.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=90.91  E-value=0.13  Score=41.12  Aligned_cols=22  Identities=32%  Similarity=0.226  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...-+-++|-+|+|||.||.++
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai  125 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAI  125 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHH
Confidence            3456789999999999999764

>PHA02624 large T antigen; Provisional

Probab=90.88  E-value=0.3  Score=43.68  Aligned_cols=31  Identities=26%  Similarity=0.124  Sum_probs=23.7

Q ss_pred             HHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          160 ESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       160 ~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+.+..+-.+-+++-++|..|.||||+|.++
T Consensus       421 lk~~l~giPKk~~il~~GPpnTGKTtf~~sL  451 (647)
T PHA02624        421 LKLIVENVPKRRYWLFKGPVNSGKTTLAAAL  451 (647)
T ss_pred             HHHHHhcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3334344456789999999999999999864

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=90.87  E-value=0.13  Score=45.38  Aligned_cols=19  Identities=26%  Similarity=0.373  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .-|+|+|..|+|||||.+.
T Consensus       349 ~riaiiG~NG~GKSTLlk~  367 (530)
T COG0488         349 DRIAIVGPNGAGKSTLLKL  367 (530)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4589999999999999875

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=90.86  E-value=0.25  Score=41.89  Aligned_cols=19  Identities=32%  Similarity=0.580  Sum_probs=16.3

Q ss_pred             eEEEEEEcCCCCcHHH-Hhc
Q 047923          170 VYILGIWGVGSIGKTT-IAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTT-la~  188 (190)
                      -+++.++|..|+|||| |||
T Consensus       203 ~~vi~LVGPTGVGKTTTlAK  222 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAK  222 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHH
Confidence            6899999999999986 454

>PRK15494 era GTPase Era; Provisional

Probab=90.78  E-value=0.14  Score=42.66  Aligned_cols=21  Identities=24%  Similarity=0.268  Sum_probs=17.6

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...-+.|+|.+|+|||||...
T Consensus        51 k~~kV~ivG~~nvGKSTLin~   71 (339)
T PRK15494         51 KTVSVCIIGRPNSGKSTLLNR   71 (339)
T ss_pred             ceeEEEEEcCCCCCHHHHHHH
Confidence            345689999999999999864

>PRK11823 DNA repair protein RadA; Provisional

Probab=90.73  E-value=0.23  Score=42.98  Aligned_cols=34  Identities=21%  Similarity=0.210  Sum_probs=24.3

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++.++|..+-..-.++-|.|-+|+|||||+.+
T Consensus        66 i~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq   99 (446)
T PRK11823         66 IGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQ   99 (446)
T ss_pred             cHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHH
Confidence            3455566654333456888999999999999864

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=90.72  E-value=0.15  Score=40.47  Aligned_cols=19  Identities=26%  Similarity=0.365  Sum_probs=16.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+.|+.|+|||||..+
T Consensus       121 ~~~~~~G~sgvGKStLiN~  139 (245)
T TIGR00157       121 RISVFAGQSGVGKSSLINA  139 (245)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3678999999999999764

The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=90.70  E-value=0.15  Score=43.13  Aligned_cols=20  Identities=35%  Similarity=0.421  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus        41 e~~~LlGpsGsGKSTLLr~I   60 (375)
T PRK09452         41 EFLTLLGPSGCGKTTVLRLI   60 (375)
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            47999999999999998753

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=90.70  E-value=0.15  Score=46.82  Aligned_cols=20  Identities=30%  Similarity=0.360  Sum_probs=17.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++++|..|+||||++..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaK  204 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAK  204 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            36999999999999998753

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=90.69  E-value=0.15  Score=43.14  Aligned_cols=20  Identities=30%  Similarity=0.479  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||.+.+
T Consensus        46 e~~~llGpsGsGKSTLLr~I   65 (377)
T PRK11607         46 EIFALLGASGCGKSTLLRML   65 (377)
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            58999999999999998753

>PRK09354 recA recombinase A; Provisional

Probab=90.68  E-value=0.33  Score=40.54  Aligned_cols=31  Identities=32%  Similarity=0.357  Sum_probs=22.3

Q ss_pred             HHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          158 IIESLLA-AESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       158 ~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .+..+|. .+=..-+++=|+|..|.||||||-
T Consensus        47 ~LD~~LG~GGip~G~IteI~G~~GsGKTtLal   78 (349)
T PRK09354         47 ALDIALGIGGLPRGRIVEIYGPESSGKTTLAL   78 (349)
T ss_pred             HHHHHhcCCCCcCCeEEEEECCCCCCHHHHHH
Confidence            3445565 332346788899999999999985

>KOG1547 consensus Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms; Cytoskeleton]

Probab=90.66  E-value=0.37  Score=38.28  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=31.0

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      -++||+|.-.+++...+....-+.. |-++|-.|.|||||..
T Consensus        24 lgyvGidtI~~Qm~~k~mk~GF~FN-IMVVgqSglgkstlin   64 (336)
T KOG1547|consen   24 LGYVGIDTIIEQMRKKTMKTGFDFN-IMVVGQSGLGKSTLIN   64 (336)
T ss_pred             cccccHHHHHHHHHHHHHhccCceE-EEEEecCCCCchhhHH
Confidence            3789999999999777665433333 4467999999999964

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=90.62  E-value=0.15  Score=46.45  Aligned_cols=20  Identities=30%  Similarity=0.338  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|..|.|||||++.+
T Consensus       506 e~vaIvG~sGsGKSTLlklL  525 (710)
T TIGR03796       506 QRVALVGGSGSGKSTIAKLV  525 (710)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999853

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.

>TIGR03453 partition_RepA plasmid partitioning protein RepA

Probab=90.62  E-value=0.41  Score=40.48  Aligned_cols=20  Identities=30%  Similarity=0.348  Sum_probs=16.7

Q ss_pred             CeEEEEEE-cCCCCcHHHHhc
Q 047923          169 DVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~-G~gGiGKTTla~  188 (190)
                      ..++|+|. .=||+||||+|-
T Consensus       103 ~~~vI~v~n~KGGvGKTT~a~  123 (387)
T TIGR03453       103 HLQVIAVTNFKGGSGKTTTAA  123 (387)
T ss_pred             CceEEEEEccCCCcCHHHHHH
Confidence            46888887 679999999875

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.

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

Probab=90.60  E-value=0.46  Score=43.71  Aligned_cols=44  Identities=20%  Similarity=0.383  Sum_probs=34.3

Q ss_pred             ccccccchhHHHHHHHhhhc------CC-CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE------SK-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~------~~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.|.-++.+.+-+...      .+ .+.+.=..|..|+|||-||+++
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaL  541 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKAL  541 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHH
Confidence            57899999999887776542      12 2667778899999999999864

>PRK08006 replicative DNA helicase; Provisional

Probab=90.58  E-value=1.5  Score=38.23  Aligned_cols=39  Identities=21%  Similarity=0.183  Sum_probs=24.3

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       204 ~~Gi~TG~~~LD~~~~-Gl~~G~LiiIaarPgmGKTafal  242 (471)
T PRK08006        204 VTGVNTGYDDLNKKTA-GLQPSDLIIVAARPSMGKTTFAM  242 (471)
T ss_pred             CCcccCCCHHHHHhhc-CCCCCcEEEEEeCCCCCHHHHHH
Confidence            4455555555555432 11123566677999999999974

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=90.54  E-value=0.3  Score=40.12  Aligned_cols=32  Identities=25%  Similarity=0.309  Sum_probs=22.3

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+|..+-..-.++=|+|.+|.||||||-.
T Consensus        90 ~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~  121 (317)
T PRK04301         90 ELDELLGGGIETQSITEFYGEFGSGKTQICHQ  121 (317)
T ss_pred             HHHHHhcCCccCCcEEEEECCCCCCHhHHHHH
Confidence            34445543323456788999999999999853

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.44  E-value=0.15  Score=41.88  Aligned_cols=21  Identities=29%  Similarity=0.251  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-+-++|-.|+|||.||.++
T Consensus       156 ~~gl~L~G~~G~GKThLa~Ai  176 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAI  176 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            455779999999999999864

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=90.34  E-value=0.17  Score=42.53  Aligned_cols=20  Identities=35%  Similarity=0.278  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.|.|..|.||||+.++
T Consensus       134 ~glilI~GpTGSGKTTtL~a  153 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAA  153 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            36899999999999999875

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.

>TIGR01842 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family

Probab=90.33  E-value=0.16  Score=44.83  Aligned_cols=20  Identities=40%  Similarity=0.438  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =..++|+|..|.|||||++.
T Consensus       344 G~~~~ivG~sGsGKSTL~~l  363 (544)
T TIGR01842       344 GEALAIIGPSGSGKSTLARL  363 (544)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999975

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.

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=90.30  E-value=0.17  Score=43.68  Aligned_cols=20  Identities=35%  Similarity=0.546  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.|+||.|..|+||||.++-
T Consensus       100 G~V~GilG~NGiGKsTalkI  119 (591)
T COG1245         100 GKVVGILGPNGIGKSTALKI  119 (591)
T ss_pred             CcEEEEEcCCCccHHHHHHH
Confidence            46899999999999998763

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=90.29  E-value=0.3  Score=40.76  Aligned_cols=31  Identities=26%  Similarity=0.327  Sum_probs=22.5

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .+.++|..+-..-.+.=|+|.+|.||||||-
T Consensus       114 ~LD~lLgGGi~~G~ItEI~G~~GsGKTql~l  144 (344)
T PLN03187        114 ALDELLGGGIETRCITEAFGEFRSGKTQLAH  144 (344)
T ss_pred             hHHhhcCCCCCCCeEEEEecCCCCChhHHHH
Confidence            3445565433345778899999999999985

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=90.26  E-value=0.17  Score=45.05  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|-.|.|||||++.+
T Consensus       362 ~~v~IvG~sGsGKSTLl~lL  381 (588)
T PRK13657        362 QTVAIVGPTGAGKSTLINLL  381 (588)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999853

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=90.25  E-value=0.16  Score=40.26  Aligned_cols=18  Identities=33%  Similarity=0.350  Sum_probs=15.4

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -..|+|..|.|||||.+.
T Consensus        59 ~W~I~G~NGsGKTTLL~l   76 (257)
T COG1119          59 HWAIVGPNGAGKTTLLSL   76 (257)
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            367889999999999874

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=90.25  E-value=0.28  Score=42.30  Aligned_cols=44  Identities=18%  Similarity=0.258  Sum_probs=32.8

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....+..+...+..-...-.-+-|.|-.|.|||++|+++
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~i  181 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHAL  181 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHH
Confidence            46889988888887777543333333569999999999999863

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

Probab=90.19  E-value=0.32  Score=39.03  Aligned_cols=43  Identities=19%  Similarity=0.200  Sum_probs=29.7

Q ss_pred             cccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++=|.|-.++++.+....           +-+.-|=+-+||.+|.|||.||++|
T Consensus       156 diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kav  209 (408)
T KOG0727|consen  156 DIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAV  209 (408)
T ss_pred             ccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHH
Confidence            445778777777664332           1123455668999999999999975

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=90.19  E-value=0.23  Score=43.78  Aligned_cols=45  Identities=22%  Similarity=0.137  Sum_probs=33.8

Q ss_pred             ccccccccchhHHHHHHHhhh-cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAA-ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~-~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|....+..+.+.+.. ...+.. +=|+|-.|.||++||+++
T Consensus       202 ~f~~~ig~s~~~~~~~~~~~~~A~~~~p-vlI~GE~GtGK~~lA~ai  247 (520)
T PRK10820        202 AFSQIVAVSPKMRQVVEQARKLAMLDAP-LLITGDTGTGKDLLAYAC  247 (520)
T ss_pred             cccceeECCHHHHHHHHHHHHHhCCCCC-EEEECCCCccHHHHHHHH
Confidence            456899999888888777653 222344 449999999999999864

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase

Probab=90.13  E-value=0.18  Score=44.38  Aligned_cols=22  Identities=14%  Similarity=0.185  Sum_probs=19.3

Q ss_pred             CCeEEEEEEcCCCCcHHHHhcc
Q 047923          168 KDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-.++-++|.+|.||||+|+.
T Consensus       367 ~~p~LVil~G~pGSGKST~A~~  388 (526)
T TIGR01663       367 APCEMVIAVGFPGAGKSHFCKK  388 (526)
T ss_pred             CCceEEEEECCCCCCHHHHHHH
Confidence            3478999999999999999974

Note that the EC number for the kinase function is: 2.7.1.78

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=90.10  E-value=0.31  Score=40.64  Aligned_cols=35  Identities=20%  Similarity=0.272  Sum_probs=25.2

Q ss_pred             hhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          154 SRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       154 ~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .-...+.++|..+-..-.++=|+|.+|+|||+||-
T Consensus       107 tG~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~  141 (342)
T PLN03186        107 TGSRELDKILEGGIETGSITEIYGEFRTGKTQLCH  141 (342)
T ss_pred             CCCHHHHHhhcCCCcCceEEEEECCCCCCccHHHH
Confidence            33445556665443446788899999999999985

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=89.95  E-value=0.19  Score=44.74  Aligned_cols=20  Identities=25%  Similarity=0.323  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|-.|.|||||++.+
T Consensus       377 ~~vaIvG~SGsGKSTL~~lL  396 (588)
T PRK11174        377 QRIALVGPSGAGKTSLLNAL  396 (588)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            67899999999999999753

>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional

Probab=89.94  E-value=0.18  Score=44.57  Aligned_cols=20  Identities=30%  Similarity=0.252  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|+|..|.|||||++.
T Consensus       349 G~~~aivG~sGsGKSTL~~l  368 (547)
T PRK10522        349 GELLFLIGGNGSGKSTLAML  368 (547)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999975

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

Probab=89.91  E-value=0.14  Score=44.68  Aligned_cols=21  Identities=29%  Similarity=0.287  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+.+=++|.+|.|||+||+++
T Consensus       276 ~~giLl~GpPGtGKT~lAkav  296 (494)
T COG0464         276 PKGVLLYGPPGTGKTLLAKAV  296 (494)
T ss_pred             CCeeEEECCCCCCHHHHHHHH
Confidence            456778999999999999974

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

Probab=89.86  E-value=0.29  Score=40.01  Aligned_cols=43  Identities=26%  Similarity=0.291  Sum_probs=28.6

Q ss_pred             ccccccch---hHHHHHHHhhhc-CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          147 NQLVGRES---RVEIIESLLAAE-SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       147 ~~~vG~d~---~~~~~~~~l~~~-~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+|-..   -++.+.++|... .....-+-|+|-.|.||||+++.
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~r   80 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIER   80 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHH
Confidence            34566543   344445555543 23467788999999999999874

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

>PRK13869 plasmid-partitioning protein RepA; Provisional

Probab=89.86  E-value=0.51  Score=40.27  Aligned_cols=20  Identities=25%  Similarity=0.327  Sum_probs=16.7

Q ss_pred             CeEEEEEE-cCCCCcHHHHhc
Q 047923          169 DVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~-G~gGiGKTTla~  188 (190)
                      +.++|+|. .-||+||||+|-
T Consensus       120 ~~~vIav~n~KGGvGKTTta~  140 (405)
T PRK13869        120 HLQVIAVTNFKGGSGKTTTSA  140 (405)
T ss_pred             CceEEEEEcCCCCCCHHHHHH
Confidence            46899998 569999999874

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=89.85  E-value=0.26  Score=44.46  Aligned_cols=44  Identities=11%  Similarity=0.141  Sum_probs=32.6

Q ss_pred             cccccccchhHHHHHHHhhhcC-CCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAES-KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~-~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|....+..+.+.+..-. .+.. |=|+|-.|.||+++|+++
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~p-vli~Ge~GtGK~~~A~~i  368 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFP-VLLCGEEGVGKALLAQAI  368 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCC-EEEECCCCcCHHHHHHHH
Confidence            4568888888888877665422 2344 459999999999999864

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=89.82  E-value=0.2  Score=44.56  Aligned_cols=19  Identities=37%  Similarity=0.539  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       342 ~~~~ivG~sGsGKSTLl~l  360 (569)
T PRK10789        342 QMLGICGPTGSGKSTLLSL  360 (569)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999975

>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed

Probab=89.81  E-value=0.17  Score=41.88  Aligned_cols=21  Identities=33%  Similarity=0.442  Sum_probs=18.0

Q ss_pred             CeEEEEE--EcCCCCcHHHHhcc
Q 047923          169 DVYILGI--WGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i--~G~gGiGKTTla~~  189 (190)
                      .+.||+|  .++||.|||+++.+
T Consensus        48 ~~pvIsVGNi~vGGtGKTP~v~~   70 (325)
T PRK00652         48 PVPVIVVGNITVGGTGKTPVVIA   70 (325)
T ss_pred             CCCEEEEcCeeCCCCChHHHHHH
Confidence            4778888  99999999999864

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=89.81  E-value=0.2  Score=44.75  Aligned_cols=20  Identities=30%  Similarity=0.290  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|+|..|.|||||++.
T Consensus       361 G~~~~ivG~sGsGKSTL~~l  380 (585)
T TIGR01192       361 GQTVAIVGPTGAGKTTLINL  380 (585)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            36789999999999999975

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=89.77  E-value=0.2  Score=43.97  Aligned_cols=21  Identities=19%  Similarity=0.167  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..++|+|..|.|||||++.+
T Consensus       348 G~~~~ivG~sGsGKSTL~~ll  368 (529)
T TIGR02857       348 GERVALVGPSGAGKSTLLNLL  368 (529)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            357899999999999999853

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

>PRK08506 replicative DNA helicase; Provisional

Probab=89.72  E-value=0.87  Score=39.69  Aligned_cols=40  Identities=18%  Similarity=0.204  Sum_probs=26.8

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..|...-...+.+++. +-..-.++-|-|.+|+||||+|-.
T Consensus       172 ~~Gi~TG~~~LD~~~~-G~~~G~LivIaarpg~GKT~fal~  211 (472)
T PRK08506        172 IIGLDTGFVELNKMTK-GFNKGDLIIIAARPSMGKTTLCLN  211 (472)
T ss_pred             CCcccCChHHHHhhcC-CCCCCceEEEEcCCCCChHHHHHH
Confidence            5566666666666542 212234677789999999999853

>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional

Probab=89.71  E-value=0.16  Score=46.06  Aligned_cols=21  Identities=33%  Similarity=0.360  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++.++|++|.||||+|+.+
T Consensus       215 ~~~~~~vglp~~GKStia~~L  235 (664)
T PTZ00322        215 SLIVIMVGLPGRGKTYVARQI  235 (664)
T ss_pred             ceeEEecccCCCChhHHHHHH
Confidence            468889999999999999853

>TIGR00368 Mg chelatase-related protein

Probab=89.71  E-value=0.22  Score=43.71  Aligned_cols=41  Identities=20%  Similarity=0.176  Sum_probs=26.6

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++|.+.-++.+.-.+    ..-..+.+.|.+|.||||||+.+
T Consensus       191 ~~dv~Gq~~~~~al~~aa----~~g~~vlliG~pGsGKTtlar~l  231 (499)
T TIGR00368       191 LKDIKGQQHAKRALEIAA----AGGHNLLLFGPPGSGKTMLASRL  231 (499)
T ss_pred             HHHhcCcHHHHhhhhhhc----cCCCEEEEEecCCCCHHHHHHHH
Confidence            345666655544433222    12346888999999999999853

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=89.64  E-value=0.19  Score=45.66  Aligned_cols=19  Identities=26%  Similarity=0.270  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       492 ~~iaIvG~sGsGKSTLlkl  510 (694)
T TIGR03375       492 EKVAIIGRIGSGKSTLLKL  510 (694)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999985

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=89.64  E-value=0.21  Score=44.48  Aligned_cols=19  Identities=21%  Similarity=0.319  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       367 ~~~aivG~sGsGKSTL~~l  385 (574)
T PRK11160        367 EKVALLGRTGCGKSTLLQL  385 (574)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999975

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=89.61  E-value=0.39  Score=38.92  Aligned_cols=29  Identities=34%  Similarity=0.346  Sum_probs=22.1

Q ss_pred             HHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          160 ESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       160 ~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .++|..+-..-+++=|+|..|.||||||-
T Consensus        50 D~~LGGGl~~g~ItEiyG~~gsGKT~lal   78 (279)
T COG0468          50 DEALGGGLPRGRITEIYGPESSGKTTLAL   78 (279)
T ss_pred             HHHhcCCcccceEEEEecCCCcchhhHHH
Confidence            35555333447899999999999999984

>PRK11670 antiporter inner membrane protein; Provisional

Probab=89.58  E-value=0.28  Score=41.30  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=16.0

Q ss_pred             eEEEEEE-cCCCCcHHHHhc
Q 047923          170 VYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~-G~gGiGKTTla~  188 (190)
                      .++|+|. |-||+||||+|-
T Consensus       107 ~~vIaV~S~KGGVGKTT~av  126 (369)
T PRK11670        107 KNIIAVSSGKGGVGKSSTAV  126 (369)
T ss_pred             CEEEEEeCCCCCCCHHHHHH
Confidence            5777776 999999999974

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=89.55  E-value=0.35  Score=41.83  Aligned_cols=21  Identities=33%  Similarity=0.449  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-+-|||-.|.|||+|++++
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai  161 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAA  161 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHH
Confidence            345779999999999999864

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

Probab=89.55  E-value=0.42  Score=38.54  Aligned_cols=45  Identities=22%  Similarity=0.242  Sum_probs=31.4

Q ss_pred             cccccccchhHHH---HHHHhhh----cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEI---IESLLAA----ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~---~~~~l~~----~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++++|.+.-+.+   +++.|..    +.+--+-+-.+|.+|.|||.+|+++
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akal  171 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKAL  171 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHH
Confidence            3578898865443   3444543    2233567779999999999999974

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=89.53  E-value=0.24  Score=43.62  Aligned_cols=44  Identities=23%  Similarity=0.242  Sum_probs=28.7

Q ss_pred             ccccccchhHHHHHH---HhhhcC------CC-eEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIES---LLAAES------KD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~---~l~~~~------~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++.-|.|+-++++++   .|....      .+ -+=|=++|.+|.|||-||++|
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAv  357 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAV  357 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHh
Confidence            456688865555544   454321      11 223447899999999999985

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=89.48  E-value=0.2  Score=45.76  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =..++|+|..|.|||||++.
T Consensus       507 Ge~vaIvG~SGsGKSTLl~l  526 (711)
T TIGR00958       507 GEVVALVGPSGSGKSTVAAL  526 (711)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999985

>PRK09563 rbgA GTPase YlqF; Reviewed

Probab=89.42  E-value=0.44  Score=38.60  Aligned_cols=29  Identities=10%  Similarity=0.173  Sum_probs=22.0

Q ss_pred             cchHHHHHHhhcccceEEEecCCCcCchh
Q 047923           18 EISESIAYAIESPAISVIIFSEGYPFSRW   46 (190)
Q Consensus        18 ~~~~~l~~ai~~s~~~ivv~S~~y~~S~w   46 (190)
                      ....++.++++++++.+.|+.-.-..+..
T Consensus        13 k~~~~l~~~l~~aDvIL~VvDar~p~~~~   41 (287)
T PRK09563         13 KARREIKENLKLVDVVIEVLDARIPLSSE   41 (287)
T ss_pred             HHHHHHHHHhhhCCEEEEEEECCCCCCCC
Confidence            34578899999999999999865544443

>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional

Probab=89.39  E-value=0.19  Score=45.27  Aligned_cols=21  Identities=29%  Similarity=0.243  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.++-+.|++|.||||+|+++
T Consensus       460 ~~~i~~~G~~gsGKst~a~~l  480 (632)
T PRK05506        460 PATVWFTGLSGSGKSTIANLV  480 (632)
T ss_pred             cEEEEecCCCCchHHHHHHHH
Confidence            578889999999999999753

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=89.31  E-value=0.16  Score=47.20  Aligned_cols=14  Identities=43%  Similarity=0.446  Sum_probs=12.0

Q ss_pred             EEEcCCCCcHHHHh
Q 047923          174 GIWGVGSIGKTTIA  187 (190)
Q Consensus       174 ~i~G~gGiGKTTla  187 (190)
                      =|.||+|.||||+-
T Consensus       689 LI~GMPGTGKTTtI  702 (1100)
T KOG1805|consen  689 LILGMPGTGKTTTI  702 (1100)
T ss_pred             eeecCCCCCchhhH
Confidence            36899999999974

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=89.30  E-value=0.22  Score=44.14  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       359 ~~v~IvG~sGsGKSTLl~l  377 (571)
T TIGR02203       359 ETVALVGRSGSGKSTLVNL  377 (571)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5689999999999999875

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.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=89.28  E-value=0.43  Score=41.52  Aligned_cols=20  Identities=15%  Similarity=0.303  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-++|+|-+++|||||..+
T Consensus       211 ~~kI~iiG~~nvGKSSLin~  230 (472)
T PRK03003        211 PRRVALVGKPNVGKSSLLNK  230 (472)
T ss_pred             ceEEEEECCCCCCHHHHHHH
Confidence            56789999999999999864

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=89.28  E-value=0.4  Score=42.97  Aligned_cols=43  Identities=19%  Similarity=0.135  Sum_probs=29.2

Q ss_pred             ccc-ccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLV-GRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~v-G~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+ |.|+-++++.+....           +.+.-+=|=.||.+|.||||+|+++
T Consensus       434 ~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkal  488 (693)
T KOG0730|consen  434 DDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKAL  488 (693)
T ss_pred             hhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHH
Confidence            334 578777777654432           1223445568999999999999975

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.25  E-value=0.34  Score=42.28  Aligned_cols=34  Identities=18%  Similarity=0.127  Sum_probs=24.5

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+.++|..+=..-.++-|.|.+|+||||||.+
T Consensus       249 i~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~  282 (484)
T TIGR02655       249 VVRLDEMCGGGFFKDSIILATGATGTGKTLLVSK  282 (484)
T ss_pred             hHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHH
Confidence            4455566655434456778899999999999864

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.

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

Probab=89.23  E-value=0.25  Score=44.00  Aligned_cols=45  Identities=22%  Similarity=0.175  Sum_probs=33.1

Q ss_pred             cccccccchhHHHHHHHhhhcC--C-------C-eEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAES--K-------D-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~--~-------~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+.-|.|+.++++.+.+..-.  .       . -+=+.++|.+|.|||.||+++
T Consensus       149 F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAv  203 (596)
T COG0465         149 FADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAV  203 (596)
T ss_pred             hhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHH
Confidence            4567799988888877765311  1       1 345678899999999999975

>PRK01889 GTPase RsgA; Reviewed

Probab=89.05  E-value=0.36  Score=40.49  Aligned_cols=30  Identities=20%  Similarity=0.487  Sum_probs=22.7

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ++++..+|..    -..++++|..|+|||||.+.
T Consensus       185 l~~L~~~L~~----g~~~~lvG~sgvGKStLin~  214 (356)
T PRK01889        185 LDVLAAWLSG----GKTVALLGSSGVGKSTLVNA  214 (356)
T ss_pred             HHHHHHHhhc----CCEEEEECCCCccHHHHHHH
Confidence            5566666643    24789999999999999764

>PHA02542 41 41 helicase; Provisional

Probab=89.00  E-value=0.89  Score=39.65  Aligned_cols=40  Identities=10%  Similarity=0.032  Sum_probs=26.7

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..|...-...+.+++..+-..-.++-|-|.+|+||||+|-
T Consensus       169 ~~gi~TG~~~LD~~t~gGl~~G~LiiIaarPgmGKTtfal  208 (473)
T PHA02542        169 ANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLC  208 (473)
T ss_pred             CCccCCCcHHHHHhccCCCCCCcEEEEEcCCCccHHHHHH
Confidence            5566666777777663222223355566999999999985

>PRK05748 replicative DNA helicase; Provisional

Probab=89.00  E-value=0.96  Score=39.04  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=24.6

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       183 ~~gi~TG~~~LD~~~~-G~~~G~livIaarpg~GKT~~al  221 (448)
T PRK05748        183 ITGIPTGFTDLDKMTS-GLQPNDLIIVAARPSVGKTAFAL  221 (448)
T ss_pred             CCCccCChHHHHHhcC-CCCCCceEEEEeCCCCCchHHHH
Confidence            3345555555555443 21223567788999999999985

>PRK09165 replicative DNA helicase; Provisional

Probab=88.91  E-value=1  Score=39.48  Aligned_cols=39  Identities=26%  Similarity=0.305  Sum_probs=24.9

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       197 ~~gi~TG~~~LD~~~g-G~~~g~livIaarpg~GKT~~al  235 (497)
T PRK09165        197 LSGISTGLRDLDSKLG-GLHPSDLIILAGRPSMGKTALAT  235 (497)
T ss_pred             CCcccCChHHHhhhcC-CCCCCceEEEEeCCCCChHHHHH
Confidence            3455555555555542 22223567778999999999984

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=88.80  E-value=0.37  Score=42.65  Aligned_cols=45  Identities=20%  Similarity=0.234  Sum_probs=33.6

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++|....++.+.+.+..-...-.-|=|.|-.|.||+++|+++
T Consensus       218 f~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~I  262 (538)
T PRK15424        218 LGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAI  262 (538)
T ss_pred             hhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHH
Confidence            345899999898888877642222234558999999999999864

>PHA02519 plasmid partition protein SopA; Reviewed

Probab=88.78  E-value=0.67  Score=39.32  Aligned_cols=20  Identities=25%  Similarity=0.298  Sum_probs=16.5

Q ss_pred             CeEEEEEE-cCCCCcHHHHhc
Q 047923          169 DVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~-G~gGiGKTTla~  188 (190)
                      +..+|+|. .-||+||||+|-
T Consensus       105 ~~~vIav~n~KGGVGKTTta~  125 (387)
T PHA02519        105 NPVVLAVMSHKGGVYKTSSAV  125 (387)
T ss_pred             CceEEEEecCCCCCcHHHHHH
Confidence            37899988 559999999874

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=88.76  E-value=0.28  Score=40.55  Aligned_cols=19  Identities=42%  Similarity=0.329  Sum_probs=16.0

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      -+-|.|-.|.||||+++++
T Consensus       146 nilI~G~tGSGKTTll~aL  164 (323)
T PRK13833        146 NIVISGGTGSGKTTLANAV  164 (323)
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            3569999999999998763

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=88.74  E-value=0.36  Score=42.62  Aligned_cols=45  Identities=22%  Similarity=0.305  Sum_probs=33.8

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++|....++.+.+.+..-...-.-|=|.|-.|.||+++|+++
T Consensus       211 f~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~I  255 (526)
T TIGR02329       211 LDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAI  255 (526)
T ss_pred             hhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHH
Confidence            356899999898888877543222234558999999999999864

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.

>smart00350 MCM minichromosome maintenance proteins

Probab=88.70  E-value=0.44  Score=41.87  Aligned_cols=45  Identities=16%  Similarity=0.127  Sum_probs=30.3

Q ss_pred             cccccccchhHHHHHHHhhhcC-----CCeE-----EEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAES-----KDVY-----ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~-----~~~~-----vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-+..+.-.|..+.     ++.+     -+=|+|-+|.|||+||+++
T Consensus       202 ~p~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l  256 (509)
T smart00350      202 APSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYV  256 (509)
T ss_pred             CccccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHH
Confidence            4578999887666654443321     1111     3668999999999999864

>PF01057 Parvo_NS1: Parvovirus non-structural protein NS1; InterPro: IPR001257 Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides

Probab=88.61  E-value=0.49  Score=38.19  Aligned_cols=32  Identities=25%  Similarity=0.273  Sum_probs=24.1

Q ss_pred             HHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          159 IESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       159 ~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +..++.....+...+.++|.++.|||.||++|
T Consensus       102 l~~~~~k~~~krNti~~~Gp~~tGKt~la~aI  133 (271)
T PF01057_consen  102 LYCWLSKQWGKRNTIWFYGPASTGKTNLADAI  133 (271)
T ss_dssp             HHHHHTTTSTT--EEEEESTTTSSHCHCHHCC
T ss_pred             HHHHHhCcccCccEEEEEcCCCCCHHHHHHHH
Confidence            44555555566899999999999999999875

Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contains two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons []. This entry represents the helicase domain of the Parvovirus NS1 protein; which is required for viral DNA replication []. This domain contains the ATP/GTP-binding site motif A (P-loop). Parvoviral NS1 also regulates host gene expression through histone acetylation []. ; GO: 0019079 viral genome replication; PDB: 3P0S_A 1S9H_A 1U0J_A.

>PRK13705 plasmid-partitioning protein SopA; Provisional

Probab=88.60  E-value=0.65  Score=39.42  Aligned_cols=20  Identities=20%  Similarity=0.278  Sum_probs=16.5

Q ss_pred             CeEEEEEEcC-CCCcHHHHhc
Q 047923          169 DVYILGIWGV-GSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G~-gGiGKTTla~  188 (190)
                      ..++|+|... ||+||||+|-
T Consensus       105 ~~~vIai~n~KGGVGKTT~a~  125 (388)
T PRK13705        105 FPPVIGVAAHKGGVYKTSVSV  125 (388)
T ss_pred             CCeEEEEECCCCCchHHHHHH
Confidence            4789999854 9999999874

>TIGR00954 3a01203 Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protei

Probab=88.56  E-value=0.26  Score=44.72  Aligned_cols=19  Identities=32%  Similarity=0.364  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       479 e~~~IvG~nGsGKSTLl~l  497 (659)
T TIGR00954       479 NHLLICGPNGCGKSSLFRI  497 (659)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4789999999999999875

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=88.55  E-value=0.48  Score=40.39  Aligned_cols=20  Identities=30%  Similarity=0.456  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      .--++++|.+|+|||||..+
T Consensus       172 ~~~v~ivG~~~~GKSsLin~  191 (429)
T TIGR03594       172 PIKIAIIGRPNVGKSTLVNA  191 (429)
T ss_pred             ceEEEEECCCCCCHHHHHHH
Confidence            34588999999999999864

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.

>PRK06904 replicative DNA helicase; Validated

Probab=88.55  E-value=2.9  Score=36.47  Aligned_cols=39  Identities=21%  Similarity=0.176  Sum_probs=25.1

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       201 ~~Gi~TG~~~LD~~t~-Gl~~G~LiiIaarPg~GKTafal  239 (472)
T PRK06904        201 VTGVTTGFTDLDKKTA-GLQPSDLIIVAARPSMGKTTFAM  239 (472)
T ss_pred             CCCccCChHHHHHHHh-ccCCCcEEEEEeCCCCChHHHHH
Confidence            4566666666665542 11223456677999999999973

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=88.49  E-value=2.3  Score=36.63  Aligned_cols=39  Identities=15%  Similarity=0.225  Sum_probs=26.0

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|.......+.++... -..-.++.+-|-+|+||||+|=
T Consensus       176 ~~Gi~tgf~~LD~~t~G-~~~~dLii~AaRP~mGKTafal  214 (435)
T COG0305         176 LIGVPTGFTDLDEITSG-FRPGDLIIVAARPGMGKTALAL  214 (435)
T ss_pred             CcccccCchhhHHHhcC-CccCCEEEEccCCCCChHHHHH
Confidence            56666666666554432 1224567788999999999983

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=88.47  E-value=0.28  Score=43.72  Aligned_cols=20  Identities=25%  Similarity=0.272  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|-.|.|||||++.+
T Consensus       368 e~iaIvG~SGsGKSTLl~lL  387 (592)
T PRK10790        368 GFVALVGHTGSGKSTLASLL  387 (592)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999853

>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter

Probab=88.44  E-value=0.27  Score=43.60  Aligned_cols=20  Identities=35%  Similarity=0.348  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|+|..|.|||||++.
T Consensus       368 G~~~aivG~sGsGKSTl~~l  387 (555)
T TIGR01194       368 GDIVFIVGENGCGKSTLAKL  387 (555)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            35899999999999999875

This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.

>PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional

Probab=88.36  E-value=0.4  Score=43.52  Aligned_cols=22  Identities=32%  Similarity=0.290  Sum_probs=19.1

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+|.|-|..|.||||+|+.+
T Consensus       441 ~~~~i~i~g~~~~gks~~~~~l  462 (661)
T PRK11860        441 RVPVICIDGPTASGKGTVAARV  462 (661)
T ss_pred             CcceEEeeCCCCCCHHHHHHHH
Confidence            3668999999999999999863

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

Probab=88.36  E-value=0.27  Score=40.20  Aligned_cols=43  Identities=26%  Similarity=0.294  Sum_probs=30.2

Q ss_pred             cccccchhHHHHHHHhhhc--C---------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAE--S---------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~--~---------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++=|.|+..+++.+-....  .         ..-.=+-+||.+|.|||-||++|
T Consensus       186 diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAV  239 (440)
T KOG0726|consen  186 DIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAV  239 (440)
T ss_pred             ccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHH
Confidence            4557888888887764431  1         01233457999999999999986

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=88.36  E-value=0.27  Score=43.57  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|-.|.|||||++.
T Consensus       367 e~i~IvG~sGsGKSTLlkl  385 (576)
T TIGR02204       367 ETVALVGPSGAGKSTLFQL  385 (576)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4689999999999999985

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PLN03211 ABC transporter G-25; Provisional

Probab=88.21  E-value=0.32  Score=44.14  Aligned_cols=21  Identities=33%  Similarity=0.379  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|..|.|||||.+.+
T Consensus        94 Ge~~aI~GpnGaGKSTLL~iL  114 (659)
T PLN03211         94 GEILAVLGPSGSGKSTLLNAL  114 (659)
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            468999999999999998753

>PRK12608 transcription termination factor Rho; Provisional

Probab=88.06  E-value=0.27  Score=41.44  Aligned_cols=18  Identities=22%  Similarity=0.030  Sum_probs=15.7

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -..|.|-.|.|||||++.
T Consensus       135 R~LIvG~pGtGKTTLl~~  152 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQ  152 (380)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            348999999999999975

>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]

Probab=88.04  E-value=0.82  Score=36.59  Aligned_cols=20  Identities=40%  Similarity=0.507  Sum_probs=16.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+|=|=|..|+||||+|..
T Consensus        89 p~IILIGGasGVGkStIA~E  108 (299)
T COG2074          89 PLIILIGGASGVGKSTIAGE  108 (299)
T ss_pred             CeEEEecCCCCCChhHHHHH
Confidence            35666779999999999964

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=88.02  E-value=0.29  Score=40.61  Aligned_cols=20  Identities=30%  Similarity=0.489  Sum_probs=17.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.-|+|+|.+++|||||..+
T Consensus       157 ~adV~lvG~pnaGKSTLl~~  176 (329)
T TIGR02729       157 LADVGLVGLPNAGKSTLISA  176 (329)
T ss_pred             cccEEEEcCCCCCHHHHHHH
Confidence            45589999999999999865

This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=88.02  E-value=0.48  Score=43.41  Aligned_cols=42  Identities=24%  Similarity=0.184  Sum_probs=30.0

Q ss_pred             ccccchhHHHHHHHhhhc-------CCC---eEEEEEEcCCCCcHHHHhccC
Q 047923          149 LVGRESRVEIIESLLAAE-------SKD---VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~-------~~~---~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +=|.+.-+.+|.+-+...       +.+   ..=|=+||.+|.|||-|||||
T Consensus       674 VGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAV  725 (953)
T KOG0736|consen  674 VGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAV  725 (953)
T ss_pred             ccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHH
Confidence            347788888887765541       122   334557999999999999986

>PRK15115 response regulator GlrR; Provisional

Probab=87.79  E-value=0.95  Score=38.72  Aligned_cols=43  Identities=19%  Similarity=0.114  Sum_probs=28.1

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++|....+..+.+....-...-..+-|.|..|.|||++|+++
T Consensus       135 ~lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~i  177 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAI  177 (444)
T ss_pred             cccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHH
Confidence            4677776666665544332222223458999999999999863

>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG

Probab=87.73  E-value=0.88  Score=36.34  Aligned_cols=35  Identities=20%  Similarity=0.123  Sum_probs=23.1

Q ss_pred             hhHHHHHHHhhh--cCCCeEEEEEE-cCCCCcHHHHhc
Q 047923          154 SRVEIIESLLAA--ESKDVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       154 ~~~~~~~~~l~~--~~~~~~vi~i~-G~gGiGKTTla~  188 (190)
                      +.++.+..-|..  ...+.++|+|. +-||.||||+|-
T Consensus        85 e~~~~l~~~l~~~~~~~~~~vi~vts~~~g~Gktt~a~  122 (274)
T TIGR03029        85 EALRALRSQLMLRWFSEGRKALAVVSAKSGEGCSYIAA  122 (274)
T ss_pred             HHHHHHHHHhhhhccCCCCeEEEEECCCCCCCHHHHHH
Confidence            344445444432  23357888888 779999999885

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).

>PRK07004 replicative DNA helicase; Provisional

Probab=87.70  E-value=2.4  Score=36.84  Aligned_cols=39  Identities=15%  Similarity=0.194  Sum_probs=23.7

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|...-...+.+++. +-..-.++-|-|-+|+||||+|..
T Consensus       194 ~gi~TG~~~LD~~t~-G~~~g~liviaarpg~GKT~~al~  232 (460)
T PRK07004        194 TGTPTGFVDLDRMTS-GMHGGELIIVAGRPSMGKTAFSMN  232 (460)
T ss_pred             CCccCCcHHhccccc-CCCCCceEEEEeCCCCCccHHHHH
Confidence            344444444444432 212234677789999999999853

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=87.68  E-value=0.31  Score=44.33  Aligned_cols=19  Identities=32%  Similarity=0.555  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|-.|.|||||++.
T Consensus       484 ~~vaivG~sGsGKSTL~~l  502 (694)
T TIGR01846       484 EFIGIVGPSGSGKSTLTKL  502 (694)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4789999999999999985

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=87.63  E-value=0.33  Score=40.39  Aligned_cols=19  Identities=21%  Similarity=0.205  Sum_probs=16.9

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++.|.|..|.||||+.++
T Consensus       123 g~ili~G~tGSGKTT~l~a  141 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLAS  141 (343)
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            5688999999999999875

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.

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

Probab=87.63  E-value=0.52  Score=42.17  Aligned_cols=44  Identities=18%  Similarity=0.173  Sum_probs=32.4

Q ss_pred             ccccccchhHHHHHHHhhhcCC----------CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESK----------DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~----------~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++=|+|..+.++.+++..-..          .-|=+=++|.+|.|||.||+++
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~Ai  243 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAI  243 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHH
Confidence            4566899999999887654211          1244557899999999999875

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=87.59  E-value=0.51  Score=43.24  Aligned_cols=45  Identities=18%  Similarity=0.135  Sum_probs=32.1

Q ss_pred             cccccccchhHHHHHHHhhh--cC-----CC---eEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAA--ES-----KD---VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~--~~-----~~---~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++-|.|+-+++|.+....  +.     -+   -+=+=++|.+|.|||=|||++
T Consensus       310 FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAi  364 (774)
T KOG0731|consen  310 FKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAI  364 (774)
T ss_pred             cccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHH
Confidence            46788999888888776442  11     01   233457899999999999985

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=87.52  E-value=0.31  Score=40.52  Aligned_cols=20  Identities=30%  Similarity=0.489  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.-|+|+|.+++|||||..+
T Consensus       158 ~adVglVG~PNaGKSTLln~  177 (335)
T PRK12299        158 LADVGLVGLPNAGKSTLISA  177 (335)
T ss_pred             cCCEEEEcCCCCCHHHHHHH
Confidence            34589999999999999764

>PRK05636 replicative DNA helicase; Provisional

Probab=87.52  E-value=1.8  Score=38.12  Aligned_cols=39  Identities=15%  Similarity=0.184  Sum_probs=24.8

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..|...-...+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       245 ~~Gi~TG~~~LD~~t~-Gl~~G~Liiiaarpg~GKT~~al  283 (505)
T PRK05636        245 ATGIPTGFKDLDDLTN-GLRGGQMIIVAARPGVGKSTLAL  283 (505)
T ss_pred             CCceecChHHHhhhcC-CCCCCceEEEEeCCCCCHHHHHH
Confidence            3455555555555432 11224567788999999999975

>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains

Probab=87.44  E-value=3.2  Score=37.85  Aligned_cols=84  Identities=19%  Similarity=0.168  Sum_probs=44.0

Q ss_pred             HHHHhHHHHHHHhhccccccCchhhhHHHHHHHHHhhhhhhhhccccccccccchhHHHHHHHhhhcCCC---eEEEEEE
Q 047923          100 EKLQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKD---VYILGIW  176 (190)
Q Consensus       100 e~v~kWr~AL~ev~~~~g~~~~e~~~i~~iv~~v~~~l~~~~~~~~~~~~vG~d~~~~~~~~~l~~~~~~---~~vi~i~  176 (190)
                      ++++..|-..-.+...-|..-.     +.+|.+|+.+|....- .........|.......++-....++   ...|.++
T Consensus        51 ~k~~~~rvkflrl~~Rlg~s~~-----~~vvaqVlyrl~l~~~-~~~~~~~s~d~a~~~a~~~ea~g~~~LdfslrIvLV  124 (763)
T TIGR00993        51 EKLQLIRVKFLRLAQRLGQTPE-----NSIAAQVLYRLGLLAG-RQGGGAFSLDAAKAMAEQLEAEGQDPLDFSLNILVL  124 (763)
T ss_pred             HHHHHHHHHHHHHHHHhCCCcc-----cchHHHHHHHHHHhhc-cCccccccchhhHHHHhhhhhhhccccCcceEEEEE
Confidence            4566666666666666664432     2245556666543221 11111112333232222222222222   4568899


Q ss_pred             cCCCCcHHHHhcc
Q 047923          177 GVGSIGKTTIARA  189 (190)
Q Consensus       177 G~gGiGKTTla~~  189 (190)
                      |..|+||||+...
T Consensus       125 GKTGVGKSSLINS  137 (763)
T TIGR00993       125 GKSGVGKSATINS  137 (763)
T ss_pred             CCCCCCHHHHHHH
Confidence            9999999999864

The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=87.35  E-value=0.57  Score=42.94  Aligned_cols=20  Identities=15%  Similarity=0.361  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-++|+|.+|+|||||..+
T Consensus       450 ~~kI~ivG~~nvGKSSLin~  469 (712)
T PRK09518        450 LRRVALVGRPNVGKSSLLNQ  469 (712)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            56789999999999999864

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=87.17  E-value=0.32  Score=44.02  Aligned_cols=43  Identities=23%  Similarity=0.176  Sum_probs=27.0

Q ss_pred             cccccchhHHHHHHHhhhcC----------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAES----------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~----------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ++.|.+..++.+.+++....          .--+-+-++|.+|.||||+|+++
T Consensus       153 di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~  205 (644)
T PRK10733        153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAI  205 (644)
T ss_pred             HHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHH
Confidence            45566665555555433210          00223779999999999999863

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=87.11  E-value=0.47  Score=39.56  Aligned_cols=20  Identities=35%  Similarity=0.250  Sum_probs=17.3

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..+.|.|..|.||||+.++
T Consensus       178 ~~~ili~G~tGsGKTTll~a  197 (340)
T TIGR03819       178 RLAFLISGGTGSGKTTLLSA  197 (340)
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            35788999999999999874

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=86.97  E-value=0.37  Score=40.95  Aligned_cols=19  Identities=37%  Similarity=0.571  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .-|+|+|.+++|||||..+
T Consensus       160 adValVG~PNaGKSTLln~  178 (390)
T PRK12298        160 ADVGLLGLPNAGKSTFIRA  178 (390)
T ss_pred             ccEEEEcCCCCCHHHHHHH
Confidence            3489999999999999765

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=86.87  E-value=0.79  Score=38.55  Aligned_cols=40  Identities=23%  Similarity=0.057  Sum_probs=31.7

Q ss_pred             ccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          151 GRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       151 G~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++.-+-++.+++..+-.+-|-+-.-|.--.||||||.++
T Consensus       136 ~~~~~i~~iL~~lv~N~PKkRy~lFkGPvNsGKTTlAAAl  175 (417)
T PF06431_consen  136 NFDDVILEILKCLVENIPKKRYWLFKGPVNSGKTTLAAAL  175 (417)
T ss_dssp             THHHHHHHHHHHHHHTBTTB-EEEEE-STTSSHHHHHHHH
T ss_pred             chHHHHHHHHHHHhcCCCcceeEEEecCcCCchHHHHHHH
Confidence            5666777788888777778899999999999999999864

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

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

Probab=86.79  E-value=0.33  Score=39.19  Aligned_cols=19  Identities=26%  Similarity=0.520  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .-++|.|-.|.||||||+.
T Consensus        70 Qr~~If~~~G~GKTtLa~~   88 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIME   88 (274)
T ss_pred             CEEEEecCCCCChhHHHHH
Confidence            4578999999999999975

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.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=86.78  E-value=0.82  Score=38.50  Aligned_cols=37  Identities=24%  Similarity=0.338  Sum_probs=24.7

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      -++.....--..+|..  +++.++.+.|-.|.|||-||=
T Consensus       227 ~prn~eQ~~ALdlLld--~dI~lV~L~G~AGtGKTlLAL  263 (436)
T COG1875         227 RPRNAEQRVALDLLLD--DDIDLVSLGGKAGTGKTLLAL  263 (436)
T ss_pred             CcccHHHHHHHHHhcC--CCCCeEEeeccCCccHhHHHH
Confidence            3444333333444433  468889999999999999984

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

Probab=86.73  E-value=0.72  Score=33.33  Aligned_cols=38  Identities=24%  Similarity=0.394  Sum_probs=32.8

Q ss_pred             CeeEEEeC-CCCC--cccchHHHHHHhhcccceEEEecCCC
Q 047923            4 NIQTFIDD-QLNR--GDEISESIAYAIESPAISVIIFSEGY   41 (190)
Q Consensus         4 gi~~f~d~-~~~~--g~~~~~~l~~ai~~s~~~ivv~S~~y   41 (190)
                      |+.|.+|. +...  +.....-+.++|+++...|+|+|+.|
T Consensus        30 g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~   70 (150)
T PF08357_consen   30 GIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY   70 (150)
T ss_pred             CCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence            99999998 7744  66788899999999999999999644

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 [].

>PRK05595 replicative DNA helicase; Provisional

Probab=86.59  E-value=1.7  Score=37.45  Aligned_cols=39  Identities=23%  Similarity=0.154  Sum_probs=26.1

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +.|.......+.+++. +-..-.++-|-|.+|+||||+|-
T Consensus       181 ~~gi~tg~~~ld~~~~-G~~~g~liviaarpg~GKT~~al  219 (444)
T PRK05595        181 TTGVASGFRELDAKTS-GFQKGDMILIAARPSMGKTTFAL  219 (444)
T ss_pred             CCcccCChHHHHHhcC-CCCCCcEEEEEecCCCChHHHHH
Confidence            4566666666666553 21223466677999999999975

>KOG4181 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.40  E-value=0.95  Score=37.88  Aligned_cols=33  Identities=24%  Similarity=0.354  Sum_probs=25.8

Q ss_pred             hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          155 RVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       155 ~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      -.+...++|... .++.|||+.|.-|.||+||..
T Consensus       174 ~~d~a~~ll~~~-tdf~VIgvlG~QgsGKStlls  206 (491)
T KOG4181|consen  174 FNDNARKLLHKT-TDFTVIGVLGGQGSGKSTLLS  206 (491)
T ss_pred             hhhHHHHHhhcC-CCeeEEEeecCCCccHHHHHH
Confidence            345566666554 579999999999999999864

>PRK13764 ATPase; Provisional

Probab=86.39  E-value=0.39  Score=43.05  Aligned_cols=20  Identities=35%  Similarity=0.242  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-|.|..|.||||+++++
T Consensus       258 ~~ILIsG~TGSGKTTll~AL  277 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQAL  277 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            34779999999999999863

>KOG2702 consensus Predicted panthothenate kinase/uridine kinase-related protein [Nucleotide transport and metabolism; Coenzyme transport and metabolism]

Probab=86.37  E-value=0.58  Score=37.02  Aligned_cols=37  Identities=22%  Similarity=0.188  Sum_probs=26.0

Q ss_pred             cchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          152 RESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       152 ~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++-.....+.|.  ++.-+.+|+.|-||.||+|++.+|
T Consensus       103 ~de~y~~~~e~L~--~n~~~l~glag~pGtgkst~~a~v  139 (323)
T KOG2702|consen  103 DDEFYPVKYEALT--SNNEELTGLAGRPGTGKSTRIAAV  139 (323)
T ss_pred             hhhhhHHHHHHhc--ccchheeeeecCCCCcchhHHHHH
Confidence            3333444455554  445678999999999999998753

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.36  E-value=1.7  Score=36.97  Aligned_cols=20  Identities=25%  Similarity=0.303  Sum_probs=17.3

Q ss_pred             CeEEEEEEcCCCCcHHHHhc
Q 047923          169 DVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~  188 (190)
                      +-.||-++|.-|.||||.+.
T Consensus       100 kpsVimfVGLqG~GKTTtc~  119 (483)
T KOG0780|consen  100 KPSVIMFVGLQGSGKTTTCT  119 (483)
T ss_pred             CCcEEEEEeccCCCcceeHH
Confidence            36799999999999999764

>PRK00093 GTP-binding protein Der; Reviewed

Probab=86.08  E-value=0.78  Score=39.25  Aligned_cols=20  Identities=25%  Similarity=0.424  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-++|+|.+|+|||||..+
T Consensus       173 ~~~v~ivG~~n~GKStlin~  192 (435)
T PRK00093        173 PIKIAIIGRPNVGKSSLINA  192 (435)
T ss_pred             ceEEEEECCCCCCHHHHHHH
Confidence            45689999999999999865

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=86.02  E-value=0.44  Score=39.64  Aligned_cols=42  Identities=21%  Similarity=0.100  Sum_probs=26.0

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +++.....-..+.+.|..--...+-+-|.|-.|.|||||+.+
T Consensus       151 dli~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlLNa  192 (355)
T COG4962         151 DLIIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLLNA  192 (355)
T ss_pred             HHHHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHHHH
Confidence            344444434444444443323345677899999999999865

>PRK09862 putative ATP-dependent protease; Provisional

Probab=85.75  E-value=0.71  Score=40.60  Aligned_cols=22  Identities=27%  Similarity=0.134  Sum_probs=18.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-..+.+.|-.|.||||||+.+
T Consensus       209 ~G~~llliG~~GsGKTtLak~L  230 (506)
T PRK09862        209 GGHNLLLIGPPGTGKTMLASRI  230 (506)
T ss_pred             CCcEEEEECCCCCcHHHHHHHH
Confidence            4568999999999999999853

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=85.62  E-value=0.42  Score=44.03  Aligned_cols=19  Identities=32%  Similarity=0.393  Sum_probs=16.7

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ++..|.|.+|.||||++++
T Consensus       369 ~~~il~G~aGTGKTtll~~  387 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKA  387 (744)
T ss_pred             CEEEEEecCCCCHHHHHHH
Confidence            4678999999999999875

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=85.49  E-value=0.44  Score=43.72  Aligned_cols=20  Identities=40%  Similarity=0.381  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++.|.|.+|.||||+++++
T Consensus       339 ~~~iitGgpGTGKTt~l~~i  358 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAI  358 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            47788999999999998753

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=85.43  E-value=0.74  Score=39.42  Aligned_cols=43  Identities=23%  Similarity=0.347  Sum_probs=31.5

Q ss_pred             ccccccchhHHHHHHHhhhc-CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE-SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~-~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....++.+...+..- ..+..++ |.|-.|.||+++|+++
T Consensus       139 ~~lig~s~~~~~l~~~i~~~a~~~~~vl-i~Ge~GtGK~~lA~~i  182 (445)
T TIGR02915       139 RGLITSSPGMQKICRTIEKIAPSDITVL-LLGESGTGKEVLARAL  182 (445)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEE-EECCCCcCHHHHHHHH
Confidence            45888888888887766542 2234444 8999999999999863

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=85.42  E-value=0.49  Score=40.71  Aligned_cols=21  Identities=14%  Similarity=0.249  Sum_probs=18.1

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-..++|.|-.|.|||||++.
T Consensus       154 ~GQ~igI~G~sGaGKSTLl~~  174 (434)
T PRK07196        154 KGQRVGLMAGSGVGKSVLLGM  174 (434)
T ss_pred             cceEEEEECCCCCCccHHHHH
Confidence            346799999999999999875

>COG4175 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]

Probab=85.34  E-value=0.59  Score=38.67  Aligned_cols=21  Identities=33%  Similarity=0.387  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+.-|-|+.|.||+||.+++
T Consensus        54 GeIfViMGLSGSGKSTLvR~~   74 (386)
T COG4175          54 GEIFVIMGLSGSGKSTLVRLL   74 (386)
T ss_pred             CeEEEEEecCCCCHHHHHHHH
Confidence            457778999999999999864

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=85.28  E-value=0.56  Score=40.52  Aligned_cols=20  Identities=25%  Similarity=0.415  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|+|-.|.|||||++.
T Consensus       165 Gqri~I~G~SGsGKTTLL~~  184 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAM  184 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45789999999999999875

>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH

Probab=85.15  E-value=0.86  Score=38.23  Aligned_cols=19  Identities=21%  Similarity=0.352  Sum_probs=16.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +-+.++|+.|+|||||-.+
T Consensus       155 ~~v~~vG~~nvGKStliN~  173 (360)
T TIGR03597       155 KDVYVVGVTNVGKSSLINK  173 (360)
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4678999999999999754

This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.

>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=85.07  E-value=0.49  Score=41.57  Aligned_cols=19  Identities=26%  Similarity=0.354  Sum_probs=16.7

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .-++|+|-.|.|||||.+.
T Consensus       365 EkvAIlG~SGsGKSTllqL  383 (573)
T COG4987         365 EKVAILGRSGSGKSTLLQL  383 (573)
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4578999999999999875

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=85.02  E-value=1  Score=35.90  Aligned_cols=45  Identities=22%  Similarity=0.326  Sum_probs=31.5

Q ss_pred             cccccccchhHHHHHHHhh-h-cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLA-A-ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~-~-~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..++|.|..++.+.+--. . ..-...-+=+||.-|.||+.|.|++
T Consensus        59 L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~  105 (287)
T COG2607          59 LADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKAL  105 (287)
T ss_pred             HHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHH
Confidence            3578999998888865322 1 1112444568999999999999874

>COG1162 Predicted GTPases [General function prediction only]

Probab=84.98  E-value=1.1  Score=36.71  Aligned_cols=31  Identities=32%  Similarity=0.461  Sum_probs=22.6

Q ss_pred             hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          155 RVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       155 ~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++++..+|...     +..+.|..|+|||||..++
T Consensus       154 ~~~~l~~~l~~~-----~svl~GqSGVGKSSLiN~L  184 (301)
T COG1162         154 GLEELAELLAGK-----ITVLLGQSGVGKSTLINAL  184 (301)
T ss_pred             cHHHHHHHhcCC-----eEEEECCCCCcHHHHHHhh
Confidence            456666666432     5678899999999997653

>PLN02772 guanylate kinase

Probab=84.90  E-value=0.64  Score=39.49  Aligned_cols=21  Identities=24%  Similarity=0.229  Sum_probs=18.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+++-|.|..|+||+||++.
T Consensus       134 ~~k~iVlsGPSGvGKsTL~~~  154 (398)
T PLN02772        134 AEKPIVISGPSGVGKGTLISM  154 (398)
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            467899999999999999875

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

Probab=84.75  E-value=0.51  Score=42.25  Aligned_cols=18  Identities=33%  Similarity=0.386  Sum_probs=15.8

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +=+||.+|.|||-|||+|
T Consensus       548 vLL~GPPGCGKTLlAKAV  565 (802)
T KOG0733|consen  548 VLLCGPPGCGKTLLAKAV  565 (802)
T ss_pred             eEEeCCCCccHHHHHHHH
Confidence            347999999999999985

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=84.57  E-value=0.65  Score=40.03  Aligned_cols=21  Identities=14%  Similarity=0.295  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..++|.|-.|.|||||++.+
T Consensus       162 GqrigI~G~sG~GKSTLL~~I  182 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMM  182 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHh
Confidence            356899999999999998753

>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

Probab=84.53  E-value=0.54  Score=41.74  Aligned_cols=20  Identities=30%  Similarity=0.579  Sum_probs=17.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      --+++++|.+|.|||||.+.
T Consensus        69 PfIvavvGPpGtGKsTLirS   88 (1077)
T COG5192          69 PFIVAVVGPPGTGKSTLIRS   88 (1077)
T ss_pred             CeEEEeecCCCCChhHHHHH
Confidence            45778999999999999874

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=84.51  E-value=0.53  Score=38.95  Aligned_cols=14  Identities=36%  Similarity=0.629  Sum_probs=12.2

Q ss_pred             EEEcCCCCcHHHHh
Q 047923          174 GIWGVGSIGKTTIA  187 (190)
Q Consensus       174 ~i~G~gGiGKTTla  187 (190)
                      =|+|-||+|||||+
T Consensus        93 ~~~gdsg~GKttll  106 (402)
T COG3598          93 ILYGDSGVGKTTLL  106 (402)
T ss_pred             EEecCCcccHhHHH
Confidence            35699999999997

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=84.48  E-value=0.79  Score=37.96  Aligned_cols=18  Identities=33%  Similarity=0.589  Sum_probs=15.9

Q ss_pred             CeEEEEEEcCCCCcHHHH
Q 047923          169 DVYILGIWGVGSIGKTTI  186 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTl  186 (190)
                      +.-|+-++|..|+||||-
T Consensus       138 ~p~Vil~vGVNG~GKTTT  155 (340)
T COG0552         138 KPFVILFVGVNGVGKTTT  155 (340)
T ss_pred             CcEEEEEEecCCCchHhH
Confidence            478999999999999984

>PLN03140 ABC transporter G family member; Provisional

Probab=84.38  E-value=0.63  Score=46.06  Aligned_cols=21  Identities=33%  Similarity=0.213  Sum_probs=18.6

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -++++|.|.+|.|||||.+.+
T Consensus       191 Ge~~~llGpnGSGKSTLLk~L  211 (1470)
T PLN03140        191 SRMTLLLGPPSSGKTTLLLAL  211 (1470)
T ss_pred             CeEEEEEcCCCCCHHHHHHHH
Confidence            578999999999999998753

>COG1084 Predicted GTPase [General function prediction only]

Probab=84.30  E-value=0.64  Score=38.38  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=19.8

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.+.+-|.|++-+|||||.++|
T Consensus       167 ~~pTivVaG~PNVGKSSlv~~l  188 (346)
T COG1084         167 DLPTIVVAGYPNVGKSSLVRKL  188 (346)
T ss_pred             CCCeEEEecCCCCcHHHHHHHH
Confidence            5899999999999999998764

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=84.18  E-value=1.2  Score=38.56  Aligned_cols=41  Identities=24%  Similarity=0.257  Sum_probs=29.6

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..+++|.+.-++.++---..+.+    +=++|.+|.|||-||+.
T Consensus       177 D~~DV~GQ~~AKrAleiAAAGgHn----Ll~~GpPGtGKTmla~R  217 (490)
T COG0606         177 DFKDVKGQEQAKRALEIAAAGGHN----LLLVGPPGTGKTMLASR  217 (490)
T ss_pred             chhhhcCcHHHHHHHHHHHhcCCc----EEEecCCCCchHHhhhh
Confidence            345678988888877644433332    55779999999999974

>PTZ00265 multidrug resistance protein (mdr1); Provisional

Probab=83.98  E-value=0.6  Score=46.22  Aligned_cols=20  Identities=25%  Similarity=0.267  Sum_probs=17.7

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||++.+
T Consensus       412 e~vaIvG~SGsGKSTLl~lL  431 (1466)
T PTZ00265        412 KTYAFVGESGCGKSTILKLI  431 (1466)
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999753

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=83.89  E-value=0.57  Score=40.52  Aligned_cols=18  Identities=39%  Similarity=0.401  Sum_probs=15.5

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      |=|-|.+|.||||.|+++
T Consensus       266 ILIAG~PGaGKsTFaqAl  283 (604)
T COG1855         266 ILIAGAPGAGKSTFAQAL  283 (604)
T ss_pred             eEEecCCCCChhHHHHHH
Confidence            556799999999999974

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=83.82  E-value=3.4  Score=35.55  Aligned_cols=19  Identities=32%  Similarity=0.340  Sum_probs=16.5

Q ss_pred             eEEEEEEcCCCCcHHHHhc
Q 047923          170 VYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~  188 (190)
                      -.+|=.+|.-|.||||.|-
T Consensus       100 P~vImmvGLQGsGKTTt~~  118 (451)
T COG0541         100 PTVILMVGLQGSGKTTTAG  118 (451)
T ss_pred             CeEEEEEeccCCChHhHHH
Confidence            4678899999999999874

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=83.48  E-value=1.5  Score=38.33  Aligned_cols=19  Identities=37%  Similarity=0.246  Sum_probs=16.4

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++.|.|..|.||||+..+
T Consensus       243 GlilitGptGSGKTTtL~a  261 (486)
T TIGR02533       243 GIILVTGPTGSGKTTTLYA  261 (486)
T ss_pred             CEEEEEcCCCCCHHHHHHH
Confidence            4788999999999999764

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=83.44  E-value=1.3  Score=36.31  Aligned_cols=46  Identities=26%  Similarity=0.289  Sum_probs=30.7

Q ss_pred             cccccccccchhHHH---HHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEI---IESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~---~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+..+||.+.-.+.   +.+++....-.-|-+-+-|.+|.|||+||-+
T Consensus        35 ~~~~g~vGQ~~AReAagiivdlik~KkmaGravLlaGppgtGKTAlAla   83 (456)
T KOG1942|consen   35 EVAAGFVGQENAREAAGIIVDLIKSKKMAGRAVLLAGPPGTGKTALALA   83 (456)
T ss_pred             ecccccccchhhhhhhhHHHHHHHhhhccCcEEEEecCCCCchhHHHHH
Confidence            345688998765553   3455544322245566889999999999854

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.41  E-value=0.69  Score=41.94  Aligned_cols=19  Identities=32%  Similarity=0.448  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++++|..|.||||+|..
T Consensus       495 e~vALVGPSGsGKSTiasL  513 (716)
T KOG0058|consen  495 EVVALVGPSGSGKSTIASL  513 (716)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4899999999999999974

>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein

Probab=83.24  E-value=0.76  Score=45.30  Aligned_cols=21  Identities=14%  Similarity=0.099  Sum_probs=18.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|..|.|||||.+.+
T Consensus        87 Ge~~aIlG~nGsGKSTLLk~L  107 (1394)
T TIGR00956        87 GELTVVLGRPGSGCSTLLKTI  107 (1394)
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            468999999999999998753

>TIGR00955 3a01204 The Eye Pigment Precursor Transporter (EPP) Family protein

Probab=83.20  E-value=0.8  Score=41.24  Aligned_cols=20  Identities=35%  Similarity=0.478  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|.|-.|.|||||-+.
T Consensus        51 Ge~~aI~G~sGsGKSTLL~~   70 (617)
T TIGR00955        51 GELLAVMGSSGAGKTTLMNA   70 (617)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46899999999999999775

>PLN03232 ABC transporter C family member; Provisional

Probab=82.94  E-value=0.7  Score=45.88  Aligned_cols=20  Identities=25%  Similarity=0.385  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..+||+|..|.|||||++.
T Consensus      1262 GekvaIVG~SGSGKSTL~~l 1281 (1495)
T PLN03232       1262 SEKVGVVGRTGAGKSSMLNA 1281 (1495)
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35799999999999999975

>PRK07773 replicative DNA helicase; Validated

Probab=82.80  E-value=2.6  Score=39.68  Aligned_cols=40  Identities=15%  Similarity=0.123  Sum_probs=24.8

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..|...-...+.+++ .+-..-.++-|-|-+|+||||+|-.
T Consensus       197 ~~Gi~TG~~~LD~l~-~Gl~~G~livIagrPg~GKT~fal~  236 (886)
T PRK07773        197 ARGVPTGFTELDAMT-NGLHPGQLIIVAARPSMGKTTFGLD  236 (886)
T ss_pred             CCCccCChhHhcccc-CCCCCCcEEEEEeCCCCCcHHHHHH
Confidence            445555555554444 1112235677889999999999853

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=82.57  E-value=0.8  Score=38.68  Aligned_cols=18  Identities=33%  Similarity=0.348  Sum_probs=15.7

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      .+-|.|..|.||||+.++
T Consensus       151 lilI~G~TGSGKTT~l~a  168 (372)
T TIGR02525       151 LGLICGETGSGKSTLAAS  168 (372)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            467899999999999875

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).

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=82.56  E-value=0.76  Score=37.24  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=18.0

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.++|.+|..|.||||+-|.
T Consensus        49 ~G~ivgflGaNGAGKSTtLKm   69 (325)
T COG4586          49 KGEIVGFLGANGAGKSTTLKM   69 (325)
T ss_pred             CCcEEEEEcCCCCcchhhHHH
Confidence            346899999999999999774

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=82.46  E-value=0.69  Score=40.03  Aligned_cols=20  Identities=25%  Similarity=0.386  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.-|+|+|..|+||+||.+.
T Consensus       613 dSRiaIVGPNGVGKSTlLkL  632 (807)
T KOG0066|consen  613 DSRIAIVGPNGVGKSTLLKL  632 (807)
T ss_pred             cceeEEECCCCccHHHHHHH
Confidence            34589999999999999764

>PRK08149 ATP synthase SpaL; Validated

Probab=82.43  E-value=0.82  Score=39.31  Aligned_cols=20  Identities=25%  Similarity=0.408  Sum_probs=17.3

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|.|-.|.|||||.+.
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~  170 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNM  170 (428)
T ss_pred             CCEEEEECCCCCChhHHHHH
Confidence            45689999999999999864

>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]

Probab=82.30  E-value=1.4  Score=37.43  Aligned_cols=22  Identities=23%  Similarity=0.240  Sum_probs=19.3

Q ss_pred             CCeEEEEEEcCCCCcHHHHhcc
Q 047923          168 KDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++-|+|+-+.|||||+..
T Consensus        71 ~~~~~vmvvG~vDSGKSTLt~~   92 (398)
T COG1341          71 GKVGVVMVVGPVDSGKSTLTTY   92 (398)
T ss_pred             cCCcEEEEECCcCcCHHHHHHH
Confidence            3578899999999999999875

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=82.30  E-value=0.84  Score=37.83  Aligned_cols=20  Identities=30%  Similarity=0.428  Sum_probs=17.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|.|-.|.|||||.+.
T Consensus        69 Gqri~I~G~sG~GKTtLl~~   88 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGM   88 (326)
T ss_pred             CcEEEEECCCCCChHHHHHH
Confidence            45689999999999999764

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PRK06321 replicative DNA helicase; Provisional

Probab=81.64  E-value=1.7  Score=37.91  Aligned_cols=40  Identities=13%  Similarity=0.184  Sum_probs=26.4

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.|.......+.+++. +-..-.++-|-|-+|+||||+|-.
T Consensus       206 ~~Gi~tG~~~LD~~t~-Gl~~G~LiiiaarPgmGKTafal~  245 (472)
T PRK06321        206 ISGIPTHFIDLDKMIN-GFSPSNLMILAARPAMGKTALALN  245 (472)
T ss_pred             CCccccCcHHHHHHhc-CCCCCcEEEEEeCCCCChHHHHHH
Confidence            4566666666666554 222234667789999999999853

>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR)

Probab=81.52  E-value=0.79  Score=45.51  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+||+|-.|.|||||+++
T Consensus      1246 ekvaIvGrSGsGKSTLl~l 1264 (1490)
T TIGR01271      1246 QRVGLLGRTGSGKSTLLSA 1264 (1490)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4689999999999999875

The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=81.31  E-value=0.66  Score=40.12  Aligned_cols=19  Identities=32%  Similarity=0.510  Sum_probs=16.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      |--|++|..|.|||||.+.
T Consensus       291 RRYGLVGPNG~GKTTLLkH  309 (807)
T KOG0066|consen  291 RRYGLVGPNGMGKTTLLKH  309 (807)
T ss_pred             ceecccCCCCCchHHHHHH
Confidence            5568999999999999874

>PRK05922 type III secretion system ATPase; Validated

Probab=81.30  E-value=0.9  Score=39.13  Aligned_cols=19  Identities=16%  Similarity=0.392  Sum_probs=16.6

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|.|-.|.|||||.+.
T Consensus       158 qrigI~G~nG~GKSTLL~~  176 (434)
T PRK05922        158 QRIGVFSEPGSGKSSLLST  176 (434)
T ss_pred             cEEEEECCCCCChHHHHHH
Confidence            4589999999999999874

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=81.29  E-value=0.95  Score=39.17  Aligned_cols=20  Identities=20%  Similarity=0.341  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|.|-.|.|||||++.
T Consensus       168 GqrigI~G~sG~GKSTLl~~  187 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGM  187 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45689999999999999875

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=81.27  E-value=0.88  Score=45.29  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+||+|..|.|||||+++
T Consensus      1313 ekiaIVGrTGsGKSTL~~l 1331 (1522)
T TIGR00957      1313 EKVGIVGRTGAGKSSLTLG 1331 (1522)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5799999999999999875

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=81.21  E-value=1.6  Score=37.43  Aligned_cols=43  Identities=23%  Similarity=0.095  Sum_probs=29.4

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++|....+..+.+.+..-...-.-+-|.|-.|.||+++|+++
T Consensus       144 ~ii~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~i  186 (457)
T PRK11361        144 HILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAI  186 (457)
T ss_pred             ceecccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHH
Confidence            4777777777776655443222233458899999999999863

>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein

Probab=81.18  E-value=1  Score=44.48  Aligned_cols=19  Identities=26%  Similarity=0.447  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.+.
T Consensus       790 e~~aI~G~sGaGKSTLL~~  808 (1394)
T TIGR00956       790 TLTALMGASGAGKTTLLNV  808 (1394)
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            5899999999999999875

>PLN03130 ABC transporter C family member; Provisional

Probab=81.18  E-value=0.89  Score=45.53  Aligned_cols=19  Identities=32%  Similarity=0.438  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+||+|..|.|||||++.
T Consensus      1266 ekVaIVGrSGSGKSTLl~l 1284 (1622)
T PLN03130       1266 EKVGIVGRTGAGKSSMLNA 1284 (1622)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5799999999999999875

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=81.17  E-value=1.9  Score=39.92  Aligned_cols=32  Identities=28%  Similarity=0.331  Sum_probs=22.7

Q ss_pred             HHHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          157 EIIESLLA-AESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       157 ~~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ..+..+|. .+=..-+++=|+|..|+||||||-
T Consensus        46 ~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal   78 (790)
T PRK09519         46 IALDVALGIGGLPRGRVIEIYGPESSGKTTVAL   78 (790)
T ss_pred             HHHHHhhcCCCccCCeEEEEECCCCCCHHHHHH
Confidence            34556665 332335677799999999999984

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=81.13  E-value=1  Score=38.85  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..++|.|-.|.|||||++.+
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i  177 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMI  177 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            457899999999999998753

>CHL00189 infB translation initiation factor 2; Provisional

Probab=81.05  E-value=0.89  Score=41.81  Aligned_cols=21  Identities=33%  Similarity=0.289  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++++|+|..|.|||||..+
T Consensus       243 r~p~V~IvGhvdvGKTSLld~  263 (742)
T CHL00189        243 RPPIVTILGHVDHGKTTLLDK  263 (742)
T ss_pred             cCCEEEEECCCCCCHHHHHHH
Confidence            367999999999999999864

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=81.03  E-value=1.5  Score=37.65  Aligned_cols=44  Identities=23%  Similarity=0.271  Sum_probs=31.5

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....+.++...+..-...-..+-|.|-.|.|||++|+++
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~i  177 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARAL  177 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHH
Confidence            35788888788877766543333234568899999999999863

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PTZ00265 multidrug resistance protein (mdr1); Provisional

Probab=81.01  E-value=0.9  Score=45.03  Aligned_cols=19  Identities=26%  Similarity=0.263  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus      1195 ~~vAIVG~SGsGKSTl~~L 1213 (1466)
T PTZ00265       1195 KTTAIVGETGSGKSTVMSL 1213 (1466)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999975

>PRK13796 GTPase YqeH; Provisional

Probab=80.98  E-value=1.8  Score=36.40  Aligned_cols=18  Identities=28%  Similarity=0.425  Sum_probs=15.4

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -+.++|+.++||+||-.+
T Consensus       162 ~v~vvG~~NvGKSTLiN~  179 (365)
T PRK13796        162 DVYVVGVTNVGKSTLINR  179 (365)
T ss_pred             eEEEEcCCCCcHHHHHHH
Confidence            467899999999999764

>PLN03140 ABC transporter G family member; Provisional

Probab=80.96  E-value=1  Score=44.60  Aligned_cols=20  Identities=30%  Similarity=0.436  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|.|..|.|||||.+.
T Consensus       906 Gel~aL~G~sGaGKTTLL~~  925 (1470)
T PLN03140        906 GVLTALMGVSGAGKTTLMDV  925 (1470)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            36899999999999999875

>PTZ00243 ABC transporter; Provisional

Probab=80.95  E-value=0.92  Score=45.27  Aligned_cols=19  Identities=32%  Similarity=0.368  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+||+|-.|.|||||++.
T Consensus      1337 ekVaIVGrTGSGKSTLl~l 1355 (1560)
T PTZ00243       1337 EKVGIVGRTGSGKSTLLLT 1355 (1560)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5689999999999999975

>PRK12297 obgE GTPase CgtA; Reviewed

Probab=80.85  E-value=0.92  Score=39.01  Aligned_cols=20  Identities=25%  Similarity=0.481  Sum_probs=17.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.-|+++|.+.+|||||-.+
T Consensus       158 ~adVglVG~pNaGKSTLLn~  177 (424)
T PRK12297        158 LADVGLVGFPNVGKSTLLSV  177 (424)
T ss_pred             cCcEEEEcCCCCCHHHHHHH
Confidence            44589999999999999764

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=80.72  E-value=0.86  Score=40.85  Aligned_cols=19  Identities=32%  Similarity=0.146  Sum_probs=15.7

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ++.-|.|.+|.||||+...
T Consensus       161 ~~~vitGgpGTGKTt~v~~  179 (586)
T TIGR01447       161 NFSLITGGPGTGKTTTVAR  179 (586)
T ss_pred             CeEEEEcCCCCCHHHHHHH
Confidence            4677899999999997653

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PHA03132 thymidine kinase; Provisional

Probab=80.65  E-value=1.1  Score=39.89  Aligned_cols=21  Identities=33%  Similarity=0.344  Sum_probs=18.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...|.|-|.=|+||||+++.+
T Consensus       257 ~~fIv~EGidGsGKTTlik~L  277 (580)
T PHA03132        257 ACFLFLEGVMGVGKTTLLNHM  277 (580)
T ss_pred             eEEEEEECCCCCCHHHHHHHH
Confidence            678889999999999998753

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=80.52  E-value=1.8  Score=38.37  Aligned_cols=36  Identities=19%  Similarity=0.277  Sum_probs=26.2

Q ss_pred             hhHHHHHHHhh-----hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          154 SRVEIIESLLA-----AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       154 ~~~~~~~~~l~-----~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.++..||.     ...-+-+++=|.|..|.||||..+.
T Consensus        89 kKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkv  129 (634)
T KOG1970|consen   89 KKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKV  129 (634)
T ss_pred             HhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHH
Confidence            34566677776     2223467999999999999997663

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=80.31  E-value=1.1  Score=39.62  Aligned_cols=21  Identities=33%  Similarity=0.347  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =+-.||||.+|.||||+-+++
T Consensus       101 g~rygLiG~nG~Gkst~L~~i  121 (614)
T KOG0927|consen  101 GRRYGLIGPNGSGKSTFLRAI  121 (614)
T ss_pred             CceEEEEcCCCCcHhHHHHHH
Confidence            356899999999999997753

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=80.26  E-value=0.95  Score=40.69  Aligned_cols=20  Identities=35%  Similarity=0.418  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+-|||-.|.|||.|++++
T Consensus       315 NpL~LyG~sGsGKTHLL~AI  334 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAI  334 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            44789999999999999864

>PRK12296 obgE GTPase CgtA; Reviewed

Probab=80.22  E-value=0.97  Score=39.67  Aligned_cols=20  Identities=35%  Similarity=0.493  Sum_probs=17.3

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.-|+|+|.+++|||||..+
T Consensus       159 ~adV~LVG~PNAGKSTLln~  178 (500)
T PRK12296        159 VADVGLVGFPSAGKSSLISA  178 (500)
T ss_pred             cceEEEEEcCCCCHHHHHHH
Confidence            45689999999999999764

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=80.19  E-value=1.1  Score=38.64  Aligned_cols=21  Identities=24%  Similarity=0.389  Sum_probs=18.1

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-..++|.|-.|.|||||++.
T Consensus       157 ~Gq~i~I~G~sG~GKStLl~~  177 (438)
T PRK07721        157 KGQRVGIFAGSGVGKSTLMGM  177 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            456889999999999999874

>TIGR01257 rim_protein retinal-specific rim ABC transporter

Probab=80.12  E-value=1  Score=46.25  Aligned_cols=19  Identities=37%  Similarity=0.541  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++||.|..|.|||||.+.
T Consensus      1966 Ei~gLLG~NGAGKTTLlkm 1984 (2272)
T TIGR01257      1966 ECFGLLGVNGAGKTTTFKM 1984 (2272)
T ss_pred             cEEEEECCCCCcHHHHHHH
Confidence            4789999999999999875

This model describes the photoreceptor protein (rim protein) in eukaryotes. It is the member of ABC transporter superfamily. Rim protein is a membrane glycoprotein which is localized in the photoreceptor outer segment discs. Mutation/s in its genetic loci is implicated in the recessive Stargardt's disease.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	190
3ozi_A	204	Crystal Structure Of The Tir Domain From The Flax D		1e-16
3jrn_A	176	Crystal Structure Of Tir Domain From Arabidopsis Th		2e-15

>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease Resistance Protein L6 Length = 204

Iteration: 1
 Score = 82.4 bits (202), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/134 (33%), Positives = 78/134 (58%), Gaps = 4/134 (2%)
Query: 2   RQNIQTF-IDDQLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
           R  I TF  DD+L +G EI  ++  AI+   I V I S GY  S+WCL EL +I++ ++E
Sbjct: 61  RYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEE 120
Query: 61  YA-HIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFI 119
               I++P FY  DPS+VR QTG +  +F K   +F  + + +Q+W++A K+      + 
Sbjct: 121 DPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKF--DGQTIQNWKDALKKVGDLKGWH 178
Query: 120 LPESELIKEVVNQI 133
           + +++    + +++
Sbjct: 179 IGKNDKQGAIADKV 192

>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana Length = 176

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 48/135 (35%), Positives = 72/135 (53%), Gaps = 5/135 (3%)
Query: 2   RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE 60
           R++I+TF DD +L  G   S  +   IE    +V++ SE Y  S WCL ELV I+ ++K+
Sbjct: 34  RRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLDELVTIMDFEKK 93
Query: 61  YAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFIL 120
            +  V+P FY  +P+ VR QTG     F K   R  E+ EK+  WR A    A       
Sbjct: 94  GSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR--EDPEKVLKWRQALTNFAQLSGDCS 151
Query: 121 --PESELIKEVVNQI 133
              +S+L+ ++ N+I
Sbjct: 152 GDDDSKLVDKIANEI 166

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	190
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	4e-55
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	3e-52
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	2e-38
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	5e-07
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	7e-05

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana} Length = 176

 Score =  171 bits (436), Expect = 4e-55
 Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 5/140 (3%)

Query: 1   SRQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKK 59
            R++I+TF DD+ L  G   S  +   IE    +V++ SE Y  S WCL ELV I+ ++K
Sbjct: 33  VRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLDELVTIMDFEK 92

Query: 60  EYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFI 119
           + +  V+P FY  +P+ VR QTG     F K   R +   EK+  WR A    A      
Sbjct: 93  KGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASREDP--EKVLKWRQALTNFAQLSGDC 150

Query: 120 L--PESELIKEVVNQILKRL 137
               +S+L+ ++ N+I  + 
Sbjct: 151 SGDDDSKLVDKIANEISNKK 170

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum} Length = 204

 Score =  165 bits (420), Expect = 3e-52
 Identities = 47/143 (32%), Positives = 76/143 (53%), Gaps = 8/143 (5%)

Query: 1   SRQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKK 59
            R  I TF DD  L +G EI  ++  AI+   I V I S GY  S+WCL EL +I++ ++
Sbjct: 60  RRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQE 119

Query: 60  EY-AHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAF 118
           E    I++P FY  DPS+VR QTG +  +F K   +F+   + +Q+W++A K+      +
Sbjct: 120 EDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDG--QTIQNWKDALKKVGDLKGW 177

Query: 119 IL----PESELIKEVVNQILKRL 137
            +     +  +  +V   I   +
Sbjct: 178 HIGKNDKQGAIADKVSADIWSHI 200

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222} Length = 154

 Score =  128 bits (323), Expect = 2e-38
 Identities = 17/109 (15%), Positives = 42/109 (38%), Gaps = 3/109 (2%)

Query: 1   SRQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKK 59
                + + DD  L  GD +  SI   + S    +++ S  +    W   EL  + + + 
Sbjct: 44  RAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLES 103

Query: 60  EYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNA 108
                ++P +++    EV S + +  +  +      +   +++ +   A
Sbjct: 104 SGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSV--DEIVADLMA 150

>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 = 48.1 bits (114), Expect = 5e-07
 Identities = 18/117 (15%), Positives = 41/117 (35%), Gaps = 6/117 (5%)

Query: 75  SEVRSQTGSFGNSFSK-LEERFNENSEKLQSWRNATKEAASFMAFILPESELIKEVVNQI 133
              R Q    G           +  ++ L+ + +        +  ++   +  ++++++ 
Sbjct: 59  RIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRK 118

Query: 134 LKRLAEVLLCDKENQLVGRESRVE-IIESLLAAESKDVYILGIWGVGSIGKTTIARA 189
           L          K+     RE  V+ +I+ L      D + L + G    GK+ IA  
Sbjct: 119 LLLGNVP----KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQ 171

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 22/139 (15%), Positives = 48/139 (34%), Gaps = 14/139 (10%)

Query: 50  ELVKILKYKKEYAHIVIPGFYRGDPSEVRSQTGSFGNSFSKLEERFNENSEKLQSWRNAT 109
           E V+    +++ A ++I         +      SF N+   L E + + +  L       
Sbjct: 41  EKVRNEPTQQQRAAMLIKMI----LKKDNDSYVSFYNA--LLHEGYKDLAALLHDGIPVV 94

Query: 110 KEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAAESKD 169
                         + +  + + +   L E  +  +    V R+  V  I+  L+    +
Sbjct: 95  SS--------SSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGE 146

Query: 170 VYILGIWGVGSIGKTTIAR 188
              + I G+   GK+ +A 
Sbjct: 147 PGWVTIHGMAGCGKSVLAA 165

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 5e-05
 Identities = 43/252 (17%), Positives = 75/252 (29%), Gaps = 90/252 (35%)

Query: 3   QNIQTFIDDQLNRGDEISESIAYAIES--PAISVIIFSEGYPFSRWCLHELV-------- 52
           Q +   ID       + S +I   I S    +  ++ S+ Y     CL  LV        
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN---CL--LVLLNVQNAK 257

Query: 53  ---------KIL---KYK--------KEYAHIVIPGFYRG-DPSEVRSQTGSF-GNSFSK 90
                    KIL   ++K            HI +        P EV+S    +       
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317

Query: 91  L--E-------------ERFNENSEKLQSWRNATKEAAS------------------FMA 117
           L  E             E   +      +W++   +  +                  F  
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Query: 118 F-ILPES-------------ELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEI--IES 161
             + P S             ++IK  V  ++ +L +  L +K+ +    ES + I  I  
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK----ESTISIPSIYL 433

Query: 162 LLAAESKDVYIL 173
            L  + ++ Y L
Sbjct: 434 ELKVKLENEYAL 445

>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 = 40.2 bits (93), Expect = 3e-04
 Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 33/149 (22%)

Query: 50  ELVKILKYKKEYAHIVIPGFYRGDPSEVRSQT----GSFGNSFSKLEERFNENSEK---- 101
               IL  K+E  HI+           V S T     +  +   ++ ++F E   +    
Sbjct: 41  MPKSILS-KEEIDHII------MSKDAV-SGTLRLFWTLLSKQEEMVQKFVEEVLRINYK 92

Query: 102 --LQSWRNATKEAASFMAFILPESELIKEVVNQILKRLAEVLLCDKENQLVGRESRV-EI 158
             +   +   ++ +         + +  E  ++ L    +V    K N  V R     ++
Sbjct: 93  FLMSPIKTEQRQPS-------MMTRMYIEQRDR-LYNDNQVF--AKYN--VSRLQPYLKL 140

Query: 159 IESLLAAESKDVYILGIWGVGSIGKTTIA 187
            ++LL  E +    + I GV   GKT +A
Sbjct: 141 RQALL--ELRPAKNVLIDGVLGSGKTWVA 167

>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 = 40.4 bits (95), Expect = 7e-05
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 1   SRQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKK 59
           S  +++ F+  +    G  I   +  A+ S    V++ + G+    WC +++++ L    
Sbjct: 35  STASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDPWCKYQMLQALTEAP 94

Query: 60  EYAHIVIPGFYRGDPSEVRSQ 80
                 IP       +    +
Sbjct: 95  GAEGCTIPLLSGLSRAAYPPE 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	190
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	100.0
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	100.0
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	99.92
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	99.82
1fyx_A	149	TOLL-like receptor 2; beta-alpha-beta fold, signal	99.68
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	99.67
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	99.66
2js7_A	160	Myeloid differentiation primary response protein M	99.65
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.22
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	98.98
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.8
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.76
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	98.62
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.99
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.95
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.87
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.8
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.74
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	97.73
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.64
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.6
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.51
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.5
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	97.46
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	97.36
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.35
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.24
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.18
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.1
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.09
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	97.08
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	97.01
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	96.98
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	96.92
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.91
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.86
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.81
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.81
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.79
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.79
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.78
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.75
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.75
3pvs_A	447	Replication-associated recombination protein A; ma	96.72
3bos_A	242	Putative DNA replication factor; P-loop containing	96.65
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.65
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.6
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.6
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.6
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.56
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.54
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.52
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.47
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.45
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.44
3fwy_A	314	Light-independent protochlorophyllide reductase I	96.41
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.38
2xxa_A	433	Signal recognition particle protein; protein trans	96.36
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.36
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.35
2og2_A	359	Putative signal recognition particle receptor; nuc	96.34
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	96.34
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.27
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.27
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.25
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.22
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.21
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.11
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.05
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.03
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.95
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.89
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.88
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.87
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	95.86
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.85
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	95.79
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.77
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.77
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.75
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.72
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.68
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.66
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.62
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.61
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.6
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.59
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.59
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.53
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	95.5
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.5
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.45
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.41
3end_A	307	Light-independent protochlorophyllide reductase ir	95.29
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.14
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.11
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.09
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	95.04
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.03
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.93
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	94.93
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.92
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.91
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.9
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.83
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.83
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	94.83
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.8
2qgz_A	308	Helicase loader, putative primosome component; str	94.75
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	94.68
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.6
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	94.59
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.57
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	94.57
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	94.56
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.53
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.51
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.44
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	94.32
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	94.18
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	94.17
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.16
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.14
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	94.13
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.09
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	94.0
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.0
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.99
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.93
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.89
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.86
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	93.82
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.8
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	93.73
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.68
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.57
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	93.35
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	93.3
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.27
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.26
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.22
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.19
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.12
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.11
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	93.08
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.03
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.02
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	93.0
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	92.99
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.96
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	92.94
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	92.88
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.87
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.8
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	92.73
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	92.67
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	92.54
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	92.46
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.42
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.4
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	92.33
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	92.32
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	92.32
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.31
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.29
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	92.28
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.27
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	92.23
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	92.14
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.01
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	91.96
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	91.7
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	91.52
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.49
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	91.47
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	91.45
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	91.32
2z43_A	324	DNA repair and recombination protein RADA; archaea	91.3
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	91.23
1u94_A	356	RECA protein, recombinase A; homologous recombinat	91.2
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.19
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	91.15
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	91.12
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	91.1
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	90.76
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	90.69
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	90.55
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	90.48
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	90.46
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	90.42
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	90.34
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	90.26
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	90.2
3ez9_A	403	Para; DNA binding, winged-HTH, partition, biosynth	90.17
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	90.0
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	89.52
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	89.36
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	89.33
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	89.15
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	88.71
2vf7_A	842	UVRA2, excinuclease ABC, subunit A.; DNA-binding p	88.58
3hyn_A	189	Putative signal transduction protein; DUF1863 fami	88.56
3ice_A	422	Transcription termination factor RHO; transcriptio	88.27
2ygr_A	993	Uvrabc system protein A; hydrolase, nucleotide exc	88.19
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	88.1
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	88.1
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	87.94
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	87.73
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	87.43
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	86.9
2r6f_A	972	Excinuclease ABC subunit A; UVRA, nucleotide excis	86.87
1xp8_A	366	RECA protein, recombinase A; recombination, radior	86.86
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	86.38
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	86.3
1of1_A	376	Thymidine kinase; transferase, antiviral drug, enz	86.15
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	85.91
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	85.81
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	85.62
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	85.61
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	84.52
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	84.45
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	84.12
3q5d_A	447	Atlastin-1; G protein, GTPase, GDP/GTP binding, hy	83.6
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	83.48
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	83.39
3ec1_A	369	YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase	83.31
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	83.21
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	83.19
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	83.14
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	82.94
1eiw_A	111	Hypothetical protein MTH538; CHEY-like fold, flavo	82.9
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	82.34
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	81.93
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	81.55
4a9a_A	376	Ribosome-interacting GTPase 1; DRG-DFRP complex, r	81.25
3h2y_A	368	GTPase family protein; GTP-binding protein YQEH, p	80.99
3l0o_A	427	Transcription termination factor RHO; helicase, RH	80.92

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana}

Probab=100.00  E-value=1.3e-47  Score=285.91  Aligned_cols=139  Identities=35%  Similarity=0.589  Sum_probs=115.9

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCcccccc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQ   80 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~Vr~q   80 (190)
                      ++||++|+|+ ++.+|++|.++|.+||++|+++|+|||+||++|+|||+||++|++|++.+++.|+||||+|+|++||+|
T Consensus        34 ~~gi~~f~D~~~l~~G~~i~~~l~~aIe~Sri~IvV~S~ny~~S~WCl~EL~~i~~~~~~~~~~ViPIfy~V~ps~Vr~q  113 (176)
T 3jrn_A           34 RRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQ  113 (176)
T ss_dssp             HTTCCEECCCC--------------CCTTEEEEEEEECTTTTTCHHHHHHHHHHHHHHHTTSCEEEEEECSSCHHHHHHT
T ss_pred             HCCCEEEEEcccccCCCchHHHHHHHHHhCCEEEEEecCCcCCChhHHHHHHHHHhhhccCCCEEEEEEecCCHHHhhhc
Confidence            5799999998 999999999999999999999999999999999999999999999999899999999999999999999


Q ss_pred             CCchhhHHHHHHHhhhhhhHHHHhHHHHHHHhhccccccCc--hhhhHHHHHHHHHhhhhhhhh
Q 047923           81 TGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP--ESELIKEVVNQILKRLAEVLL  142 (190)
Q Consensus        81 ~g~~~~~f~~~~~~~~~~~e~v~kWr~AL~ev~~~~g~~~~--e~~~i~~iv~~v~~~l~~~~~  142 (190)
                      +|.||++|.+|+.+  .+.+++++||.||+++++++|+++.  |+++|++||++|+++|+.++|
T Consensus       114 ~g~fg~af~~~~~~--~~~~~~~~Wr~AL~~va~~~G~~~~~~e~~~i~~Iv~~v~~~l~~~~~  175 (176)
T 3jrn_A          114 TGVLAEQFKKHASR--EDPEKVLKWRQALTNFAQLSGDCSGDDDSKLVDKIANEISNKKTIYAT  175 (176)
T ss_dssp             CTHHHHHHHHHHTT--SCHHHHHHHHHHHHHHTTSCCEECCSCHHHHHHHHHHHHHTTCC----
T ss_pred             cCcHHHHHHHHHhc--cCHHHHHHHHHHHHHHhcccceecCCCHHHHHHHHHHHHHHHhcCCCC
Confidence            99999999999887  4557899999999999999999986  999999999999999987765

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum}

Probab=100.00  E-value=1e-45  Score=280.13  Aligned_cols=136  Identities=35%  Similarity=0.661  Sum_probs=128.0

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhc-CCeeEEeEEeecCCccccc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKE-YAHIVIPGFYRGDPSEVRS   79 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~-~~~~v~PvFy~v~ps~Vr~   79 (190)
                      ++||++|+|+ ++++|+.|.++|++||++|+++|+|||+||++|+|||+||++|++|++. ++++|+||||+|+|++||+
T Consensus        61 ~~GI~~f~D~~el~~G~~I~~~l~~aIe~Sri~IvV~S~nYa~S~WCl~EL~~I~e~~~~~~~~~ViPIFY~VdPs~Vr~  140 (204)
T 3ozi_A           61 RYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRH  140 (204)
T ss_dssp             HTTCCEEEEETTTCCGGGTTTTHHHHHHHCSEEEEEECTTGGGCHHHHHHHHHHHHHHHHCTTSEECCEEESSCHHHHHH
T ss_pred             HCCCcEEEeCCccCCCCchHHHHHHHHHhCcEeeEEEEcccccCcHHHHHHHHHHHHHHhcCCeeeEEEEeecCHHHHHh
Confidence            5799999998 9999999999999999999999999999999999999999999999875 5789999999999999999


Q ss_pred             cCCchhhHHHHHHHhhhhhhHHHHhHHHHHHHhhccccccCc----hhhhHHHHHHHHHhhhhh
Q 047923           80 QTGSFGNSFSKLEERFNENSEKLQSWRNATKEAASFMAFILP----ESELIKEVVNQILKRLAE  139 (190)
Q Consensus        80 q~g~~~~~f~~~~~~~~~~~e~v~kWr~AL~ev~~~~g~~~~----e~~~i~~iv~~v~~~l~~  139 (190)
                      |+|.||++|.+|+.++..  +++++||.||+++++++||++.    +.+++++|+.+|+.+|++
T Consensus       141 q~g~fg~af~~~~~~~~~--~~v~~Wr~AL~~va~lsG~~~~~~~~e~~~i~~Iv~di~~kl~~  202 (204)
T 3ozi_A          141 QTGCYKKAFRKHANKFDG--QTIQNWKDALKKVGDLKGWHIGKNDKQGAIADKVSADIWSHISK  202 (204)
T ss_dssp             TCTTHHHHHHHHTTTSCH--HHHHHHHHHHHHHHTSCBEEECTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHhhCH--HHHHHHHHHHHHHhccCceecCCCCCHHHHHHHHHHHHHHHhcc
Confidence            999999999999887743  5799999999999999999986    778999999999999875

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222}

Probab=99.92  E-value=1.2e-26  Score=170.63  Aligned_cols=90  Identities=18%  Similarity=0.313  Sum_probs=84.7

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCcccccc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQ   80 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~Vr~q   80 (190)
                      ++||++|+|+ ++.+|+++.++|.+||++|+++|+|||++|++|.||++||..+++|...+++.|+||||+|+|++||+|
T Consensus        45 ~~gi~v~~D~~~l~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPV~~~v~p~~v~~~  124 (154)
T 3h16_A           45 AAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASF  124 (154)
T ss_dssp             HHTCCEECGGGEECTTCCHHHHHHHHHTSEEEEEEEEEHHHHTTCCCHHHHHHHTCCCTTSCCCEEEEEESCCTGGGTTT
T ss_pred             HCCCcEEEcHHhCCCccHHHHHHHHHHHhCcEEEEEeCcchhcChHHHHHHHHHHHHHhcCCCEEEEEEecCCHHHHhhC
Confidence            4699999999 899999999999999999999999999999999999999999999987788899999999999999999


Q ss_pred             CCchhhHHHHH
Q 047923           81 TGSFGNSFSKL   91 (190)
Q Consensus        81 ~g~~~~~f~~~   91 (190)
                      .|.|++.|...
T Consensus       125 ~~~~~~~~~~~  135 (154)
T 3h16_A          125 SPTMADKLAFN  135 (154)
T ss_dssp             CCCCCSSCCEE
T ss_pred             CccHHHHHhhh
Confidence            99999877443

>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=99.82  E-value=2.6e-22  Score=145.96  Aligned_cols=107  Identities=13%  Similarity=0.211  Sum_probs=65.9

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEEeecCCccccccC
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGFYRGDPSEVRSQT   81 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvFy~v~ps~Vr~q~   81 (190)
                      +|+++|+|+ ++.+|+++.++|.+||++|+.+|+|||++|++|.||+.||..++.+.......||||||+|+++++....
T Consensus        37 ~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~I~VlS~~y~~S~wc~~El~~al~~~~~~~~~vIpv~~~v~~~~lp~~L  116 (146)
T 3ub2_A           37 ASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDPWCKYQMLQALTEAPGAEGCTIPLLSGLSRAAYPPEL  116 (146)
T ss_dssp             ----------------CCCEEECCTTCCEEEEEEEECHHHHHCHHHHHHHHHHHHTSSSSSSEEEEEECSCCGGGSCGGG
T ss_pred             CCeEEEEECccccccccHHHHHHHHHHhCCEEEEEECcccccCHHHHHHHHHHHHHHhhcCCcEEEEEcCCChhhCCHHH
Confidence            699999999 9999999999999999999999999999999999999999999998633334778999999976653322


Q ss_pred             Cch-hhHHHHHHHhhhhhhHHHHhHHHHH
Q 047923           82 GSF-GNSFSKLEERFNENSEKLQSWRNAT  109 (190)
Q Consensus        82 g~~-~~~f~~~~~~~~~~~e~v~kWr~AL  109 (190)
                      ..+ ...+..+...+....+.+.+|++||
T Consensus       117 r~~~~id~~~~d~~f~~l~~~v~~~~~~~  145 (146)
T 3ub2_A          117 RFMYYVDGRGPDGGFRQVKEAVMRYLQTL  145 (146)
T ss_dssp             GGSCCEETTSGGGGHHHHHHHHHHHHTTC
T ss_pred             hCeeeeeccChHhhHHHHHHHHHHHHHhc
Confidence            111 0111112223333335678887764

>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=99.68  E-value=1.7e-18  Score=126.29  Aligned_cols=75  Identities=19%  Similarity=0.194  Sum_probs=66.4

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHH-hhhcCCeeEEeEEee-cCCccc
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILK-YKKEYAHIVIPGFYR-GDPSEV   77 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~-~~~~~~~~v~PvFy~-v~ps~V   77 (190)
                      .|+++|+|+ ++.+|+++.++|.+||++|++.|+|||++|++|.||+.||..++. +.+.++..||||||. +++..+
T Consensus        33 ~g~~~~~~~rd~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~S~wc~~El~~a~~~~~~~~~~~vIpv~~~~i~~~~~  110 (149)
T 1fyx_A           33 PPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWXKYELDFSHFRLFDENNDAAILILLEPIEKKAI  110 (149)
T ss_dssp             SCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHHHHSCCSCCTTCGGGTTCCEEEESSCCCTTTS
T ss_pred             CCeEEeeccccCCCchhHHHHHHHHHHHcCEEEEEeCcchhccchHHHHHHHHHHHHHhcCCCEEEEEEecCCChhhc
Confidence            499999999 999999999999999999999999999999999999999999885 345566789999997 555444

>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=99.67  E-value=4.7e-18  Score=127.25  Aligned_cols=74  Identities=20%  Similarity=0.241  Sum_probs=61.9

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhh-hcCCeeEEeEEee-cCCc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYK-KEYAHIVIPGFYR-GDPS   75 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~-~~~~~~v~PvFy~-v~ps   75 (190)
                      ++|+++|+|+ |+.+|+++.++|.+||++|+..|+|||++|++|.||+.||..++.+. +.++..||||||. +.+.
T Consensus        62 ~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~IvVlS~~yl~S~wc~~El~~a~~~~~~~~~~~vIpV~~~~i~~~  138 (178)
T 2j67_A           62 DGSILICLYESYFDPGKSISENIVSFIEKSYKSIFVLSPNFVQNEWCHYEFYFAHHNLFHENSDHIILILLEPIPFY  138 (178)
T ss_dssp             C-CCCEEEHHHHCCTTSCHHHHHHHHHHTEEEEEEEECHHHHHHTGGGTHHHHTTCC-------CEEEEESSCCCGG
T ss_pred             cCCeEEEEecccCCCCccHHHHHHHHHHhCCEEEEEecccccccchHHHHHHHHHHHHHhcCCCEEEEEEecCCChH
Confidence            3799999999 99999999999999999999999999999999999999999998643 4566789999998 4433

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens}

Probab=99.66  E-value=2.5e-17  Score=121.22  Aligned_cols=73  Identities=19%  Similarity=0.187  Sum_probs=66.8

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCc-CchhhHHHHHHHHHhh-hcCCeeEEeEEeecCC
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYP-FSRWCLHELVKILKYK-KEYAHIVIPGFYRGDP   74 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~-~S~wcl~El~~i~~~~-~~~~~~v~PvFy~v~p   74 (190)
                      ++|+++|+|+ |+.+|+++.++|.+||++|+..|+|||++|+ .|.||+.|+..++.+. +.++..||||||.--+
T Consensus        39 ~~g~~l~~~~rD~~~G~~i~~~i~~~I~~Sr~~IvVlS~~y~~~S~wc~~El~~a~~~~~~~~~~~vI~I~~~~~~  114 (159)
T 1t3g_A           39 HYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELR  114 (159)
T ss_dssp             TSCCCEECHHHHCCCCTTHHHHHHHHHHTBSEEEEEECHHHHHTTTTHHHHHSHHHHHHHHTTSSEEEEEECSCCC
T ss_pred             CCCeEEEEEcccccCccchHHHHHHHHHHcCEEEEEEccchhhcChHHHHHHHHHHHHHHhcCCCEEEEEEecccc
Confidence            5899999999 9999999999999999999999999999997 9999999999999876 5667899999988444

>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=99.65  E-value=1.4e-17  Score=122.78  Aligned_cols=72  Identities=18%  Similarity=0.178  Sum_probs=65.1

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhh-cccceEEEecCCCcCchhhHHHHHHHHHhh-hcCCeeEEeEEeecCC
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIE-SPAISVIIFSEGYPFSRWCLHELVKILKYK-KEYAHIVIPGFYRGDP   74 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~-~s~~~ivv~S~~y~~S~wcl~El~~i~~~~-~~~~~~v~PvFy~v~p   74 (190)
                      .|+++|+|+ ++.+|+++.++|.+||+ .|+.+|+|||++|++|.||+.||..++.+. +.++..||||||..-+
T Consensus        43 ~g~~~~~~~rd~~~G~~i~~~i~~~I~~~Sr~~IvVlS~~y~~S~wc~~El~~a~~~~~~~~~~~vIpV~~~~~~  117 (160)
T 2js7_A           43 YRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMK  117 (160)
T ss_dssp             SCCCCEESCCSSSSSCSCCCCCGGGHHHHEEEEEEECCHHHHHSHHHHHHHHHHHHHCTTHHHHTEEEEESSCCC
T ss_pred             CceEEEEeCCCCCCCCcHHHHHHHHHHHhCCEEEEEECcchhcCHHHHHHHHHHHHHHHccCCCEEEEEEEcccc
Confidence            579999999 99999999999999999 799999999999999999999999999875 4455789999998543

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.22  E-value=4.7e-12  Score=114.56  Aligned_cols=74  Identities=14%  Similarity=0.174  Sum_probs=66.4

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhh-hcCCeeEEeEEeecCCc
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYK-KEYAHIVIPGFYRGDPS   75 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~-~~~~~~v~PvFy~v~ps   75 (190)
                      ++|+++|+++ |+.+|+.+.+++.+||++||..|+|+|++|+.|.||..|+..++.+. +.++..||||||+--|.
T Consensus       700 ~~~~~~~~~~rd~~~G~~~~~~i~~~i~~sr~~i~vls~~~~~s~wc~~e~~~a~~~~~~~~~~~~i~i~~~~~~~  775 (844)
T 3j0a_A          700 QNRFNLCFEERDFVPGENRIANIQDAIWNSRKIVCLVSRHFLRDGWCLEAFSYAQGRCLSDLNSALIMVVVGSLSQ  775 (844)
T ss_dssp             TTCSCEECSSSSCCSSSCHHHHHHHHHHHSSEEEEEECTTHHHHTSTTHHHHHHHSCCCCSSCTTEEEEESSCCCS
T ss_pred             CCceEEEEEccccCCCchHHHHHHHHHHHhCeEEEEeccccccChHHHHHHHHHHHHHHHhcCCcEEEEEeccCCh
Confidence            5789999999 99999999999999999999999999999999999999998877654 55677899999985443

>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=98.98  E-value=5.4e-10  Score=96.77  Aligned_cols=41  Identities=27%  Similarity=0.285  Sum_probs=36.1

Q ss_pred             cccchhHHHHHHHhhhc-CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          150 VGRESRVEIIESLLAAE-SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~-~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +||+.+++++.++|... ...+++++|+||||+||||||+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v  172 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQA  172 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHH
Confidence            59999999999999765 335899999999999999999863

>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=98.80  E-value=2.6e-09  Score=99.21  Aligned_cols=46  Identities=22%  Similarity=0.282  Sum_probs=40.9

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .....+|||+..++++.++|....+.+++++|+||||+||||||+.
T Consensus       121 ~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~  166 (1249)
T 3sfz_A          121 QRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAE  166 (1249)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHH
Confidence            4556799999999999999977666799999999999999999974

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.76  E-value=4.1e-09  Score=91.58  Aligned_cols=46  Identities=22%  Similarity=0.281  Sum_probs=40.3

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .....+|||+..++.+.++|...+.+.++++|+||||+||||||+.
T Consensus       121 ~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~  166 (591)
T 1z6t_A          121 QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAE  166 (591)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHH
T ss_pred             CCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHH
Confidence            4556899999999999999986556689999999999999999974

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=98.62  E-value=6e-09  Score=95.56  Aligned_cols=40  Identities=25%  Similarity=0.066  Sum_probs=35.4

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|||+..++.+.++|... +.+++++|+||||+||||||++
T Consensus       130 ~VGRe~eLeeL~elL~~~-d~~RVV~IvGmGGIGKTTLAk~  169 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALD  169 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHC-CSSCEEEECCSTTSSHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhcc-CCCeEEEEEcCCCccHHHHHHH
Confidence            499999999999998753 3489999999999999999985

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.99  E-value=3e-06  Score=69.92  Aligned_cols=46  Identities=28%  Similarity=0.270  Sum_probs=35.4

Q ss_pred             cccccccccchhHHHHHHHh-hh---c---CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLL-AA---E---SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l-~~---~---~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+..++||+.+++.+..+| ..   +   ....-+|||+|++|+||||||++
T Consensus        19 ~~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~   71 (412)
T 1w5s_A           19 YIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKF   71 (412)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHH
Confidence            34578999999999999888 53   1   22345556699999999999985

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.95  E-value=4.6e-06  Score=60.91  Aligned_cols=43  Identities=21%  Similarity=0.306  Sum_probs=34.7

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++|++..++.+.+.+...  ..+.+-|+|.+|+||||||++
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~   62 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEG   62 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSCHHHHHHH
T ss_pred             cccccccchHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHH
Confidence            4467999999999998888653  234467999999999999975

>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=97.87  E-value=5e-06  Score=67.66  Aligned_cols=46  Identities=26%  Similarity=0.357  Sum_probs=37.8

Q ss_pred             cccccccccchhHHHHHHHhhhc--CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAE--SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~--~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+..++||+..++.+.+++...  ....+.+.|+|.+|+||||||++
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~   64 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKF   64 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHH
Confidence            34578999999999999988742  33456788999999999999985

>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=97.80  E-value=1.2e-05  Score=65.66  Aligned_cols=45  Identities=13%  Similarity=0.072  Sum_probs=36.8

Q ss_pred             cccccccchhHHHHHHHhhh--cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAA--ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~--~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +..++|++..++.+..++..  .....+.+-|+|.+|+||||||+++
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l   65 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYI   65 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHH
Confidence            46899999999999988764  2333568899999999999999853

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.74  E-value=1.1e-05  Score=65.67  Aligned_cols=47  Identities=23%  Similarity=0.294  Sum_probs=37.9

Q ss_pred             cccccccccchhHHHHHHHhhhc--CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE--SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~--~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+..++|++..++.+..++...  ....+.+-|+|.+|+||||||+++
T Consensus        16 ~~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~   64 (387)
T 2v1u_A           16 YVPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLV   64 (387)
T ss_dssp             CCCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHH
Confidence            34578999999999999988543  334567889999999999999853

>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=97.73  E-value=2.5e-05  Score=58.91  Aligned_cols=45  Identities=24%  Similarity=0.257  Sum_probs=36.0

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+++|++..++.+..++..... -+.+-|+|.+|+||||||++
T Consensus        20 ~~~~~~~g~~~~~~~l~~~l~~~~~-~~~~ll~G~~G~GKT~l~~~   64 (250)
T 1njg_A           20 QTFADVVGQEHVLTALANGLSLGRI-HHAYLFSGTRGVGKTSIARL   64 (250)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHTCC-CSEEEEECSTTSCHHHHHHH
T ss_pred             ccHHHHhCcHHHHHHHHHHHHcCCC-CeEEEEECCCCCCHHHHHHH
Confidence            3446799999999999988876421 23678999999999999975

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.64  E-value=1.9e-05  Score=57.43  Aligned_cols=43  Identities=21%  Similarity=0.324  Sum_probs=34.1

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+++|++..++.+.+.+...  ..+.+-|+|.+|+||||||++
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~--~~~~vll~G~~G~GKT~la~~   62 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSRR--TKNNPILLGDPGVGKTAIVEG   62 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSS--SSCEEEEESCGGGCHHHHHHH
T ss_pred             ccchhhcchHHHHHHHHHHhCC--CCCceEEECCCCCCHHHHHHH
Confidence            3467999999999998887653  233456999999999999975

>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=97.60  E-value=3.8e-05  Score=62.61  Aligned_cols=46  Identities=22%  Similarity=0.216  Sum_probs=36.7

Q ss_pred             cccccccccchhHHHHHHHhhhc----CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAE----SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~----~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+..++|++..++.+..++...    ....+.+.|+|.+|+||||||++
T Consensus        14 ~~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~   63 (389)
T 1fnn_A           14 YVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRK   63 (389)
T ss_dssp             CCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHH
Confidence            34468999999999998888652    22245788999999999999975

>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=97.51  E-value=4.4e-05  Score=62.42  Aligned_cols=65  Identities=18%  Similarity=0.207  Sum_probs=43.3

Q ss_pred             hhhhHHHHHHHHHhhhhhhhhccccccccccchhHHHHHHHhhh----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          122 ESELIKEVVNQILKRLAEVLLCDKENQLVGRESRVEIIESLLAA----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       122 e~~~i~~iv~~v~~~l~~~~~~~~~~~~vG~d~~~~~~~~~l~~----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +..+++.+...+....+   + ....+++|.+..++.+.+.+..          .....+-+-|+|.+|+||||||+++
T Consensus        63 ~~~~~~~i~~~i~~~~~---~-~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~ai  137 (357)
T 3d8b_A           63 EPKMIELIMNEIMDHGP---P-VNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCI  137 (357)
T ss_dssp             CHHHHHHHHHHTBCCSC---C-CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHH
T ss_pred             ChHHHHHHHhhcccCCC---C-CCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHH
Confidence            44555555554433322   2 3446799999999999887653          1112456779999999999999864

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.50  E-value=5.3e-05  Score=59.91  Aligned_cols=47  Identities=19%  Similarity=0.240  Sum_probs=35.5

Q ss_pred             cccccccccchhHHHHHHHhhhc----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+++...          ....+.+-|+|.+|.||||||+++
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~l   74 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAV   74 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHH
Confidence            34568999999999998876431          112356789999999999999863

>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=97.46  E-value=9.3e-05  Score=58.85  Aligned_cols=44  Identities=30%  Similarity=0.344  Sum_probs=35.7

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+++|++..++.+..++..+.  ...+-++|.+|+||||+|++
T Consensus        22 ~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~   65 (327)
T 1iqp_A           22 QRLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALA   65 (327)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHH
T ss_pred             CCHHHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHH
Confidence            344679999999999998887653  33378999999999999985

>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=97.36  E-value=0.00013  Score=57.85  Aligned_cols=44  Identities=20%  Similarity=0.320  Sum_probs=35.3

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+++|++..++.+.+++..+.  ...+-++|.+|+||||+|++
T Consensus        18 ~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~   61 (323)
T 1sxj_B           18 QVLSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHC   61 (323)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHH
T ss_pred             CCHHHHHCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHH
Confidence            334679999999999998886543  23378999999999999975

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.35  E-value=9.4e-05  Score=58.04  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=35.6

Q ss_pred             cccccccccchhHHHHHHHhhhc-----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE-----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~-----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+.+...           ....+-+-|+|.+|+||||||+++
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~l   71 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAV   71 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHH
Confidence            44567999999999988876431           122345779999999999999864

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.24  E-value=0.00014  Score=58.42  Aligned_cols=46  Identities=24%  Similarity=0.282  Sum_probs=36.1

Q ss_pred             ccccccccchhHHHHHHHhhhc---CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAE---SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~---~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|++..++.+..++...   ......+-|+|.+|+||||||+++
T Consensus        27 ~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i   75 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANII   75 (338)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHH
Confidence            3467999999999998888652   223445779999999999999863

>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=97.18  E-value=0.00023  Score=57.31  Aligned_cols=45  Identities=16%  Similarity=0.265  Sum_probs=35.3

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+..++....  ...+-++|.+|+||||+|+++
T Consensus        34 ~~~~~i~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l   78 (353)
T 1sxj_D           34 KNLDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILAL   78 (353)
T ss_dssp             SSTTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHH
T ss_pred             CCHHHhhCCHHHHHHHHHHHhcCC--CCEEEEECCCCCCHHHHHHHH
Confidence            344679999999999988886542  222789999999999999863

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=97.10  E-value=0.00023  Score=57.56  Aligned_cols=44  Identities=23%  Similarity=0.294  Sum_probs=32.2

Q ss_pred             ccccccchhHHHHHHHhhhc---CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE---SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~---~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.++|.+.-++.+...+...   ......+.++|.+|.||||||+++
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~i   71 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHII   71 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHH
Confidence            46788877777776655432   223466899999999999999863

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.09  E-value=0.00026  Score=56.11  Aligned_cols=42  Identities=24%  Similarity=0.242  Sum_probs=30.7

Q ss_pred             cccccchhHHHHHHHhhhc-------------CCCeEEEEEEcCCCCcHHHHhcc
Q 047923          148 QLVGRESRVEIIESLLAAE-------------SKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~-------------~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++|.+..++.+.+++..-             .....-+-|+|.+|+||||||++
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~   86 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALK   86 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHH
Confidence            4788888877777655421             22344677999999999999975

>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=97.08  E-value=0.0013  Score=56.18  Aligned_cols=20  Identities=30%  Similarity=0.511  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||++.
T Consensus       293 GeVI~LVGpNGSGKTTLl~~  312 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGK  312 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHH
Confidence            46999999999999999875

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=97.01  E-value=0.0018  Score=52.27  Aligned_cols=20  Identities=35%  Similarity=0.403  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|.+|.||||++..
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~  124 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAK  124 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            67999999999999999864

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=96.98  E-value=0.00041  Score=56.30  Aligned_cols=45  Identities=22%  Similarity=0.155  Sum_probs=32.6

Q ss_pred             cccccccchhHHHHHHHhh---hcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLA---AESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~---~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++|.+..++.+..++.   .....-+.+-|+|.+|+||||||+++
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~l   90 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGM   90 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHH
Confidence            5689999988777654443   22222246779999999999999863

>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=96.92  E-value=0.00052  Score=58.78  Aligned_cols=47  Identities=26%  Similarity=0.242  Sum_probs=36.5

Q ss_pred             cccccccccchhHHHHHHHhhhcC---------------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAES---------------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~---------------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|++..++.+.+++....               ...+.+-|+|.+|+||||||+++
T Consensus        36 ~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~l   97 (516)
T 1sxj_A           36 TNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLV   97 (516)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHH
Confidence            344679999999999999886410               12467889999999999999863

>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=96.91  E-value=0.00051  Score=55.14  Aligned_cols=47  Identities=21%  Similarity=0.243  Sum_probs=34.7

Q ss_pred             cccccccccchhHHHHHHHhhh----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAA----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+++..          ....-+-+-++|.+|.|||+||+++
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~ai   71 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV   71 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHH
T ss_pred             CCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHH
Confidence            3446799999999998887631          1111345779999999999999864

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.86  E-value=0.00032  Score=52.15  Aligned_cols=45  Identities=18%  Similarity=0.052  Sum_probs=27.7

Q ss_pred             cccccccchhHH----HHHHHhhhcCCCe--EEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVE----IIESLLAAESKDV--YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~----~~~~~l~~~~~~~--~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++++.+....    .+.+++.......  +.+-|+|.+|+||||||+++
T Consensus        24 f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i   74 (202)
T 2w58_A           24 LSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAI   74 (202)
T ss_dssp             TTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHH
T ss_pred             HhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHH
Confidence            356776553333    3334443322211  57789999999999999863

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.81  E-value=0.0029  Score=51.14  Aligned_cols=20  Identities=30%  Similarity=0.416  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||++.
T Consensus       129 g~vi~lvG~nGaGKTTll~~  148 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAK  148 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            57999999999999999874

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.00033  Score=56.54  Aligned_cols=44  Identities=11%  Similarity=-0.049  Sum_probs=34.9

Q ss_pred             ccccccchhHHHHHHHhhh--cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA--ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~--~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-+.|||.+.+.+...|..  ....-..+=|+|.+|.|||+++++|
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v   65 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDV   65 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHH
Confidence            3488999999999887764  2334566789999999999999864

>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=96.79  E-value=0.00071  Score=55.22  Aligned_cols=47  Identities=21%  Similarity=0.233  Sum_probs=34.1

Q ss_pred             cccccccccchhHHHHHHHhhhc----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAE----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+.+...          ....+-+-|+|.+|+||||||+++
T Consensus        48 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~al  104 (355)
T 2qp9_X           48 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV  104 (355)
T ss_dssp             CCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHH
Confidence            34467999999999888776321          111234678999999999999864

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.79  E-value=0.00065  Score=57.54  Aligned_cols=42  Identities=24%  Similarity=0.378  Sum_probs=33.2

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|++..++.+...|..... - -+-|+|.+|+||||||+++
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~~-~-~~LL~G~pG~GKT~la~~l  221 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRTK-N-NPVLIGEPGVGKTAIAEGL  221 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSS-C-EEEEESCTTTTTHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccCC-C-CeEEECCCCCCHHHHHHHH
Confidence            5689999999999988865322 2 2358999999999999863

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.78  E-value=0.0015  Score=52.36  Aligned_cols=41  Identities=15%  Similarity=0.130  Sum_probs=31.9

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+..++.+...+....    -+-++|.+|+|||+||+++
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~l   66 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTL   66 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHH
T ss_pred             ccceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHH
Confidence            3578999988888877665532    3668999999999999863

>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=96.75  E-value=0.0032  Score=50.16  Aligned_cols=20  Identities=40%  Similarity=0.544  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++++.|.+|+||||++..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~  117 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGK  117 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            57899999999999999864

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.75  E-value=0.0006  Score=53.96  Aligned_cols=44  Identities=16%  Similarity=0.339  Sum_probs=33.4

Q ss_pred             ccccccchhHHHHHHHhhhcC------C-CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAES------K-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~------~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+..++.+...+....      . ....+.++|.+|+||||+|+++
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~l   67 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTL   67 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHH
Confidence            458899888888877765421      1 1457889999999999999863

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=96.72  E-value=0.00079  Score=56.77  Aligned_cols=44  Identities=23%  Similarity=0.386  Sum_probs=33.8

Q ss_pred             ccccccccchhH---HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRV---EIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~---~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|.+..+   ..+...+...  ....+-|||.+|+||||||+++
T Consensus        24 ~l~~ivGq~~~~~~~~~L~~~i~~~--~~~~vLL~GppGtGKTtlAr~i   70 (447)
T 3pvs_A           24 NLAQYIGQQHLLAAGKPLPRAIEAG--HLHSMILWGPPGTGKTTLAEVI   70 (447)
T ss_dssp             STTTCCSCHHHHSTTSHHHHHHHHT--CCCEEEEECSTTSSHHHHHHHH
T ss_pred             CHHHhCCcHHHHhchHHHHHHHHcC--CCcEEEEECCCCCcHHHHHHHH
Confidence            346789998777   6666666654  3467889999999999999863

>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=96.65  E-value=0.0007  Score=51.10  Aligned_cols=42  Identities=17%  Similarity=0.273  Sum_probs=26.3

Q ss_pred             cccccccc---hhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          146 ENQLVGRE---SRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       146 ~~~~vG~d---~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++++|.+   ..++.+..++...  ..+.+-|+|.+|+||||||++
T Consensus        27 ~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~   71 (242)
T 3bos_A           27 FTSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHA   71 (242)
T ss_dssp             TTTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHH
T ss_pred             hhhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHH
Confidence            35677743   3333444443332  345677999999999999975

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.65  E-value=0.001  Score=52.16  Aligned_cols=46  Identities=22%  Similarity=0.216  Sum_probs=30.5

Q ss_pred             ccccccccchhHHHHHHHhhhc---------CCC-eEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAE---------SKD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~---------~~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++++|.+..++++.++...-         +-. -+-+.|+|..|.||||||+++
T Consensus        38 ~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i   93 (278)
T 1iy2_A           38 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAV   93 (278)
T ss_dssp             CGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHH
Confidence            3456788887777666554321         001 112889999999999999863

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.60  E-value=0.0039  Score=49.92  Aligned_cols=20  Identities=30%  Similarity=0.476  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.|+|.+|.||||++..
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~  123 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGK  123 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHH
Confidence            57999999999999999864

>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=96.60  E-value=0.0019  Score=50.26  Aligned_cols=44  Identities=16%  Similarity=0.098  Sum_probs=29.8

Q ss_pred             ccccccchhHHHHHH-------Hhhhc-CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIES-------LLAAE-SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~-------~l~~~-~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.+...+.+..       .+... .....-+-|+|.+|+||||||+++
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~i   84 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKI   84 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHH
Confidence            457777766655554       22211 234667789999999999999863

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.60  E-value=0.00098  Score=54.88  Aligned_cols=46  Identities=20%  Similarity=0.281  Sum_probs=34.8

Q ss_pred             ccccccccchhHHHHHHHhhhc----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAE----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|.+..++.+.+++...          ....+-+-|+|.+|+|||+||+++
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~ai  168 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAV  168 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHH
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHH
Confidence            3467999999999998876321          011356779999999999999864

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.56  E-value=0.0073  Score=48.19  Aligned_cols=20  Identities=35%  Similarity=0.277  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||++.
T Consensus       100 g~vi~lvG~nGsGKTTll~~  119 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGK  119 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHH
Confidence            46999999999999999875

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.54  E-value=0.0095  Score=50.12  Aligned_cols=20  Identities=35%  Similarity=0.341  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.++|.+|+||||++..
T Consensus       100 p~vIlivG~~G~GKTTt~~k  119 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAK  119 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHH
Confidence            67999999999999998753

>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=96.52  E-value=0.0018  Score=52.14  Aligned_cols=43  Identities=16%  Similarity=0.251  Sum_probs=32.6

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-++.+...+..+  .+..+.++|..|.||||+|+++
T Consensus        24 ~~~~~g~~~~~~~L~~~i~~g--~~~~~ll~Gp~G~GKTtla~~l   66 (340)
T 1sxj_C           24 LDEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVAL   66 (340)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHH
Confidence            356789888788777777654  3333789999999999999863

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.47  E-value=0.0021  Score=52.37  Aligned_cols=33  Identities=30%  Similarity=0.364  Sum_probs=23.9

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+...+........+|+|.|.+|+|||||+..
T Consensus        66 ~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~   98 (355)
T 3p32_A           66 QQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEA   98 (355)
T ss_dssp             HHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHH
T ss_pred             HHHHHHhHhhcCCceEEEEECCCCCCHHHHHHH
Confidence            334444443445678999999999999999864

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.45  E-value=0.009  Score=50.13  Aligned_cols=20  Identities=40%  Similarity=0.494  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+++.++|.+|+||||++..
T Consensus        97 ~~vI~lvG~~GsGKTTt~~k  116 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGK  116 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            58999999999999999753

>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=96.44  E-value=0.0012  Score=55.41  Aligned_cols=47  Identities=19%  Similarity=0.202  Sum_probs=34.7

Q ss_pred             cccccccccchhHHHHHHHhhh----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAA----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+.+.+..          .....+-+-|+|.+|+|||+||+++
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~ai  187 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAV  187 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHH
Confidence            3446799999999888876631          0112356779999999999999864

>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=96.41  E-value=0.0015  Score=52.47  Aligned_cols=21  Identities=29%  Similarity=0.651  Sum_probs=18.2

Q ss_pred             CCeEEEEEEcCCCCcHHHHhc
Q 047923          168 KDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ++.++|+|.|=||+||||.|-
T Consensus        46 ~~aKVIAIaGKGGVGKTTtav   66 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSS   66 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHH
Confidence            358999999999999999873

>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=96.38  E-value=0.0019  Score=55.06  Aligned_cols=45  Identities=24%  Similarity=0.287  Sum_probs=34.5

Q ss_pred             cccccccchhHHHHHHHhhhc-----------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAE-----------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~-----------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+++|.+..++.+.+++...           ...-+-+-|+|.+|.|||+||+++
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lArai  258 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAV  258 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHH
Confidence            356899999999998877532           222345679999999999999864

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.36  E-value=0.0092  Score=50.05  Aligned_cols=21  Identities=24%  Similarity=0.215  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|.++|.||+||||+|-.
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~  119 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGK  119 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            368999999999999999853

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.35  E-value=0.0018  Score=57.95  Aligned_cols=42  Identities=24%  Similarity=0.378  Sum_probs=33.4

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|++..++.+...|..... - -+-++|.+|+||||+|+++
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~~-~-~vLL~G~pGtGKT~la~~l  221 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRTK-N-NPVLIGEPGVGKTAIAEGL  221 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSS-C-EEEEESCTTTTTHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCCCC-C-CeEEECCCCCCHHHHHHHH
Confidence            5689999999999988865321 2 2458999999999999863

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.34  E-value=0.013  Score=47.86  Aligned_cols=20  Identities=35%  Similarity=0.277  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||++.
T Consensus       157 g~vi~lvG~nGsGKTTll~~  176 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGK  176 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHH
Confidence            46999999999999999875

>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=96.34  E-value=0.0021  Score=54.11  Aligned_cols=46  Identities=24%  Similarity=0.212  Sum_probs=32.8

Q ss_pred             ccccccccchhHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|.+..++.+..++..   +...-+-+-++|.+|.||||||+++
T Consensus        35 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~al   83 (456)
T 2c9o_A           35 AASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAI   83 (456)
T ss_dssp             EETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHH
T ss_pred             chhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHH
Confidence            346899999888876655442   2212244668999999999999863

>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=96.27  E-value=0.0025  Score=50.82  Aligned_cols=45  Identities=20%  Similarity=0.080  Sum_probs=34.6

Q ss_pred             ccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|.+..++.+.+++..+.. -.++=+.|.+|+||||+|+++
T Consensus        24 ~~~~ivg~~~~~~~l~~~l~~~~~-~~~~L~~G~~G~GKT~la~~l   68 (324)
T 3u61_B           24 TIDECILPAFDKETFKSITSKGKI-PHIILHSPSPGTGKTTVAKAL   68 (324)
T ss_dssp             STTTSCCCHHHHHHHHHHHHTTCC-CSEEEECSSTTSSHHHHHHHH
T ss_pred             CHHHHhCcHHHHHHHHHHHHcCCC-CeEEEeeCcCCCCHHHHHHHH
Confidence            346799999999999988875421 245567788999999999863

>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=96.27  E-value=0.0015  Score=59.35  Aligned_cols=42  Identities=19%  Similarity=0.329  Sum_probs=33.6

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++|++..++.+...|....  .+-+-++|-+|+||||||+.
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~  210 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEG  210 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHH
Confidence            3568999999999998886532  23356899999999999985

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.25  E-value=0.0055  Score=49.43  Aligned_cols=21  Identities=43%  Similarity=0.675  Sum_probs=19.0

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++||.|..|.||||||+.
T Consensus        91 ~p~iigI~GpsGSGKSTl~~~  111 (321)
T 3tqc_A           91 VPYIIGIAGSVAVGKSTTSRV  111 (321)
T ss_dssp             CCEEEEEECCTTSSHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            467999999999999999975

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.22  E-value=0.0039  Score=53.29  Aligned_cols=40  Identities=20%  Similarity=0.161  Sum_probs=31.3

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+..++.+...+..+.    -+-++|.+|+|||+||+++
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraL   61 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRL   61 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHG
T ss_pred             hhhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHH
Confidence            468999988887776665432    3568999999999999864

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.21  E-value=0.0012  Score=47.24  Aligned_cols=21  Identities=24%  Similarity=0.453  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -..++|+|..|.|||||++++
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i   56 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAW   56 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            457899999999999999863

>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=96.11  E-value=0.0029  Score=56.51  Aligned_cols=42  Identities=29%  Similarity=0.349  Sum_probs=33.4

Q ss_pred             cccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          146 ENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++|++..++.+.+.|....  -.-+-++|-+|+||||||++
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~  226 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEG  226 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHH
Confidence            3568999999999988886542  22346899999999999985

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=96.05  E-value=0.0022  Score=51.53  Aligned_cols=22  Identities=36%  Similarity=0.564  Sum_probs=19.4

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .-.++||.|..|.|||||++.+
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L  110 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVL  110 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHH
Confidence            4679999999999999999853

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=96.03  E-value=0.0022  Score=50.59  Aligned_cols=21  Identities=33%  Similarity=0.803  Sum_probs=18.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+|+|.|+.|.||||+|+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~   94 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQR   94 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            467899999999999999985

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.95  E-value=0.0022  Score=50.46  Aligned_cols=18  Identities=33%  Similarity=0.338  Sum_probs=16.6

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +.++|.+|.||||||+++
T Consensus        47 vlL~Gp~GtGKTtLakal   64 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAV   64 (274)
T ss_dssp             EEEESSTTSCHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHH
Confidence            899999999999999864

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.89  E-value=0.0056  Score=51.31  Aligned_cols=44  Identities=16%  Similarity=0.165  Sum_probs=32.6

Q ss_pred             ccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++++.+.+..           +-..-+=+=++|.+|.|||+||+++
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAi  226 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAV  226 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHH
Confidence            5678999988888776542           1122345668999999999999974

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.88  E-value=0.0045  Score=50.51  Aligned_cols=20  Identities=25%  Similarity=0.202  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-++|.+|+||||||+++
T Consensus        73 ~~ill~Gp~GtGKT~la~~l   92 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTL   92 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHH
Confidence            34668999999999999863

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=95.87  E-value=0.0069  Score=50.80  Aligned_cols=20  Identities=30%  Similarity=0.363  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      .++|.|+|.+|+||||+|..
T Consensus        99 ~~vI~ivG~~GvGKTTla~~  118 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAK  118 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46899999999999999864

>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=95.86  E-value=0.0025  Score=49.07  Aligned_cols=18  Identities=39%  Similarity=0.490  Sum_probs=16.4

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +.|+|..|.||||||+++
T Consensus        52 ~ll~G~~G~GKTtl~~~i   69 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAV   69 (254)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            889999999999999863

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.85  E-value=0.006  Score=51.26  Aligned_cols=44  Identities=18%  Similarity=0.246  Sum_probs=32.7

Q ss_pred             ccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++++.+.+..           +-...+=+=++|.+|.|||+||++|
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAi  235 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAV  235 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHH
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHH
Confidence            5677999988888776542           1112355668999999999999974

>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=95.79  E-value=0.0076  Score=48.79  Aligned_cols=27  Identities=26%  Similarity=0.368  Sum_probs=21.3

Q ss_pred             hhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          163 LAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       163 l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +........+++|.|.+|.|||||+..
T Consensus        49 l~~~~~~~~~i~i~G~~g~GKSTl~~~   75 (341)
T 2p67_A           49 IMPYCGNTLRLGVTGTPGAGKSTFLEA   75 (341)
T ss_dssp             HGGGCSCSEEEEEEECTTSCHHHHHHH
T ss_pred             CCcccCCCEEEEEEcCCCCCHHHHHHH
Confidence            333344678999999999999999864

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.77  E-value=0.0025  Score=49.57  Aligned_cols=19  Identities=26%  Similarity=0.335  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..|.|.|+.|.||||+++.
T Consensus        49 ~~i~l~G~~GsGKSTl~~~   67 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKI   67 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3689999999999999985

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.77  E-value=0.0028  Score=48.82  Aligned_cols=18  Identities=33%  Similarity=0.350  Sum_probs=16.2

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +.|+|.+|.||||||+++
T Consensus        48 vll~G~~GtGKT~la~~l   65 (257)
T 1lv7_A           48 VLMVGPPGTGKTLLAKAI   65 (257)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHH
Confidence            679999999999999864

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.75  E-value=0.0039  Score=53.27  Aligned_cols=46  Identities=22%  Similarity=0.220  Sum_probs=32.0

Q ss_pred             ccccccccchhHHHHHHHhhhc-C--------CC-eEEEEEEcCCCCcHHHHhccC
Q 047923          145 KENQLVGRESRVEIIESLLAAE-S--------KD-VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~~-~--------~~-~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+++|.+..++++.++...- .        -. -+-+.|+|.+|.||||||+++
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraI   84 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAV   84 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHH
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHH
Confidence            3467889988877777654321 0        01 123789999999999999864

>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=95.72  E-value=0.0035  Score=50.03  Aligned_cols=21  Identities=43%  Similarity=0.583  Sum_probs=18.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.++||.|..|.|||||++.
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~   99 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARV   99 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            467999999999999999985

>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=95.68  E-value=0.0088  Score=43.09  Aligned_cols=22  Identities=27%  Similarity=0.348  Sum_probs=18.9

Q ss_pred             CCeEEEEEEcCCCCcHHHHhcc
Q 047923          168 KDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..-.+++|.|..|.|||||.+.
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~   52 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRG   52 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHH
Confidence            3456899999999999999885

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.66  E-value=0.011  Score=47.86  Aligned_cols=31  Identities=26%  Similarity=0.371  Sum_probs=23.1

Q ss_pred             HHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          159 IESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       159 ~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +.+-+...-..-.+++|.|.+|.|||||.+.
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~   74 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTTIDA   74 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHHH
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHHHHH
Confidence            3333444444578999999999999999864

>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=95.62  E-value=0.0038  Score=50.05  Aligned_cols=45  Identities=20%  Similarity=0.125  Sum_probs=28.8

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+..++.+...+....  ..-+=|+|-+|+|||+||+++
T Consensus        21 ~~f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~l   65 (350)
T 1g8p_A           21 FPFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRAL   65 (350)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHH
T ss_pred             CCchhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHH
Confidence            344678999875554432222111  112668999999999999863

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.61  E-value=0.0054  Score=53.51  Aligned_cols=40  Identities=25%  Similarity=0.408  Sum_probs=32.1

Q ss_pred             ccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+.-++.+...+..+    ..+.|+|..|.||||||+++
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~i   80 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAM   80 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHH
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHH
Confidence            56889988887777666554    36889999999999999863

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.60  E-value=0.0063  Score=50.57  Aligned_cols=44  Identities=20%  Similarity=0.258  Sum_probs=32.2

Q ss_pred             ccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++-|.+..++++.+.+..           +-..-+=+=++|.+|.|||+||+++
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAi  202 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAV  202 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHH
Confidence            5677999999888776542           1112344568999999999999974

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.59  E-value=0.008  Score=50.43  Aligned_cols=45  Identities=20%  Similarity=0.215  Sum_probs=32.9

Q ss_pred             cccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++.|.+..++++.+.+..           +-..-+=+=+||.+|.|||+||+++
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAi  235 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARAC  235 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHH
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHH
Confidence            35778999999888775432           1112455668999999999999974

>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=95.59  E-value=0.0058  Score=51.27  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...+-|+|.+|+||||||+++
T Consensus       130 ~~~lll~Gp~G~GKTtLa~ai  150 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSI  150 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHH
Confidence            566889999999999999863

>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=95.53  E-value=0.0042  Score=49.45  Aligned_cols=20  Identities=25%  Similarity=0.305  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++++|.+|.||||++..
T Consensus       105 g~vi~lvG~~GsGKTTl~~~  124 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAK  124 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            46899999999999999864

>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=95.50  E-value=0.004  Score=49.39  Aligned_cols=21  Identities=29%  Similarity=0.254  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -+.+-|+|.+|.||||||+++
T Consensus        49 ~~~vLL~Gp~GtGKT~la~al   69 (301)
T 3cf0_A           49 SKGVLFYGPPGCGKTLLAKAI   69 (301)
T ss_dssp             CSEEEEECSSSSSHHHHHHHH
T ss_pred             CceEEEECCCCcCHHHHHHHH
Confidence            346789999999999999864

>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=95.50  E-value=0.0086  Score=49.35  Aligned_cols=24  Identities=29%  Similarity=0.113  Sum_probs=19.8

Q ss_pred             cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          166 ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       166 ~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-..-++++|+|..|.|||||+++
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~  188 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAA  188 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHH
Confidence            333456899999999999999985

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.45  E-value=0.0076  Score=50.92  Aligned_cols=44  Identities=20%  Similarity=0.249  Sum_probs=32.4

Q ss_pred             ccccccchhHHHHHHHhhh-----------cCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----------ESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----------~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++++.+.+..           +-...+=+=++|.+|.|||+||++|
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAi  263 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAV  263 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHH
Confidence            4678999999988775432           1122445568999999999999974

>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=95.41  E-value=0.005  Score=49.22  Aligned_cols=20  Identities=30%  Similarity=0.371  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|.+|.|||||++.
T Consensus       102 g~vi~lvG~nGsGKTTll~~  121 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAK  121 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            56899999999999999875

>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=95.14  E-value=0.012  Score=50.77  Aligned_cols=44  Identities=32%  Similarity=0.305  Sum_probs=31.1

Q ss_pred             ccccccchhHHHHHHHhhhc----CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE----SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~----~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.+.-.+.+.+.+...    ...-..+.++|.+|+||||||+++
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~i  128 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSI  128 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHH
Confidence            34788887777765543321    113457899999999999999863

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.11  E-value=0.012  Score=52.71  Aligned_cols=44  Identities=20%  Similarity=0.354  Sum_probs=33.5

Q ss_pred             ccccccchhHHHHHHHhhhcC-------CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAES-------KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~-------~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+..++.+...+....       .....+-++|.+|+|||+||+++
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~al  541 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARAL  541 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHH
Confidence            568899998888877765421       11346789999999999999864

>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=95.09  E-value=0.014  Score=52.58  Aligned_cols=44  Identities=25%  Similarity=0.336  Sum_probs=32.7

Q ss_pred             ccccccchhHHHHHHHhhh---c-----C---CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA---E-----S---KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~---~-----~---~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++.|.+..++++.+++..   .     .   ...+-|=++|.+|.|||+||++|
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LArai  258 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAV  258 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHH
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHH
Confidence            5678999999888876542   1     1   12355678999999999999974

>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=95.04  E-value=0.0077  Score=47.13  Aligned_cols=20  Identities=25%  Similarity=0.327  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||.+.
T Consensus        50 Gei~~liG~NGsGKSTLlk~   69 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRC   69 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHH
T ss_pred             CCEEEEEcCCCCcHHHHHHH
Confidence            35799999999999999875

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.03  E-value=0.0085  Score=47.58  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++++|.+|.||||++..
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~  117 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAK  117 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            47899999999999999864

>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=94.93  E-value=0.0086  Score=46.64  Aligned_cols=19  Identities=42%  Similarity=0.573  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.+.
T Consensus        42 ei~~l~G~NGsGKSTLlk~   60 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRI   60 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            4799999999999999875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=94.93  E-value=0.0076  Score=48.37  Aligned_cols=20  Identities=25%  Similarity=0.318  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+-++|.+|.|||+||+++
T Consensus        46 ~~iLL~GppGtGKT~la~al   65 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAV   65 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHH
Confidence            45778999999999999864

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.92  E-value=0.015  Score=49.68  Aligned_cols=21  Identities=24%  Similarity=0.295  Sum_probs=17.4

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|.|+|.+|+||||++..
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~k  120 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSK  120 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            367999999999999999864

>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=94.91  E-value=0.0087  Score=46.83  Aligned_cols=19  Identities=26%  Similarity=0.414  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus        47 e~~~l~G~NGsGKSTLlk~   65 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSAT   65 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5799999999999999875

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.90  E-value=0.009  Score=46.58  Aligned_cols=19  Identities=32%  Similarity=0.361  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus        47 e~~~i~G~nGsGKSTLl~~   65 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKL   65 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4799999999999999875

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.83  E-value=0.0095  Score=46.74  Aligned_cols=20  Identities=25%  Similarity=0.308  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||.+.
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~   64 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAAL   64 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35799999999999999875

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=94.83  E-value=0.005  Score=47.63  Aligned_cols=18  Identities=33%  Similarity=0.366  Sum_probs=15.7

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +-|+|.+|+||||||+++
T Consensus        47 vll~G~~GtGKT~la~~l   64 (268)
T 2r62_A           47 VLLVGPPGTGKTLLAKAV   64 (268)
T ss_dssp             CCCBCSSCSSHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHH
Confidence            558999999999999864

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.83  E-value=0.019  Score=48.08  Aligned_cols=44  Identities=25%  Similarity=0.304  Sum_probs=32.3

Q ss_pred             ccccccchhHHHHHHHhhh---c--------CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA---E--------SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~---~--------~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++-|.+..++++.+.+..   .        -..-+=+=++|.+|.|||.||+++
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAi  236 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAV  236 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHH
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHH
Confidence            4677899988888776542   1        112345668999999999999874

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.80  E-value=0.0096  Score=46.95  Aligned_cols=19  Identities=26%  Similarity=0.371  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus        48 e~~~liG~NGsGKSTLlk~   66 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNI   66 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            4799999999999999875

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=94.75  E-value=0.017  Score=46.10  Aligned_cols=21  Identities=29%  Similarity=0.224  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.-+-|||..|+|||+||+++
T Consensus       152 ~~~lll~G~~GtGKT~La~ai  172 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAM  172 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            356779999999999999763

>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=94.68  E-value=0.012  Score=47.53  Aligned_cols=19  Identities=32%  Similarity=0.427  Sum_probs=16.4

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +++-|+|.+|+||||||.+
T Consensus       124 sviLI~GpPGsGKTtLAlq  142 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHA  142 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHH
Confidence            4567999999999999975

>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=94.60  E-value=0.015  Score=47.33  Aligned_cols=31  Identities=26%  Similarity=0.377  Sum_probs=22.4

Q ss_pred             HHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          159 IESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       159 ~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..+|..+-..-.++.|+|..|.|||||+..
T Consensus       120 LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~  150 (349)
T 1pzn_A          120 LDKLLGGGIETQAITEVFGEFGSGKTQLAHT  150 (349)
T ss_dssp             HHHHHTSSEESSEEEEEEESTTSSHHHHHHH
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHH
Confidence            3345543222357999999999999999874

>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=94.59  E-value=0.015  Score=51.89  Aligned_cols=44  Identities=16%  Similarity=0.213  Sum_probs=32.8

Q ss_pred             ccccccchhHHHHHHHhhhcC------C-CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAES------K-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~------~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+..++.+...+....      + ....+-++|.+|+|||+||+++
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~l  508 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQL  508 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHH
Confidence            468899988888877665321      1 2446789999999999999863

>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=94.57  E-value=0.012  Score=47.15  Aligned_cols=23  Identities=17%  Similarity=0.224  Sum_probs=19.1

Q ss_pred             CCeEEEEEEcCCCCcHHHHhccC
Q 047923          168 KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       168 ~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..-.+++|+|..|.|||||++.+
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL  146 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSL  146 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHH
Confidence            34467999999999999999753

>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=94.57  E-value=0.011  Score=46.39  Aligned_cols=19  Identities=37%  Similarity=0.408  Sum_probs=16.0

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      -+-++|.+|+||||||+++
T Consensus        52 ~vll~G~~GtGKT~la~~l   70 (310)
T 1ofh_A           52 NILMIGPTGVGKTEIARRL   70 (310)
T ss_dssp             CEEEECCTTSSHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            3558999999999999863

>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=94.56  E-value=0.43  Score=37.37  Aligned_cols=29  Identities=10%  Similarity=0.093  Sum_probs=23.3

Q ss_pred             chHHHHHHhhcccceEEEecCCCcCchhh
Q 047923           19 ISESIAYAIESPAISVIIFSEGYPFSRWC   47 (190)
Q Consensus        19 ~~~~l~~ai~~s~~~ivv~S~~y~~S~wc   47 (190)
                      ...++.+.++++++.+.|+.-.-..+..|
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            45688899999999999998766666665

>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=94.53  E-value=0.01  Score=49.33  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=18.6

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.+|-|+|++|.||||+|+.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~  277 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQE  277 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            357889999999999999985

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.51  E-value=0.015  Score=43.95  Aligned_cols=33  Identities=18%  Similarity=0.267  Sum_probs=22.9

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..+..++.. -.+-+.+-|+|.+|.||||+|.+
T Consensus        45 ~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~a   77 (212)
T 1tue_A           45 LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMS   77 (212)
T ss_dssp             HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHH
T ss_pred             HHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHH
Confidence            5555555543 22334688999999999999864

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.44  E-value=0.035  Score=46.61  Aligned_cols=39  Identities=15%  Similarity=0.171  Sum_probs=24.8

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|.......+..++. +-..-.++.|.|-+|+||||||..
T Consensus       184 ~~i~tG~~~LD~~~g-Gl~~G~liiI~G~pG~GKTtl~l~  222 (454)
T 2r6a_A          184 TGIPTGFTELDRMTS-GFQRSDLIIVAARPSVGKTAFALN  222 (454)
T ss_dssp             CSBCCSCHHHHHHHS-SBCTTCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCCCcHHHHhhcC-CCCCCCEEEEECCCCCCHHHHHHH
Confidence            344444445555542 211235788999999999999864

>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=94.32  E-value=0.015  Score=48.44  Aligned_cols=32  Identities=19%  Similarity=0.245  Sum_probs=22.9

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+.+.|..-.+...+++|+|..|.|||||.++
T Consensus        57 ~i~~~L~~~~~~~~~valvG~nGaGKSTLln~   88 (413)
T 1tq4_A           57 AISDALKEIDSSVLNVAVTGETGSGKSSFINT   88 (413)
T ss_dssp             HHHHHHHHHHHCCEEEEEEECTTSSHHHHHHH
T ss_pred             hhhhhhhhcccCCeEEEEECCCCCcHHHHHHH
Confidence            34444443333466899999999999999875

>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=94.18  E-value=0.016  Score=47.25  Aligned_cols=20  Identities=25%  Similarity=0.335  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++|+|..|.|||||++.
T Consensus       170 g~k~~IvG~nGsGKSTLlk~  189 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNK  189 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHH
Confidence            57899999999999999985

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=94.17  E-value=0.012  Score=50.95  Aligned_cols=21  Identities=33%  Similarity=0.427  Sum_probs=18.5

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+++|.|+.|.|||||++++
T Consensus       369 G~iI~LiG~sGSGKSTLar~L  389 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARAL  389 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHH
Confidence            468999999999999999863

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.16  E-value=0.04  Score=44.68  Aligned_cols=41  Identities=15%  Similarity=0.151  Sum_probs=27.4

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+.|...-...+..++. +-..-.++-|.|.+|+||||||..
T Consensus        25 ~~~gi~TG~~~LD~~~g-Gl~~G~LiiIaG~pG~GKTt~al~   65 (338)
T 4a1f_A           25 EVTGIPTGFVQLDNYTS-GFNKGSLVIIGARPSMGKTSLMMN   65 (338)
T ss_dssp             CCCSBCCSCHHHHHHHC-SBCTTCEEEEEECTTSCHHHHHHH
T ss_pred             CcCcccCCChHHHHHhc-CCCCCcEEEEEeCCCCCHHHHHHH
Confidence            45566655666666663 211234677899999999999853

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.14  E-value=0.016  Score=42.11  Aligned_cols=21  Identities=24%  Similarity=0.104  Sum_probs=17.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....+.++|.+|+|||||..+
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~   67 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTL   67 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            345688999999999999864

>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=94.13  E-value=0.016  Score=45.90  Aligned_cols=19  Identities=26%  Similarity=0.391  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus        65 e~~~i~G~NGsGKSTLlk~   83 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLMM   83 (290)
T ss_dssp             CEEEEEESTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            5799999999999999875

>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=94.09  E-value=0.031  Score=43.78  Aligned_cols=33  Identities=21%  Similarity=0.248  Sum_probs=23.7

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+..+|.....+...+-++|.+|.|||++|.++
T Consensus        92 ~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~al  124 (267)
T 1u0j_A           92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAI  124 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHH
T ss_pred             HHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHH
Confidence            345555543233556889999999999999863

>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=94.00  E-value=0.016  Score=49.15  Aligned_cols=18  Identities=39%  Similarity=0.422  Sum_probs=16.1

Q ss_pred             EEEEcCCCCcHHHHhccC
Q 047923          173 LGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~v  190 (190)
                      +-|+|.+|.||||||+++
T Consensus        52 vLL~GppGtGKT~Larai   69 (476)
T 2ce7_A           52 ILLVGPPGTGKTLLARAV   69 (476)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            669999999999999864

>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=94.00  E-value=0.017  Score=46.94  Aligned_cols=20  Identities=25%  Similarity=0.189  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-++|.+|+||||+|+++
T Consensus        52 ~~vll~GppGtGKT~la~~i   71 (363)
T 3hws_A           52 SNILLIGPTGSGKTLLAETL   71 (363)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            35678999999999999864

>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=93.99  E-value=0.013  Score=46.90  Aligned_cols=20  Identities=35%  Similarity=0.401  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||++.
T Consensus        80 Ge~vaivG~sGsGKSTLl~l   99 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRL   99 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHH
T ss_pred             CCEEEEECCCCchHHHHHHH
Confidence            35799999999999999975

>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=93.93  E-value=0.019  Score=47.06  Aligned_cols=20  Identities=35%  Similarity=0.577  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||.+.
T Consensus        54 Gei~~IiGpnGaGKSTLlr~   73 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRC   73 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHH
T ss_pred             CCEEEEEcCCCchHHHHHHH
Confidence            35799999999999999875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.89  E-value=0.035  Score=44.31  Aligned_cols=38  Identities=24%  Similarity=0.161  Sum_probs=24.5

Q ss_pred             ccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          151 GRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       151 G~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      |...-...+..++ .+-..-.++-|.|.+|+||||||..
T Consensus        50 ~i~TG~~~LD~~l-gGl~~G~l~li~G~pG~GKTtl~l~   87 (315)
T 3bh0_A           50 GVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALK   87 (315)
T ss_dssp             SBCCSCHHHHHHH-SSBCTTCEEEEECCTTSSHHHHHHH
T ss_pred             CccCChHHHHhhc-CCCCCCcEEEEEeCCCCCHHHHHHH
Confidence            4444445555555 2212235677899999999999864

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.86  E-value=0.024  Score=45.99  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=18.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+++|.|.+|.|||||..+
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~   93 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEY   93 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHH
Confidence            478999999999999999764

>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=93.82  E-value=0.037  Score=45.22  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=18.1

Q ss_pred             CCeEEEEEEc-CCCCcHHHHhc
Q 047923          168 KDVYILGIWG-VGSIGKTTIAR  188 (190)
Q Consensus       168 ~~~~vi~i~G-~gGiGKTTla~  188 (190)
                      ...++|+|++ -||+||||+|-
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~  162 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAA  162 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHH
T ss_pred             CCceEEEEECCCCCChHHHHHH
Confidence            3589999995 99999999985

>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=93.80  E-value=0.027  Score=51.12  Aligned_cols=44  Identities=16%  Similarity=0.342  Sum_probs=33.3

Q ss_pred             ccccccchhHHHHHHHhhhc----C--C-CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE----S--K-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~----~--~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+..++.+...+...    .  + ....+-|+|-.|+|||+||+++
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~l  608 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTL  608 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHH
Confidence            45789998888887776532    1  1 1457889999999999999863

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=93.73  E-value=0.024  Score=45.93  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+|.|.|+.|+||||||..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~   59 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSID   59 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            35789999999999999874

>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=93.68  E-value=0.024  Score=47.37  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++.++|.+|.||||++..
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~  117 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAK  117 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            57899999999999999864

>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=93.57  E-value=0.058  Score=46.17  Aligned_cols=21  Identities=5%  Similarity=0.031  Sum_probs=18.2

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+|-+.|+.|.||||+|+++
T Consensus       395 ~~~I~l~GlsGsGKSTIa~~L  415 (511)
T 1g8f_A          395 GFSIVLGNSLTVSREQLSIAL  415 (511)
T ss_dssp             CEEEEECTTCCSCHHHHHHHH
T ss_pred             ceEEEecccCCCCHHHHHHHH
Confidence            467888999999999999863

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=93.35  E-value=0.042  Score=47.85  Aligned_cols=45  Identities=13%  Similarity=0.065  Sum_probs=29.3

Q ss_pred             cccccccchhHHHHHHHhhhcCCC------e---EEEEEEcCCCCcHHHHhccC
Q 047923          146 ENQLVGRESRVEIIESLLAAESKD------V---YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       146 ~~~~vG~d~~~~~~~~~l~~~~~~------~---~vi~i~G~gGiGKTTla~~v  190 (190)
                      ...++|.+.-++.+...|..+...      .   .-+=++|-+|+|||+||+++
T Consensus       294 ~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~l  347 (595)
T 3f9v_A          294 APSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFI  347 (595)
T ss_dssp             SSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSS
T ss_pred             cchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHH
Confidence            356889987666554333322100      0   03568999999999999975

>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=93.30  E-value=0.077  Score=43.55  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=17.9

Q ss_pred             CCeEEEEEE-cCCCCcHHHHhc
Q 047923          168 KDVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       168 ~~~~vi~i~-G~gGiGKTTla~  188 (190)
                      ...++|.|+ |-||+||||+|-
T Consensus       106 ~~~~vIav~s~KGGvGKTT~a~  127 (398)
T 3ez2_A          106 SEAYVIFISNLKGGVSKTVSTV  127 (398)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHH
T ss_pred             CCCeEEEEEeCCCCccHHHHHH
Confidence            347899998 889999999885

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.27  E-value=0.029  Score=45.77  Aligned_cols=19  Identities=42%  Similarity=0.618  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.+.
T Consensus        42 e~~~llGpnGsGKSTLLr~   60 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRL   60 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            4789999999999999875

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.26  E-value=0.07  Score=44.60  Aligned_cols=38  Identities=18%  Similarity=0.167  Sum_probs=23.9

Q ss_pred             ccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          151 GRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       151 G~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      |...-...+..++ .+-..-.++-|.|.+|+||||||..
T Consensus       182 ~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~  219 (444)
T 2q6t_A          182 GVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALT  219 (444)
T ss_dssp             -CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHH
T ss_pred             cccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHH
Confidence            4444444555555 2222234778899999999999853

>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=93.22  E-value=0.03  Score=44.46  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=16.9

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++++.|..|+|||||.++
T Consensus       166 ~i~~l~G~sG~GKSTLln~  184 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSR  184 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            3789999999999999875

>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=93.19  E-value=0.032  Score=48.92  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=18.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+|-+.|+.|.||||+|+++
T Consensus        52 g~lIvLtGlsGSGKSTlAr~L   72 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMAL   72 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHH
Confidence            568899999999999999863

>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=93.11  E-value=0.029  Score=45.23  Aligned_cols=20  Identities=25%  Similarity=0.162  Sum_probs=17.4

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||.+++
T Consensus       172 ~~v~i~G~~GsGKTTll~~l  191 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSI  191 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHG
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            36899999999999998863

>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=93.08  E-value=0.032  Score=45.58  Aligned_cols=18  Identities=28%  Similarity=0.388  Sum_probs=16.4

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      +++|+|..|+|||||.+.
T Consensus       217 ~~~lvG~sG~GKSTLln~  234 (358)
T 2rcn_A          217 ISIFAGQSGVGKSSLLNA  234 (358)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCccHHHHHHH
Confidence            689999999999999875

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.03  E-value=0.032  Score=45.35  Aligned_cols=20  Identities=25%  Similarity=0.408  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|.|-.|.|||||.+.
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~   90 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGM   90 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35799999999999999875

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.02  E-value=0.032  Score=48.01  Aligned_cols=20  Identities=40%  Similarity=0.596  Sum_probs=17.6

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||++.+
T Consensus       313 e~~~i~G~NGsGKSTLlk~l  332 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKML  332 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            47899999999999999853

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=93.00  E-value=0.033  Score=48.00  Aligned_cols=19  Identities=58%  Similarity=0.802  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||++.
T Consensus       295 ei~~i~G~nGsGKSTLl~~  313 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARI  313 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3789999999999999985

>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=92.99  E-value=0.036  Score=45.25  Aligned_cols=34  Identities=29%  Similarity=0.241  Sum_probs=24.0

Q ss_pred             HHHHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLA-AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+..+|. .+-..-+++.|+|-+|+||||||..
T Consensus        46 ~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~   80 (356)
T 3hr8_A           46 SLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALH   80 (356)
T ss_dssp             CHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHH
T ss_pred             CHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHH
Confidence            345556665 2222346899999999999999864

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=92.96  E-value=0.037  Score=48.06  Aligned_cols=21  Identities=33%  Similarity=0.321  Sum_probs=18.3

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      -.+|-|.|+.|.||||+|+++
T Consensus       396 ~~~I~l~GlsGSGKSTiA~~L  416 (573)
T 1m8p_A          396 GFTIFLTGYMNSGKDAIARAL  416 (573)
T ss_dssp             CEEEEEECSTTSSHHHHHHHH
T ss_pred             ceEEEeecCCCCCHHHHHHHH
Confidence            468899999999999999863

>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=92.94  E-value=0.031  Score=46.97  Aligned_cols=19  Identities=37%  Similarity=0.408  Sum_probs=16.2

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      -+-++|.+|.||||+|+++
T Consensus        52 ~iLl~GppGtGKT~lar~l   70 (444)
T 1g41_A           52 NILMIGPTGVGKTEIARRL   70 (444)
T ss_dssp             CEEEECCTTSSHHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHHH
Confidence            3668999999999999863

>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=92.88  E-value=0.031  Score=46.37  Aligned_cols=33  Identities=18%  Similarity=0.303  Sum_probs=23.0

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      ...+..+|..+-..-.++.|+|-.|.|||||+.
T Consensus       164 ~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~  196 (400)
T 3lda_A          164 SKNLDTLLGGGVETGSITELFGEFRTGKSQLCH  196 (400)
T ss_dssp             CHHHHHHTTTSEETTSEEEEEESTTSSHHHHHH
T ss_pred             ChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHH
Confidence            344555564322223589999999999999997

>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=92.87  E-value=0.039  Score=45.22  Aligned_cols=20  Identities=20%  Similarity=0.229  Sum_probs=17.8

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.+++|+|..|.|||||.++
T Consensus       136 g~~i~ivG~~GsGKTTll~~  155 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIAS  155 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            46899999999999999875

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.80  E-value=0.028  Score=45.81  Aligned_cols=19  Identities=32%  Similarity=0.431  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||+++
T Consensus       176 ~~i~ivG~sGsGKSTll~~  194 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKA  194 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4689999999999999875

>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=92.73  E-value=0.038  Score=44.94  Aligned_cols=34  Identities=26%  Similarity=0.284  Sum_probs=23.1

Q ss_pred             HHHHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLA-AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+..+|. .+-..-+++.|+|-+|.||||||..
T Consensus        46 ~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~   80 (349)
T 2zr9_A           46 SISLDVALGIGGLPRGRVIEIYGPESSGKTTVALH   80 (349)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHH
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHH
Confidence            334455565 2212245789999999999999864

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=92.67  E-value=0.039  Score=47.51  Aligned_cols=20  Identities=30%  Similarity=0.491  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||.+.
T Consensus        47 Ge~~~LvG~NGaGKSTLlk~   66 (538)
T 1yqt_A           47 GMVVGIVGPNGTGKSTAVKI   66 (538)
T ss_dssp             TSEEEEECCTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35799999999999999985

>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=92.54  E-value=0.041  Score=48.09  Aligned_cols=19  Identities=42%  Similarity=0.679  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.+.
T Consensus       383 ei~~i~G~NGsGKSTLlk~  401 (607)
T 3bk7_A          383 EVIGIVGPNGIGKTTFVKM  401 (607)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            3789999999999999985

>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=92.46  E-value=0.075  Score=42.93  Aligned_cols=32  Identities=22%  Similarity=0.308  Sum_probs=23.0

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+|..+-..-.++-|+|-+|.||||||..
T Consensus       110 ~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~  141 (343)
T 1v5w_A          110 EFDKLLGGGIESMAITEAFGEFRTGKTQLSHT  141 (343)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHHH
T ss_pred             hHHHHhcCCCCCCeEEEEECCCCCCHHHHHHH
Confidence            44455643323357889999999999999864

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.42  E-value=0.043  Score=47.95  Aligned_cols=19  Identities=37%  Similarity=0.469  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||++.
T Consensus       379 Eiv~iiG~NGsGKSTLlk~  397 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKL  397 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHH
Confidence            4689999999999999985

>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=92.40  E-value=0.044  Score=45.30  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      =.+++|.|..|.|||||.+.+
T Consensus        47 Ge~~~llGpsGsGKSTLLr~i   67 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAF   67 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHH
Confidence            357999999999999998753

>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=92.33  E-value=0.1  Score=43.45  Aligned_cols=21  Identities=33%  Similarity=0.472  Sum_probs=17.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..-++|+|.+|+|||||.+.
T Consensus       179 ~~~kvaivG~~gvGKSTLln~  199 (439)
T 1mky_A          179 DAIKVAIVGRPNVGKSTLFNA  199 (439)
T ss_dssp             SCEEEEEECSTTSSHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHH
Confidence            356789999999999999864

>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP- binding, hydrolase, magnesium, metal-binding, nucleotide- binding, potassium; HET: GDP FON; 2.95A {Chlorobium tepidum} PDB: 3gei_A*

Probab=92.32  E-value=0.83  Score=38.61  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=17.3

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +++ +.|+|.+|+|||||..++
T Consensus       233 ~~k-V~ivG~~nvGKSSLln~L  253 (476)
T 3gee_A          233 GVS-TVIAGKPNAGKSTLLNTL  253 (476)
T ss_dssp             CEE-EEEECCTTSSHHHHHHHC
T ss_pred             CCE-EEEECCCCCCHHHHHHHH
Confidence            354 889999999999998653

>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=92.32  E-value=0.047  Score=44.50  Aligned_cols=19  Identities=26%  Similarity=0.211  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.++
T Consensus       124 g~i~I~GptGSGKTTlL~~  142 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAA  142 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4899999999999999875

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.31  E-value=0.051  Score=46.90  Aligned_cols=20  Identities=30%  Similarity=0.396  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+|.+.|+.|.||||+|+.
T Consensus       372 ~~~I~l~G~~GsGKSTia~~  391 (546)
T 2gks_A          372 GFCVWLTGLPCAGKSTIAEI  391 (546)
T ss_dssp             CEEEEEECSTTSSHHHHHHH
T ss_pred             ceEEEccCCCCCCHHHHHHH
Confidence            56899999999999999985

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.29  E-value=0.037  Score=46.76  Aligned_cols=20  Identities=30%  Similarity=0.292  Sum_probs=17.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||++.
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~  157 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRT  157 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999985

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.28  E-value=0.041  Score=46.00  Aligned_cols=21  Identities=19%  Similarity=0.248  Sum_probs=17.8

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+--++|+|..|.|||||.+.
T Consensus        41 ei~~vaLvG~nGaGKSTLln~   61 (427)
T 2qag_B           41 FCFNILCVGETGLGKSTLMDT   61 (427)
T ss_dssp             CEEEEEEECSTTSSSHHHHHH
T ss_pred             CeeEEEEECCCCCCHHHHHHH
Confidence            344599999999999999875

>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=92.27  E-value=0.049  Score=43.17  Aligned_cols=18  Identities=28%  Similarity=0.540  Sum_probs=16.4

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      +++|+|..|.|||||.++
T Consensus       171 iv~l~G~sG~GKSTll~~  188 (301)
T 1u0l_A          171 ISTMAGLSGVGKSSLLNA  188 (301)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHH
Confidence            689999999999999875

>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=92.23  E-value=0.047  Score=47.70  Aligned_cols=19  Identities=37%  Similarity=0.592  Sum_probs=17.4

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus       118 e~~~LiG~NGsGKSTLlki  136 (607)
T 3bk7_A          118 MVVGIVGPNGTGKTTAVKI  136 (607)
T ss_dssp             SEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHH
Confidence            5799999999999999875

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=92.14  E-value=0.071  Score=46.16  Aligned_cols=20  Identities=20%  Similarity=0.235  Sum_probs=17.9

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||++.+
T Consensus       368 ~~~~ivG~sGsGKSTll~~l  387 (578)
T 4a82_A          368 ETVAFVGMSGGGKSTLINLI  387 (578)
T ss_dssp             CEEEEECSTTSSHHHHHTTT
T ss_pred             CEEEEECCCCChHHHHHHHH
Confidence            57899999999999999864

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.01  E-value=0.052  Score=47.45  Aligned_cols=19  Identities=37%  Similarity=0.655  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus       104 ei~~LvGpNGaGKSTLLki  122 (608)
T 3j16_B          104 QVLGLVGTNGIGKSTALKI  122 (608)
T ss_dssp             SEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHH
Confidence            4799999999999999875

>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=91.96  E-value=0.021  Score=45.65  Aligned_cols=18  Identities=22%  Similarity=0.340  Sum_probs=16.5

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      +++|+|..|+|||||.++
T Consensus       175 ~~~lvG~sG~GKSTLln~  192 (307)
T 1t9h_A          175 TTVFAGQSGVGKSSLLNA  192 (307)
T ss_dssp             EEEEEESHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            789999999999999875

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=91.70  E-value=0.15  Score=42.74  Aligned_cols=39  Identities=23%  Similarity=0.157  Sum_probs=24.6

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|.......+.+++. +-..-.++-|.|.+|+||||||-.
T Consensus       178 ~gi~TG~~~LD~~lg-Gl~~G~liiIaG~pG~GKTtlal~  216 (444)
T 3bgw_A          178 TGVPSGFTELDRMTY-GYKRRNFVLIAARPSMGKTAFALK  216 (444)
T ss_dssp             CSBCCSCHHHHHHHS-SBCSSCEEEEEECSSSSHHHHHHH
T ss_pred             CCcCCCcHHHHhhcC-CCCCCcEEEEEeCCCCChHHHHHH
Confidence            344444455555552 212235677899999999999853

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=91.52  E-value=0.062  Score=45.05  Aligned_cols=20  Identities=15%  Similarity=0.346  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =..++|.|-.|.|||||.+.
T Consensus       157 Gq~~~IvG~sGsGKSTLl~~  176 (438)
T 2dpy_A          157 GQRMGLFAGSGVGKSVLLGM  176 (438)
T ss_dssp             TCEEEEEECTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999999875

>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=91.49  E-value=0.15  Score=42.42  Aligned_cols=21  Identities=29%  Similarity=0.164  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.+++|.|..|.|||||.++
T Consensus       166 ~ggii~I~GpnGSGKTTlL~a  186 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYA  186 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHH
Confidence            346899999999999999875

>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=91.47  E-value=0.056  Score=44.15  Aligned_cols=21  Identities=29%  Similarity=0.483  Sum_probs=17.9

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ++++++|+|.+|+|||||.++
T Consensus       178 ~~~~V~lvG~~naGKSTLln~  198 (364)
T 2qtf_A          178 NIPSIGIVGYTNSGKTSLFNS  198 (364)
T ss_dssp             -CCEEEEECBTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            467799999999999999764

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=91.45  E-value=0.088  Score=45.72  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||++.+
T Consensus       370 e~~~ivG~sGsGKSTll~~l  389 (587)
T 3qf4_A          370 SLVAVLGETGSGKSTLMNLI  389 (587)
T ss_dssp             CEEEEECSSSSSHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999864

>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=91.32  E-value=0.072  Score=46.16  Aligned_cols=19  Identities=32%  Similarity=0.400  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||++.
T Consensus       370 ~~~~ivG~sGsGKSTll~~  388 (582)
T 3b5x_A          370 KTVALVGRSGSGKSTIANL  388 (582)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5799999999999999975

>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=91.30  E-value=0.062  Score=42.98  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=21.6

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+|..+-..-.++-|+|.+|.||||||..
T Consensus        95 ~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~  126 (324)
T 2z43_A           95 ALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQ  126 (324)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHH
T ss_pred             hHHHhcCCCCCCCcEEEEECCCCCCHhHHHHH
Confidence            34455542211235788999999999999864

>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=91.23  E-value=0.068  Score=46.30  Aligned_cols=19  Identities=32%  Similarity=0.391  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||++.
T Consensus       370 ~~~~ivG~sGsGKSTLl~~  388 (582)
T 3b60_A          370 KTVALVGRSGSGKSTIASL  388 (582)
T ss_dssp             CEEEEEECTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5789999999999999875

>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=91.20  E-value=0.075  Score=43.33  Aligned_cols=35  Identities=26%  Similarity=0.217  Sum_probs=23.0

Q ss_pred             hHHHHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLA-AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      -...+..+|. .+-..-+++-|.|-+|+||||||..
T Consensus        47 G~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~   82 (356)
T 1u94_A           47 GSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQ   82 (356)
T ss_dssp             SCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHH
T ss_pred             CCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHH
Confidence            3344555564 2111235788999999999999864

>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=91.19  E-value=0.085  Score=41.96  Aligned_cols=32  Identities=25%  Similarity=0.262  Sum_probs=22.1

Q ss_pred             HHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          158 IIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       158 ~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..+|..+-..-.++-|+|-+|+||||||..
T Consensus        86 ~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~  117 (322)
T 2i1q_A           86 ELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQ  117 (322)
T ss_dssp             HHHHHTTSSEETTEEEEEEESTTSSHHHHHHH
T ss_pred             hHHHhcCCCccCCeEEEEECCCCCCHHHHHHH
Confidence            34455542212246889999999999999863

>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=91.15  E-value=0.092  Score=44.05  Aligned_cols=18  Identities=28%  Similarity=0.353  Sum_probs=16.1

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      .+-|.|.+|.||||++.+
T Consensus        47 ~~li~G~aGTGKT~ll~~   64 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKF   64 (459)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHH
Confidence            788999999999999864

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=91.12  E-value=0.077  Score=43.00  Aligned_cols=21  Identities=29%  Similarity=0.453  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++++|.+|+|||||...
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~  186 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKA  186 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            467899999999999999764

>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=91.10  E-value=0.072  Score=45.54  Aligned_cols=20  Identities=25%  Similarity=0.199  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|.|..|.|||||++.
T Consensus       281 G~i~~i~G~~GsGKSTLl~~  300 (525)
T 1tf7_A          281 DSIILATGATGTGKTLLVSR  300 (525)
T ss_dssp             SCEEEEEECTTSSHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHH
Confidence            35899999999999999875

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=90.76  E-value=0.18  Score=42.03  Aligned_cols=21  Identities=24%  Similarity=0.476  Sum_probs=17.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..-++++|.+|+|||||..+
T Consensus       174 ~~~ki~lvG~~nvGKSSLin~  194 (436)
T 2hjg_A          174 EVIQFCLIGRPNVGKSSLVNA  194 (436)
T ss_dssp             TCEEEEEECSTTSSHHHHHHH
T ss_pred             cCcEEEEEcCCCCCHHHHHHH
Confidence            456788999999999999764

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=90.69  E-value=0.1  Score=41.82  Aligned_cols=18  Identities=33%  Similarity=0.373  Sum_probs=15.9

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -|.|+|.+|+|||||...
T Consensus       167 kI~ivG~~~vGKSsLl~~  184 (329)
T 3o47_A          167 RILMVGLDAAGKTTILYK  184 (329)
T ss_dssp             EEEEEESTTSSHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHH
Confidence            478999999999999865

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=90.55  E-value=0.52  Score=41.74  Aligned_cols=38  Identities=26%  Similarity=0.205  Sum_probs=23.8

Q ss_pred             cchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          152 RESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       152 ~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++.+...+..-......|+|+|..|.|||||..+
T Consensus        51 l~~~l~~L~~~~~~l~~~~~~V~VvG~~naGKSSLlNa   88 (695)
T 2j69_A           51 LERDIEDITIASKNLQQGVFRLLVLGDMKRGKSTFLNA   88 (695)
T ss_dssp             CHHHHHHHHHHHHHHHHCCEEEEEECCTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCEEEEECCCCCCHHHHHHH
Confidence            33444445443332112345688999999999999764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=90.48  E-value=0.082  Score=45.21  Aligned_cols=18  Identities=33%  Similarity=0.217  Sum_probs=16.2

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      .++|.|..|.|||||.++
T Consensus       262 ~i~I~GptGSGKTTlL~a  279 (511)
T 2oap_1          262 SAIVVGETASGKTTTLNA  279 (511)
T ss_dssp             CEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            489999999999999875

>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=90.42  E-value=0.27  Score=38.28  Aligned_cols=20  Identities=35%  Similarity=0.297  Sum_probs=16.9

Q ss_pred             CeEEEEEEc-CCCCcHHHHhc
Q 047923          169 DVYILGIWG-VGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G-~gGiGKTTla~  188 (190)
                      ..++|.|.+ .||+||||+|-
T Consensus        81 ~~kvI~vts~kgG~GKTt~a~  101 (271)
T 3bfv_A           81 AVQSIVITSEAPGAGKSTIAA  101 (271)
T ss_dssp             CCCEEEEECSSTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCcHHHHHH
Confidence            468899996 59999999985

>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=90.34  E-value=0.063  Score=44.72  Aligned_cols=20  Identities=25%  Similarity=0.433  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...++|+|.+|.|||||.++
T Consensus       157 g~~VgLVG~~gAGKSTLL~~  176 (416)
T 1udx_A          157 IADVGLVGYPNAGKSSLLAA  176 (416)
T ss_dssp             SCSEEEECCGGGCHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            45689999999999999875

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=90.26  E-value=0.08  Score=46.05  Aligned_cols=19  Identities=32%  Similarity=0.335  Sum_probs=17.4

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||++.
T Consensus       382 ~~~~ivG~sGsGKSTll~~  400 (598)
T 3qf4_B          382 QKVALVGPTGSGKTTIVNL  400 (598)
T ss_dssp             CEEEEECCTTSSTTHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            5899999999999999875

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=90.20  E-value=0.27  Score=38.83  Aligned_cols=20  Identities=35%  Similarity=0.368  Sum_probs=17.0

Q ss_pred             CeEEEEEEcC-CCCcHHHHhc
Q 047923          169 DVYILGIWGV-GSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G~-gGiGKTTla~  188 (190)
                      ..++|.|.|. ||+||||+|.
T Consensus       103 ~~kvI~vts~kgG~GKTtva~  123 (299)
T 3cio_A          103 ENNILMITGATPDSGKTFVSS  123 (299)
T ss_dssp             SCCEEEEEESSSSSCHHHHHH
T ss_pred             CCeEEEEECCCCCCChHHHHH
Confidence            4678999985 8999999985

>3ez9_A Para; DNA binding, winged-HTH, partition, biosynthetic protein; 2.80A {Salmonella enterica subsp} PDB: 3ezf_A

Probab=90.17  E-value=0.088  Score=43.31  Aligned_cols=21  Identities=24%  Similarity=0.284  Sum_probs=10.1

Q ss_pred             CCeEEEEEE-cCCCCcHHHHhc
Q 047923          168 KDVYILGIW-GVGSIGKTTIAR  188 (190)
Q Consensus       168 ~~~~vi~i~-G~gGiGKTTla~  188 (190)
                      ...++|.|+ |-||+||||+|-
T Consensus       109 ~~~~vIav~s~KGGvGKTT~a~  130 (403)
T 3ez9_A          109 KSPYVIFVVNLKGGVSKTVSTV  130 (403)
T ss_dssp             CSCEEEEECCC--------CHH
T ss_pred             CCceEEEEEcCCCCchHHHHHH
Confidence            457899998 889999999874

>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=90.00  E-value=0.18  Score=39.66  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=16.1

Q ss_pred             eEEEEEEcCCCCcHHHHhc
Q 047923          170 VYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~  188 (190)
                      .--+.++|.+|+|||||..
T Consensus       155 ~~~i~i~G~~~~GKssli~  173 (332)
T 2wkq_A          155 LIKCVVVGDGAVGKTCLLI  173 (332)
T ss_dssp             CEEEEEEESTTSSHHHHHH
T ss_pred             eeEEEEECCCCCChHHHHH
Confidence            4457899999999999984

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=89.52  E-value=0.17  Score=44.48  Aligned_cols=19  Identities=26%  Similarity=0.475  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||++.
T Consensus       349 e~vaIiGpnGsGKSTLl~~  367 (670)
T 3ux8_A          349 TFVAVTGVSGSGKSTLVNE  367 (670)
T ss_dssp             SEEEEECSTTSSHHHHHTT
T ss_pred             CEEEEEeeCCCCHHHHHHH
Confidence            4789999999999999864

>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=89.36  E-value=0.13  Score=47.47  Aligned_cols=19  Identities=42%  Similarity=0.578  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus       462 e~v~LiGpNGsGKSTLLk~  480 (986)
T 2iw3_A          462 RRYGICGPNGCGKSTLMRA  480 (986)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4689999999999999875

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=89.33  E-value=0.12  Score=40.16  Aligned_cols=29  Identities=14%  Similarity=0.088  Sum_probs=23.1

Q ss_pred             chHHHHHHhhcccceEEEecCCCcCchhh
Q 047923           19 ISESIAYAIESPAISVIIFSEGYPFSRWC   47 (190)
Q Consensus        19 ~~~~l~~ai~~s~~~ivv~S~~y~~S~wc   47 (190)
                      ...++.+.++++++.+.|++-.-..+..|
T Consensus        11 a~~~~~~~l~~~D~vl~VvDar~P~~~~~   39 (262)
T 3cnl_A           11 AKRQIKDLLRLVNTVVEVRDARAPFATSA   39 (262)
T ss_dssp             TTHHHHHHHTTCSEEEEEEETTSTTTTSC
T ss_pred             HHHHHHHHHhhCCEEEEEeeCCCCCcCcC
Confidence            45688999999999999998765555554

>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=89.15  E-value=0.17  Score=41.00  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=17.4

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.-|+++|.+++|||||..++
T Consensus       158 la~V~lvG~~nvGKSTLln~L  178 (342)
T 1lnz_A          158 LADVGLVGFPSVGKSTLLSVV  178 (342)
T ss_dssp             CCCEEEESSTTSSHHHHHHHS
T ss_pred             cCeeeeeCCCCCCHHHHHHHH
Confidence            345899999999999998653

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=88.71  E-value=0.14  Score=43.80  Aligned_cols=19  Identities=26%  Similarity=0.433  Sum_probs=16.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      --|+++|.+|+|||||...
T Consensus        42 ~kV~lvG~~~vGKSSLl~~   60 (535)
T 3dpu_A           42 IKVHLIGDGMAGKTSLLKQ   60 (535)
T ss_dssp             EEEEEESSSCSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4477999999999999864

>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A*

Probab=88.58  E-value=0.21  Score=45.35  Aligned_cols=19  Identities=26%  Similarity=0.447  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||++.
T Consensus       524 eiv~I~G~nGSGKSTLl~~  542 (842)
T 2vf7_A          524 VMTSVTGVSGSGKSTLVSQ  542 (842)
T ss_dssp             SEEEEECCTTSSHHHHCCC
T ss_pred             CEEEEEcCCCcCHHHHHHH
Confidence            3789999999999999985

>3hyn_A Putative signal transduction protein; DUF1863 family protein, nucleotide-binding protein, structur genomics; HET: MSE; 1.20A {Eubacterium rectale atcc 33656}

Probab=88.56  E-value=0.71  Score=33.91  Aligned_cols=50  Identities=12%  Similarity=0.038  Sum_probs=40.7

Q ss_pred             ccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhhhcCCeeEEeEE
Q 047923           17 DEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYKKEYAHIVIPGF   69 (190)
Q Consensus        17 ~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~v~PvF   69 (190)
                      ..|-+.|.+.|..|+..|+++|++...|.|-.-|+....+   ..+..||=|+
T Consensus        67 ~tIKrrLReRI~~Sk~vIllIs~~T~~s~~v~wEIe~Ai~---~~~~PII~Vy  116 (189)
T 3hyn_A           67 KTLKPRLHTRLDNSKNIILFLSSITANSRALREEMNYGIG---TKGLPVIVIY  116 (189)
T ss_dssp             TTHHHHHHHHHHTEEEEEEECCTTCCCCHHHHHHHHHHTT---TTCCCEEEEE
T ss_pred             HHHHHHHHHHHHhcCcEEEEEecCccccchhHHHHHHHHH---hcCCcEEEEE
Confidence            3577899999999999999999999999998888877662   2345666664

>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=88.27  E-value=0.15  Score=42.22  Aligned_cols=20  Identities=20%  Similarity=-0.062  Sum_probs=17.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -..++|+|-.|.|||||++.
T Consensus       174 GQr~~IvG~sG~GKTtLl~~  193 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQN  193 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHH
Confidence            34689999999999999964

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=88.10  E-value=0.42  Score=37.53  Aligned_cols=20  Identities=30%  Similarity=0.311  Sum_probs=16.6

Q ss_pred             CeEEEEEEc-CCCCcHHHHhc
Q 047923          169 DVYILGIWG-VGSIGKTTIAR  188 (190)
Q Consensus       169 ~~~vi~i~G-~gGiGKTTla~  188 (190)
                      ..++|.|.+ -||+||||+|-
T Consensus        91 ~~kvI~vts~kgG~GKTtva~  111 (286)
T 3la6_A           91 QNNVLMMTGVSPSIGMTFVCA  111 (286)
T ss_dssp             TCCEEEEEESSSSSSHHHHHH
T ss_pred             CCeEEEEECCCCCCcHHHHHH
Confidence            467888886 59999999985

>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=88.10  E-value=0.17  Score=43.79  Aligned_cols=19  Identities=26%  Similarity=0.338  Sum_probs=16.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +++-|.|.+|.||||++.+
T Consensus       205 ~~~~I~G~pGTGKTt~i~~  223 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKA  223 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHH
Confidence            4677899999999999864

>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=87.94  E-value=0.18  Score=42.66  Aligned_cols=18  Identities=28%  Similarity=0.682  Sum_probs=16.1

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      .++|+|-.|+|||||++.
T Consensus       153 ~~~i~G~sGvGKTtL~~~  170 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQE  170 (473)
T ss_dssp             EEEEECCSSSCHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHH
Confidence            478999999999999874

>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=87.73  E-value=0.12  Score=47.70  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|+|..|.|||||.+.
T Consensus       700 eivaIiGpNGSGKSTLLkl  718 (986)
T 2iw3_A          700 SRIAVIGPNGAGKSTLINV  718 (986)
T ss_dssp             CEEEECSCCCHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4789999999999999875

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=87.43  E-value=0.2  Score=43.64  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .+..++|+|-.|.|||||.++
T Consensus        44 ~lp~iaIvG~nGsGKSTLL~~   64 (608)
T 3szr_A           44 ALPAIAVIGDQSSGKSSVLEA   64 (608)
T ss_dssp             CCCCEECCCCTTSCHHHHHHH
T ss_pred             cCCeEEEECCCCChHHHHHHH
Confidence            367799999999999999875

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=86.90  E-value=0.22  Score=47.28  Aligned_cols=19  Identities=26%  Similarity=0.440  Sum_probs=17.3

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .++||+|..|.|||||++.
T Consensus      1060 e~v~ivG~sGsGKSTl~~~ 1078 (1284)
T 3g5u_A         1060 QTLALVGSSGCGKSTVVQL 1078 (1284)
T ss_dssp             SEEEEECSSSTTHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4799999999999999975

>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, at cassette, DNA damage, DNA excision; HET: ADP; 3.20A {Geobacillus stearothermophilus} PDB: 3uwx_A

Probab=86.87  E-value=0.23  Score=45.67  Aligned_cols=20  Identities=25%  Similarity=0.415  Sum_probs=17.5

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|.|..|.|||||++.+
T Consensus       651 eiv~I~G~nGSGKSTLl~~l  670 (972)
T 2r6f_A          651 TFVAVTGVSGSGKSTLVNEV  670 (972)
T ss_dssp             SEEECCBCTTSSHHHHHTTT
T ss_pred             CEEEEEcCCCCCHHHHHHHH
Confidence            37899999999999999863

>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=86.86  E-value=0.31  Score=39.78  Aligned_cols=35  Identities=31%  Similarity=0.229  Sum_probs=22.3

Q ss_pred             hHHHHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLA-AESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      -...+..+|. .+-..-+++-|+|-+|+||||||..
T Consensus        58 G~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~   93 (366)
T 1xp8_A           58 GSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALA   93 (366)
T ss_dssp             SCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHH
T ss_pred             CCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHH
Confidence            3444555564 1111234677899999999999853

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=86.38  E-value=0.099  Score=42.93  Aligned_cols=18  Identities=28%  Similarity=0.327  Sum_probs=16.6

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      +.+|+|-.|.|||||.++
T Consensus        62 ~~~lvG~NGaGKStLl~a   79 (415)
T 4aby_A           62 FCAFTGETGAGKSIIVDA   79 (415)
T ss_dssp             EEEEEESHHHHHHHHTHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            889999999999999865

>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=86.30  E-value=0.4  Score=39.29  Aligned_cols=43  Identities=21%  Similarity=0.221  Sum_probs=31.3

Q ss_pred             ccccccchhHHHHHHHhhhcC-CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAES-KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~~-~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....++++.+.+..-. .+..+ -|.|-.|.|||++|+++
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a~~~~~v-li~Ge~GtGK~~lAr~i  180 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKISCAECPV-LITGESGVGKEVVARLI  180 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHTTCCSCE-EEECSTTSSHHHHHHHH
T ss_pred             hhhhhccHHhhHHHHHHHHhcCCCCCe-EEecCCCcCHHHHHHHH
Confidence            357888877888877665422 23444 68999999999999863

>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=86.15  E-value=0.27  Score=40.34  Aligned_cols=21  Identities=29%  Similarity=0.278  Sum_probs=18.4

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....|.|-|.=|+||||+++.
T Consensus        48 ~~~fIt~EG~dGsGKTT~~~~   68 (376)
T 1of1_A           48 TLLRVYIDGPHGMGKTTTTQL   68 (376)
T ss_dssp             EEEEEEECSSTTSSHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHH
Confidence            467889999999999999875

>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=85.91  E-value=0.21  Score=45.07  Aligned_cols=44  Identities=20%  Similarity=0.205  Sum_probs=30.1

Q ss_pred             ccccccchhHHHHHHHhhhc--------C---CCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE--------S---KDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~--------~---~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++.|.+..++++.+.+...        .   ...+-+=++|.+|.|||.||+++
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkai  531 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAI  531 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHH
Confidence            35568888888877654421        0   11233558999999999999874

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=85.81  E-value=0.36  Score=42.46  Aligned_cols=17  Identities=24%  Similarity=0.470  Sum_probs=15.6

Q ss_pred             EEEEEEcCCCCcHHHHh
Q 047923          171 YILGIWGVGSIGKTTIA  187 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla  187 (190)
                      .+++|+|..|.|||||+
T Consensus        45 e~~~liGpNGaGKSTLl   61 (670)
T 3ux8_A           45 KLVVLTGLSGSGKSSLA   61 (670)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHh
Confidence            47999999999999995

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=85.62  E-value=0.34  Score=45.91  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+++|+|..|.|||||++.+
T Consensus       417 ~~~~ivG~sGsGKSTl~~ll  436 (1284)
T 3g5u_A          417 QTVALVGNSGCGKSTTVQLM  436 (1284)
T ss_dssp             CEEEEECCSSSSHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            57899999999999999864

>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=85.61  E-value=0.5  Score=39.52  Aligned_cols=21  Identities=24%  Similarity=0.476  Sum_probs=17.7

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...-+.++|.+|+|||||..+
T Consensus       194 ~~~ki~ivG~~~vGKSslin~  214 (456)
T 4dcu_A          194 EVIQFCLIGRPNVGKSSLVNA  214 (456)
T ss_dssp             TCEEEEEECSTTSSHHHHHHH
T ss_pred             ccceeEEecCCCCCHHHHHHH
Confidence            356788999999999999764

>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=84.52  E-value=0.28  Score=42.74  Aligned_cols=19  Identities=37%  Similarity=0.218  Sum_probs=16.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +.+-|.|.+|.||||++..
T Consensus       165 ~~~vi~G~pGTGKTt~l~~  183 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAK  183 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHH
Confidence            4678899999999998753

>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=84.45  E-value=0.7  Score=37.56  Aligned_cols=43  Identities=23%  Similarity=0.290  Sum_probs=30.4

Q ss_pred             ccccccchhHHHHHHHhhhc-CCCeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAAE-SKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~~-~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|....+..+...+..- ..+.. +-|+|-.|.||+++|+++
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~~~~~-vli~GesGtGKe~lAr~i  172 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAKSKAP-VLITGESGTGKEIVARLI  172 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHTSCSC-EEEECCTTSSHHHHHHHH
T ss_pred             ccccccchHHHHHHhhhhhhhccchh-heEEeCCCchHHHHHHHH
Confidence            45788888777777766532 22333 348899999999999863

>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=84.12  E-value=0.32  Score=43.67  Aligned_cols=19  Identities=32%  Similarity=0.337  Sum_probs=17.4

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .+++|.|..|.|||||.+.
T Consensus       577 ~i~~I~GpNGsGKSTlLr~  595 (765)
T 1ewq_A          577 ELVLITGPNMAGKSTFLRQ  595 (765)
T ss_dssp             CEEEEESCSSSSHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHH
Confidence            5899999999999999875

>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=83.60  E-value=0.75  Score=38.62  Aligned_cols=35  Identities=17%  Similarity=0.239  Sum_probs=25.5

Q ss_pred             hHHHHHHHhhh---cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLAA---ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~~---~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+.+..+|..   ....+.+|+|+|....||+||...
T Consensus        49 ~~eal~~iL~~~~~~~~~v~vVsV~G~~~~GKStLLN~   86 (447)
T 3q5d_A           49 DETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDF   86 (447)
T ss_dssp             CHHHHHHHHCCTTTTTSBEEEEEEEESTTSSHHHHHHH
T ss_pred             CHHHHHHHHhccccCCCceEEEEEECCCCCcHHHHHHH
Confidence            34555556553   234599999999999999999653

>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=83.48  E-value=0.38  Score=40.71  Aligned_cols=20  Identities=10%  Similarity=0.024  Sum_probs=16.6

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -.++-|.|.+|+||||||-.
T Consensus       242 G~l~li~G~pG~GKT~lal~  261 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQ  261 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHH
Confidence            35677899999999999853

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=83.39  E-value=0.37  Score=41.49  Aligned_cols=21  Identities=24%  Similarity=0.172  Sum_probs=18.4

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....|.|+|..|+|||||..+
T Consensus        64 ~~~~V~vvG~~n~GKSTLIN~   84 (550)
T 2qpt_A           64 GKPMVLVAGQYSTGKTSFIQY   84 (550)
T ss_dssp             SCCEEEEEEBTTSCHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            467899999999999999764

>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus}

Probab=83.31  E-value=0.72  Score=37.53  Aligned_cols=35  Identities=20%  Similarity=0.261  Sum_probs=23.5

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|.+.-++.+.+++..     +.+.++|..|+|||||..+
T Consensus       147 ~gi~~L~~~I~~~~~~-----~~i~~vG~~nvGKStliN~  181 (369)
T 3ec1_A          147 IGMAKVMEAINRYREG-----GDVYVVGCTNVGKSTFINR  181 (369)
T ss_dssp             BTHHHHHHHHHHHHTT-----SCEEEECCTTSSHHHHHHH
T ss_pred             CCHHHHHHHHHhhccc-----CcEEEEcCCCCchHHHHHH
Confidence            3555555555554422     2478899999999999754

>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=83.21  E-value=0.29  Score=46.53  Aligned_cols=19  Identities=26%  Similarity=0.389  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+||+|..|.|||||++.
T Consensus      1106 e~vaIVG~SGsGKSTL~~l 1124 (1321)
T 4f4c_A         1106 QTLALVGPSGCGKSTVVAL 1124 (1321)
T ss_dssp             CEEEEECSTTSSTTSHHHH
T ss_pred             CEEEEECCCCChHHHHHHH
Confidence            4689999999999999975

>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=83.19  E-value=0.37  Score=43.45  Aligned_cols=20  Identities=35%  Similarity=0.250  Sum_probs=18.0

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      -++++|.|..|.|||||.+.
T Consensus       607 g~i~~ItGpNGsGKSTlLr~  626 (800)
T 1wb9_A          607 RRMLIITGPNMGGKSTYMRQ  626 (800)
T ss_dssp             SCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHH
Confidence            46899999999999999875

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=83.14  E-value=1  Score=39.35  Aligned_cols=30  Identities=33%  Similarity=0.329  Sum_probs=19.5

Q ss_pred             hhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHh
Q 047923          154 SRVEIIESLLAAESKDVYILGIWGVGSIGKTTIA  187 (190)
Q Consensus       154 ~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla  187 (190)
                      ++.+.+...|..  .+  +.-|+|++|.||||..
T Consensus       193 ~Q~~AV~~al~~--~~--~~lI~GPPGTGKT~ti  222 (646)
T 4b3f_X          193 SQKEAVLFALSQ--KE--LAIIHGPPGTGKTTTV  222 (646)
T ss_dssp             HHHHHHHHHHHC--SS--EEEEECCTTSCHHHHH
T ss_pred             HHHHHHHHHhcC--CC--ceEEECCCCCCHHHHH
Confidence            445556555542  22  3458999999999754

>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=82.94  E-value=0.39  Score=40.43  Aligned_cols=19  Identities=26%  Similarity=0.483  Sum_probs=16.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ++ +.|+|.+|+|||||..+
T Consensus       225 ~k-V~ivG~~nvGKSSLln~  243 (462)
T 3geh_A          225 LK-VAIVGRPNVGKSSLLNA  243 (462)
T ss_dssp             EE-EEEEECTTSSHHHHHHH
T ss_pred             CE-EEEEcCCCCCHHHHHHH
Confidence            44 78999999999999764

>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=82.90  E-value=0.69  Score=31.14  Aligned_cols=32  Identities=9%  Similarity=-0.153  Sum_probs=26.4

Q ss_pred             HHhhcccceEEEecCCCcCchhhHHHHHHHHH
Q 047923           25 YAIESPAISVIIFSEGYPFSRWCLHELVKILK   56 (190)
Q Consensus        25 ~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~   56 (190)
                      ..|+.|.+.||+.+++-..|+||..|+....+
T Consensus        34 ~~I~~~~~vIvL~G~~t~~s~wv~~EI~~A~~   65 (111)
T 1eiw_A           34 ATPEDADAVIVLAGLWGTRRDEILGAVDLARK   65 (111)
T ss_dssp             CCSSSCSEEEEEGGGTTTSHHHHHHHHHHHTT
T ss_pred             CccccCCEEEEEeCCCcCCChHHHHHHHHHHH
Confidence            35788999999999999999999999865443

>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=81.93  E-value=0.78  Score=36.65  Aligned_cols=19  Identities=32%  Similarity=0.205  Sum_probs=16.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      +-+.|.|..|+||||||.+
T Consensus       145 ~~vl~~G~sG~GKSt~a~~  163 (314)
T 1ko7_A          145 VGVLITGDSGIGKSETALE  163 (314)
T ss_dssp             EEEEEEESTTSSHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHH
Confidence            4577899999999999864

>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=81.55  E-value=0.49  Score=45.02  Aligned_cols=19  Identities=26%  Similarity=0.372  Sum_probs=17.1

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus       445 ~~vaivG~sGsGKSTll~l  463 (1321)
T 4f4c_A          445 QTVALVGSSGCGKSTIISL  463 (1321)
T ss_dssp             CEEEEEECSSSCHHHHHHH
T ss_pred             cEEEEEecCCCcHHHHHHH
Confidence            4789999999999999975

>4a9a_A Ribosome-interacting GTPase 1; DRG-DFRP complex, ribosome binding GTPase; 2.67A {Saccharomyces cerevisiae}

Probab=81.25  E-value=0.48  Score=38.88  Aligned_cols=21  Identities=33%  Similarity=0.501  Sum_probs=18.2

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      +..-|||+|.+.+|||||-.+
T Consensus        71 g~a~V~ivG~PNvGKSTL~n~   91 (376)
T 4a9a_A           71 GVASVGFVGFPSVGKSTLLSK   91 (376)
T ss_dssp             SSEEEEEECCCCHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHH
Confidence            467899999999999999754

>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str}

Probab=80.99  E-value=0.6  Score=38.02  Aligned_cols=35  Identities=20%  Similarity=0.219  Sum_probs=23.0

Q ss_pred             cccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          150 VGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       150 vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .|.+.-++.+.+++..     ..+.++|..|+|||||..+
T Consensus       145 ~gi~~L~~~l~~~~~~-----~~i~~vG~~nvGKStliN~  179 (368)
T 3h2y_A          145 QGIAELADAIEYYRGG-----KDVYVVGCTNVGKSTFINR  179 (368)
T ss_dssp             TTHHHHHHHHHHHHTT-----SCEEEEEBTTSSHHHHHHH
T ss_pred             cCHHHHHhhhhhhccc-----ceEEEecCCCCChhHHHHH
Confidence            3555555555444321     2478899999999999754

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=80.92  E-value=0.54  Score=39.01  Aligned_cols=19  Identities=32%  Similarity=0.109  Sum_probs=16.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      .-++|.|-.|+|||||++.
T Consensus       176 QR~lIfg~~g~GKT~Ll~~  194 (427)
T 3l0o_A          176 QRGMIVAPPKAGKTTILKE  194 (427)
T ss_dssp             CEEEEEECTTCCHHHHHHH
T ss_pred             ceEEEecCCCCChhHHHHH
Confidence            3578999999999999864

---

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	190
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-06
d1fyva_	161	c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (H	2e-05
d1fyxa_	149	c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (H	1e-04

>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 = 45.6 bits (107), Expect = 1e-06
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 145 KENQLVGRESRVE-IIESLLAAESKDVYILGIWGVGSIGKTTIARA 189
           K+     RE  V+ +I+ L      D + L + G    GK+ IA  
Sbjct: 18  KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQ 63

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 2/82 (2%)

Query: 2   RQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKIL-KYKK 59
           ++ +Q  + ++    G  I E+I   IE    S+ + S  +  S WC +EL         
Sbjct: 37  KEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHYELYFAHHNLFH 96

Query: 60  EYAHIVIPGFYRGDPSEVRSQT 81
           E ++ +I       P      +
Sbjct: 97  EGSNSLILILLEPIPQYSIPSS 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 = 38.5 bits (89), Expect = 1e-04
 Identities = 16/81 (19%), Positives = 27/81 (33%), Gaps = 2/81 (2%)

Query: 2   RQNIQTFIDDQ-LNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKY-KK 59
               +  +  +    G  I ++I  +IE    +V + SE +  S WC +EL         
Sbjct: 32  NPPFKLCLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWCKYELDFSHFRLFD 91

Query: 60  EYAHIVIPGFYRGDPSEVRSQ 80
           E     I         +   Q
Sbjct: 92  ENNDAAILILLEPIEKKAIPQ 112

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	190
d1fyva_	161	Toll-like receptor 1, TLR1 {Human (Homo sapiens) [	99.4
d1fyxa_	149	Toll-like receptor 2, TLR2 {Human (Homo sapiens) [	99.37
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.27
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.59
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.09
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.87
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.65
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.49
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	96.34
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.28
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.11
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.81
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.66
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	95.6
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.56
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	95.43
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.32
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.09
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.02
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.95
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	94.83
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.45
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.91
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	93.87
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	92.85
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.76
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.55
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.27
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	90.14
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	89.7
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	89.0
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	86.14
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	86.07
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	85.56
d1tuea_	205	Replication protein E1 helicase domain {Human papi	85.23
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	85.23
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	82.28
d1xpua3	289	Transcription termination factor Rho, ATPase domai	82.06
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	80.68

>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=99.40  E-value=1.8e-14  Score=104.37  Aligned_cols=70  Identities=23%  Similarity=0.347  Sum_probs=63.7

Q ss_pred             CCCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHhh-hcCCeeEEeEEee
Q 047923            2 RQNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKYK-KEYAHIVIPGFYR   71 (190)
Q Consensus         2 ~~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~~-~~~~~~v~PvFy~   71 (190)
                      ++|+++|+|+ ++.+|+.+.++|.+||++|+..|+|+|++|..|.||..|+..++.+. +.+...+|||++.
T Consensus        37 ~~g~~v~~d~~d~~~G~~~~~~i~~~i~~s~~~i~vlS~~~~~s~w~~~E~~~a~~~~~~~~~~~lIpV~l~  108 (161)
T d1fyva_          37 KEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLE  108 (161)
T ss_dssp             TTTCCEECTTTTCCTTSCHHHHHHHHHHHEEEEEEEESHHHHHHTSHHHHHHTTSCCCSCSSCSSEEEEESS
T ss_pred             hCCCcceEeccccccccccHHHHHHHHHhCCEEEEEecCccccChHHHHHHHHHHHHHHHcCCCceeEEEEe
Confidence            5799999999 99999999999999999999999999999999999999999887654 3455689999887

>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=99.37  E-value=5.1e-14  Score=100.67  Aligned_cols=70  Identities=21%  Similarity=0.238  Sum_probs=62.1

Q ss_pred             CCeeEEEeC-CCCCcccchHHHHHHhhcccceEEEecCCCcCchhhHHHHHHHHHh-hhcCCeeEEeEEeec
Q 047923            3 QNIQTFIDD-QLNRGDEISESIAYAIESPAISVIIFSEGYPFSRWCLHELVKILKY-KKEYAHIVIPGFYRG   72 (190)
Q Consensus         3 ~gi~~f~d~-~~~~g~~~~~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~~~-~~~~~~~v~PvFy~v   72 (190)
                      .|+++|+|+ ++.+|+++.++|.++|+.|+..|+|+|++|..|.||..|+...+.. .+.++..+|||++.-
T Consensus        33 ~g~~~~~~~rd~~~G~~~~~~i~~~i~~S~~~i~vlS~~~l~s~wc~~E~~~a~~~~~~~~~~~iIpV~l~~  104 (149)
T d1fyxa_          33 PPFKLCLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWCKYELDFSHFRLFDENNDAAILILLEP  104 (149)
T ss_dssp             SCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHHHHSCCSCCTTCGGGTTCCEEEESSC
T ss_pred             CCceEEEecccccccchHHHHHHHHHHhCCEEEEEEcCccccccchHHHHHHHHHHHHHcCCceEEEEEecc
Confidence            589999999 9999999999999999999999999999999999999999765543 245667899999873

>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=99.27  E-value=1.4e-12  Score=101.97  Aligned_cols=45  Identities=27%  Similarity=0.264  Sum_probs=38.6

Q ss_pred             ccccccccchhHHHHHHHhhh-cCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          145 KENQLVGRESRVEIIESLLAA-ESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       145 ~~~~~vG~d~~~~~~~~~l~~-~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ....++||+.+++.+.++|.. .+++.++++|+||||+||||||++
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~   63 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQ   63 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHH
T ss_pred             CCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHH
Confidence            345688999999999998875 444689999999999999999975

>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=1.6e-05  Score=58.94  Aligned_cols=45  Identities=29%  Similarity=0.314  Sum_probs=36.6

Q ss_pred             cccccccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          144 DKENQLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       144 ~~~~~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ....+++|.+.-.+.+..++....  ..-+=++|.+|+||||+|+++
T Consensus        21 ~~~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~i   65 (231)
T d1iqpa2          21 QRLDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALAL   65 (231)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHH
Confidence            455789999999999999987653  344669999999999999853

>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=97.09  E-value=0.00014  Score=52.73  Aligned_cols=40  Identities=23%  Similarity=0.361  Sum_probs=31.6

Q ss_pred             cccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          148 QLVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+|||..++.+...|.....  .-+-++|-+|+|||||+..
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~k--~n~lLvG~pGVGKTalv~~   62 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRTK--NNPVLIGEPGVGKTAIVEG   62 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSCHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhccCC--CCeEEEecCCcccHHHHHH
Confidence            488999999999998875321  1245889999999999863

>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=96.87  E-value=0.00026  Score=52.63  Aligned_cols=22  Identities=23%  Similarity=0.126  Sum_probs=18.5

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+.+-|+|.+|+||||+|+++
T Consensus        42 ~~~~lll~GppGtGKT~l~~~l   63 (276)
T d1fnna2          42 HYPRATLLGRPGTGKTVTLRKL   63 (276)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCCceEEECCCCCCHHHHHHHH
Confidence            3567789999999999999863

>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=96.65  E-value=0.0011  Score=51.61  Aligned_cols=30  Identities=23%  Similarity=0.357  Sum_probs=22.5

Q ss_pred             HHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          159 IESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       159 ~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +...+.....+..+|||.|.+|.|||||..
T Consensus        40 ~~~~~~~~~~~~~~igitG~pGaGKSTli~   69 (323)
T d2qm8a1          40 LIDAVLPQTGRAIRVGITGVPGVGKSTTID   69 (323)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHH
T ss_pred             HHHHhhhccCCceEEeeeCCCCCCHHHHHH
Confidence            333333445568999999999999999964

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.49  E-value=0.001  Score=51.88  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=21.2

Q ss_pred             hhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          163 LAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       163 l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +...+.+..+|||.|.+|.|||||..
T Consensus        47 ~~~~~~~~~~IgitG~pGaGKSTLi~   72 (327)
T d2p67a1          47 IMPYCGNTLRLGVTGTPGAGKSTFLE   72 (327)
T ss_dssp             HGGGCSCSEEEEEEECTTSCHHHHHH
T ss_pred             hhhccCCceEEEeeCCCCCCHHHHHH
Confidence            33445568999999999999999975

>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=96.34  E-value=0.00038  Score=51.93  Aligned_cols=21  Identities=43%  Similarity=0.496  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++-++|.+|+||||+++++
T Consensus        46 ~~~l~l~GppGtGKT~l~~~l   66 (287)
T d1w5sa2          46 NMIYGSIGRVGIGKTTLAKFT   66 (287)
T ss_dssp             EEEEECTTCCSSSHHHHHHHH
T ss_pred             ceEEEeECCCCCCHHHHHHHH
Confidence            456678899999999999863

>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=96.28  E-value=0.00098  Score=53.21  Aligned_cols=38  Identities=21%  Similarity=0.434  Sum_probs=30.1

Q ss_pred             cccccchhHHHHHHHhhhc-CCCeEEEEEEcCCCCcHHHHhc
Q 047923          148 QLVGRESRVEIIESLLAAE-SKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~~-~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .++|||..++.+...|... .+.+   -++|.+|+|||+|+.
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k~n~---llvG~~GvGKtaiv~   61 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTKNNP---VLIGEPGVGKTAIVE   61 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSCCCC---EEEECTTSCHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhcCCCCCC---eEECCCCCCHHHHHH
Confidence            4889999999999988743 2223   356999999999875

>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=96.11  E-value=0.0037  Score=48.22  Aligned_cols=20  Identities=45%  Similarity=0.675  Sum_probs=18.5

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      --+|||.|-.|+||||+|+.
T Consensus        80 P~iIGIaG~sgSGKSTla~~   99 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARV   99 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHH
T ss_pred             CEEEEEeCCCCCCCcHHHHH
Confidence            67999999999999999985

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=95.81  E-value=0.0027  Score=50.10  Aligned_cols=42  Identities=24%  Similarity=0.016  Sum_probs=28.1

Q ss_pred             ccccchhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhccC
Q 047923          149 LVGRESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       149 ~vG~d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      +.|.+....+..+.+..+..+-+.+-++|.+|.|||++|+++
T Consensus       133 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~  174 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAAL  174 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHH
Confidence            445554444443433344455678899999999999999863

>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=95.66  E-value=0.0015  Score=50.32  Aligned_cols=20  Identities=35%  Similarity=0.353  Sum_probs=17.0

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+-++|.+|+|||.||+++
T Consensus        50 ~~iLl~GPpG~GKT~lAkal   69 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIARRL   69 (309)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            44568999999999999974

>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=95.60  E-value=0.0015  Score=48.22  Aligned_cols=21  Identities=33%  Similarity=0.333  Sum_probs=17.9

Q ss_pred             eEEEEEEcCCCCcHHHHhccC
Q 047923          170 VYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .+.+-++|.+|+||||+|+++
T Consensus        52 ~~~lll~GPpG~GKTt~a~~l   72 (253)
T d1sxja2          52 FRAAMLYGPPGIGKTTAAHLV   72 (253)
T ss_dssp             CSEEEEECSTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            456779999999999999864

>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=95.56  E-value=0.0084  Score=46.17  Aligned_cols=44  Identities=16%  Similarity=0.207  Sum_probs=31.8

Q ss_pred             ccccccchhHHHHHHHhhh-----cC-C-CeEEEEEEcCCCCcHHHHhccC
Q 047923          147 NQLVGRESRVEIIESLLAA-----ES-K-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       147 ~~~vG~d~~~~~~~~~l~~-----~~-~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|.+.-++.+...+..     .+ + ...++-++|..|+|||.||+++
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~l   72 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQL   72 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHH
Confidence            3578888888877654431     11 2 2567889999999999999863

>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=95.43  E-value=0.075  Score=39.59  Aligned_cols=34  Identities=15%  Similarity=0.139  Sum_probs=26.2

Q ss_pred             HHHHHHhhcccceEEEecCCCcCchhhHHHHHHHH
Q 047923           21 ESIAYAIESPAISVIIFSEGYPFSRWCLHELVKIL   55 (190)
Q Consensus        21 ~~l~~ai~~s~~~ivv~S~~y~~S~wcl~El~~i~   55 (190)
                      .++.++|+.+++.+.|+==.-.-|.+|. +|.+++
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            4677899999999999987777777774 355555

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.32  E-value=0.0054  Score=45.60  Aligned_cols=22  Identities=23%  Similarity=0.148  Sum_probs=18.3

Q ss_pred             CeEEEEEEcCCCCcHHHHhccC
Q 047923          169 DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..+-+=++|.+|.|||+||+++
T Consensus        39 p~~~vLL~GppGtGKT~la~al   60 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKI   60 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHH
Confidence            3556679999999999999864

>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=95.09  E-value=0.0033  Score=47.11  Aligned_cols=19  Identities=32%  Similarity=0.391  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus        42 e~iaivG~sGsGKSTLl~l   60 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASL   60 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHH
Confidence            4699999999999999985

>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=95.02  E-value=0.0037  Score=46.77  Aligned_cols=19  Identities=26%  Similarity=0.372  Sum_probs=17.2

Q ss_pred             EEEEEEcCCCCcHHHHhcc
Q 047923          171 YILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~  189 (190)
                      ..++|+|..|.|||||++.
T Consensus        41 e~vaivG~sGsGKSTLl~l   59 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAAL   59 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            4699999999999999985

>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=94.95  E-value=0.0038  Score=47.49  Aligned_cols=20  Identities=30%  Similarity=0.287  Sum_probs=17.7

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      =.+++|+|..|.|||||.+.
T Consensus        62 Ge~vaivG~nGsGKSTLl~~   81 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLML   81 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHH
Confidence            35799999999999999975

>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=94.83  E-value=0.0067  Score=45.43  Aligned_cols=20  Identities=20%  Similarity=0.235  Sum_probs=17.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      ..++|+|..|.|||||++.+
T Consensus        45 e~vaivG~sGsGKSTLl~ll   64 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLI   64 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTT
T ss_pred             CEEEEECCCCCcHHHHHHHH
Confidence            47899999999999999864

>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=94.45  E-value=0.0047  Score=46.01  Aligned_cols=19  Identities=37%  Similarity=0.385  Sum_probs=16.3

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      -+=++|.+|.|||+||+++
T Consensus        44 giLl~GppGtGKT~la~ai   62 (247)
T d1ixza_          44 GVLLVGPPGVGKTHLARAV   62 (247)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             eEEEecCCCCChhHHHHHH
Confidence            3568999999999999864

>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=93.91  E-value=0.013  Score=45.10  Aligned_cols=43  Identities=16%  Similarity=0.356  Sum_probs=30.4

Q ss_pred             cccccchhHHHHHHHhhh-----cC-C-CeEEEEEEcCCCCcHHHHhccC
Q 047923          148 QLVGRESRVEIIESLLAA-----ES-K-DVYILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       148 ~~vG~d~~~~~~~~~l~~-----~~-~-~~~vi~i~G~gGiGKTTla~~v  190 (190)
                      .++|.+.-++.+...+..     .+ + ...++-++|..|+|||.||+.+
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~l   73 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTL   73 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHH
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHH
Confidence            477888777777554431     11 1 2557789999999999999853

>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=93.87  E-value=0.0084  Score=44.84  Aligned_cols=20  Identities=30%  Similarity=0.205  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+-++|.+|.|||+||+++
T Consensus        46 ~~iLL~GppGtGKT~la~~i   65 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAI   65 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             CeEEeeCCCCCCccHHHHHH
Confidence            44569999999999999864

>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=92.85  E-value=0.017  Score=44.58  Aligned_cols=19  Identities=32%  Similarity=0.445  Sum_probs=15.7

Q ss_pred             EEEEEcCCCCcHHHHhccC
Q 047923          172 ILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~v  190 (190)
                      ++=++|.+|+|||.||+++
T Consensus       125 ~~l~~G~pG~GKT~la~al  143 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHAL  143 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHH
Confidence            4446899999999999864

>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=92.76  E-value=0.012  Score=44.07  Aligned_cols=20  Identities=30%  Similarity=0.283  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCCcHHHHhccC
Q 047923          171 YILGIWGVGSIGKTTIARAN  190 (190)
Q Consensus       171 ~vi~i~G~gGiGKTTla~~v  190 (190)
                      +-+=++|.+|.|||+||+++
T Consensus        42 ~giLL~Gp~GtGKT~l~~al   61 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAI   61 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCcchhHHHHH
Confidence            34559999999999999864

>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=92.55  E-value=0.047  Score=42.74  Aligned_cols=20  Identities=25%  Similarity=0.223  Sum_probs=16.2

Q ss_pred             eEEEEEEcCCCCcHHHHhcc
Q 047923          170 VYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       170 ~~vi~i~G~gGiGKTTla~~  189 (190)
                      ...+=.+|..|+|||-|||+
T Consensus        68 ~~niLfiGPTGvGKTElAk~   87 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQT   87 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHH
T ss_pred             CcceeeeCCCCccHHHHHHH
Confidence            33466779999999999985

>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=91.27  E-value=0.037  Score=38.18  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=18.3

Q ss_pred             CeEEEEEEcCCCCcHHHHhcc
Q 047923          169 DVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       169 ~~~vi~i~G~gGiGKTTla~~  189 (190)
                      .-.+|.+.|-=|.||||++|.
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~   52 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRG   52 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHH
T ss_pred             CCeEEEEecCCCccHHHHHHH
Confidence            456789999999999999985

>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=90.14  E-value=0.088  Score=38.32  Aligned_cols=29  Identities=24%  Similarity=0.483  Sum_probs=20.8

Q ss_pred             HHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          156 VEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       156 ~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ++.+.++|..   +  +..+.|..|+|||||..+
T Consensus        86 ~~~L~~~l~~---k--t~~~~G~SGVGKSTLiN~  114 (225)
T d1u0la2          86 IEELKEYLKG---K--ISTMAGLSGVGKSSLLNA  114 (225)
T ss_dssp             HHHHHHHHSS---S--EEEEECSTTSSHHHHHHH
T ss_pred             HhhHHHHhcC---C--eEEEECCCCCCHHHHHHh
Confidence            5566666632   2  456889999999999764

>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=89.70  E-value=0.1  Score=38.90  Aligned_cols=33  Identities=21%  Similarity=0.278  Sum_probs=24.8

Q ss_pred             HHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          157 EIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       157 ~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      ..+..+|.....+-..+-++|.|+.||||++.+
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~  123 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEA  123 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHH
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHH
Confidence            344555655545577888999999999999975

>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=89.00  E-value=0.041  Score=42.35  Aligned_cols=17  Identities=29%  Similarity=0.341  Sum_probs=15.2

Q ss_pred             EEEEcCCCCcHHHHhcc
Q 047923          173 LGIWGVGSIGKTTIARA  189 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~  189 (190)
                      +-|.|..|.||||+.++
T Consensus       169 ili~G~tgSGKTT~l~a  185 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYIKS  185 (323)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             EEEEeeccccchHHHHH
Confidence            67899999999999875

>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=86.14  E-value=0.1  Score=40.62  Aligned_cols=31  Identities=26%  Similarity=0.077  Sum_probs=20.8

Q ss_pred             chhHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          153 ESRVEIIESLLAAESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       153 d~~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      +..+..+...+.     -++.-|.|.+|.||||++.
T Consensus       151 ~~Q~~A~~~al~-----~~~~vI~G~pGTGKTt~i~  181 (359)
T d1w36d1         151 NWQKVAAAVALT-----RRISVISGGPGTGKTTTVA  181 (359)
T ss_dssp             CHHHHHHHHHHT-----BSEEEEECCTTSTHHHHHH
T ss_pred             cHHHHHHHHHHc-----CCeEEEEcCCCCCceehHH
Confidence            445555554442     2467789999999999763

>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=86.07  E-value=0.12  Score=41.49  Aligned_cols=17  Identities=41%  Similarity=0.569  Sum_probs=14.4

Q ss_pred             EEEEcCCCCcHHHHhcc
Q 047923          173 LGIWGVGSIGKTTIARA  189 (190)
Q Consensus       173 i~i~G~gGiGKTTla~~  189 (190)
                      |=++|..|+|||-||+.
T Consensus        52 ILliGPTGvGKTlLAr~   68 (443)
T d1g41a_          52 ILMIGPTGVGKTEIARR   68 (443)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            44669999999999985

>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=85.56  E-value=0.16  Score=37.70  Aligned_cols=31  Identities=29%  Similarity=0.298  Sum_probs=20.9

Q ss_pred             HHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          158 IIESLLA-AESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       158 ~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .+..+|. .+-..-++.-|+|-+|.||||||-
T Consensus        41 ~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l   72 (263)
T d1u94a1          41 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTL   72 (263)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHhcCCCccCceEEEEecCCCcHHHHHHH
Confidence            4445553 211123588899999999999984

>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=85.23  E-value=0.18  Score=35.98  Aligned_cols=34  Identities=18%  Similarity=0.216  Sum_probs=25.4

Q ss_pred             hHHHHHHHhhhcCCCeEEEEEEcCCCCcHHHHhcc
Q 047923          155 RVEIIESLLAAESKDVYILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       155 ~~~~~~~~l~~~~~~~~vi~i~G~gGiGKTTla~~  189 (190)
                      -+..+..+|. +..+-..+-++|.++.|||++|.+
T Consensus        39 Fl~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~s   72 (205)
T d1tuea_          39 FLGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMS   72 (205)
T ss_dssp             HHHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCceEEEEECCCCccHHHHHHH
Confidence            3455566664 335677889999999999999864

>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=85.23  E-value=0.17  Score=39.83  Aligned_cols=18  Identities=17%  Similarity=0.283  Sum_probs=15.6

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -|+|.|.+|+|||||..+
T Consensus        58 ~Iai~G~~n~GKSSLiNa   75 (400)
T d1tq4a_          58 NVAVTGETGSGKSSFINT   75 (400)
T ss_dssp             EEEEEECTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            479999999999999754

>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=82.28  E-value=0.26  Score=36.64  Aligned_cols=31  Identities=32%  Similarity=0.284  Sum_probs=21.3

Q ss_pred             HHHHHhh-hcCCCeEEEEEEcCCCCcHHHHhc
Q 047923          158 IIESLLA-AESKDVYILGIWGVGSIGKTTIAR  188 (190)
Q Consensus       158 ~~~~~l~-~~~~~~~vi~i~G~gGiGKTTla~  188 (190)
                      .+..+|. .+-..-++.-|+|-+|.||||||-
T Consensus        44 ~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l   75 (268)
T d1xp8a1          44 SLDLALGVGGIPRGRITEIYGPESGGKTTLAL   75 (268)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHH
T ss_pred             HHHHHhcCCCccCceEEEEecCCccchHHHHH
Confidence            3445554 221224588999999999999984

>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=82.06  E-value=0.21  Score=37.60  Aligned_cols=18  Identities=22%  Similarity=0.023  Sum_probs=15.7

Q ss_pred             EEEEEcCCCCcHHHHhcc
Q 047923          172 ILGIWGVGSIGKTTIARA  189 (190)
Q Consensus       172 vi~i~G~gGiGKTTla~~  189 (190)
                      -++|.|-.|+|||||+..
T Consensus        45 r~~I~g~~g~GKT~l~~~   62 (289)
T d1xpua3          45 RGLIVAPPKAGKTMLLQN   62 (289)
T ss_dssp             EEEEEECSSSSHHHHHHH
T ss_pred             eeeEeCCCCCCHHHHHHH
Confidence            478999999999999864

>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=80.68  E-value=0.11  Score=37.92  Aligned_cols=16  Identities=25%  Similarity=0.422  Sum_probs=13.9

Q ss_pred             EEEcCCCCcHHHHhcc
Q 047923          174 GIWGVGSIGKTTIARA  189 (190)
Q Consensus       174 ~i~G~gGiGKTTla~~  189 (190)
                      .+.|..|+|||||..+
T Consensus       101 vl~G~SGVGKSSLiN~  116 (231)
T d1t9ha2         101 VFAGQSGVGKSSLLNA  116 (231)
T ss_dssp             EEEESHHHHHHHHHHH
T ss_pred             EEECCCCccHHHHHHh
Confidence            4889999999999764