Citrus Sinensis ID: 042778

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-
Protein Sequence
MAAYSSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEcccccccccccHHHHHHHHHHccccEEEcccccccccccHHHHHHHHHccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHHHccccccEEccccHHHHcccccHHHHHHHHHHHHHccccccccHHHHHHHHccccEEEEEccccccHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccccccHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccEEEcccccccccccHHHHHHHHHccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccccccHHHcccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHHHHHHHHHHHHHccccHHHHHccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHcccEEEEEEccccccccHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHccccccccHHHHHcc
Coil and Loop (DISEMBL)
maayssspsspssprnhkydvfqsfrgednrdnftGHLYSALSQKGIETFIDdqlnrgdeISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAaglsgfhsqnirlaevspcsnknqlvGVESRVEEIESLLgaeskdvyaLGIWGIGGIDRTTIARAIFNKISsnfegscflqnvreesqrpgglgFLQQKLLSKLLQdgivipdiALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSrhafkqnnphigfeelssr
Flexible Loop (DISEMBL)
maayssspsspssprnhKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRlaevspcsnknQLVGVESRVEEIESLLgaeskdvyaLGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRhafkqnnphigfeelssr
Low Complexity Region (SEG)
MAAYssspsspsspRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPgglgflqqkllskllqDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Disordered region (IsUnstruct)
********************************NFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKEN*EKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVRE****PGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAF***************
Disordered Region (DISOPRED)
*******************DVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Disordered Region (DISEMBL)
****************HKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Disordered Region (DISPRO)
**************RNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAYSSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSSR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	311	2.2.26 [Sep-21-2011]
O82500	1095	Putative disease resistan	no	no	0.932	0.264	0.355	3e-48
Q40392	1144	TMV resistance protein N	N/A	no	0.922	0.250	0.361	5e-46
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.954	0.228	0.318	3e-38
Q9FL92	1372	Probable WRKY transcripti	no	no	0.823	0.186	0.278	5e-21
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.848	0.139	0.288	6e-21
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.890	0.171	0.244	1e-16
Q9FH83	1288	Probable WRKY transcripti	no	no	0.717	0.173	0.273	2e-13
Q9C5Q9	411	Protein PHLOEM PROTEIN 2-	no	no	0.257	0.194	0.476	5e-13
Q9FHE9	354	Protein PHLOEM PROTEIN 2-	no	no	0.411	0.361	0.315	2e-12
Q9SYC9	571	Vesicle-associated protei	no	no	0.250	0.136	0.430	6e-10

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

 Score =  192 bits (487), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 128/360 (35%), Positives = 180/360 (50%), Gaps = 70/360 (19%)

Query: 12  SSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEA 71
           SS  + +YDVF SFRGED R+NF  HL      KGI TF DD + R   I   L  AI  
Sbjct: 4   SSSNSWRYDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDHIKRSHTIGHELRAAIRE 63

Query: 72  SAISLIIFSEAYASSRWCLDELVKILTRELEEMFK------------------------- 106
           S IS+++FSE YASS WCLDEL++I+  + E+  K                         
Sbjct: 64  SKISVVLFSENYASSSWCLDELIEIMKCKEEQGLKVMPVFYKVDPSDIRKQTGKFGMSFL 123

Query: 107 -----ENSEKLQTWRNALKEAAGLSGFHSQN-----IRLAEVS----------PCSNKNQ 146
                +  E+   WR AL +AA + G H QN      ++  +S          P  + N 
Sbjct: 124 ETCCGKTEERQHNWRRALTDAANILGDHPQNWDNEAYKITTISKDVLEKLNATPSRDFND 183

Query: 147 LVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVR 206
           LVG+E+ + ++ESLL  ES+ V  +GIWG  G+ +TTIARA++N+   NF  S F++NVR
Sbjct: 184 LVGMEAHIAKMESLLCLESQGVRIVGIWGPAGVGKTTIARALYNQYHENFNLSIFMENVR 243

Query: 207 EESQRPG----GLGF-LQQKLLSKLL-QDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQ 260
           E     G    GL   LQQ+ LSKLL Q  + +  +     +L  +KVLI+LDDV    Q
Sbjct: 244 ESYGEAGLDDYGLKLHLQQRFLSKLLDQKDLRVRHLGAIEERLKSQKVLIILDDVDNIEQ 303

Query: 261 IKSLIG-------------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNP 301
           +K+L                     +L +  +   Y++       AL +F +HAFKQ++P
Sbjct: 304 LKALAKENQWFGNKSRIVVTTQNKQLLVSHDINHMYQVAYPSKQEALTIFCQHAFKQSSP 363

Arabidopsis thaliana (taxid: 3702)

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

 Score =  185 bits (469), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 133/368 (36%), Positives = 189/368 (51%), Gaps = 81/368 (22%)

Query: 19  YDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEASAISLI 77
           YDVF SFRGED R  FT HLY  L+ KGI+TF DD+ L  G  I   L  AIE S  +++
Sbjct: 12  YDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKAIEESQFAIV 71

Query: 78  IFSEAYASSRWCLDELVKIL---TR-----------------------------ELEEMF 105
           +FSE YA+SRWCL+ELVKI+   TR                             E E  +
Sbjct: 72  VFSENYATSRWCLNELVKIMECKTRFKQTVIPIFYDVDPSHVRNQKESFAKAFEEHETKY 131

Query: 106 KENSEKLQTWRNALKEAAGLSG----------------FHSQNIRLAEVSPCSNKNQLVG 149
           K++ E +Q WR AL EAA L G                    + +L ++S  S    +VG
Sbjct: 132 KDDVEGIQRWRIALNEAANLKGSCDNRDKTDADCIRQIVDQISSKLCKIS-LSYLQNIVG 190

Query: 150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI------SSNFEGSCFLQ 203
           +++ +E+IESLL      V  +GIWG+GG+ +TTIARAIF+ +      S  F+G+CFL+
Sbjct: 191 IDTHLEKIESLLEIGINGVRIMGIWGMGGVGKTTIARAIFDTLLGRMDSSYQFDGACFLK 250

Query: 204 NVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRR----KVLIVLDDV---- 255
           +++E  +   G+  LQ  LLS+LL++     +      Q++ R    KVLIVLDD+    
Sbjct: 251 DIKENKR---GMHSLQNALLSELLREKANYNNEEDGKHQMASRLRSKKVLIVLDDIDNKD 307

Query: 256 ----------TCFRQIKSLIGMLRNCCVKEK----YEMKELGDDHALELFSRHAFKQNNP 301
                       F     +I   R+  + EK    YE+  L D  +++LF +HAF +  P
Sbjct: 308 HYLEYLAGDLDWFGNGSRIIITTRDKHLIEKNDIIYEVTALPDHESIQLFKQHAFGKEVP 367

Query: 302 HIGFEELS 309
           +  FE+LS
Sbjct: 368 NENFEKLS 375

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

 Score =  159 bits (402), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 116/364 (31%), Positives = 182/364 (50%), Gaps = 67/364 (18%)

Query: 12  SSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEA 71
           SS  + +YDVF SFRGED RD+F  HL   L  K I TFIDD++ R   I   L+ AI+ 
Sbjct: 5   SSSGSRRYDVFPSFRGEDVRDSFLSHLLKELRGKAI-TFIDDEIERSRSIGPELLSAIKE 63

Query: 72  SAISLIIFSEAYASSRWCLDELVKI-----------------------------LTRELE 102
           S I+++IFS+ YASS WCL+ELV+I                               +  E
Sbjct: 64  SRIAIVIFSKNYASSTWCLNELVEIHKCYTNLNQMVIPIFFHVDASEVKKQTGEFGKVFE 123

Query: 103 EMFKENSE-KLQTWRNALKEAAGLSGFH--------------SQNIRLAEVSPCSNKNQL 147
           E  K  SE + Q+W+ AL   A ++G+               ++++    ++P  +   L
Sbjct: 124 ETCKAKSEDEKQSWKQALAAVAVMAGYDLRKWPSEAAMIEELAEDVLRKTMTPSDDFGDL 183

Query: 148 VGVESRVEEIESLLGAESKDV-YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVR 206
           VG+E+ +E I+S+L  ESK+    +GIWG  GI ++TI RA+++K+S  F    F+    
Sbjct: 184 VGIENHIEAIKSVLCLESKEARIMVGIWGQSGIGKSTIGRALYSKLSIQFHHRAFITYKS 243

Query: 207 EESQRPGGLGFLQQK-LLSKLL-QDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSL 264
                  G+    +K LLS++L Q  I I    +  ++L ++KVLI+LDDV     +K+L
Sbjct: 244 TSGSDVSGMKLRWEKELLSEILGQKDIKIEHFGVVEQRLKQQKVLILLDDVDSLEFLKTL 303

Query: 265 IG-------------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGF 305
           +G                   +L+   +   YE++   +  AL +  R AF +++P   F
Sbjct: 304 VGKAEWFGSGSRIIVITQDRQLLKAHEIDLIYEVEFPSEHLALTMLCRSAFGKDSPPDDF 363

Query: 306 EELS 309
           +EL+
Sbjct: 364 KELA 367

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

 Score =  102 bits (253), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 155/302 (51%), Gaps = 46/302 (15%)

Query: 28  EDNRDNFTGHLYSALSQKGI-ETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASS 86
           E+ R +F  HL  AL +KG+ + FID   +  +E SQS+V   E + +S++I       S
Sbjct: 14  EEVRYSFVSHLSKALQRKGVNDVFIDSDDSLSNE-SQSMV---ERARVSVMILPGNRTVS 69

Query: 87  RWCLDELVKILTRE-------LEEMFKENSEKLQTWRNALKEAAGLSGFH--------SQ 131
              LD+LVK+L  +       +  ++   S + + W +AL ++ G S  H        SQ
Sbjct: 70  ---LDKLVKVLDCQKNKDQVVVPVLYGVRSSETE-WLSAL-DSKGFSSVHHSRKECSDSQ 124

Query: 132 NIR--LAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIF 189
            ++  + +V       + +G+ S++ EIE ++  +  D+  +GIWG+ GI +TT+A+A+F
Sbjct: 125 LVKETVRDVYEKLFYMERIGIYSKLLEIEKMINKQPLDIRCVGIWGMPGIGKTTLAKAVF 184

Query: 190 NKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVL 249
           +++S  F+  CF+++  +  Q  G    L+++ L +       +  ++L   +L+ ++VL
Sbjct: 185 DQMSGEFDAHCFIEDYTKAIQEKGVYCLLEEQFLKENAGASGTVTKLSLLRDRLNNKRVL 244

Query: 250 IVLDDVTCFRQIKSLIG-------------------MLRNCCVKEKYEMKELGDDHALEL 290
           +VLDDV     ++S +G                   + R C V + YE++ L +  AL+L
Sbjct: 245 VVLDDVRSPLVVESFLGGFDWFGPKSLIIITSKDKSVFRLCRVNQIYEVQGLNEKEALQL 304

Query: 291 FS 292
           FS
Sbjct: 305 FS 306

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  101 bits (252), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 95/329 (28%), Positives = 155/329 (47%), Gaps = 65/329 (19%)

Query: 19  YDVFQSF-RGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           YDV   + R + + ++F  HL ++L ++GI  +  ++ N         VDA+    + +I
Sbjct: 668 YDVVIRYGRADISNEDFISHLRASLCRRGISVY--EKFNE--------VDALPKCRVLII 717

Query: 78  IFSEAYASS--------RWCLDELV-KILTRELEEMFKENSEKLQ---------TWRNAL 119
           + +  Y  S        +   D +V  I  R     F  NS+  +          W+ AL
Sbjct: 718 VLTSTYVPSNLLNILEHQHTEDRVVYPIFYRLSPYDFVCNSKNYERFYLQDEPKKWQAAL 777

Query: 120 KEAAGLSGFHSQN----------IRLAEVSPCS-NKNQLVGVESRVEEIESLLGAESKDV 168
           KE   + G+   +          +R A    CS +K  ++G++ +VEEI SLL  ES DV
Sbjct: 778 KEITQMPGYTLTDKSESELIDEIVRDALKVLCSADKVNMIGMDMQVEEILSLLCIESLDV 837

Query: 169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQ 228
            ++GIWG  GI +TTIA  IF KIS  +E    L+++ +E +  G    +++  LS++L+
Sbjct: 838 RSIGIWGTVGIGKTTIAEEIFRKISVQYETCVVLKDLHKEVEVKGH-DAVRENFLSEVLE 896

Query: 229 ---DGIVIPDIALSF--RQLSRRKVLIVLDDVTCFRQIKSLIGML-------------RN 270
                I I DI  SF   +L R+++L++LDDV  +R + + +G L             RN
Sbjct: 897 VEPHVIRISDIKTSFLRSRLQRKRILVILDDVNDYRDVDTFLGTLNYFGPGSRIIMTSRN 956

Query: 271 ------CCVKEKYEMKELGDDHALELFSR 293
                 C +   YE+K L    +L L  R
Sbjct: 957 RRVFVLCKIDHVYEVKPLDIPKSLLLLDR 985

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 87.0 bits (214), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 50/327 (15%)

Query: 33  NFTGHLYSALSQKGIETFIDD---QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWC 89
           +   HL +AL ++GI  F+D    Q  +   I Q+      A  + ++I  E      W 
Sbjct: 31  SLVSHLSAALRREGISVFVDACGLQETKFFSIKQNQPLTDGARVLVVVISDEVEFYDPW- 89

Query: 90  LDELVKILT------RELEEMFK--ENSEKLQTWRNALKEAAGLSGFHSQNIR------- 134
             + +K++         +  +F   ++  ++  W N+  EA  L+   S+ +        
Sbjct: 90  FPKFLKVIQGWQNNGHVVVPVFYGVDSLTRVYGWANSWLEAEKLTSHQSKILSNNVLTDS 149

Query: 135 ------LAEVSPCSNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAI 188
                 + +V       + VG+ +R+ EIE LL  + +D+ ++GIWG+ GI +TT+A+A+
Sbjct: 150 ELVEEIVRDVYGKLYPAERVGIYARLLEIEKLLYKQHRDIRSIGIWGMPGIGKTTLAKAV 209

Query: 189 FNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR--- 245
           FN +S++++ SCF++N  E   + G    L+++ + K+L+D   I    +    L R   
Sbjct: 210 FNHMSTDYDASCFIENFDEAFHKEGLHRLLKER-IGKILKDEFDIESSYIMRPTLHRDKL 268

Query: 246 --RKVLIVLDDVTCFRQIKSLIGML-------------------RNCCVKEKYEMKELGD 284
             +++L+VLDDV      +S +  L                     C + + Y ++ L  
Sbjct: 269 YDKRILVVLDDVRDSLAAESFLKRLDWFGSGSLIIITSVDKQVFAFCQINQIYTVQGLNV 328

Query: 285 DHALELFSRHAFKQNNPHIGFEELSSR 311
             AL+LFS+  F  N P     +LS +
Sbjct: 329 HEALQLFSQSVFGINEPEQNDRKLSMK 355

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FH83|WRK52_ARATH Probable WRKY transcription factor 52 OS=Arabidopsis thaliana GN=WRKY52 PE=2 SV=3

 Score = 76.6 bits (187), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 22/245 (8%)

Query: 28  EDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSR 87
           E+ R +F  HL  AL +KGI   + D         +S    IE + +S+++       S 
Sbjct: 17  EEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQA-KIEKAGVSVMVLPGNCDPSE 75

Query: 88  WCLDELVKIL-------TRELEEMFKENSEKLQTWRNALKEAAGLSGFH------SQNIR 134
             LD+  K+L        + +  +   +S     W + L +  GLS  H      S +I 
Sbjct: 76  VWLDKFAKVLECQRNNKDQAVVSVLYGDSLLRDQWLSEL-DFRGLSRIHQSRKECSDSIL 134

Query: 135 LAEVSPCSNKNQL----VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN 190
           + E+     +       +G+ S++ EIE+++  +   +  +GIWG+ GI +TT+A+A+F+
Sbjct: 135 VEEIVRDVYETHFYVGRIGIYSKLLEIENMVNKQPIGIRCVGIWGMPGIGKTTLAKAVFD 194

Query: 191 KISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLI 250
           ++SS F+ SCF+++  +     G    L+++LL     D  ++   +L  R L+ ++VL+
Sbjct: 195 QMSSAFDASCFIEDYDKSIHEKGLYCLLEEQLLPG--NDATIMKLSSLRDR-LNSKRVLV 251

Query: 251 VLDDV 255
           VLDDV
Sbjct: 252 VLDDV 256

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 75.5 bits (184), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/86 (47%), Positives = 52/86 (60%), Gaps = 6/86 (6%)

Query: 11 PSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIE 70
          P+ P+     VF +FRG+D R  F   L  AL ++ I  FID+Q  RG  +  SL D I 
Sbjct: 19 PTGPQ-----VFINFRGKDLRKGFMSFLKPALKKEKINVFIDEQEERGKYLI-SLFDTIG 72

Query: 71 ASAISLIIFSEAYASSRWCLDELVKI 96
           S I+L+IFSE Y  S WC+DELVKI
Sbjct: 73 ESKIALVIFSEGYCESHWCMDELVKI 98

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.6 bits (179), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 78/171 (45%), Gaps = 43/171 (25%)

Query: 1   MAAYSSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDE 60
           MAA SS   +P+ P+     VF +FRG+D R+ F   L  A+ +  I  FID     G +
Sbjct: 1   MAASSSVRPTPTGPQ-----VFINFRGKDLRNGFLSFLEPAMREANINVFIDKDEVVGTD 55

Query: 61  ISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKI------------------------ 96
           +    V  I+ S ++++IFS+ Y SS WCLDEL +I                        
Sbjct: 56  LVNLFV-RIQESRVAVVIFSKDYTSSEWCLDELAEIKDCINQGGLNAIPIFYKLAPSSVL 114

Query: 97  --------LTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVS 139
                     R L+E +K + E+ Q W+ AL+    L G     +RLAE S
Sbjct: 115 ELKGGFGDTFRVLKEKYKNDPERTQKWQEALESIPKLKG-----LRLAEKS 160

Arabidopsis thaliana (taxid: 3702)

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

 Score = 65.1 bits (157), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           +Y VF +FRG++ R++F G L  A+  + I  F D+   RG  ++  L   IE S +++ 
Sbjct: 357 QYQVFINFRGDELRNSFVGFLVKAMRLEKINVFTDEVELRGTNLNY-LFRRIEESRVAVA 415

Query: 78  IFSEAYASSRWCLDELVKI 96
           IFSE Y  S WCLDELVK+
Sbjct: 416 IFSERYTESCWCLDELVKM 434

May play a role in vesicle trafficking.

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	311
255564976	944	TMV resistance protein N, putative [Rici	0.938	0.309	0.430	2e-63
224145716	532	tir-nbs-lrr resistance protein [Populus	0.971	0.567	0.409	6e-60
255561496	876	TMV resistance protein N, putative [Rici	0.961	0.341	0.4	3e-59
255555357	1094	leucine-rich repeat-containing protein,	0.906	0.257	0.419	4e-59
224127754	1125	tir-nbs-lrr resistance protein [Populus	0.935	0.258	0.394	5e-59
359493487	1162	PREDICTED: TMV resistance protein N-like	0.929	0.248	0.419	6e-59
224144414	520	tir-nbs-lrr resistance protein [Populus	0.942	0.563	0.408	2e-58
255569048	1084	leucine-rich repeat-containing protein,	0.922	0.264	0.423	2e-58
359493483	1274	PREDICTED: TMV resistance protein N-like	0.929	0.226	0.417	2e-58
451798990	1335	TMV resistance protein N-like protein 7	0.929	0.216	0.417	3e-58

>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 =  249 bits (635), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 156/362 (43%), Positives = 203/362 (56%), Gaps = 70/362 (19%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED RDNFT HLY+AL QK I+ F+DD+L+RG+EIS +LV  IE S +S+I
Sbjct: 15  KYDVFVSFRGEDTRDNFTSHLYAALHQKQIKAFVDDKLSRGEEISAALVKVIEESMVSVI 74

Query: 78  IFSEAYASSRWCLDELVKILT--------------------------------RELEEMF 105
           IFSE YA S WCLDELVKIL                                  E E+ F
Sbjct: 75  IFSENYAFSPWCLDELVKILECKKTVGQIVLPVFYHVDPSDVAEQKGGFGAAFIEHEKCF 134

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQNIR----------------LAEVSPCSNKNQLVG 149
           KE  +KLQ WR AL EAA +SG+ S  IR                L  +S  ++   LVG
Sbjct: 135 KERIDKLQKWRAALTEAANISGWSSSVIRSESKLIQEIAEDILKKLNHMSSSTDSKGLVG 194

Query: 150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREES 209
           + SR+++IE LL  E  DV  LG+WG+GG  +TT A  +FN+IS+ F+  CFL NV EES
Sbjct: 195 INSRIDKIELLLCVELADVRFLGLWGMGGAGKTTTAEVVFNRISTQFDSCCFLANVNEES 254

Query: 210 QRPGGLGFLQQKLLSKLL-QDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIG-- 266
           +R G L  LQ++L SKLL QD +   +      +L  RKVLIVLDDV   RQ+++L G  
Sbjct: 255 ERYGLLK-LQRQLFSKLLGQDNVNYAEGIFDKSRLKHRKVLIVLDDVNNLRQLENLAGEH 313

Query: 267 -----------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELS 309
                            +L+N      Y++++L    AL+LFS +AF+Q  P   + +LS
Sbjct: 314 NWFGPGSRIILTSRDKDVLKN-KTDAIYKIEDLDHHEALQLFSLNAFRQECPKADYMKLS 372

Query: 310 SR 311
            R
Sbjct: 373 KR 374

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145716|ref|XP_002325741.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|224145719|ref|XP_002325742.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222862616|gb|EEF00123.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222862617|gb|EEF00124.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 154/376 (40%), Positives = 199/376 (52%), Gaps = 74/376 (19%)

Query: 10  SPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDA 68
           S SS     YDVF SFRG+D R NFT HLY+AL Q GI TF DD +L RG+EIS  LV A
Sbjct: 1   SSSSRHRWNYDVFLSFRGKDTRKNFTDHLYTALIQAGIHTFRDDNELPRGEEISPQLVKA 60

Query: 69  IEASAISLIIFSEAYASSRWCLDELVKILT------------------------------ 98
           IE S IS+++FS+ YASSRWCLDELVKI+                               
Sbjct: 61  IEGSRISIVVFSKQYASSRWCLDELVKIVECRQKIDQVVLPIFYDTEPSDVRKQTGSYAK 120

Query: 99  --RELEEMFKENSEKLQTWRNALKEAAGLSGFHSQN----------IRLAEVSPCSNKNQ 146
              E EE FKE  EK+  WR AL EA  LSG+   N           R+     C   N+
Sbjct: 121 AFDEHEEHFKEEMEKVNKWRGALAEAGNLSGWGLNNEANGYEAEFIKRIVSDVACKLGNK 180

Query: 147 L-------VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGS 199
                   VG+ SRV+ I SLL     DV  +GI GI GI +TTIA+A+FNK+   FEGS
Sbjct: 181 TLHVAKHPVGIYSRVQGIISLLKGAKPDVGIVGIHGIAGIGKTTIAKAVFNKLYFGFEGS 240

Query: 200 CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPDIALSFRQLSRRKVLIVLDD 254
            FL +V+E S +P GL  LQ++LL  +L+  +     V   + L   +L R+K+L+V DD
Sbjct: 241 SFLLDVKEISDKPNGLVELQERLLHDILKPNVWKLSNVYEGMNLIKERLHRKKILVVFDD 300

Query: 255 VTCFRQIKSLIG-------------------MLRNCCVKEKYEMKELGDDHALELFSRHA 295
           V    Q+++L+G                   +L    V E Y  KEL  D +L+LFS HA
Sbjct: 301 VDKREQLEALMGERCWFGAGSIIIVVTKNKHLLAEVGVDEMYHAKELDRDQSLQLFSLHA 360

Query: 296 FKQNNPHIGFEELSSR 311
           F++ +P   +EELS +
Sbjct: 361 FRETHPAKNYEELSGK 376

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

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 =  234 bits (597), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 150/375 (40%), Positives = 217/375 (57%), Gaps = 76/375 (20%)

Query: 10  SPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAI 69
           +P +    KYDVF SFRGED RDNFT HLYSAL++K I TF+D ++ RG+EIS S+  AI
Sbjct: 2   APLATSEKKYDVFLSFRGEDTRDNFTSHLYSALNKKKIFTFMDKEIKRGEEISPSIAKAI 61

Query: 70  EASAISLIIFSEAYASSRWCLDELVKILT------------------------------- 98
           + S +S+IIFSE YA S+WCLDEL KIL                                
Sbjct: 62  KGSKLSVIIFSEKYAFSKWCLDELTKILECKKMNGQIVIPVFYRVDPVHVRNQRGSFACA 121

Query: 99  -RELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIR----------------LAEVSPC 141
             + EE  KE  EK+++WR+AL EA  +SG++S   R                L + SP 
Sbjct: 122 FAKHEETLKERMEKVESWRSALNEAGSISGWNSLVARPESKLIEEIVKDISKKLNQTSP- 180

Query: 142 SNKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCF 201
           S+   LVG++SR+E+IES+L  +  DV  +G+WG+GGI +TT+A AIF++IS+ +E S F
Sbjct: 181 SHSIGLVGIDSRLEQIESMLCLDMSDVRIIGVWGMGGIGKTTLAGAIFDQISAQYESSYF 240

Query: 202 LQNVREESQRPGGLGFLQQKLLSKLLQDGIV---IPDIALSFRQ--LSRRKVLIVLDDVT 256
           L NVRE+ +R   L  L++KL SK+L++  +    P++  +F +  LSR+K+L+VLDDV 
Sbjct: 241 LGNVREQLKR-CLLAELREKLFSKILEEKNLDTRTPNLGNTFLKDRLSRKKILVVLDDVD 299

Query: 257 CFRQIKSLIG--------------------MLRNCCVKEKYEMKELGDDHALELFSRHAF 296
              Q++ L+                     +L+N  V E Y+++ L    AL+LFS +AF
Sbjct: 300 STMQLQELLPGQHDLFGPGSRIIVTSRDKQVLKN-VVDEIYKVEGLNQHEALQLFSLNAF 358

Query: 297 KQNNPHIGFEELSSR 311
           K+N+P     E+S+R
Sbjct: 359 KKNSPTNDRVEISTR 373

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  234 bits (597), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 149/355 (41%), Positives = 200/355 (56%), Gaps = 73/355 (20%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED R NFT HL++AL+ K I TFIDD L RG+EIS SL+ AIE S IS++
Sbjct: 22  KYDVFLSFRGEDTRYNFTSHLHAALNGKKIPTFIDDDLERGNEISPSLLKAIEESKISVV 81

Query: 78  IFSEAYASSRWCLDELVKIL-------------------------TRELEEMFKEN---- 108
           I S+ Y SS+WCL+ELVKIL                         T   E++F  +    
Sbjct: 82  IISQDYPSSKWCLEELVKILECMKNRGQMVIPVFYRVDPSHVRNQTGSFEDVFARHEESL 141

Query: 109 ---SEKLQTWRNALKEAAGLSGFHSQNIR----------------LAEVSPCSNKNQLVG 149
               EK+Q+WR ALKE A LSG+HS + R                L ++SP      LVG
Sbjct: 142 SVSKEKVQSWRAALKEVANLSGWHSTSTRPEAEAVKEIIEVIVKKLNQMSPNCYSRGLVG 201

Query: 150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREES 209
           +ESR++EIESLL   S +V  +GIWG+GG+ +TT+ARAI+++I+  FE   FL N RE+ 
Sbjct: 202 MESRIQEIESLLCLRSSNVRIVGIWGMGGLGKTTLARAIYDRIAPQFEICYFLSNAREQL 261

Query: 210 QRPGGLGFLQQKLLSKLLQDGIVIPDIALSF--RQLSRRKVLIVLDDVTCFRQIKSLI-- 265
           QR   L  LQ +L S LL++   + ++  SF   +L R+KVLIV+DD     Q++ L+  
Sbjct: 262 QR-CTLSELQNQLFSTLLEEQSTL-NLQRSFIKDRLCRKKVLIVIDDADDSTQLQELLLE 319

Query: 266 -------------------GMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNP 301
                               +LRN    + Y M++L    AL+LFS  AFKQ+NP
Sbjct: 320 SEPDYFGSGSRIIITSRDKQVLRNIARDKIYAMQKLKKHEALQLFSLKAFKQDNP 374

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  234 bits (596), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 145/368 (39%), Positives = 207/368 (56%), Gaps = 77/368 (20%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED R  F  HLY+AL +K I TFID +LNRG+EIS SL+ AIE S +S++
Sbjct: 14  KYDVFLSFRGEDTRVCFVSHLYAALKRKQISTFIDYKLNRGEEISPSLLKAIEDSKLSVV 73

Query: 78  IFSEAYASSRWCLDELVKILT--------------------------------RELEEMF 105
           +FS+ YASS+WCL+EL KIL                                    +++ 
Sbjct: 74  VFSDNYASSKWCLEELAKILECKKVKGQMVIPVFYRVDPSHVRNQTGSFADAFARHDQLL 133

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQNIR----------------LAEVSPCSNKNQLVG 149
           KE  EK+  WR A++EAA LSG+ S NI+                L + S  ++   L+G
Sbjct: 134 KEKMEKVLNWRAAMREAANLSGWDSHNIKSESEFVDDIVRDILNKLHQTSMSTHHTSLIG 193

Query: 150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREES 209
           +++R++++E+LL  ES+DV  +GIWG+GGI +TTIA+A+++ +S+ FEG  F+ NVREE 
Sbjct: 194 IDARIKKVETLLKMESQDVRIVGIWGMGGIGKTTIAKAVYDNVSAQFEGFLFVANVREEI 253

Query: 210 QRPGGLGFLQQKLLSKLLQDGIVIPDIALSF------RQLSRRKVLIVLDDVTCFRQIKS 263
           +R   +G LQ+ +L +LL D  ++    LSF       +L R+KVLIVLDDV   RQ++ 
Sbjct: 254 KRHSVVG-LQKNILPELL-DQDILNTGPLSFGNAFVMDRLLRKKVLIVLDDVDSSRQLEE 311

Query: 264 LIG--------------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHI 303
           L+                     +L N  V E Y+++ L    AL+LF+  AFK  NP I
Sbjct: 312 LLPEPHVSFGPGSKILLTSRDKQVLTN-VVDEIYDVERLNHHEALQLFNMKAFKNYNPTI 370

Query: 304 GFEELSSR 311
              EL  +
Sbjct: 371 DHSELVEK 378

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493487|ref|XP_003634612.1| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  233 bits (595), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 152/362 (41%), Positives = 202/362 (55%), Gaps = 73/362 (20%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED R +FT HL++AL QKGI TF+DDQL RG++IS +L++AIE S  S+I
Sbjct: 21  KYDVFLSFRGEDTRKSFTDHLHTALCQKGINTFMDDQLRRGEQISPALLNAIEESRFSII 80

Query: 78  IFSEAYASSRWCLDELVKILT-------REL-------------------------EEMF 105
           IFS+ YASS WCLDELVKIL        R L                         E+ +
Sbjct: 81  IFSDNYASSSWCLDELVKILDCIKVMGHRALPVFYNLNPSHVKKQTGSFAEAFAKHEQEY 140

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQNI---------------RLAEVSPCSNKNQLVGV 150
           +E  EK+  WR AL E A +SG+ S++                +L   SP   K  LVG+
Sbjct: 141 REKMEKVVKWREALTEVATISGWDSRDRHESKLIEEIVRDIWNKLVGTSPSYMKG-LVGM 199

Query: 151 ESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQ 210
           ESR+E ++SLL   S DV  +GIWG+ GI +TTIA+ I+ +I + FEG CFL NVREES 
Sbjct: 200 ESRLEAMDSLLSMFSDDVRMVGIWGMAGIGKTTIAKVIYERIYTQFEGCCFLSNVREESY 259

Query: 211 RPGGLGFLQQKLLSKLLQD-----GIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLI 265
           +  GL +LQ +LLS++L++     G+    I      L  RKVLI+LDDV   +Q++ L 
Sbjct: 260 K-HGLPYLQMELLSQILKERKPNAGLFNKGINFMKDVLHSRKVLIILDDVDQRQQLEDLA 318

Query: 266 GM------------------LRNCC-VKEKYEMKELGDDHALELFSRHAFKQNNPHIGFE 306
           G                   L  C  V   YE+KEL +D AL+LF  +AF+  +    F 
Sbjct: 319 GYNNWFGLGSRIIITTRDRHLLTCQEVDAIYEVKELDNDEALKLFCLYAFRHRHGTEDFR 378

Query: 307 EL 308
           +L
Sbjct: 379 QL 380

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144414|ref|XP_002325282.1| tir-nbs-lrr resistance protein [Populus trichocarpa] gi|222862157|gb|EEE99663.1| tir-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  232 bits (592), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 150/367 (40%), Positives = 194/367 (52%), Gaps = 74/367 (20%)

Query: 19  YDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLI 77
           YDVF SFRGED R NFT HLY+AL   GI TF DD +L RG+EIS  L+ AIE S IS++
Sbjct: 1   YDVFLSFRGEDTRKNFTDHLYTALGNAGIHTFRDDNELPRGEEISPQLLKAIEGSRISIV 60

Query: 78  IFSEAYASSRWCLDELVKILT--------------------------------RELEEMF 105
           +FS+ YASSRWCLDELVKI+                                  E EE F
Sbjct: 61  VFSKHYASSRWCLDELVKIIECRQKIGQVVLPIFYDTEPSDVRKQTGSYAKAFDEHEERF 120

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQN----------IRLAEVSPCSNKNQL-------V 148
           KE  EK+  WR AL EA  LSG+   N           R+     C   N+        V
Sbjct: 121 KEEMEKVNKWRGALAEAGNLSGWGLHNEANGYEAEFIKRIVSDVACKLGNKTLHVAKHPV 180

Query: 149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREE 208
           G+ SRV+ I SLL     DV  +GI GI GI +TTIA+A+FNK+   FEGS FL +V+E 
Sbjct: 181 GIYSRVQGIISLLKGAKPDVGIVGIHGIAGIGKTTIAKAVFNKLYFGFEGSSFLSDVKEI 240

Query: 209 SQRPGGLGFLQQKLLSKLLQDGI-----VIPDIALSFRQLSRRKVLIVLDDVTCFRQIKS 263
           S +P GL  LQ++LL  +L+  +     V   + L   +L R+K+L+V DDV    Q+++
Sbjct: 241 SDKPNGLVELQERLLHDILKPRVWKVSNVYEGMNLIKERLHRKKILVVFDDVDKREQLEA 300

Query: 264 LIG-------------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNPHIG 304
           L+G                   +L    V   Y  KEL  D +LELFS HAF++ +P   
Sbjct: 301 LMGERCWFGAGSIIIVVTKNKHLLTEVGVDGMYHAKELDRDQSLELFSLHAFRETHPAKD 360

Query: 305 FEELSSR 311
           +EELS +
Sbjct: 361 YEELSGK 367

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569048|ref|XP_002525493.1| leucine-rich repeat-containing protein, putative [Ricinus communis] gi|223535172|gb|EEF36851.1| leucine-rich repeat-containing protein, putative [Ricinus communis]

 Score =  232 bits (591), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 152/359 (42%), Positives = 207/359 (57%), Gaps = 72/359 (20%)

Query: 9   SSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDA 68
           SS +SP+  K+DVF SFRG+D RDNFT HLY AL +K I+TFID+ L RG+EI+ +L+  
Sbjct: 3   SSSNSPK-RKFDVFLSFRGKDTRDNFTSHLYDALCRKKIKTFIDNGLERGEEITPALLRT 61

Query: 69  IEASAISLIIFSEAYASSRWCLDELVKIL-TRE--------------------------- 100
           IE S IS+I+FSE YASS WCLDE+VKIL  RE                           
Sbjct: 62  IEESLISVIVFSENYASSPWCLDEMVKILECRETHGQAVLPVFYHVDPSDVEEQNGSFAL 121

Query: 101 -LEEMFKENSEKLQTWRNALKEAAGLSGFHSQNI----------------RLAEVSPCSN 143
            L E+ K   +K+  WR  L +AA +SG+ S+ I                +L + S    
Sbjct: 122 TLVELEKNFKDKVSKWRTDLMKAASISGWDSRAIGSEAKLVKHIVEHILQKLNKASSTDL 181

Query: 144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ 203
           K  L+G++S + +I+ LL     D+  +G+WG+ GI +TTIA AIFN +SS FEG CFL+
Sbjct: 182 KG-LIGLDSHIRKIKKLLQIGLPDIRTVGLWGMSGIGKTTIAGAIFNTLSSQFEGCCFLE 240

Query: 204 NVREESQRPGGLGFLQQKLLSKLLQDG---IVIPDIALSF--RQLSRRKVLIVLDDVTCF 258
           N++EES+R  GL  L+ KLLS++L +G   I  P I  +    +L  +KVL+VLDDV   
Sbjct: 241 NIKEESER-CGLVPLRDKLLSEILMEGNVHIATPSIGSTSLKNRLRHKKVLLVLDDVNDV 299

Query: 259 RQIKSLIG------------------MLRNCCVKEKYEMKELGDDHALELFSRHAFKQN 299
            QI++LIG                  +L+N  V E YE++ L DD AL+LF+ HAFK N
Sbjct: 300 DQIETLIGRCDFGLGSRVLVTSRDKQVLKN-VVDEIYEVEGLSDDEALQLFNLHAFKDN 357

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493483|ref|XP_003634610.1| PREDICTED: TMV resistance protein N-like, partial [Vitis vinifera]

 Score =  231 bits (590), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 151/362 (41%), Positives = 200/362 (55%), Gaps = 73/362 (20%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED R +FT HL++AL QKGI TF+DDQL RG+++S +L++AIE S  S+I
Sbjct: 15  KYDVFLSFRGEDTRKSFTDHLHTALCQKGINTFMDDQLRRGEQVSPALLNAIEESRFSII 74

Query: 78  IFSEAYASSRWCLDELVKIL-------------------------TRELEEMF------- 105
           IFS+ YASS WCLDELVKIL                         T    E F       
Sbjct: 75  IFSDNYASSSWCLDELVKILDCIKVMGHRALPVFYNVNPSHVKKQTGSFAEAFAKHEQEN 134

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQNI---------------RLAEVSPCSNKNQLVGV 150
           +E  EK+  WR AL E A +SG+ S++                +L   SP   K  LVG+
Sbjct: 135 REKMEKVVKWREALTEVATISGWDSRDRHESKLIEEIVRDIWNKLVGTSPSYMKG-LVGM 193

Query: 151 ESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQ 210
           ESR+E ++SLL   S DV  +GIWG+ GI +TTIA+ I+ +I + FEG CFL NVREES 
Sbjct: 194 ESRLEAMDSLLCIGSLDVRMVGIWGMAGIGKTTIAKVIYERIYTQFEGCCFLSNVREESY 253

Query: 211 RPGGLGFLQQKLLSKLLQD-----GIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLI 265
           +  GL +LQ +LLS++L++     G+    I      L  RKVLI+LDDV   +Q++ L 
Sbjct: 254 K-HGLPYLQMELLSQILKERNPNAGLFNKGINFMKDVLHSRKVLIILDDVDQRKQLEDLA 312

Query: 266 G------------------MLRNCC-VKEKYEMKELGDDHALELFSRHAFKQNNPHIGFE 306
           G                   L  C  V   YE+KEL +D AL+LF  +AF+  +    F 
Sbjct: 313 GDNNWFGSGSRIIITTRDRHLLTCQEVDAIYEVKELDNDEALKLFCLYAFRHKHGTEDFR 372

Query: 307 EL 308
           +L
Sbjct: 373 QL 374

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|451798990|gb|AGF69193.1| TMV resistance protein N-like protein 7 [Vitis labrusca]

 Score =  231 bits (589), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 151/362 (41%), Positives = 200/362 (55%), Gaps = 73/362 (20%)

Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
           KYDVF SFRGED R +FT HL++AL QKGI TF+DDQL RG+++S +L++AIE S  S+I
Sbjct: 15  KYDVFLSFRGEDTRKSFTDHLHTALCQKGINTFMDDQLRRGEQVSPALLNAIEESRFSII 74

Query: 78  IFSEAYASSRWCLDELVKIL-------------------------TRELEEMF------- 105
           IFS+ YASS WCLDELVKIL                         T    E F       
Sbjct: 75  IFSDNYASSSWCLDELVKILDCIKVMGHRALPVFYNVNPSHVKKQTGSFAEAFAKHEQEN 134

Query: 106 KENSEKLQTWRNALKEAAGLSGFHSQNI---------------RLAEVSPCSNKNQLVGV 150
           +E  EK+  WR AL E A +SG+ S++                +L   SP   K  LVG+
Sbjct: 135 REKMEKVVKWREALTEVATISGWDSRDRHESKLIEEIVRDIWNKLVGTSPSYMKG-LVGM 193

Query: 151 ESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQ 210
           ESR+E ++SLL   S DV  +GIWG+ GI +TTIA+ I+ +I + FEG CFL NVREES 
Sbjct: 194 ESRLEAMDSLLCIGSLDVRMVGIWGMAGIGKTTIAKVIYERIYTQFEGCCFLSNVREESY 253

Query: 211 RPGGLGFLQQKLLSKLLQD-----GIVIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLI 265
           +  GL +LQ +LLS++L++     G+    I      L  RKVLI+LDDV   +Q++ L 
Sbjct: 254 K-HGLPYLQMELLSQILKERNPNAGLFNKGINFMKDVLHSRKVLIILDDVDQRKQLEDLA 312

Query: 266 G------------------MLRNCC-VKEKYEMKELGDDHALELFSRHAFKQNNPHIGFE 306
           G                   L  C  V   YE+KEL +D AL+LF  +AF+  +    F 
Sbjct: 313 GDNNWFGSGSRIIITTRDRHLLTCQEVDAIYEVKELDNDEALKLFCLYAFRHKHGTEDFR 372

Query: 307 EL 308
           +L
Sbjct: 373 QL 374

Source: Vitis labrusca

Species: Vitis labrusca

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	311
TAIR|locus:2118106	1219	AT4G12010 [Arabidopsis thalian	0.254	0.064	0.6	1.9e-41
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.279	0.076	0.555	6.4e-41
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.286	0.081	0.516	9.2e-41
TAIR|locus:2167457	1191	AT5G36930 [Arabidopsis thalian	0.254	0.066	0.562	1.7e-40
TAIR|locus:2205824	1384	AT1G27170 [Arabidopsis thalian	0.250	0.056	0.562	6.3e-40
TAIR|locus:2175075	1068	AT5G41750 [Arabidopsis thalian	0.257	0.074	0.475	9.6e-38
TAIR|locus:2175991	1294	AT5G17680 [Arabidopsis thalian	0.257	0.061	0.506	5.8e-37
TAIR|locus:2076043	1194	RPP1 "recognition of peronospo	0.266	0.069	0.469	7.9e-37
TAIR|locus:2032602	1163	AT1G72860 [Arabidopsis thalian	0.286	0.076	0.511	3.6e-36
TAIR|locus:2174920	1017	AT5G40100 [Arabidopsis thalian	0.282	0.086	0.505	2.3e-35

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

 Score = 244 (91.0 bits), Expect = 1.9e-41, Sum P(3) = 1.9e-41
 Identities = 48/80 (60%), Positives = 62/80 (77%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
             ++DVF SFRG D R+NFTGHL  AL  +GI++FIDD+L RGD ++ +L D IE S I++I
Sbjct:    10 EFDVFLSFRGFDTRNNFTGHLQKALRLRGIDSFIDDRLRRGDNLT-ALFDRIEKSKIAII 68

Query:    78 IFSEAYASSRWCLDELVKIL 97
             +FS  YA+S WCL ELVKIL
Sbjct:    69 VFSTNYANSAWCLRELVKIL 88

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

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

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

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

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

 Score = 240 (89.5 bits), Expect = 6.4e-41, Sum P(3) = 6.4e-41
 Identities = 50/90 (55%), Positives = 62/90 (68%)

Query:    19 YDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEASAISLI 77
             YDVF SFRGED R  FT HLY  L+ KGI+TF DD+ L  G  I   L  AIE S  +++
Sbjct:    12 YDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKAIEESQFAIV 71

Query:    78 IFSEAYASSRWCLDELVKILTRELEEMFKE 107
             +FSE YA+SRWCL+ELVKI+  E +  FK+
Sbjct:    72 VFSENYATSRWCLNELVKIM--ECKTRFKQ 99

GO:0005515 "protein binding" evidence=IPI

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

 Score = 228 (85.3 bits), Expect = 9.2e-41, Sum P(3) = 9.2e-41
 Identities = 46/89 (51%), Positives = 57/89 (64%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
             +YDVF SFRGED R+NF  HL      KGI TF DD + R   I   L  AI  S IS++
Sbjct:    10 RYDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDHIKRSHTIGHELRAAIRESKISVV 69

Query:    78 IFSEAYASSRWCLDELVKILTRELEEMFK 106
             +FSE YASS WCLDEL++I+  + E+  K
Sbjct:    70 LFSENYASSSWCLDELIEIMKCKEEQGLK 98

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:2167457 AT5G36930 [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 1.7e-40, Sum P(3) = 1.7e-40
 Identities = 45/80 (56%), Positives = 58/80 (72%)

Query:    19 YDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLI 77
             YDVF SFRG D R NF  HLY +L + GI TF+DD +L RG+ IS  L++AIE S I ++
Sbjct:    17 YDVFVSFRGADVRKNFLSHLYDSLRRCGISTFMDDVELQRGEYISPELLNAIETSKILIV 76

Query:    78 IFSEAYASSRWCLDELVKIL 97
             + ++ YASS WCLDELV I+
Sbjct:    77 VLTKDYASSAWCLDELVHIM 96

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:2205824 AT1G27170 [Arabidopsis thaliana (taxid:3702)]

 Score = 219 (82.2 bits), Expect = 6.3e-40, Sum P(3) = 6.3e-40
 Identities = 45/80 (56%), Positives = 54/80 (67%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEASAISL 76
             KYDVF SFRG D RDNF  HLY AL  K +  F D++ + RGDEIS SL   +E SA S+
Sbjct:    13 KYDVFLSFRGADTRDNFGDHLYKALKDK-VRVFRDNEGMERGDEISSSLKAGMEDSAASV 71

Query:    77 IIFSEAYASSRWCLDELVKI 96
             I+ S  Y+ SRWCLDEL  +
Sbjct:    72 IVISRNYSGSRWCLDELAML 91

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 209 (78.6 bits), Expect = 9.6e-38, Sum P(3) = 9.6e-38
 Identities = 38/80 (47%), Positives = 52/80 (65%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLI 77
             +Y VF SF G D R  F  HL+S  + KGI TF D +++RG  I   L+  I  + +S++
Sbjct:    12 RYQVFSSFHGPDVRKGFLSHLHSVFASKGITTFNDQKIDRGQTIGPELIQGIREARVSIV 71

Query:    78 IFSEAYASSRWCLDELVKIL 97
             + S+ YASS WCLDELV+IL
Sbjct:    72 VLSKKYASSSWCLDELVEIL 91

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2175991 AT5G17680 [Arabidopsis thaliana (taxid:3702)]

 Score = 208 (78.3 bits), Expect = 5.8e-37, Sum P(4) = 5.8e-37
 Identities = 41/81 (50%), Positives = 53/81 (65%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISL 76
             K DVF SFRGED R  F  HL+    + GI+ F DD  L RG  IS  L+DAI+ S  ++
Sbjct:    17 KTDVFVSFRGEDVRKTFVSHLFCEFDRMGIKAFRDDLDLQRGKSISPELIDAIKGSRFAI 76

Query:    77 IIFSEAYASSRWCLDELVKIL 97
             ++ S  YA+S WCLDEL+KI+
Sbjct:    77 VVVSRNYAASSWCLDELLKIM 97

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2076043 RPP1 "recognition of peronospora parasitica 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 7.9e-37, Sum P(3) = 7.9e-37
 Identities = 39/83 (46%), Positives = 54/83 (65%)

Query:    15 RNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAI 74
             RN K+DVF SF G D R  F  H+  +  +KGI+TFID+ + R   I   L +AI+ S I
Sbjct:    94 RNWKHDVFPSFHGADVRRTFLSHIMESFRRKGIDTFIDNNIERSKSIGPELKEAIKGSKI 153

Query:    75 SLIIFSEAYASSRWCLDELVKIL 97
             ++++ S  YASS WCLDEL +I+
Sbjct:   154 AIVLLSRKYASSSWCLDELAEIM 176

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0002239 "response to oomycetes" evidence=IDA

GO:0000139 "Golgi membrane" evidence=IDA

GO:0005789 "endoplasmic reticulum membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0030275 "LRR domain binding" evidence=ISS

TAIR|locus:2032602 AT1G72860 [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 3.6e-36, Sum P(3) = 3.6e-36
 Identities = 46/90 (51%), Positives = 57/90 (63%)

Query:    18 KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEASAISL 76
             KYDVF SFRGED R N   HL+  L  KG+ TF DD+ L  GD IS+ +  AI+ S  +L
Sbjct:    11 KYDVFLSFRGEDTRKNIVSHLHKQLVDKGVVTFKDDKKLELGDSISEEISRAIQNSTYAL 70

Query:    77 IIFSEAYASSRWCLDELVKILTRELEEMFK 106
             +I SE YASS WCLDEL  ++   L+   K
Sbjct:    71 VILSENYASSSWCLDELRMVMDLHLKNKIK 100

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:2174920 AT5G40100 [Arabidopsis thaliana (taxid:3702)]

 Score = 218 (81.8 bits), Expect = 2.3e-35, Sum P(3) = 2.3e-35
 Identities = 45/89 (50%), Positives = 57/89 (64%)

Query:    15 RNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEASA 73
             R   YDVF SFRGED R +   HLY AL+ +GI TF DD+ L  GD IS+ L  AIE S 
Sbjct:     8 RASSYDVFLSFRGEDTRHSIVSHLYEALTSRGIATFKDDKRLELGDHISEELQRAIEGSD 67

Query:    74 ISLIIFSEAYASSRWCLDELVKILTRELE 102
               +++ SE Y +SRWCL EL  I+  ++E
Sbjct:    68 FVVVVLSENYPTSRWCLMELQSIMELQME 96

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

---

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

Your Input: gw1.XIX.314.1 annotation not avaliable (532 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	311
PLN03210	1153	PLN03210, PLN03210, Resistant to P	3e-50
smart00255	140	smart00255, TIR, Toll - interleukin 1 - resistance	9e-22
pfam01582	135	pfam01582, TIR, TIR domain	1e-21
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	1e-14
pfam13676	102	pfam13676, TIR_2, TIR domain	4e-10
PLN03194	187	PLN03194, PLN03194, putative disease resistance pr	5e-08

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

 Score =  178 bits (453), Expect = 3e-50
 Identities = 121/378 (32%), Positives = 179/378 (47%), Gaps = 77/378 (20%)

Query: 9   SSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDA 68
           SS SS RN  YDVF SF GED R  F  H    L +K I  F D+++ R   +   L  A
Sbjct: 3   SSSSSSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQA 62

Query: 69  IEASAISLIIFSEAYASSRWCLDELVKIL-------------------------TRELEE 103
           I  S I++++FS+ YASS WCL+EL++I+                         T +  E
Sbjct: 63  IRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGE 122

Query: 104 MF------KENSEKLQTWRNALKEAAGLSGFHSQN----IRLAE-----------VSPCS 142
            F      K   EK+Q W+ AL + A + G+HSQN     ++ E           ++P +
Sbjct: 123 AFEKTCQNKTEDEKIQ-WKQALTDVANILGYHSQNWPNEAKMIEEIANDVLGKLNLTPSN 181

Query: 143 NKNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL 202
           +    VG+E  + ++ SLL  ES++V  +GIWG  GI +TTIARA+F+++S  F+ S F+
Sbjct: 182 DFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFI 241

Query: 203 QNVREESQRPGGLG----------FLQQKLLSKLL-QDGIVIPDIALSFRQLSRRKVLIV 251
                                    LQ+  LS++L +  I I  +     +L  RKVLI 
Sbjct: 242 DRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIF 301

Query: 252 LDDVTCFRQIKSLIG-------------------MLRNCCVKEKYEMKELGDDHALELFS 292
           +DD+     + +L G                    LR   +   YE+    ++ ALE+F 
Sbjct: 302 IDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFC 361

Query: 293 RHAFKQNNPHIGFEELSS 310
           R AFK+N+P  GF EL+S
Sbjct: 362 RSAFKKNSPPDGFMELAS 379

syringae 6; Provisional. Length = 1153

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

 Score = 88.9 bits (221), Expect = 9e-22
 Identities = 39/87 (44%), Positives = 50/87 (57%), Gaps = 2/87 (2%)

Query: 18  KYDVFQSFRG-EDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISL 76
           +YDVF S+ G ED R+ F  HL   L   G+  FIDD    G    + + +AIE S I++
Sbjct: 1   EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFE-PGGGDLEEIDEAIEKSRIAI 59

Query: 77  IIFSEAYASSRWCLDELVKILTRELEE 103
           ++ S  YA S WCLDELV  L   LEE
Sbjct: 60  VVLSPNYAESEWCLDELVAALENALEE 86

Length = 140

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

 Score = 88.1 bits (219), Expect = 1e-21
 Identities = 42/84 (50%), Positives = 55/84 (65%), Gaps = 1/84 (1%)

Query: 21  VFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIF 79
           VF SF G+D+RD F  HL   L +KGI+  IDD     G+ I ++L +AIE S  +++IF
Sbjct: 1   VFVSFSGKDDRDTFVSHLLKELEEKGIKLCIDDRDELPGESILENLFEAIEKSRRAIVIF 60

Query: 80  SEAYASSRWCLDELVKILTRELEE 103
           S  YASS WCLDELV+I+   LE 
Sbjct: 61  SSNYASSEWCLDELVEIVKCALEG 84

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|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 72.4 bits (178), Expect = 1e-14
 Identities = 42/188 (22%), Positives = 80/188 (42%), Gaps = 34/188 (18%)

Query: 150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISSNFEGSCFLQNVRE 207
            E  +E +   L   S ++  +GI G+GG+ +TT+A+ I+N   +  +F+   ++   + 
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 208 ESQRPGGLGFLQQKLLSKLLQDGIVIPDIALS------FRQLSRRKVLIVLDDV------ 255
            ++       LQ+ +L +L  D     +   S         L R++ L+VLDDV      
Sbjct: 61  YTEFR-----LQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDW 115

Query: 256 ----TCF--RQIKSLIGM--------LRNCCVKEKYEMKELGDDHALELFSRHAFKQNNP 301
                 F   +  S + +         R     + +E++ L  + + ELFS   F++  P
Sbjct: 116 DKIGVPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELP 175

Query: 302 -HIGFEEL 308
                EE+
Sbjct: 176 PCPELEEV 183

Length = 285

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 21 VFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFS 80
          VF S+   D    +   L  AL   GI  ++D  +  G++    + +A+ ++ + L++ S
Sbjct: 1  VFISYASADRE--WAEWLADALEAAGIRVWLDWDIPPGEDWRDEIEEALRSADVVLVLLS 58

Query: 81 EAYASSRWCLDEL 93
           AY +S WC  E 
Sbjct: 59 PAYLASPWCRAEW 71

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

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

 Score = 51.7 bits (124), Expect = 5e-08
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 8   PSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLV 66
           PSS SS +    DVF + RG D +      LY  LS+  +  F+D++ +  GD++   + 
Sbjct: 18  PSSSSSAKPC--DVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKIN 75

Query: 67  DAIEASAISLIIFSEAYASSRWCLDELVKIL 97
            AI    + + +FS  Y  S +CL EL  I+
Sbjct: 76  SAIRNCKVGVAVFSPRYCESYFCLHELALIM 106

Length = 187

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	311
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PLN03194	187	putative disease resistance protein; Provisional	100.0
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.92
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.9
PF01582	141	TIR: TIR domain; InterPro: IPR000157 In Drosophila	99.67
smart00255	140	TIR Toll - interleukin 1 - resistance.	99.63
PF13676	102	TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_	99.47
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.98
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.94
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.88
PF05729	166	NACHT: NACHT domain	98.81
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.68
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.62
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.59
PRK13342	413	recombination factor protein RarA; Reviewed	98.58
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.54
KOG2028	554	consensus ATPase related to the helicase subunit o	98.52
cd01128	249	rho_factor Transcription termination factor rho is	98.5
PRK09376	416	rho transcription termination factor Rho; Provisio	98.5
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.45
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.45
PTZ00202	550	tuzin; Provisional	98.39
PRK13341	725	recombination factor protein RarA/unknown domain f	98.37
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.37
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.34
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.33
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.31
TIGR00767	415	rho transcription termination factor Rho. Members	98.3
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.28
PRK06893	229	DNA replication initiation factor; Validated	98.25
KOG3678	832	consensus SARM protein (with sterile alpha and arm	98.25
PF13173	128	AAA_14: AAA domain	98.21
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.1
PRK08727	233	hypothetical protein; Validated	98.09
PRK04195	482	replication factor C large subunit; Provisional	98.09
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.09
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.07
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.04
PRK04841	903	transcriptional regulator MalT; Provisional	98.04
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.03
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.03
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.01
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.96
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.94
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.94
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.93
PLN03025	319	replication factor C subunit; Provisional	97.92
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.89
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.87
PRK05642	234	DNA replication initiation factor; Validated	97.87
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.85
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.81
PRK12402	337	replication factor C small subunit 2; Reviewed	97.81
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.8
PF00004	132	AAA: ATPase family associated with various cellula	97.8
PF08937	130	DUF1863: MTH538 TIR-like domain (DUF1863); InterPr	97.79
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.79
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.77
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.77
smart00382	148	AAA ATPases associated with a variety of cellular	97.76
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.75
PHA00729	226	NTP-binding motif containing protein	97.75
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.74
PRK10865	857	protein disaggregation chaperone; Provisional	97.74
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.74
PRK08118	167	topology modulation protein; Reviewed	97.71
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.7
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.67
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.66
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.65
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.65
CHL00095	821	clpC Clp protease ATP binding subunit	97.63
PRK08084	235	DNA replication initiation factor; Provisional	97.63
PRK09087	226	hypothetical protein; Validated	97.62
PRK12377	248	putative replication protein; Provisional	97.62
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.62
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.6
PF08357	150	SEFIR: SEFIR domain; InterPro: IPR013568 This doma	97.6
CHL00176	638	ftsH cell division protein; Validated	97.59
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.58
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.57
PRK08116	268	hypothetical protein; Validated	97.57
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.56
PRK07261	171	topology modulation protein; Provisional	97.56
PRK12422	445	chromosomal replication initiation protein; Provis	97.55
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.53
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.52
PRK07952	244	DNA replication protein DnaC; Validated	97.52
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.52
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.52
PHA02544	316	44 clamp loader, small subunit; Provisional	97.51
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.49
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.48
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.47
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.47
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.47
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.47
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.45
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.45
PRK12608	380	transcription termination factor Rho; Provisional	97.44
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.44
COG3903	414	Predicted ATPase [General function prediction only	97.43
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.42
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.42
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.41
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK06696	223	uridine kinase; Validated	97.36
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.36
PRK06620	214	hypothetical protein; Validated	97.34
CHL00181	287	cbbX CbbX; Provisional	97.33
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.31
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.3
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.3
PRK07667	193	uridine kinase; Provisional	97.29
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.29
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.28
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.27
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.27
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.26
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.25
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.24
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.22
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.2
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.18
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.17
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.16
PRK06921	266	hypothetical protein; Provisional	97.15
PRK06835	329	DNA replication protein DnaC; Validated	97.15
PRK08181	269	transposase; Validated	97.15
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.12
COG3899	849	Predicted ATPase [General function prediction only	97.11
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.11
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.1
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.08
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.08
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.07
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.07
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.07
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.06
PRK05541	176	adenylylsulfate kinase; Provisional	97.06
PRK09183	259	transposase/IS protein; Provisional	97.06
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.05
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.05
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.05
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.03
PRK06526	254	transposase; Provisional	97.02
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.02
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.99
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.99
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.98
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.97
CHL00095	821	clpC Clp protease ATP binding subunit	96.96
PRK10865	857	protein disaggregation chaperone; Provisional	96.94
PRK06217	183	hypothetical protein; Validated	96.94
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.94
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.93
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.92
CHL00195	489	ycf46 Ycf46; Provisional	96.89
PRK08939	306	primosomal protein DnaI; Reviewed	96.89
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.88
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.88
PRK05480	209	uridine/cytidine kinase; Provisional	96.87
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.83
PRK08233	182	hypothetical protein; Provisional	96.82
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.82
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK03839	180	putative kinase; Provisional	96.81
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.81
PRK06762	166	hypothetical protein; Provisional	96.81
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.77
PTZ00301	210	uridine kinase; Provisional	96.76
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.75
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.74
PRK00131	175	aroK shikimate kinase; Reviewed	96.74
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.74
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.72
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.72
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.71
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.71
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.7
PRK04040	188	adenylate kinase; Provisional	96.69
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.69
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.69
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.68
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.68
PRK15455	644	PrkA family serine protein kinase; Provisional	96.67
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.66
PRK00625	173	shikimate kinase; Provisional	96.66
PRK09354	349	recA recombinase A; Provisional	96.62
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.62
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.61
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.61
PRK13947	171	shikimate kinase; Provisional	96.6
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.6
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.59
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.58
PF14516	331	AAA_35: AAA-like domain	96.57
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.56
PF07726	131	AAA_3: ATPase family associated with various cellu	96.55
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.55
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.54
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.54
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.53
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.53
PRK06547	172	hypothetical protein; Provisional	96.51
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.51
PRK08356	195	hypothetical protein; Provisional	96.5
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.49
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.47
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.46
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.46
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.43
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.43
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	96.43
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.41
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.4
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.36
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.36
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.33
PRK03846	198	adenylylsulfate kinase; Provisional	96.33
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.33
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	96.32
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.32
PRK00889	175	adenylylsulfate kinase; Provisional	96.32
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.32
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.3
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.29
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.28
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	96.27
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.26
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.26
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.25
PRK13946	184	shikimate kinase; Provisional	96.25
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.24
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.24
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.23
PRK13949	169	shikimate kinase; Provisional	96.23
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.22
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.2
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	96.2
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.2
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	96.18
PRK08149	428	ATP synthase SpaL; Validated	96.16
PRK13531	498	regulatory ATPase RavA; Provisional	96.16
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.15
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	96.15
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.15
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.12
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.11
PRK11823	446	DNA repair protein RadA; Provisional	96.1
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.1
PRK13948	182	shikimate kinase; Provisional	96.08
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.07
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.06
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.06
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.05
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.04
PRK04182	180	cytidylate kinase; Provisional	96.04
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.02
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	96.02
PRK13975	196	thymidylate kinase; Provisional	96.0
PTZ00035	337	Rad51 protein; Provisional	96.0
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.98
PRK05057	172	aroK shikimate kinase I; Reviewed	95.98
PRK14974	336	cell division protein FtsY; Provisional	95.96
PRK06936	439	type III secretion system ATPase; Provisional	95.95
PRK03731	171	aroL shikimate kinase II; Reviewed	95.95
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	95.93
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.93
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.92
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.91
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.9
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.9
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.89
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.88
PRK14530	215	adenylate kinase; Provisional	95.88
PRK05922	434	type III secretion system ATPase; Validated	95.88
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.88
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	95.88
PRK13765	637	ATP-dependent protease Lon; Provisional	95.88
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	95.87
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.87
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.87
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.86
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.85
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.85
PLN02318	656	phosphoribulokinase/uridine kinase	95.85
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.85
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.85
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.83
PTZ00088	229	adenylate kinase 1; Provisional	95.83
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	95.82
PRK14738	206	gmk guanylate kinase; Provisional	95.81
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.81
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.8
PRK05439	311	pantothenate kinase; Provisional	95.8
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.8
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.8
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.79
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.78
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.78
PRK00300	205	gmk guanylate kinase; Provisional	95.76
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	95.76
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.76
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.74
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	95.74
PRK12678	672	transcription termination factor Rho; Provisional	95.73
KOG1514	767	consensus Origin recognition complex, subunit 1, a	95.72
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.7
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.7
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.69
PRK04296	190	thymidine kinase; Provisional	95.68
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.67
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.66
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	95.65
PRK15453	290	phosphoribulokinase; Provisional	95.64
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.64
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.62
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.62
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	95.62
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.62
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.62
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.6
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.59
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.55
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.54
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.53
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.53
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	95.53
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.51
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.5
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.49
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.49
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	95.47
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	95.45
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	95.45
PLN02924	220	thymidylate kinase	95.44
PRK13768	253	GTPase; Provisional	95.44
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.41
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.41
PRK13695	174	putative NTPase; Provisional	95.41
PLN02200	234	adenylate kinase family protein	95.4
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.39
PRK10867	433	signal recognition particle protein; Provisional	95.38
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.38
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.37
PRK06761	282	hypothetical protein; Provisional	95.37
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.37
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	95.36
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.36
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.36
PLN02348	395	phosphoribulokinase	95.35
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.35
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	95.34
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.34
PRK14527	191	adenylate kinase; Provisional	95.31
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.31
PRK09825	176	idnK D-gluconate kinase; Provisional	95.31
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.3
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.29
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.28
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.28
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.27
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	95.27
PRK01184	184	hypothetical protein; Provisional	95.25
PRK06067	234	flagellar accessory protein FlaH; Validated	95.25
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.24
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.23
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.23
PRK10416	318	signal recognition particle-docking protein FtsY;	95.23
CHL00060	494	atpB ATP synthase CF1 beta subunit	95.23
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.22
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	95.21
PRK14532	188	adenylate kinase; Provisional	95.2
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.19
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.19
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	95.19
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	95.18
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.17
PRK07594	433	type III secretion system ATPase SsaN; Validated	95.17
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.16
cd02034	116	CooC The accessory protein CooC, which contains a	95.16
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	95.15
cd02117	212	NifH_like This family contains the NifH (iron prot	95.14
COG1100	219	GTPase SAR1 and related small G proteins [General	95.14
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.12
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.12
CHL00059	485	atpA ATP synthase CF1 alpha subunit	95.1
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	95.08
PHA02530	300	pseT polynucleotide kinase; Provisional	95.08
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.07
PF10137	125	TIR-like: Predicted nucleotide-binding protein con	95.06
PRK14531	183	adenylate kinase; Provisional	95.06
PRK08099	399	bifunctional DNA-binding transcriptional repressor	95.06
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	95.04
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	95.04
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.03
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.03
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.02
PF00005	137	ABC_tran: ABC transporter This structure is on hol	95.02
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.01
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.0
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	94.99
PRK14737	186	gmk guanylate kinase; Provisional	94.98
cd03116	159	MobB Molybdenum is an essential trace element in t	94.97
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	94.97
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	94.95
PLN02796	347	D-glycerate 3-kinase	94.94
COG0714	329	MoxR-like ATPases [General function prediction onl	94.94
PHA02244	383	ATPase-like protein	94.94
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	94.94
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	94.93
) 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	94.92
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	94.91
PRK11608	326	pspF phage shock protein operon transcriptional ac	94.9
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	94.9
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	94.89
PRK00698	205	tmk thymidylate kinase; Validated	94.89
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	94.89
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	94.88
PRK12338	319	hypothetical protein; Provisional	94.86
PRK13230	279	nitrogenase reductase-like protein; Reviewed	94.85
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.85
TIGR00017	217	cmk cytidylate kinase. This family consists of cyt	94.85
PRK14490	369	putative bifunctional molybdopterin-guanine dinucl	94.84
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.84
TIGR02236	310	recomb_radA DNA repair and recombination protein R	94.82
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	94.81
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	94.8
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.78
cd03114	148	ArgK-like The function of this protein family is u	94.78
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	94.78
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.77
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.76
PRK14529	223	adenylate kinase; Provisional	94.76
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	94.76
PRK06820	440	type III secretion system ATPase; Validated	94.74
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	94.74
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	94.74
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	94.73
cd02040	270	NifH NifH gene encodes component II (iron protein)	94.73
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.71
PRK09099	441	type III secretion system ATPase; Provisional	94.71
PRK02496	184	adk adenylate kinase; Provisional	94.7
PF13614	157	AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ	94.69
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.69
TIGR01663	526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	94.69
PRK13232	273	nifH nitrogenase reductase; Reviewed	94.68
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	94.68
PF00142	273	Fer4_NifH: 4Fe-4S iron sulfur cluster binding prot	94.67
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	94.66
PRK00279	215	adk adenylate kinase; Reviewed	94.64
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	94.64
PLN02165	334	adenylate isopentenyltransferase	94.63
PRK04196	460	V-type ATP synthase subunit B; Provisional	94.63
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	94.61
PRK10536	262	hypothetical protein; Provisional	94.61
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.59
PRK07429	327	phosphoribulokinase; Provisional	94.58
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	94.58
PTZ00185	574	ATPase alpha subunit; Provisional	94.58
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	94.57
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	94.57
PRK14730	195	coaE dephospho-CoA kinase; Provisional	94.56
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	94.56
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	94.56
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.55
TIGR00959	428	ffh signal recognition particle protein. This mode	94.55
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	94.54
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	94.54
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	94.53
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	94.53
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.52
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	94.52
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.52
TIGR00101	199	ureG urease accessory protein UreG. This model rep	94.52
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.51
KOG0736	953	consensus Peroxisome assembly factor 2 containing	94.49
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	94.48
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	94.48
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	94.46
PRK13233	275	nifH nitrogenase reductase; Reviewed	94.44
PRK02118	436	V-type ATP synthase subunit B; Provisional	94.44
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	94.44
cd03269	210	ABC_putative_ATPase This subfamily is involved in	94.43
PRK07165	507	F0F1 ATP synthase subunit alpha; Validated	94.43
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	94.42
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	94.41
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	94.39
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.38
PRK14528	186	adenylate kinase; Provisional	94.38
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	94.38
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	94.37
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	94.37
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	94.37
PRK04220	301	2-phosphoglycerate kinase; Provisional	94.36

>PLN03210 Resistant to P

Probab=100.00  E-value=6.7e-63  Score=520.99  Aligned_cols=296  Identities=37%  Similarity=0.602  Sum_probs=257.2

Q ss_pred             CCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeCCCCCCCcchHHHHHHHHhccceeeeeccCcccccchHHHHH
Q 042778           15 RNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELV   94 (311)
Q Consensus        15 ~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~   94 (311)
                      +.++|||||||||+|+|++|++||+++|.++||++|+|+++++|+.|.+++.+||++|+++|||||+|||+|.|||+||+
T Consensus         9 ~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~   88 (1153)
T PLN03210          9 RNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELL   88 (1153)
T ss_pred             CCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHH
Confidence            46899999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             HHHhhH-------------------------hHHHHhHhH-----HHHHHHHHHHHHHhhhcCCccCCCC-c--------
Q 042778           95 KILTRE-------------------------LEEMFKENS-----EKLQTWRNALKEAAGLSGFHSQNIR-L--------  135 (311)
Q Consensus        95 ~i~e~~-------------------------~~~~~~~~~-----~~v~~w~~~l~~~~~~~g~~~~~~~-e--------  135 (311)
                      +|++|+                         ||++|.+|+     +++++||+||++++++.||++.... |        
T Consensus        89 ~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~~~~E~~~i~~Iv  168 (1153)
T PLN03210         89 EIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQNWPNEAKMIEEIA  168 (1153)
T ss_pred             HHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcccchhHHHHHHHHHHHHhCcCceecCCCCCHHHHHHHHH
Confidence            999997                         999999886     7899999999999999999887644 4        


Q ss_pred             ccccCCCC------CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecC--cc
Q 042778          136 AEVSPCSN------KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNV--RE  207 (311)
Q Consensus       136 ~~i~~~l~------~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~--~~  207 (311)
                      ++|..+++      .+++||++.++++|..+|..+.+++++||||||||+||||||+++|+++..+|++.+|+.+.  ..
T Consensus       169 ~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~v~~  248 (1153)
T PLN03210        169 NDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISK  248 (1153)
T ss_pred             HHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeecccccc
Confidence            56666654      56899999999999999987777899999999999999999999999999999999998642  11


Q ss_pred             c---cCC----C-CChHHHHHHHHHHHhcCCC-CCCCHHHHHHHhCCCeEEEEEecCCChHHHHHhhccCCC--------
Q 042778          208 E---SQR----P-GGLGFLQQKLLSKLLQDGI-VIPDIALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRN--------  270 (311)
Q Consensus       208 ~---s~~----~-~~~~~l~~~ll~~l~~~~~-~~~~~~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~~~--------  270 (311)
                      .   ...    . .....++++++.++..... .......++++|+++|+||||||||+.++|+.+.+...|        
T Consensus       249 ~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrII  328 (1153)
T PLN03210        249 SMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRII  328 (1153)
T ss_pred             chhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEE
Confidence            1   000    0 1134677788888776544 444457789999999999999999999999999765443        


Q ss_pred             -----------cCCceEEEcCCCChHHHHHHHHHhhcCCCCCCCcHHHhhc
Q 042778          271 -----------CCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELSS  310 (311)
Q Consensus       271 -----------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~~~~~~~~~l~~  310 (311)
                                 ++.+.+|+|+.|++++||+||+++||++..|+++|+++++
T Consensus       329 iTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~  379 (1153)
T PLN03210        329 VITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELAS  379 (1153)
T ss_pred             EEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHH
Confidence                       3467899999999999999999999998888888998875

syringae 6; Provisional

>PLN03194 putative disease resistance protein; Provisional

Probab=100.00  E-value=2.5e-36  Score=250.47  Aligned_cols=123  Identities=27%  Similarity=0.496  Sum_probs=108.8

Q ss_pred             CCCCCCCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccc
Q 042778           10 SPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRW   88 (311)
Q Consensus        10 ~s~~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~w   88 (311)
                      +|+++...+|||||||||+|+|++|++||+++|+++||+||+|+ ++++|+.|.+.|.+||++|+++||||||||++|.|
T Consensus        18 ~~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~W   97 (187)
T PLN03194         18 PSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYF   97 (187)
T ss_pred             ccCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchh
Confidence            44555668899999999999999999999999999999999999 99999999999999999999999999999999999


Q ss_pred             hHHHHHHHHhhH------h-H---HHHhH------hHHHHHHHHHHHHHHhhhcCCccCC
Q 042778           89 CLDELVKILTRE------L-E---EMFKE------NSEKLQTWRNALKEAAGLSGFHSQN  132 (311)
Q Consensus        89 cl~El~~i~e~~------~-~---~~~~~------~~~~v~~w~~~l~~~~~~~g~~~~~  132 (311)
                      ||+||++|++|+      | .   .....      ..+++++||+||.+++++.|+.+..
T Consensus        98 CLdEL~~I~e~~~~ViPIFY~VdPsdVr~q~~~~~~~e~v~~Wr~AL~~va~l~G~~~~~  157 (187)
T PLN03194         98 CLHELALIMESKKRVIPIFCDVKPSQLRVVDNGTCPDEEIRRFNWALEEAKYTVGLTFDS  157 (187)
T ss_pred             HHHHHHHHHHcCCEEEEEEecCCHHHhhccccCCCCHHHHHHHHHHHHHHhccccccCCC
Confidence            999999999987      1 1   11111      1178999999999999999987653

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.92  E-value=1.1e-24  Score=222.31  Aligned_cols=156  Identities=26%  Similarity=0.360  Sum_probs=134.0

Q ss_pred             cchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh---hccCcCceEEEecCccccCCCCChHHHHHHHHH
Q 042778          148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK---ISSNFEGSCFLQNVREESQRPGGLGFLQQKLLS  224 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~---~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~  224 (311)
                      ||.+..++++.+.|..++.  .++||+||||+||||||+.++|+   +..+|+..+||.    +|+ .++...++.+|+.
T Consensus       161 VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~----VSk-~f~~~~iq~~Il~  233 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVV----VSK-EFTTRKIQQTILE  233 (889)
T ss_pred             ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEE----Ecc-cccHHhHHHHHHH
Confidence            9999999999999986543  99999999999999999999996   678999999999    999 9999999999999


Q ss_pred             HHhcCCCC--C---CCH-HHHHHHhCCCeEEEEEecCCChHHHHHhhccCC-----C---------------cCCceEEE
Q 042778          225 KLLQDGIV--I---PDI-ALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLR-----N---------------CCVKEKYE  278 (311)
Q Consensus       225 ~l~~~~~~--~---~~~-~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~~-----~---------------~~~~~~y~  278 (311)
                      .++.....  .   ... ..|.+.|.+||+||||||||+...|+.+..+.+     +               +++...++
T Consensus       234 ~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~  313 (889)
T KOG4658|consen  234 RLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIE  313 (889)
T ss_pred             HhccCCcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCcccc
Confidence            98875552  1   122 889999999999999999999999999964332     2               56678899


Q ss_pred             cCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          279 MKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       279 v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                      +++|+.+|||+||++.||... ...+++++++|
T Consensus       314 v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak  346 (889)
T KOG4658|consen  314 VECLTPEEAWDLFQKKVGPNTLGSHPDIEELAK  346 (889)
T ss_pred             ccccCccccHHHHHHhhccccccccccHHHHHH
Confidence            999999999999999999863 34445777775

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=99.90  E-value=7.1e-24  Score=192.50  Aligned_cols=145  Identities=29%  Similarity=0.422  Sum_probs=113.7

Q ss_pred             hhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hccCcCceEEEecCccccCCCCChHHHHHHHHHHHh
Q 042778          150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLL  227 (311)
Q Consensus       150 r~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~  227 (311)
                      ||.++++|.+.|....++.++|+|+||||+||||||+.++++  +..+|+.++|+.    .+. ......++..|+..+.
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~----~~~-~~~~~~~~~~i~~~l~   75 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVS----LSK-NPSLEQLLEQILRQLG   75 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEE----EES--SCCHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccc----ccc-cccccccccccccccc
Confidence            688999999999876677999999999999999999999998  899999999999    666 7777999999999988


Q ss_pred             cCCCCC---CCH----HHHHHHhCCCeEEEEEecCCChHHHHHhhccC-----CC---------------cCCceEEEcC
Q 042778          228 QDGIVI---PDI----ALSFRQLSRRKVLIVLDDVTCFRQIKSLIGML-----RN---------------CCVKEKYEMK  280 (311)
Q Consensus       228 ~~~~~~---~~~----~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~-----~~---------------~~~~~~y~v~  280 (311)
                      ......   .+.    ..+++.|.++++||||||||+...|+.+....     ++               ......|+|+
T Consensus        76 ~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~  155 (287)
T PF00931_consen   76 EPDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELE  155 (287)
T ss_dssp             CC-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECS
T ss_pred             ccccccccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccc
Confidence            774322   222    88999999999999999999999997774321     11               1125789999


Q ss_pred             CCChHHHHHHHHHhhcCCC
Q 042778          281 ELGDDHALELFSRHAFKQN  299 (311)
Q Consensus       281 ~L~~~ea~~Lf~~~af~~~  299 (311)
                      +|+.+||++||++.++...
T Consensus       156 ~L~~~ea~~L~~~~~~~~~  174 (287)
T PF00931_consen  156 PLSEEEALELFKKRAGRKE  174 (287)
T ss_dssp             S--HHHHHHHHHHHHTSHS
T ss_pred             ccccccccccccccccccc
Confidence            9999999999999999755

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

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

Probab=99.67  E-value=1.6e-17  Score=135.45  Aligned_cols=80  Identities=36%  Similarity=0.684  Sum_probs=72.9

Q ss_pred             EEecCccccCCCChHHHHHHHHHhC--CCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccchHHHHHHHH
Q 042778           21 VFQSFRGEDNRDNFTGHLYSALSQK--GIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKIL   97 (311)
Q Consensus        21 vFis~~g~D~~~~f~~~L~~~L~~~--gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i~   97 (311)
                      |||||++.+.+..|+++|..+|++.  |+++|+++ |+.+|..+.+++.++|++|+++|+|||++|+.|.||+.||..++
T Consensus         1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~   80 (141)
T PF01582_consen    1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL   80 (141)
T ss_dssp             EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred             cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence            7999999544567999999999999  99999998 99999999999999999999999999999999999999999988


Q ss_pred             hhH
Q 042778           98 TRE  100 (311)
Q Consensus        98 e~~  100 (311)
                      ++.
T Consensus        81 ~~~   83 (141)
T PF01582_consen   81 ERL   83 (141)
T ss_dssp             HHH
T ss_pred             hhc
Confidence            754

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=99.63  E-value=1.2e-15  Score=123.80  Aligned_cols=82  Identities=44%  Similarity=0.783  Sum_probs=71.2

Q ss_pred             cccEEecCcc-ccCCCChHHHHHHHHHhCCCcEEeeCCCCCCCcchHHHHHHHHhccceeeeeccCcccccchHHHHHHH
Q 042778           18 KYDVFQSFRG-EDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKI   96 (311)
Q Consensus        18 ~~dvFis~~g-~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i   96 (311)
                      .|||||||++ ++....|+.+|...|...|+.+|.|+....|... .+|.++|++|++.|+|+||+|..|.||..|+..+
T Consensus         1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a   79 (140)
T smart00255        1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA   79 (140)
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence            4899999999 5666789999999999999999999844333334 3999999999999999999999999999999988


Q ss_pred             HhhH
Q 042778           97 LTRE  100 (311)
Q Consensus        97 ~e~~  100 (311)
                      +++.
T Consensus        80 ~~~~   83 (140)
T smart00255       80 LENA   83 (140)
T ss_pred             HHHH
Confidence            8753

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

Probab=99.47  E-value=7.6e-15  Score=112.77  Aligned_cols=74  Identities=32%  Similarity=0.583  Sum_probs=65.0

Q ss_pred             EEecCccccCCCChHHHHHHHHHhCCCcEEeeCCCCCCCcchHHHHHHHHhccceeeeeccCcccccchHHHHHHH
Q 042778           21 VFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKI   96 (311)
Q Consensus        21 vFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i   96 (311)
                      |||||+++|.  .|+.+|...|+.+|+++|.|.++.+|+.+...|.++|++|+..|+++||+|..|.||..|+..+
T Consensus         1 VFIS~~~~D~--~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a   74 (102)
T PF13676_consen    1 VFISYSSEDR--EFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAA   74 (102)
T ss_dssp             EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHH
T ss_pred             eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHH
Confidence            8999999994  5999999999999999999988899999999999999999999999999999999999998544

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

Probab=98.98  E-value=3.4e-09  Score=97.86  Aligned_cols=107  Identities=23%  Similarity=0.381  Sum_probs=80.1

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHH-HHHh
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALS-FRQL  243 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l-~~~L  243 (311)
                      .+.+..+-+||++|+||||||+.+.......|...         +....+..++...+              +.- +.+.
T Consensus        45 ~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~---------sAv~~gvkdlr~i~--------------e~a~~~~~  101 (436)
T COG2256          45 AGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEAL---------SAVTSGVKDLREII--------------EEARKNRL  101 (436)
T ss_pred             cCCCceeEEECCCCCCHHHHHHHHHHhhCCceEEe---------ccccccHHHHHHHH--------------HHHHHHHh
Confidence            34578889999999999999999999887777542         11134555554433              222 3444


Q ss_pred             CCCeEEEEEecCC--ChHHHHHhhccCCC---------------------cCCceEEEcCCCChHHHHHHHHHh
Q 042778          244 SRRKVLIVLDDVT--CFRQIKSLIGMLRN---------------------CCVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       244 ~~kr~LlVLDdV~--~~~~l~~l~~~~~~---------------------~~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                      .+++.+|.+|.|+  +..|.+.|++....                     .....+|++++|+.++-.+++.+-
T Consensus       102 ~gr~tiLflDEIHRfnK~QQD~lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra  175 (436)
T COG2256         102 LGRRTILFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRA  175 (436)
T ss_pred             cCCceEEEEehhhhcChhhhhhhhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHH
Confidence            5899999999997  67788888764433                     456789999999999999999983

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.94  E-value=2.2e-08  Score=95.06  Aligned_cols=147  Identities=14%  Similarity=0.176  Sum_probs=98.9

Q ss_pred             CCCccchhhhHHHHHHhhccc--CCCeEEEEEeccCcchhHHHHHHHHHhhccCcC--ceEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE--SKDVYALGIWGIGGIDRTTIARAIFNKISSNFE--GSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~--~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      ++.++||+.++++|...|...  ......+.|+|++|+|||++++.++++......  ..+++.    ... ..+...+.
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in----~~~-~~~~~~~~  103 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYIN----CQI-DRTRYAIF  103 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEE----CCc-CCCHHHHH
Confidence            678999999999999988543  233556789999999999999999998765442  234444    222 44567888


Q ss_pred             HHHHHHHhcCCC-C-C---CCH-HHHHHHhC--CCeEEEEEecCCChH------HHHHhhcc----CCC-----------
Q 042778          220 QKLLSKLLQDGI-V-I---PDI-ALSFRQLS--RRKVLIVLDDVTCFR------QIKSLIGM----LRN-----------  270 (311)
Q Consensus       220 ~~ll~~l~~~~~-~-~---~~~-~~l~~~L~--~kr~LlVLDdV~~~~------~l~~l~~~----~~~-----------  270 (311)
                      ..++.++.+... . .   ... ..+.+.+.  ++..+||||+++...      .+..+...    ...           
T Consensus       104 ~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~  183 (394)
T PRK00411        104 SEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDL  183 (394)
T ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCc
Confidence            888888876322 1 1   112 55555554  456899999998643      34443211    110           


Q ss_pred             ------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                  .-....+.+++++.++..+++..++
T Consensus       184 ~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~  220 (394)
T PRK00411        184 TFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRV  220 (394)
T ss_pred             chhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHH
Confidence                        0012456899999999999998775

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.88  E-value=5.6e-08  Score=91.36  Aligned_cols=147  Identities=14%  Similarity=0.268  Sum_probs=97.2

Q ss_pred             CCCccchhhhHHHHHHhhccc--CCCeEEEEEeccCcchhHHHHHHHHHhhccCcC------ceEEEecCccccCCCCCh
Q 042778          144 KNQLVGVESRVEEIESLLGAE--SKDVYALGIWGIGGIDRTTIARAIFNKISSNFE------GSCFLQNVREESQRPGGL  215 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~------~~~wv~~~~~~s~~~~~~  215 (311)
                      ++.++||+.++++|...|...  ......+.|+|++|+|||++++.+++++....+      ..+++.    ... ..+.
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in----~~~-~~~~   88 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVN----CQI-LDTL   88 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEE----CCC-CCCH
Confidence            678999999999999988642  233567899999999999999999997643322      234554    222 3456


Q ss_pred             HHHHHHHHHHHhc--CCC---CCC--CH-HHHHHHhC--CCeEEEEEecCCCh-----HHHHHhhcc-----CC-C----
Q 042778          216 GFLQQKLLSKLLQ--DGI---VIP--DI-ALSFRQLS--RRKVLIVLDDVTCF-----RQIKSLIGM-----LR-N----  270 (311)
Q Consensus       216 ~~l~~~ll~~l~~--~~~---~~~--~~-~~l~~~L~--~kr~LlVLDdV~~~-----~~l~~l~~~-----~~-~----  270 (311)
                      ..+...|+.++..  ...   ...  +. ..+.+.+.  +++++||||+++..     +.+..+...     .. .    
T Consensus        89 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~l  168 (365)
T TIGR02928        89 YQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGV  168 (365)
T ss_pred             HHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEE
Confidence            7788888888852  111   111  11 44555553  56889999999865     123333211     00 0    


Q ss_pred             -------------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 -------------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 -------------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                         .-....+.+++++.+|-.+++..++
T Consensus       169 I~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~  212 (365)
T TIGR02928       169 IGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRA  212 (365)
T ss_pred             EEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHH
Confidence                               0012457899999999999999875

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.

>PF05729 NACHT: NACHT domain

Probab=98.81  E-value=4.1e-08  Score=81.09  Aligned_cols=122  Identities=16%  Similarity=0.229  Sum_probs=71.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCc------CceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHH-
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNF------EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFR-  241 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F------~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~-  241 (311)
                      |++.|.|.+|+||||+++.++.++....      ...+|+. .+.... ......+...|..+.........  ..+.. 
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~l~~~l~~~~~~~~~~~~--~~~~~~   76 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS-LRDISD-SNNSRSLADLLFDQLPESIAPIE--ELLQEL   76 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEe-ehhhhh-ccccchHHHHHHHhhccchhhhH--HHHHHH
Confidence            5789999999999999999998754443      3344443 333332 22222344433333322211111  11222 


Q ss_pred             HhCCCeEEEEEecCCChHH-------------HHHhhcc--CCC------------------cCCceEEEcCCCChHHHH
Q 042778          242 QLSRRKVLIVLDDVTCFRQ-------------IKSLIGM--LRN------------------CCVKEKYEMKELGDDHAL  288 (311)
Q Consensus       242 ~L~~kr~LlVLDdV~~~~~-------------l~~l~~~--~~~------------------~~~~~~y~v~~L~~~ea~  288 (311)
                      ....+++|||||++++...             +..+...  +..                  ......++|++|++++..
T Consensus        77 ~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~  156 (166)
T PF05729_consen   77 LEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIK  156 (166)
T ss_pred             HHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHH
Confidence            2257899999999985332             2233322  111                  234468999999999999


Q ss_pred             HHHHHh
Q 042778          289 ELFSRH  294 (311)
Q Consensus       289 ~Lf~~~  294 (311)
                      +++.++
T Consensus       157 ~~~~~~  162 (166)
T PF05729_consen  157 QYLRKY  162 (166)
T ss_pred             HHHHHH
Confidence            988554

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

Probab=98.68  E-value=3.7e-07  Score=82.03  Aligned_cols=122  Identities=11%  Similarity=0.077  Sum_probs=75.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCC--H-HHHHHH--
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPD--I-ALSFRQ--  242 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~--~-~~l~~~--  242 (311)
                      ..++.|+|++|+|||||++.+++.....=-..+|+.     .. ..+...++..++..++........  . ..+...  
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~-----~~-~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~  116 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLV-----NT-RVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLI  116 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeee-----CC-CCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHH
Confidence            558899999999999999999998653211223333     12 345667777777766543222111  1 333332  


Q ss_pred             ---hCCCeEEEEEecCCChH--HHHHhh---ccC---CC-------------------------cCCceEEEcCCCChHH
Q 042778          243 ---LSRRKVLIVLDDVTCFR--QIKSLI---GML---RN-------------------------CCVKEKYEMKELGDDH  286 (311)
Q Consensus       243 ---L~~kr~LlVLDdV~~~~--~l~~l~---~~~---~~-------------------------~~~~~~y~v~~L~~~e  286 (311)
                         ..+++++||+||++...  .++.+.   ...   ..                         ......+++++|+.+|
T Consensus       117 ~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e  196 (269)
T TIGR03015       117 EQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPLDREE  196 (269)
T ss_pred             HHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCCCHHH
Confidence               26788999999998643  444432   100   00                         0123457899999999


Q ss_pred             HHHHHHHhh
Q 042778          287 ALELFSRHA  295 (311)
Q Consensus       287 a~~Lf~~~a  295 (311)
                      ..+++...+
T Consensus       197 ~~~~l~~~l  205 (269)
T TIGR03015       197 TREYIEHRL  205 (269)
T ss_pred             HHHHHHHHH
Confidence            999888765

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.

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

Probab=98.62  E-value=6.6e-08  Score=81.54  Aligned_cols=50  Identities=30%  Similarity=0.502  Sum_probs=35.4

Q ss_pred             CccchhhhHHHHHHhhcc-cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          146 QLVGVESRVEEIESLLGA-ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .||||+.+++++...|.. .....+.+.|+|.+|+|||+|.++++.++...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            489999999999999952 33447999999999999999999999987666

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.59  E-value=1.2e-07  Score=82.53  Aligned_cols=55  Identities=16%  Similarity=0.358  Sum_probs=40.3

Q ss_pred             ccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          147 LVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       147 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      |+||+.++++|.+++..+  ..+.+.|+|..|+|||+|++.+.+.....-...+|+.
T Consensus         1 F~gR~~el~~l~~~l~~~--~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~   55 (234)
T PF01637_consen    1 FFGREKELEKLKELLESG--PSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYID   55 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHC
T ss_pred             CCCHHHHHHHHHHHHHhh--cCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEe
Confidence            689999999999988753  3567899999999999999999998744322344444

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

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.58  E-value=4e-07  Score=87.20  Aligned_cols=128  Identities=21%  Similarity=0.396  Sum_probs=79.9

Q ss_pred             CCCccchhhhHHH---HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHH
Q 042778          144 KNQLVGVESRVEE---IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      .+++||.+..+..   +..++..  +....+.|+|++|+||||||+.+++.....|..   +..   .   ..+...+ +
T Consensus        11 l~d~vGq~~~v~~~~~L~~~i~~--~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~---l~a---~---~~~~~~i-r   78 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRMIEA--GRLSSMILWGPPGTGKTTLARIIAGATDAPFEA---LSA---V---TSGVKDL-R   78 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHHHHc--CCCceEEEECCCCCCHHHHHHHHHHHhCCCEEE---Eec---c---cccHHHH-H
Confidence            3468888877655   6666653  346678889999999999999999987655432   110   0   1122222 1


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhhccCCC---------------------cCCceEE
Q 042778          221 KLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLIGMLRN---------------------CCVKEKY  277 (311)
Q Consensus       221 ~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~~~~~---------------------~~~~~~y  277 (311)
                      .++....            .....+++.+|+||+++.  ..+.+.|......                     .....++
T Consensus        79 ~ii~~~~------------~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~iilI~att~n~~~~l~~aL~SR~~~~  146 (413)
T PRK13342         79 EVIEEAR------------QRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVF  146 (413)
T ss_pred             HHHHHHH------------HhhhcCCceEEEEechhhhCHHHHHHHHHHhhcCcEEEEEeCCCChhhhccHHHhccceee
Confidence            2222211            011235778999999985  3455555321110                     2233678


Q ss_pred             EcCCCChHHHHHHHHHhh
Q 042778          278 EMKELGDDHALELFSRHA  295 (311)
Q Consensus       278 ~v~~L~~~ea~~Lf~~~a  295 (311)
                      .+++|+.++..+++.+.+
T Consensus       147 ~~~~ls~e~i~~lL~~~l  164 (413)
T PRK13342        147 ELKPLSEEDIEQLLKRAL  164 (413)
T ss_pred             EeCCCCHHHHHHHHHHHH
Confidence            999999999999998854

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.54  E-value=2.9e-07  Score=84.46  Aligned_cols=143  Identities=17%  Similarity=0.196  Sum_probs=87.0

Q ss_pred             CCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      .++||++..+++|..++...   ......+.++|++|+|||+||+.+++.....+..   +. ....    ..... ...
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~---~~-~~~~----~~~~~-l~~   74 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKI---TS-GPAL----EKPGD-LAA   74 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEE---ec-cchh----cCchh-HHH
Confidence            46899999999998888632   2235668899999999999999999987654321   11 1001    11111 122


Q ss_pred             HHHHHhcCCC----CCCCH-----HHHHHHhCCCeEEEEEecCCChHHHHHhhccCCC---------------cCCceEE
Q 042778          222 LLSKLLQDGI----VIPDI-----ALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRN---------------CCVKEKY  277 (311)
Q Consensus       222 ll~~l~~~~~----~~~~~-----~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~~~---------------~~~~~~y  277 (311)
                      ++..+.....    ++..+     +.+...+.+.+..+|+|+..+..++....+....               ......+
T Consensus        75 ~l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~~~~~  154 (305)
T TIGR00635        75 ILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIIL  154 (305)
T ss_pred             HHHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhcceEE
Confidence            2233322211    11111     4555666667777888877666555433221110               1124568


Q ss_pred             EcCCCChHHHHHHHHHhhc
Q 042778          278 EMKELGDDHALELFSRHAF  296 (311)
Q Consensus       278 ~v~~L~~~ea~~Lf~~~af  296 (311)
                      ++++++.++..+++.+.+-
T Consensus       155 ~l~~l~~~e~~~il~~~~~  173 (305)
T TIGR00635       155 RLEFYTVEELAEIVSRSAG  173 (305)
T ss_pred             EeCCCCHHHHHHHHHHHHH
Confidence            9999999999999998764

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

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

Probab=98.52  E-value=6.2e-07  Score=82.11  Aligned_cols=112  Identities=16%  Similarity=0.284  Sum_probs=76.8

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLS  244 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~  244 (311)
                      .+.+..+.+||.+|+||||||+.+.+.-+.+-  ..||.    .|....+..+ .+.++.+...           ...|.
T Consensus       159 q~~ipSmIlWGppG~GKTtlArlia~tsk~~S--yrfve----lSAt~a~t~d-vR~ife~aq~-----------~~~l~  220 (554)
T KOG2028|consen  159 QNRIPSMILWGPPGTGKTTLARLIASTSKKHS--YRFVE----LSATNAKTND-VRDIFEQAQN-----------EKSLT  220 (554)
T ss_pred             cCCCCceEEecCCCCchHHHHHHHHhhcCCCc--eEEEE----EeccccchHH-HHHHHHHHHH-----------HHhhh
Confidence            45688899999999999999999998755442  44565    3331222222 2233333221           13356


Q ss_pred             CCeEEEEEecCC--ChHHHHHhhccCCC---------------------cCCceEEEcCCCChHHHHHHHHHh
Q 042778          245 RRKVLIVLDDVT--CFRQIKSLIGMLRN---------------------CCVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       245 ~kr~LlVLDdV~--~~~~l~~l~~~~~~---------------------~~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                      .+|.+|.+|.|.  +..|.+.++|....                     .....++.+++|+.++-..++.+-
T Consensus       221 krkTilFiDEiHRFNksQQD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~ra  293 (554)
T KOG2028|consen  221 KRKTILFIDEIHRFNKSQQDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRA  293 (554)
T ss_pred             cceeEEEeHHhhhhhhhhhhcccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHH
Confidence            789999999997  56777777654333                     455678999999999999988873

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

Probab=98.50  E-value=3.5e-07  Score=81.42  Aligned_cols=88  Identities=19%  Similarity=0.157  Sum_probs=60.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH----------
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI----------  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~----------  236 (311)
                      -..++|.|.+|+|||||++.+|+.+.. +|+..+|+..+++-   ..++.++++.+...+.....+....          
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er---~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~   92 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDER---PEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVL   92 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCC---CccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHH
Confidence            457899999999999999999998543 79999999843321   3688898888833332221111110          


Q ss_pred             HHHHHH-hCCCeEEEEEecCCCh
Q 042778          237 ALSFRQ-LSRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ~~l~~~-L~~kr~LlVLDdV~~~  258 (311)
                      ...+.+ -.+++++|++|++...
T Consensus        93 ~~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          93 EKAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHHCCCCEEEEEECHHHh
Confidence            222222 3479999999999754

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.50  E-value=2.8e-07  Score=86.15  Aligned_cols=90  Identities=18%  Similarity=0.154  Sum_probs=60.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH----------
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI----------  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~----------  236 (311)
                      -...+|+|.+|+||||||+.+|+.+.. +|+..+|+..+++-   ...+.++++.++..+.....+....          
T Consensus       169 GQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER---~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~i  245 (416)
T PRK09376        169 GQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDER---PEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVI  245 (416)
T ss_pred             CceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCc---hhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHH
Confidence            456889999999999999999998654 79999999944331   2377888888763322111111100          


Q ss_pred             HHHHHH-hCCCeEEEEEecCCChHH
Q 042778          237 ALSFRQ-LSRRKVLIVLDDVTCFRQ  260 (311)
Q Consensus       237 ~~l~~~-L~~kr~LlVLDdV~~~~~  260 (311)
                      +..+.+ -.++++||++|++.....
T Consensus       246 e~Ae~~~e~G~dVlL~iDsItR~ar  270 (416)
T PRK09376        246 EKAKRLVEHGKDVVILLDSITRLAR  270 (416)
T ss_pred             HHHHHHHHcCCCEEEEEEChHHHHH
Confidence            222222 367999999999975443

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

Probab=98.45  E-value=7.4e-07  Score=77.27  Aligned_cols=54  Identities=26%  Similarity=0.464  Sum_probs=39.0

Q ss_pred             CCCccchhhhHHHHHHhhcc---cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          144 KNQLVGVESRVEEIESLLGA---ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      -+++||.+..+..+.-++..   ..+....+-+||++|+||||||..+++.....|.
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~   79 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNFK   79 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--EE
T ss_pred             HHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCeE
Confidence            57899999988887766643   2234788999999999999999999999887774

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.

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

Probab=98.45  E-value=4.1e-07  Score=72.42  Aligned_cols=86  Identities=20%  Similarity=0.217  Sum_probs=59.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-----cCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH----HH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-----FEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI----AL  238 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-----F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~----~~  238 (311)
                      -+.+.|+|.+|+|||++++.+.+.....     -...+|+.    ... ..+...+...++..+........+.    +.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~-~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~   78 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVN----CPS-SRTPRDFAQEILEALGLPLKSRQTSDELRSL   78 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEE----HHH-HSSHHHHHHHHHHHHT-SSSSTS-HHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEE----eCC-CCCHHHHHHHHHHHhCccccccCCHHHHHHH
Confidence            4678999999999999999999986542     23456777    555 5578999999999988665541222    56


Q ss_pred             HHHHhCCC-eEEEEEecCCCh
Q 042778          239 SFRQLSRR-KVLIVLDDVTCF  258 (311)
Q Consensus       239 l~~~L~~k-r~LlVLDdV~~~  258 (311)
                      +.+.+... ..+||+||++..
T Consensus        79 ~~~~l~~~~~~~lviDe~~~l   99 (131)
T PF13401_consen   79 LIDALDRRRVVLLVIDEADHL   99 (131)
T ss_dssp             HHHHHHHCTEEEEEEETTHHH
T ss_pred             HHHHHHhcCCeEEEEeChHhc
Confidence            66666554 459999999765

>PTZ00202 tuzin; Provisional

Probab=98.39  E-value=2.3e-06  Score=80.87  Aligned_cols=138  Identities=12%  Similarity=0.090  Sum_probs=89.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCC-CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESK-DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~-~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      ..+|+||+.++..|...|...+. ..+++.|.|++|+|||||++.+.....    ..+++.|       ..+..+++..+
T Consensus       261 ~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~~qL~vN-------prg~eElLr~L  329 (550)
T PTZ00202        261 IRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----MPAVFVD-------VRGTEDTLRSV  329 (550)
T ss_pred             ccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----ceEEEEC-------CCCHHHHHHHH
Confidence            67899999999999999974333 367999999999999999999997654    2244432       33678999999


Q ss_pred             HHHHhcCCC-CCCCH-HHHHHHh-----C-CCeEEEEEecCCChHHHHHhhc-----cCCC-------------------
Q 042778          223 LSKLLQDGI-VIPDI-ALSFRQL-----S-RRKVLIVLDDVTCFRQIKSLIG-----MLRN-------------------  270 (311)
Q Consensus       223 l~~l~~~~~-~~~~~-~~l~~~L-----~-~kr~LlVLDdV~~~~~l~~l~~-----~~~~-------------------  270 (311)
                      +..++.+.. ...++ ..|.+.|     . +++.+||+-= .+-+.+....+     .++.                   
T Consensus       330 L~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~l-reg~~l~rvyne~v~la~drr~ch~v~evpleslt~~~~  408 (550)
T PTZ00202        330 VKALGVPNVEACGDLLDFISEACRRAKKMNGETPLLVLKL-REGSSLQRVYNEVVALACDRRLCHVVIEVPLESLTIANT  408 (550)
T ss_pred             HHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEEEEEe-cCCCcHHHHHHHHHHHHccchhheeeeeehHhhcchhcc
Confidence            999986433 22233 3333332     3 5777777642 11111111100     0111                   


Q ss_pred             -cCCceEEEcCCCChHHHHHHHHH
Q 042778          271 -CCVKEKYEMKELGDDHALELFSR  293 (311)
Q Consensus       271 -~~~~~~y~v~~L~~~ea~~Lf~~  293 (311)
                       .+.-.-|-++.++.++|.+.-..
T Consensus       409 ~lprldf~~vp~fsr~qaf~y~~h  432 (550)
T PTZ00202        409 LLPRLDFYLVPNFSRSQAFAYTQH  432 (550)
T ss_pred             cCccceeEecCCCCHHHHHHHHhh
Confidence             34456789999999998876544

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

Probab=98.37  E-value=2.6e-06  Score=86.50  Aligned_cols=126  Identities=23%  Similarity=0.375  Sum_probs=77.9

Q ss_pred             CCccchhhhHH---HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHH
Q 042778          145 NQLVGVESRVE---EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       145 ~~~vGr~~~~~---~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      ++++|.+..+.   .+...+..  +....+.|+|++|+||||||+.+++.....|..   +..+      ..++..+ +.
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~--~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~---lna~------~~~i~di-r~   95 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKA--DRVGSLILYGPPGVGKTTLARIIANHTRAHFSS---LNAV------LAGVKDL-RA   95 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHhcCccee---ehhh------hhhhHHH-HH
Confidence            46789887764   35455542  346677899999999999999999987665522   2100      1112221 11


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHh--CCCeEEEEEecCC--ChHHHHHhhccCCC---------------------cCCceE
Q 042778          222 LLSKLLQDGIVIPDIALSFRQL--SRRKVLIVLDDVT--CFRQIKSLIGMLRN---------------------CCVKEK  276 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L--~~kr~LlVLDdV~--~~~~l~~l~~~~~~---------------------~~~~~~  276 (311)
                      ++.             .....+  .+++.+||||||+  +..+.+.|.+....                     .....+
T Consensus        96 ~i~-------------~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g~IiLI~aTTenp~~~l~~aL~SR~~v  162 (725)
T PRK13341         96 EVD-------------RAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSRL  162 (725)
T ss_pred             HHH-------------HHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhcCceEEEEEecCCChHhhhhhHhhccccc
Confidence            111             111111  2467799999997  45556555431111                     122467


Q ss_pred             EEcCCCChHHHHHHHHHhh
Q 042778          277 YEMKELGDDHALELFSRHA  295 (311)
Q Consensus       277 y~v~~L~~~ea~~Lf~~~a  295 (311)
                      +.+++|+.++...++.+.+
T Consensus       163 ~~l~pLs~edi~~IL~~~l  181 (725)
T PRK13341        163 FRLKSLSDEDLHQLLKRAL  181 (725)
T ss_pred             eecCCCCHHHHHHHHHHHH
Confidence            9999999999999998765

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.37  E-value=6.5e-07  Score=83.14  Aligned_cols=145  Identities=15%  Similarity=0.207  Sum_probs=85.1

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      ..+++|++..++.+..++...   ......+.|+|++|+||||||+.+++.....+.   ++. ...... ..    -..
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~---~~~-~~~~~~-~~----~l~   94 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR---ITS-GPALEK-PG----DLA   94 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeE---EEe-cccccC-hH----HHH
Confidence            467999999999998877531   233667889999999999999999998765432   111 110111 11    122


Q ss_pred             HHHHHHhcCCC----CCCC----H-HHHHHHhCCCeEEEEEecCCChHHHHHhhccCC---------C------cCCceE
Q 042778          221 KLLSKLLQDGI----VIPD----I-ALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLR---------N------CCVKEK  276 (311)
Q Consensus       221 ~ll~~l~~~~~----~~~~----~-~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~~---------~------~~~~~~  276 (311)
                      .++..+.....    ++..    . +.+...+.+.+..+|+|+..+..++....+...         .      ......
T Consensus        95 ~~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf~~~  174 (328)
T PRK00080         95 AILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIV  174 (328)
T ss_pred             HHHHhcccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhcCee
Confidence            33333322111    1111    1 444555556666677776555443321111100         0      112356


Q ss_pred             EEcCCCChHHHHHHHHHhhcC
Q 042778          277 YEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       277 y~v~~L~~~ea~~Lf~~~af~  297 (311)
                      +++++++.++..+++.+.+-.
T Consensus       175 ~~l~~~~~~e~~~il~~~~~~  195 (328)
T PRK00080        175 QRLEFYTVEELEKIVKRSARI  195 (328)
T ss_pred             eecCCCCHHHHHHHHHHHHHH
Confidence            899999999999999988654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.34  E-value=3.9e-06  Score=79.08  Aligned_cols=147  Identities=17%  Similarity=0.270  Sum_probs=86.0

Q ss_pred             CCCccchhhhHHHHHHhhccc--C---------CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC
Q 042778          144 KNQLVGVESRVEEIESLLGAE--S---------KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP  212 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~---------~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~  212 (311)
                      ..++.|++..+++|.+.+...  .         ...+-+.|+|++|+|||+||+++++.....|-..         ..  
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v---------~~--  189 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRV---------VG--  189 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEec---------ch--
Confidence            457889999999998876421  1         1245689999999999999999999876554221         11  


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCCHHHHHHH-hCCCeEEEEEecCCChH----------------HHHHhh----cc--CC
Q 042778          213 GGLGFLQQKLLSKLLQDGIVIPDIALSFRQ-LSRRKVLIVLDDVTCFR----------------QIKSLI----GM--LR  269 (311)
Q Consensus       213 ~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~-L~~kr~LlVLDdV~~~~----------------~l~~l~----~~--~~  269 (311)
                         ..+....    .+...  ..+..+.+. -.....+|+|||++...                .+..+.    +.  .+
T Consensus       190 ---~~l~~~~----~g~~~--~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~  260 (364)
T TIGR01242       190 ---SELVRKY----IGEGA--RLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRG  260 (364)
T ss_pred             ---HHHHHHh----hhHHH--HHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCC
Confidence               0111110    00000  000111111 12356799999987431                122221    10  00


Q ss_pred             C--------------------cCCceEEEcCCCChHHHHHHHHHhhcCCCCCC-CcHHHhhc
Q 042778          270 N--------------------CCVKEKYEMKELGDDHALELFSRHAFKQNNPH-IGFEELSS  310 (311)
Q Consensus       270 ~--------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~~~~-~~~~~l~~  310 (311)
                      .                    ...+..++++..+.++..++|+.++.+...+. .++.+|++
T Consensus       261 ~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~  322 (364)
T TIGR01242       261 NVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAK  322 (364)
T ss_pred             CEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHH
Confidence            1                    12356889999999999999999987654332 45666653

Many proteins may score above the trusted cutoff because an internal

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

Probab=98.33  E-value=4.5e-06  Score=66.60  Aligned_cols=54  Identities=30%  Similarity=0.350  Sum_probs=40.2

Q ss_pred             cchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +|++..+..+...+...  ..+.+.|+|.+|+|||||++.+++.....-...+++.
T Consensus         1 ~~~~~~~~~i~~~~~~~--~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   54 (151)
T cd00009           1 VGQEEAIEALREALELP--PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLN   54 (151)
T ss_pred             CchHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEe
Confidence            47778888888877642  3567889999999999999999998753323344444

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

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.31  E-value=6.9e-06  Score=83.37  Aligned_cols=147  Identities=13%  Similarity=0.168  Sum_probs=90.7

Q ss_pred             CCCccchhhhHHHHHHhhcc---cCCCeEEEEEeccCcchhHHHHHHHHHhhcc-----CcCc--eEEEecCccccCCCC
Q 042778          144 KNQLVGVESRVEEIESLLGA---ESKDVYALGIWGIGGIDRTTIARAIFNKISS-----NFEG--SCFLQNVREESQRPG  213 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-----~F~~--~~wv~~~~~~s~~~~  213 (311)
                      ++.++||+.++++|...|..   ++....++-|+|++|.|||++++.|.+++..     ....  +++|.+.    . -.
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm----~-Ls  828 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM----N-VV  828 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC----c-cC
Confidence            78899999999999998864   2222457789999999999999999887532     1221  3444411    1 24


Q ss_pred             ChHHHHHHHHHHHhcCCC--CCCCH---HHHHHHhC---CCeEEEEEecCCChH-----HHHHhhcc---CCC-------
Q 042778          214 GLGFLQQKLLSKLLQDGI--VIPDI---ALSFRQLS---RRKVLIVLDDVTCFR-----QIKSLIGM---LRN-------  270 (311)
Q Consensus       214 ~~~~l~~~ll~~l~~~~~--~~~~~---~~l~~~L~---~kr~LlVLDdV~~~~-----~l~~l~~~---~~~-------  270 (311)
                      ....+...|..++.+..+  .....   ..+...+.   ....+||||+|+...     .|-.|...   ...       
T Consensus       829 tp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGI  908 (1164)
T PTZ00112        829 HPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAI  908 (1164)
T ss_pred             CHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEe
Confidence            566777778777755443  22222   33444332   224599999998532     12222110   000       


Q ss_pred             -----------------cCCceEEEcCCCChHHHHHHHHHhhc
Q 042778          271 -----------------CCVKEKYEMKELGDDHALELFSRHAF  296 (311)
Q Consensus       271 -----------------~~~~~~y~v~~L~~~ea~~Lf~~~af  296 (311)
                                       ++ ...+..++++.++-.+++..++-
T Consensus       909 SNdlDLperLdPRLRSRLg-~eeIvF~PYTaEQL~dILk~RAe  950 (1164)
T PTZ00112        909 SNTMDLPERLIPRCRSRLA-FGRLVFSPYKGDEIEKIIKERLE  950 (1164)
T ss_pred             cCchhcchhhhhhhhhccc-cccccCCCCCHHHHHHHHHHHHH
Confidence                             11 12245688888888888888764

>TIGR00767 rho transcription termination factor Rho

Probab=98.30  E-value=2.4e-06  Score=80.28  Aligned_cols=89  Identities=18%  Similarity=0.158  Sum_probs=62.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH----------
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI----------  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~----------  236 (311)
                      -..++|+|.+|.|||||++.+++.+..+ |+..+|+..+++-   ...+.++++.++..+.....+....          
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER---~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDER---PEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCC---CccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            4578999999999999999999986555 9999999944331   4688899998865543322211111          


Q ss_pred             HHHHHH-hCCCeEEEEEecCCChH
Q 042778          237 ALSFRQ-LSRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ~~l~~~-L~~kr~LlVLDdV~~~~  259 (311)
                      +..+.. -.+++++|++|++....
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~a  268 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRLA  268 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHHH
Confidence            222222 35799999999997543

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

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

Probab=98.28  E-value=5.4e-06  Score=77.89  Aligned_cols=109  Identities=17%  Similarity=0.269  Sum_probs=79.2

Q ss_pred             CCCccchhhhHHHHHHhhccc--CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCc--eEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE--SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEG--SCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~--~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      ++.+.+|+.+++++...|..-  .+...-+.|+|..|.|||+.++.+.+++......  ++.|.    ... ......+.
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yIN----c~~-~~t~~~i~   90 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYIN----CLE-LRTPYQVL   90 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEe----eee-CCCHHHHH
Confidence            566999999999999888642  2223448999999999999999999987665322  45565    222 56788889


Q ss_pred             HHHHHHHhcCCC-CCCCH---HHHHHHhC--CCeEEEEEecCCC
Q 042778          220 QKLLSKLLQDGI-VIPDI---ALSFRQLS--RRKVLIVLDDVTC  257 (311)
Q Consensus       220 ~~ll~~l~~~~~-~~~~~---~~l~~~L~--~kr~LlVLDdV~~  257 (311)
                      .+|+.++..... .....   +.+.+.+.  ++.++||||+++.
T Consensus        91 ~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~  134 (366)
T COG1474          91 SKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDA  134 (366)
T ss_pred             HHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhh
Confidence            999998863333 22222   66666665  4889999999975

>PRK06893 DNA replication initiation factor; Validated

Probab=98.25  E-value=7.9e-06  Score=72.00  Aligned_cols=106  Identities=18%  Similarity=0.335  Sum_probs=65.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRK  247 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr  247 (311)
                      .+.+.|||..|+|||+|++++++....+...+.|+.    ...    .......++                 +.+. +.
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~----~~~----~~~~~~~~~-----------------~~~~-~~   92 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIP----LSK----SQYFSPAVL-----------------ENLE-QQ   92 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEee----HHH----hhhhhHHHH-----------------hhcc-cC
Confidence            467899999999999999999998655545556776    211    001111111                 1111 22


Q ss_pred             EEEEEecCCCh---HHHH----H----hhccCC-------------C----------cCCceEEEcCCCChHHHHHHHHH
Q 042778          248 VLIVLDDVTCF---RQIK----S----LIGMLR-------------N----------CCVKEKYEMKELGDDHALELFSR  293 (311)
Q Consensus       248 ~LlVLDdV~~~---~~l~----~----l~~~~~-------------~----------~~~~~~y~v~~L~~~ea~~Lf~~  293 (311)
                      -+|||||++..   .+|+    .    +.....             |          ...+.++++++++.++.++++.+
T Consensus        93 dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~  172 (229)
T PRK06893         93 DLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQR  172 (229)
T ss_pred             CEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHH
Confidence            37888888752   2222    1    110000             0          23456899999999999999999


Q ss_pred             hhcCCC
Q 042778          294 HAFKQN  299 (311)
Q Consensus       294 ~af~~~  299 (311)
                      +++...
T Consensus       173 ~a~~~~  178 (229)
T PRK06893        173 NAYQRG  178 (229)
T ss_pred             HHHHcC
Confidence            998543

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

Probab=98.25  E-value=1.9e-06  Score=80.97  Aligned_cols=70  Identities=23%  Similarity=0.387  Sum_probs=60.4

Q ss_pred             CCCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCccc
Q 042778           14 PRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYAS   85 (311)
Q Consensus        14 ~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~   85 (311)
                      +.....|||||||..- ....++-|.-.|+-+|++||+|- .+..|. +.+.+.+.|..++.+|.|++||-.+
T Consensus       608 ~~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLD  678 (832)
T KOG3678|consen  608 MLSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLD  678 (832)
T ss_pred             cccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHH
Confidence            3456789999999874 45699999999999999999998 888885 7789999999999999999999543

>PF13173 AAA_14: AAA domain

Probab=98.21  E-value=7.7e-06  Score=65.25  Aligned_cols=77  Identities=10%  Similarity=0.108  Sum_probs=46.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeE
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKV  248 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~  248 (311)
                      +++.|.|+.|+|||||++.++++.. .-...+++.    ...    ..........          -.+.+.+....++.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi~----~~~----~~~~~~~~~~----------~~~~~~~~~~~~~~   63 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL-PPENILYIN----FDD----PRDRRLADPD----------LLEYFLELIKPGKK   63 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc-ccccceeec----cCC----HHHHHHhhhh----------hHHHHHHhhccCCc
Confidence            5889999999999999999998765 333445554    111    1111000000          00233333445788


Q ss_pred             EEEEecCCChHHHHHh
Q 042778          249 LIVLDDVTCFRQIKSL  264 (311)
Q Consensus       249 LlVLDdV~~~~~l~~l  264 (311)
                      +|+||+|.....|...
T Consensus        64 ~i~iDEiq~~~~~~~~   79 (128)
T PF13173_consen   64 YIFIDEIQYLPDWEDA   79 (128)
T ss_pred             EEEEehhhhhccHHHH
Confidence            9999999877666554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.10  E-value=4.5e-05  Score=72.52  Aligned_cols=51  Identities=16%  Similarity=0.337  Sum_probs=39.8

Q ss_pred             CCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +++.|++..+++|.+.+...           -...+-|.++|.+|+|||+||++++++....
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~  192 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT  192 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCC
Confidence            45779999999998866321           1235668999999999999999999986544

>PRK08727 hypothetical protein; Validated

Probab=98.09  E-value=3e-05  Score=68.50  Aligned_cols=35  Identities=23%  Similarity=0.209  Sum_probs=28.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+.|+|..|+|||.|++++++....+.....|+.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            45999999999999999999998655544456665

>PRK04195 replication factor C large subunit; Provisional

Probab=98.09  E-value=8e-06  Score=79.81  Aligned_cols=134  Identities=21%  Similarity=0.292  Sum_probs=81.5

Q ss_pred             CCccchhhhHHHHHHhhcccC--CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAES--KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~--~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      .+++|.+..+.++..++....  ...+.+.|+|++|+||||+|+++++++.  |+. +-+.    .+. ..... ....+
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~--~~~-ieln----asd-~r~~~-~i~~~   84 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG--WEV-IELN----ASD-QRTAD-VIERV   84 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC--CCE-EEEc----ccc-cccHH-HHHHH
Confidence            468999999999999986422  2267899999999999999999999874  222 1122    122 22222 22222


Q ss_pred             HHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH------HHHHhh---ccCCC-----------------cCCceE
Q 042778          223 LSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR------QIKSLI---GMLRN-----------------CCVKEK  276 (311)
Q Consensus       223 l~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~------~l~~l~---~~~~~-----------------~~~~~~  276 (311)
                      +.......          .....++-+||||+++...      .+..|.   .....                 ......
T Consensus        85 i~~~~~~~----------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~~~~~iIli~n~~~~~~~k~Lrsr~~~  154 (482)
T PRK04195         85 AGEAATSG----------SLFGARRKLILLDEVDGIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLM  154 (482)
T ss_pred             HHHhhccC----------cccCCCCeEEEEecCcccccccchhHHHHHHHHHHcCCCCEEEeccCccccchhhHhccceE
Confidence            22221110          1111367799999998642      233332   11111                 123466


Q ss_pred             EEcCCCChHHHHHHHHHhhcC
Q 042778          277 YEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       277 y~v~~L~~~ea~~Lf~~~af~  297 (311)
                      +++++++.++....+.+.+..
T Consensus       155 I~f~~~~~~~i~~~L~~i~~~  175 (482)
T PRK04195        155 IEFKRLSTRSIVPVLKRICRK  175 (482)
T ss_pred             EEecCCCHHHHHHHHHHHHHH
Confidence            788999999988888776644

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

Probab=98.09  E-value=2.3e-05  Score=72.44  Aligned_cols=111  Identities=22%  Similarity=0.351  Sum_probs=79.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCC-eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKD-VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      .+++.+|+.++..+..++...+.. ..+|-|+|-.|.|||.+.+.+++....   ..+|++    .-+ .+....+..+|
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~---~~vw~n----~~e-cft~~~lle~I   76 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL---ENVWLN----CVE-CFTYAILLEKI   76 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC---cceeee----hHH-hccHHHHHHHH
Confidence            457889999999999999865554 556699999999999999999998733   346887    444 78899999999


Q ss_pred             HHHHhcCCC---CCC----CH----HHHHH--HhC--CCeEEEEEecCCChHHHH
Q 042778          223 LSKLLQDGI---VIP----DI----ALSFR--QLS--RRKVLIVLDDVTCFRQIK  262 (311)
Q Consensus       223 l~~l~~~~~---~~~----~~----~~l~~--~L~--~kr~LlVLDdV~~~~~l~  262 (311)
                      +.+.+..+.   ...    ++    ..+.+  -..  ++.++||||+++...+.+
T Consensus        77 L~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~  131 (438)
T KOG2543|consen   77 LNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMD  131 (438)
T ss_pred             HHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccc
Confidence            999852222   111    11    22222  122  468999999998655443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.07  E-value=2.4e-05  Score=68.28  Aligned_cols=52  Identities=15%  Similarity=0.256  Sum_probs=37.3

Q ss_pred             hhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          150 VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       150 r~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .+..++.+..++..  .....+.|+|..|+|||+||+.++++........+++.
T Consensus        22 ~~~~~~~l~~~~~~--~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~   73 (226)
T TIGR03420        22 NAELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP   73 (226)
T ss_pred             cHHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEe
Confidence            34466666666542  33668899999999999999999998654444445555

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

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.04  E-value=6e-05  Score=77.27  Aligned_cols=136  Identities=17%  Similarity=0.236  Sum_probs=80.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCC-eEEEEEeccCcchhHHHHHHHHHhhccCc--Cc-eEEEec------------Ccc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKD-VYALGIWGIGGIDRTTIARAIFNKISSNF--EG-SCFLQN------------VRE  207 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F--~~-~~wv~~------------~~~  207 (311)
                      ..++||.+..+..|.+.+..+  . ...+.++|..|+||||+|+.+++.+...-  .. -|-.|+            +-+
T Consensus        15 FddIIGQe~Iv~~LknaI~~~--rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviE   92 (944)
T PRK14949         15 FEQMVGQSHVLHALTNALTQQ--RLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIE   92 (944)
T ss_pred             HHHhcCcHHHHHHHHHHHHhC--CCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEE
Confidence            357899999999998888643  3 44568999999999999999999865431  10 011110            000


Q ss_pred             --ccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhhccC----CC---------
Q 042778          208 --ESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLIGML----RN---------  270 (311)
Q Consensus       208 --~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~~~----~~---------  270 (311)
                        ... ..++..+ +.|+..+.            ..-..+++-++|||+++.  .+.++.|+...    ..         
T Consensus        93 idAas-~~kVDdI-ReLie~v~------------~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe  158 (944)
T PRK14949         93 VDAAS-RTKVDDT-RELLDNVQ------------YRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTD  158 (944)
T ss_pred             ecccc-ccCHHHH-HHHHHHHH------------hhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCC
Confidence              000 0111111 22222111            111235677999999985  45566654211    10         


Q ss_pred             --------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 --------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 --------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                              ......|++++|+.++..+.+.+.+
T Consensus       159 ~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il  191 (944)
T PRK14949        159 PQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHIL  191 (944)
T ss_pred             chhchHHHHHhheEEeCCCCCHHHHHHHHHHHH
Confidence                    2335789999999999998887644

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.04  E-value=8.9e-05  Score=77.74  Aligned_cols=138  Identities=14%  Similarity=0.157  Sum_probs=83.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      ..++|-|+...+    .|.. ....+++.|.|++|.||||++..+.++.    +.++|+.    ....+.+...+...|+
T Consensus        13 ~~~~~~R~rl~~----~l~~-~~~~~~~~v~apaG~GKTtl~~~~~~~~----~~~~w~~----l~~~d~~~~~f~~~l~   79 (903)
T PRK04841         13 LHNTVVRERLLA----KLSG-ANNYRLVLVTSPAGYGKTTLISQWAAGK----NNLGWYS----LDESDNQPERFASYLI   79 (903)
T ss_pred             ccccCcchHHHH----HHhc-ccCCCeEEEECCCCCCHHHHHHHHHHhC----CCeEEEe----cCcccCCHHHHHHHHH
Confidence            456666664444    3432 2358899999999999999999988643    3688997    4331456666767777


Q ss_pred             HHHhcCCC-------------CCCCH----HHHHHHhC--CCeEEEEEecCCCh------HHHHHhhcc-CCC-------
Q 042778          224 SKLLQDGI-------------VIPDI----ALSFRQLS--RRKVLIVLDDVTCF------RQIKSLIGM-LRN-------  270 (311)
Q Consensus       224 ~~l~~~~~-------------~~~~~----~~l~~~L~--~kr~LlVLDdV~~~------~~l~~l~~~-~~~-------  270 (311)
                      ..+.....             ...+.    ..+-..|.  ..+++|||||+...      +.+..+... +..       
T Consensus        80 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~s  159 (903)
T PRK04841         80 AALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLS  159 (903)
T ss_pred             HHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEe
Confidence            66642111             00122    22222222  67899999999753      234444321 111       


Q ss_pred             -----c------CCceEEEcC----CCChHHHHHHHHHh
Q 042778          271 -----C------CVKEKYEMK----ELGDDHALELFSRH  294 (311)
Q Consensus       271 -----~------~~~~~y~v~----~L~~~ea~~Lf~~~  294 (311)
                           .      ......++.    +|+.+|+.+||...
T Consensus       160 R~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~  198 (903)
T PRK04841        160 RNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQR  198 (903)
T ss_pred             CCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhc
Confidence                 0      112344565    89999999999764

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

Probab=98.03  E-value=3.4e-05  Score=79.10  Aligned_cols=48  Identities=23%  Similarity=0.301  Sum_probs=39.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -+.++||+.++..+...|....  ..-+.++|.+|+|||+||+.+++++.
T Consensus       181 l~~~igr~~ei~~~~~~L~~~~--~~n~lL~G~pG~GKT~l~~~la~~~~  228 (731)
T TIGR02639       181 IDPLIGREDELERTIQVLCRRK--KNNPLLVGEPGVGKTAIAEGLALRIA  228 (731)
T ss_pred             CCcccCcHHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHHHH
Confidence            3578999999999999886432  33467999999999999999999853

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.03  E-value=2.3e-05  Score=76.44  Aligned_cols=52  Identities=23%  Similarity=0.394  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.++.|.+..++++.+.+..           +-...+-+.++|++|+|||++|+++++.+...
T Consensus       181 ~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~  243 (512)
T TIGR03689       181 YADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQR  243 (512)
T ss_pred             HHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccc
Confidence            35678899999888876532           11225568999999999999999999987554

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.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.01  E-value=5.3e-05  Score=76.32  Aligned_cols=49  Identities=24%  Similarity=0.271  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++||.+..++.|.+.+..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        15 FdEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLn   63 (830)
T PRK07003         15 FASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALN   63 (830)
T ss_pred             HHHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3578999999999998887432 245567999999999999999998754

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=0.00011  Score=71.96  Aligned_cols=145  Identities=14%  Similarity=0.124  Sum_probs=83.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc--CcCceEEEecCcc-ccC-CCCChHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS--NFEGSCFLQNVRE-ESQ-RPGGLGFLQQ  220 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F~~~~wv~~~~~-~s~-~~~~~~~l~~  220 (311)
                      ++++|.+..+..|...+..+. -...+.++|+.|+||||+|+.+++.+..  .+...||.|..-. +.. ...++.    
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~----   88 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVL----   88 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceE----
Confidence            468999988888888877432 2456799999999999999999998642  2333445441000 000 000000    


Q ss_pred             HHHHHHhcCCC-CCCCHHHHHHHh-----CCCeEEEEEecCCCh--HHHHHhhcc----CCC-----------------c
Q 042778          221 KLLSKLLQDGI-VIPDIALSFRQL-----SRRKVLIVLDDVTCF--RQIKSLIGM----LRN-----------------C  271 (311)
Q Consensus       221 ~ll~~l~~~~~-~~~~~~~l~~~L-----~~kr~LlVLDdV~~~--~~l~~l~~~----~~~-----------------~  271 (311)
                          .+..... .+..+..+++.+     ..++-+||||+++..  ..++.|+..    ...                 .
T Consensus        89 ----el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~  164 (504)
T PRK14963         89 ----EIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTIL  164 (504)
T ss_pred             ----EecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHh
Confidence                0000000 111112222222     245568899999853  345555311    111                 2


Q ss_pred             CCceEEEcCCCChHHHHHHHHHhhcCC
Q 042778          272 CVKEKYEMKELGDDHALELFSRHAFKQ  298 (311)
Q Consensus       272 ~~~~~y~v~~L~~~ea~~Lf~~~af~~  298 (311)
                      .....|++.+|+.++..+.+.+.+-+.
T Consensus       165 SRc~~~~f~~ls~~el~~~L~~i~~~e  191 (504)
T PRK14963        165 SRTQHFRFRRLTEEEIAGKLRRLLEAE  191 (504)
T ss_pred             cceEEEEecCCCHHHHHHHHHHHHHHc
Confidence            345689999999999999998876543

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=0.00012  Score=71.19  Aligned_cols=49  Identities=24%  Similarity=0.226  Sum_probs=38.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -+++||.+..+..|...+..+. -...+.++|++|+||||+|+.+++.+.
T Consensus        13 ~~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~l~   61 (472)
T PRK14962         13 FSEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKSLN   61 (472)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3578999888787777776331 135688999999999999999998753

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.94  E-value=5.8e-05  Score=78.39  Aligned_cols=49  Identities=12%  Similarity=0.267  Sum_probs=40.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -+.++||+.++..+...|....  ..-+.++|.+|+||||||+.+++++..
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~--~~n~lLvG~pGvGKTal~~~La~~i~~  234 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRR--QNNPILTGEAGVGKTAVVEGLALRIAA  234 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCC--cCceeEECCCCCCHHHHHHHHHHHHhh
Confidence            4678999999999999886432  334569999999999999999998643

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.94  E-value=0.00015  Score=71.56  Aligned_cols=50  Identities=18%  Similarity=0.249  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..++.|...+..+ .-...+.++|+.|+||||+|+.+++.+..
T Consensus        15 f~diiGq~~~v~~L~~~i~~~-rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c   64 (546)
T PRK14957         15 FAEVAGQQHALNSLVHALETQ-KVHHAYLFTGTRGVGKTTLGRLLAKCLNC   64 (546)
T ss_pred             HHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            357899999999888888643 22456789999999999999999987543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.93  E-value=7.7e-05  Score=66.99  Aligned_cols=47  Identities=26%  Similarity=0.344  Sum_probs=33.4

Q ss_pred             CccchhhhHHHHHHh---hcc-------c---CCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVGVESRVEEIESL---LGA-------E---SKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~---L~~-------~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|++...++|.++   +..       +   ......+.++|.+|+||||+|+.+++.+
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l   66 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLF   66 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHH
Confidence            578888766665533   211       0   1235678899999999999999998864

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.

>PLN03025 replication factor C subunit; Provisional

Probab=97.92  E-value=8.2e-05  Score=68.82  Aligned_cols=136  Identities=16%  Similarity=0.236  Sum_probs=77.6

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .+++|.+..+..|..++..+  ..+.+-++|.+|+||||+|+++++.+.. .|...+.-.|   .+. ..+...+. .++
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln---~sd-~~~~~~vr-~~i   85 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDG--NMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELN---ASD-DRGIDVVR-NKI   85 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeec---ccc-cccHHHHH-HHH
Confidence            46789888888888776632  3455779999999999999999998633 3432211111   122 23333222 222


Q ss_pred             HHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh---cc--CCC----------------cCCceEEEcC
Q 042778          224 SKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI---GM--LRN----------------CCVKEKYEMK  280 (311)
Q Consensus       224 ~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~---~~--~~~----------------~~~~~~y~v~  280 (311)
                      .........         .-.++.-++|||+++..  .....|.   ..  ...                ......++++
T Consensus        86 ~~~~~~~~~---------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~  156 (319)
T PLN03025         86 KMFAQKKVT---------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFS  156 (319)
T ss_pred             HHHHhcccc---------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCC
Confidence            211110000         00134568999999853  2333332   11  000                1224578899


Q ss_pred             CCChHHHHHHHHHhhc
Q 042778          281 ELGDDHALELFSRHAF  296 (311)
Q Consensus       281 ~L~~~ea~~Lf~~~af  296 (311)
                      ++++++..+.+.+.+=
T Consensus       157 ~l~~~~l~~~L~~i~~  172 (319)
T PLN03025        157 RLSDQEILGRLMKVVE  172 (319)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999998888877664

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.89  E-value=0.00029  Score=66.38  Aligned_cols=49  Identities=24%  Similarity=0.293  Sum_probs=40.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.+..++.+.+.+..+ .-...+.++|+.|+||||+|+.+++.+.
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~-~~~h~~L~~Gp~G~GKTtla~~la~~l~   63 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLG-RIHHAWLLSGTRGVGKTTIARLLAKSLN   63 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcC-CCCeEEEEecCCCCCHHHHHHHHHHHhc
Confidence            357899999999988888643 2245678999999999999999999864

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.87  E-value=0.00024  Score=69.55  Aligned_cols=50  Identities=24%  Similarity=0.251  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..+..|...+..+ .-...+.++|..|+||||+|+.+++.+..
T Consensus        20 f~dliGq~~vv~~L~~ai~~~-ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc   69 (507)
T PRK06645         20 FAELQGQEVLVKVLSYTILND-RLAGGYLLTGIRGVGKTTSARIIAKAVNC   69 (507)
T ss_pred             HHHhcCcHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            357899999888888766533 22467889999999999999999998543

>PRK05642 DNA replication initiation factor; Validated

Probab=97.87  E-value=0.0001  Score=65.09  Aligned_cols=104  Identities=18%  Similarity=0.298  Sum_probs=62.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRK  247 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr  247 (311)
                      ...+.|||..|+|||.|++++.+.....-..++|++    ...       +....              ..+.+.+.+-.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~----~~~-------~~~~~--------------~~~~~~~~~~d   99 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLP----LAE-------LLDRG--------------PELLDNLEQYE   99 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEee----HHH-------HHhhh--------------HHHHHhhhhCC
Confidence            367899999999999999999987654334456666    111       11100              11222222222


Q ss_pred             EEEEEecCCCh---HHHH----Hhhc---cCC-------------C----------cCCceEEEcCCCChHHHHHHHHHh
Q 042778          248 VLIVLDDVTCF---RQIK----SLIG---MLR-------------N----------CCVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       248 ~LlVLDdV~~~---~~l~----~l~~---~~~-------------~----------~~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                       +||+||+...   .+|+    .+..   ..+             +          .....++++++++.++-.+++.++
T Consensus       100 -~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~k  178 (234)
T PRK05642        100 -LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLR  178 (234)
T ss_pred             -EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHH
Confidence             6788998521   2222    2211   000             0          234578999999999999999977


Q ss_pred             hcC
Q 042778          295 AFK  297 (311)
Q Consensus       295 af~  297 (311)
                      +..
T Consensus       179 a~~  181 (234)
T PRK05642        179 ASR  181 (234)
T ss_pred             HHH
Confidence            754

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

Probab=97.85  E-value=4.4e-05  Score=72.92  Aligned_cols=102  Identities=18%  Similarity=0.156  Sum_probs=64.5

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc--CcCceEEEecCccccCCCCChHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS--NFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      .++++.+..++.+...|..    .+.+.++|++|+|||++|+.+++.+..  .|+.+.|++    +++ ..+...+...+
T Consensus       175 ~d~~i~e~~le~l~~~L~~----~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~Vt----FHp-sySYeDFI~G~  245 (459)
T PRK11331        175 NDLFIPETTIETILKRLTI----KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQ----FHQ-SYSYEDFIQGY  245 (459)
T ss_pred             hcccCCHHHHHHHHHHHhc----CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEe----ecc-cccHHHHhccc
Confidence            4577788888888887763    346788999999999999999998643  456667777    555 55544433211


Q ss_pred             HHHHhcCCCC-CCCH--HHHHHHhC--CCeEEEEEecCCC
Q 042778          223 LSKLLQDGIV-IPDI--ALSFRQLS--RRKVLIVLDDVTC  257 (311)
Q Consensus       223 l~~l~~~~~~-~~~~--~~l~~~L~--~kr~LlVLDdV~~  257 (311)
                      .-  .+.... ....  +.++....  .++++||+|+++.
T Consensus       246 rP--~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINR  283 (459)
T PRK11331        246 RP--NGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINR  283 (459)
T ss_pred             CC--CCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhc
Confidence            00  000001 1111  33443332  3689999999974

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00014  Score=72.30  Aligned_cols=50  Identities=24%  Similarity=0.292  Sum_probs=40.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+++||.+..++.|.+.+..+. -...+.++|..|+||||+|+.+.+.+..
T Consensus        15 FddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323         15 FTTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             HHHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3578999999999998887432 2456789999999999999999997643

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=0.00027  Score=68.31  Aligned_cols=50  Identities=18%  Similarity=0.278  Sum_probs=40.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++||.+..+..|..++..+. -...+.++|..|+||||+|+.+++.+..
T Consensus        17 f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnc   66 (484)
T PRK14956         17 FRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNC   66 (484)
T ss_pred             HHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCc
Confidence            4578999999998888887432 1346889999999999999999998654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.81  E-value=0.00029  Score=65.24  Aligned_cols=48  Identities=19%  Similarity=0.326  Sum_probs=39.7

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+++|++..++.+..++..+  ..+.+.++|..|+||||+|+++.+.+..
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~GtGKT~la~~~~~~l~~   62 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP--NLPHLLVQGPPGSGKTAAVRALARELYG   62 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            56899999999998888643  3456789999999999999999998643

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.80  E-value=6.3e-05  Score=66.35  Aligned_cols=35  Identities=17%  Similarity=0.425  Sum_probs=30.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.++|.|..|.|||||...+.......|.++..++
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t   48 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLIT   48 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEe
Confidence            36789999999999999999999999997776665

This is thought to be an ATPase involved in viral DNA packaging [].

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

Probab=97.80  E-value=6.7e-05  Score=59.32  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=21.6

Q ss_pred             EEEeccCcchhHHHHHHHHHhhcc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      |.|+|..|+||||+|+.+++....
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~   24 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGF   24 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTS
T ss_pred             CEEECcCCCCeeHHHHHHHhhccc
Confidence            568999999999999999999753

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>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=97.79  E-value=2.9e-05  Score=62.19  Aligned_cols=79  Identities=19%  Similarity=0.351  Sum_probs=41.9

Q ss_pred             ccEEecCccccCCCChHHHHHHHHHhC-------CCcE----------EeeC-CCCCCCcchHHHHHHHHhccceeeeec
Q 042778           19 YDVFQSFRGEDNRDNFTGHLYSALSQK-------GIET----------FIDD-QLNRGDEISQSLVDAIEASAISLIIFS   80 (311)
Q Consensus        19 ~dvFis~~g~D~~~~f~~~L~~~L~~~-------gi~~----------f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S   80 (311)
                      |.|||||.+.|.. .....|...+...       .+..          +.+. +......|...|.++|..|.++||+.|
T Consensus         1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig   79 (130)
T PF08937_consen    1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG   79 (130)
T ss_dssp             ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred             CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence            5799999999864 3666666666663       2221          1222 333445789999999999999999999


Q ss_pred             cCcccccchHHHHHHHHh
Q 042778           81 EAYASSRWCLDELVKILT   98 (311)
Q Consensus        81 ~~y~~S~wcl~El~~i~e   98 (311)
                      ++-..|.|+-.|+...++
T Consensus        80 ~~T~~s~wV~~EI~~A~~   97 (130)
T PF08937_consen   80 PNTAKSKWVNWEIEYALK   97 (130)
T ss_dssp             TT----HHHHHHHHHHTT
T ss_pred             CCcccCcHHHHHHHHHHH
Confidence            999999999999876554

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.79  E-value=0.00018  Score=74.97  Aligned_cols=49  Identities=14%  Similarity=0.299  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -+.++||+.++..+...|....  ..-+.++|.+|+|||+||+.+.+++..
T Consensus       172 ~~~~igr~~ei~~~~~~l~r~~--~~n~lL~G~pGvGKT~l~~~la~~i~~  220 (852)
T TIGR03346       172 LDPVIGRDEEIRRTIQVLSRRT--KNNPVLIGEPGVGKTAIVEGLAQRIVN  220 (852)
T ss_pred             CCcCCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3568999999999999887532  334558999999999999999998644

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.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.00031  Score=70.08  Aligned_cols=50  Identities=28%  Similarity=0.274  Sum_probs=40.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++||.+..++.|..++..+. -...+.++|..|+||||+|+.+++.+..
T Consensus        14 FddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~LnC   63 (702)
T PRK14960         14 FNELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCLNC   63 (702)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3578999999999998887432 2567899999999999999999988643

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=0.00038  Score=69.55  Aligned_cols=49  Identities=22%  Similarity=0.319  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++||.+..++.|.+++..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        15 f~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~Ln   63 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSLN   63 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3578999988888888887432 246678999999999999999988754

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

Probab=97.77  E-value=0.0002  Score=64.92  Aligned_cols=109  Identities=15%  Similarity=0.137  Sum_probs=75.5

Q ss_pred             CCCccchh---hhHHHHHHhhccc-CCCeEEEEEeccCcchhHHHHHHHHHhhccCcC------ceEEEecCccccCCCC
Q 042778          144 KNQLVGVE---SRVEEIESLLGAE-SKDVYALGIWGIGGIDRTTIARAIFNKISSNFE------GSCFLQNVREESQRPG  213 (311)
Q Consensus       144 ~~~~vGr~---~~~~~l~~~L~~~-~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~------~~~wv~~~~~~s~~~~  213 (311)
                      .+..||..   ..++.|.++|... ....+-+.|+|-+|+|||+|++.+.+.....++      .++.+.    +.. .+
T Consensus        33 ~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq----~P~-~p  107 (302)
T PF05621_consen   33 ADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQ----MPP-EP  107 (302)
T ss_pred             cCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEe----cCC-CC
Confidence            45666654   3455666667643 234678999999999999999999987544443      234444    566 89


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCCH----HHHHHHhCCC-eEEEEEecCCC
Q 042778          214 GLGFLQQKLLSKLLQDGIVIPDI----ALSFRQLSRR-KVLIVLDDVTC  257 (311)
Q Consensus       214 ~~~~l~~~ll~~l~~~~~~~~~~----~~l~~~L~~k-r~LlVLDdV~~  257 (311)
                      +...+...||..++.........    ......|+.- -=+||+|++.+
T Consensus       108 ~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~  156 (302)
T PF05621_consen  108 DERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHN  156 (302)
T ss_pred             ChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHH
Confidence            99999999999998776522232    3344555553 34899999986

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

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.76  E-value=0.00011  Score=57.76  Aligned_cols=35  Identities=26%  Similarity=0.349  Sum_probs=27.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+.|+|.+|+||||+|+.+...........+++.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~   37 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYID   37 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEEC
Confidence            47899999999999999999998766553344444

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

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.75  E-value=0.00034  Score=70.19  Aligned_cols=141  Identities=15%  Similarity=0.132  Sum_probs=80.3

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      ..++||.+..+..|...+..+. -...+.++|..|+||||+|+.+++.+......         ... .++.....+.|.
T Consensus        15 f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~---------~~~-pCg~C~~C~~i~   83 (647)
T PRK07994         15 FAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNCETGI---------TAT-PCGECDNCREIE   83 (647)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhhccCC---------CCC-CCCCCHHHHHHH
Confidence            4578999999998888887432 14556899999999999999999876443110         000 111111111111


Q ss_pred             HH-------HhcCC-CCCCCHHHHHHH-----hCCCeEEEEEecCCC--hHHHHHhhc----cCCC--------------
Q 042778          224 SK-------LLQDG-IVIPDIALSFRQ-----LSRRKVLIVLDDVTC--FRQIKSLIG----MLRN--------------  270 (311)
Q Consensus       224 ~~-------l~~~~-~~~~~~~~l~~~-----L~~kr~LlVLDdV~~--~~~l~~l~~----~~~~--------------  270 (311)
                      ..       +.... ..++++..+.+.     ..+++-++|+|+|+.  ....+.|+.    .+..              
T Consensus        84 ~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl  163 (647)
T PRK07994         84 QGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLP  163 (647)
T ss_pred             cCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccc
Confidence            00       00000 001111111111     235666899999984  445665531    1111              


Q ss_pred             ---cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ---CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ---~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                         ......|++++|+.++..+.+.+.+
T Consensus       164 ~TI~SRC~~~~f~~Ls~~ei~~~L~~il  191 (647)
T PRK07994        164 VTILSRCLQFHLKALDVEQIRQQLEHIL  191 (647)
T ss_pred             hHHHhhheEeeCCCCCHHHHHHHHHHHH
Confidence               2335789999999999988887654

>PHA00729 NTP-binding motif containing protein

Probab=97.75  E-value=7.4e-05  Score=65.24  Aligned_cols=101  Identities=14%  Similarity=0.164  Sum_probs=59.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCc-------------CceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNF-------------EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVI  233 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-------------~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~  233 (311)
                      +...|.|.|.+|+||||||.++.+++..++             ..+.+++           ...+...|-.         
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid-----------~~~Ll~~L~~---------   75 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFE-----------LPDALEKIQD---------   75 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEE-----------HHHHHHHHHH---------
Confidence            455789999999999999999999854211             1122222           3333333321         


Q ss_pred             CCHHHHHHHhCC-Ce-EEEEEecC--CChH-HHH--------HhhccCCCcCCceEEEcCCCChHHHHHHHHHhhcC
Q 042778          234 PDIALSFRQLSR-RK-VLIVLDDV--TCFR-QIK--------SLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       234 ~~~~~l~~~L~~-kr-~LlVLDdV--~~~~-~l~--------~l~~~~~~~~~~~~y~v~~L~~~ea~~Lf~~~af~  297 (311)
                              ...+ .+ =|||+||+  |-.. .|.        .+.+..  ......+.+.+++.++..+++..+.+.
T Consensus        76 --------a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aL--rSR~~l~il~~ls~edL~~~Lr~Rg~~  142 (226)
T PHA00729         76 --------AIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALI--RTRVSAVIFTTPSPEDLAFYLREKGWY  142 (226)
T ss_pred             --------HHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHH--HhhCcEEEEecCCHHHHHHHHHhCCCc
Confidence                    1111 11 28999993  3221 111        111111  123466889999999999999998774

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

Probab=97.74  E-value=9e-05  Score=66.63  Aligned_cols=89  Identities=16%  Similarity=0.239  Sum_probs=58.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-H-----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-I-----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-~-----  236 (311)
                      -..++|.|-.|.|||||++.++++++.+|+..+++..+++-   ......+...+...-.....     ..++ .     
T Consensus        69 GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer---~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~  145 (274)
T cd01133          69 GGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGER---TREGNDLYHEMKESGVLSKTALVYGQMNEPPGARAR  145 (274)
T ss_pred             CCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccC---cHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            45789999999999999999999998888777777655442   34555555555432111100     1111 0     


Q ss_pred             -----HHHHHHh---CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL---SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L---~~kr~LlVLDdV~~~~  259 (311)
                           -.+.+++   .++++||++||+....
T Consensus       146 ~~~~a~~~AEyfr~~~g~~Vl~~~Dsltr~a  176 (274)
T cd01133         146 VALTGLTMAEYFRDEEGQDVLLFIDNIFRFT  176 (274)
T ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEeChhHHH
Confidence                 3344444   3799999999997543

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.74  E-value=0.00011  Score=76.63  Aligned_cols=49  Identities=14%  Similarity=0.284  Sum_probs=40.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -+.++||+.++..+++.|....  ..-+.++|.+|+||||||+.+..++..
T Consensus       177 l~~vigr~~ei~~~i~iL~r~~--~~n~lL~G~pGvGKT~l~~~la~~i~~  225 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIIN  225 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcCC--cCceEEECCCCCCHHHHHHHHHHHhhc
Confidence            4578999999999999887432  334568999999999999999998643

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.74  E-value=0.00035  Score=64.14  Aligned_cols=48  Identities=27%  Similarity=0.351  Sum_probs=39.6

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+++|++..++.+..++..+  ..+.+.|+|..|+||||+|+.+.+....
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~--~~~~~ll~G~~G~GKt~~~~~l~~~l~~   64 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEK--NMPHLLFAGPPGTGKTTAALALARELYG   64 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence            56889999999999888643  3445799999999999999999998543

>PRK08118 topology modulation protein; Reviewed

Probab=97.71  E-value=2.8e-05  Score=65.13  Aligned_cols=34  Identities=21%  Similarity=0.409  Sum_probs=28.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc---cCcCceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS---SNFEGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~---~~F~~~~wv~  203 (311)
                      .|.|+|++|+||||||+.+++...   .+||..+|-.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~   39 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKP   39 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhccc
Confidence            588999999999999999999854   3577777654

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.70  E-value=0.00027  Score=61.84  Aligned_cols=113  Identities=18%  Similarity=0.266  Sum_probs=66.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCc--eEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEG--SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~--~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ...+-|||..|+|||.|.+++++.+......  +++++           ...+...+...+..     .....+++.++.
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~-----------~~~f~~~~~~~~~~-----~~~~~~~~~~~~   97 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS-----------AEEFIREFADALRD-----GEIEEFKDRLRS   97 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE-----------HHHHHHHHHHHHHT-----TSHHHHHHHHCT
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec-----------HHHHHHHHHHHHHc-----ccchhhhhhhhc
Confidence            4567899999999999999999986654332  34444           23344444443332     122445555653


Q ss_pred             CeEEEEEecCCCh---HHHH-Hhh---------c---------cCC-C----------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF---RQIK-SLI---------G---------MLR-N----------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~---~~l~-~l~---------~---------~~~-~----------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                      - =+|+||||+..   ..|+ .+.         +         .+. .          ....-++++++++.++-.+++.
T Consensus        98 ~-DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~  176 (219)
T PF00308_consen   98 A-DLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQ  176 (219)
T ss_dssp             S-SEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHH
T ss_pred             C-CEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHH
Confidence            3 36788998642   2121 121         0         000 0          3456789999999999999999


Q ss_pred             HhhcC
Q 042778          293 RHAFK  297 (311)
Q Consensus       293 ~~af~  297 (311)
                      ++|-.
T Consensus       177 ~~a~~  181 (219)
T PF00308_consen  177 KKAKE  181 (219)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98754

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

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

Probab=97.67  E-value=0.00044  Score=65.82  Aligned_cols=52  Identities=17%  Similarity=0.340  Sum_probs=39.6

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++.|.+..+++|.+.+..           +-...+-+.++|.+|+|||+||+++++.....|
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~f  207 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATF  207 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCE
Confidence            4678999888888776531           112356789999999999999999999865543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.66  E-value=0.00051  Score=69.02  Aligned_cols=49  Identities=29%  Similarity=0.342  Sum_probs=40.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++||.+..++.|..++..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        15 FddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~Ln   63 (709)
T PRK08691         15 FADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKSLN   63 (709)
T ss_pred             HHHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhc
Confidence            3578999999999999887432 245789999999999999999988753

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.65  E-value=0.00045  Score=63.71  Aligned_cols=132  Identities=14%  Similarity=0.169  Sum_probs=77.4

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc------cCcCceEEEecCccccCCCCChHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS------SNFEGSCFLQNVREESQRPGGLGFL  218 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~------~~F~~~~wv~~~~~~s~~~~~~~~l  218 (311)
                      .+++|.+..++.+...+..+ .-.....++|+.|+||||+|+.+++.+.      .+.|...|...-   .. ......+
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~-~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~---~~-~i~v~~i   78 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKN-RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN---KK-SIGVDDI   78 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcC-CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc---CC-CCCHHHH
Confidence            46789988889898888643 2256778999999999999999999742      234444443310   11 2333332


Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCC--ChHHHHHhhc----cCC-C----------------cCCce
Q 042778          219 QQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVT--CFRQIKSLIG----MLR-N----------------CCVKE  275 (311)
Q Consensus       219 ~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~--~~~~l~~l~~----~~~-~----------------~~~~~  275 (311)
                      . .+...+...           -...++| ++|+|+++  +...++.|+.    +++ .                .....
T Consensus        79 r-~~~~~~~~~-----------p~~~~~k-v~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~  145 (313)
T PRK05564         79 R-NIIEEVNKK-----------PYEGDKK-VIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQ  145 (313)
T ss_pred             H-HHHHHHhcC-----------cccCCce-EEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhce
Confidence            2 232322111           0112344 44555543  4555555541    111 1                23357


Q ss_pred             EEEcCCCChHHHHHHHHHh
Q 042778          276 KYEMKELGDDHALELFSRH  294 (311)
Q Consensus       276 ~y~v~~L~~~ea~~Lf~~~  294 (311)
                      .+++++++.++..+.+.+.
T Consensus       146 ~~~~~~~~~~~~~~~l~~~  164 (313)
T PRK05564        146 IYKLNRLSKEEIEKFISYK  164 (313)
T ss_pred             eeeCCCcCHHHHHHHHHHH
Confidence            8899999999988877654

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.65  E-value=0.00069  Score=65.95  Aligned_cols=49  Identities=22%  Similarity=0.243  Sum_probs=38.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++||.+..++.|.+.+..+. -...+.++|..|+||||+|+.+++.+.
T Consensus        12 f~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~Ln   60 (491)
T PRK14964         12 FKDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCLN   60 (491)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHHc
Confidence            4578999988888887776432 145788999999999999999988653

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.63  E-value=0.00015  Score=75.44  Aligned_cols=48  Identities=23%  Similarity=0.410  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -+.++||+.+++.+.+.|....  ..-+.++|.+|+|||+||+.++.++.
T Consensus       178 ~~~~igr~~ei~~~~~~L~r~~--~~n~lL~G~pGvGKTal~~~la~~i~  225 (821)
T CHL00095        178 LDPVIGREKEIERVIQILGRRT--KNNPILIGEPGVGKTAIAEGLAQRIV  225 (821)
T ss_pred             CCCCCCcHHHHHHHHHHHcccc--cCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            3578999999999999997432  23456999999999999999999854

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.63  E-value=0.0004  Score=61.41  Aligned_cols=36  Identities=14%  Similarity=0.246  Sum_probs=27.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .+.+.|+|+.|+|||+|++++++.....-..+.++.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~   80 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVP   80 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            467899999999999999999998654433345554

>PRK09087 hypothetical protein; Validated

Probab=97.62  E-value=0.00015  Score=63.81  Aligned_cols=25  Identities=20%  Similarity=0.078  Sum_probs=22.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.+.|||..|+|||+|++++++..
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~   68 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKS   68 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhc
Confidence            4568999999999999999988764

>PRK12377 putative replication protein; Provisional

Probab=97.62  E-value=0.00018  Score=64.00  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=29.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...+.|+|..|+|||+||.++.+.+......+.++.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~  136 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVT  136 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEE
Confidence            457899999999999999999999766544556665

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.62  E-value=0.0012  Score=62.71  Aligned_cols=50  Identities=28%  Similarity=0.274  Sum_probs=40.3

Q ss_pred             CCccchhhhHHHHHHhhcccCC--------CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGAESK--------DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++++|.+..++.|...+..+.+        -...+.++|+.|+||||+|+.+++.+-.
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c   62 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQC   62 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            4688999999999998875431        2567889999999999999999887543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.60  E-value=0.00046  Score=67.79  Aligned_cols=49  Identities=20%  Similarity=0.265  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++||.+..++.|.+.+..+. -...+.++|+.|+||||+|+.+.+.+.
T Consensus        15 f~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk~l~   63 (509)
T PRK14958         15 FQEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAKCLN   63 (509)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHHHhc
Confidence            3578999999999999886431 245678999999999999999999754

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

Probab=97.60  E-value=7.6e-05  Score=61.12  Aligned_cols=65  Identities=25%  Similarity=0.392  Sum_probs=55.8

Q ss_pred             cEEecCccccC-CCChHHHHHHHHHhC-CCcEEeeC-CCCC--CCcchHHHHHHHHhccceeeeeccCcc
Q 042778           20 DVFQSFRGEDN-RDNFTGHLYSALSQK-GIETFIDD-QLNR--GDEISQSLVDAIEASAISLIIFSEAYA   84 (311)
Q Consensus        20 dvFis~~g~D~-~~~f~~~L~~~L~~~-gi~~f~d~-~~~~--G~~~~~~i~~ai~~s~~~i~v~S~~y~   84 (311)
                      -|||||+.... ...+|-.|+..|++. |+.|.+|. +...  +..+...+.+.|++++..|+|+||.|.
T Consensus         2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~~   71 (150)
T PF08357_consen    2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGYK   71 (150)
T ss_pred             eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccchh
Confidence            49999999543 346799999999999 99999998 6644  678889999999999999999998763

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 [].

>CHL00176 ftsH cell division protein; Validated

Probab=97.59  E-value=0.00034  Score=70.35  Aligned_cols=51  Identities=24%  Similarity=0.291  Sum_probs=37.4

Q ss_pred             CCCccchhhhHHHHHHhhcc---c-------CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGA---E-------SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---~-------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+...+++.+++..   .       ..-.+-+.++|.+|+|||+||++++.....
T Consensus       182 f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~  242 (638)
T CHL00176        182 FRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEV  242 (638)
T ss_pred             HHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            56788998777776665422   1       111456899999999999999999987543

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

Probab=97.58  E-value=0.00043  Score=66.53  Aligned_cols=52  Identities=25%  Similarity=0.424  Sum_probs=40.0

Q ss_pred             CCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          145 NQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++.|++..+++|.+.+...           -...+-+.++|.+|+|||+||+++++.....|
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~f  245 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATF  245 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCE
Confidence            35678999999888866421           12345688999999999999999999876655

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.57  E-value=0.00068  Score=61.71  Aligned_cols=47  Identities=19%  Similarity=0.304  Sum_probs=31.6

Q ss_pred             CccchhhhHHHHHHhhc---c-------c--CC-CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVGVESRVEEIESLLG---A-------E--SK-DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~---~-------~--~~-~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|.+...++|.++..   .       +  .. ...-+.++|.+|.||||+|+.+++.+
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l   82 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQIL   82 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHH
Confidence            57787766666554321   1       0  01 12358899999999999998888764

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.

>PRK08116 hypothetical protein; Validated

Probab=97.57  E-value=0.00016  Score=65.24  Aligned_cols=74  Identities=26%  Similarity=0.356  Sum_probs=44.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeE
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKV  248 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~  248 (311)
                      .-+.|+|..|+|||.||.++++.+..+-..++++.           ...+...+........  ......+.+.+.+-. 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~-----------~~~ll~~i~~~~~~~~--~~~~~~~~~~l~~~d-  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN-----------FPQLLNRIKSTYKSSG--KEDENEIIRSLVNAD-  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE-----------HHHHHHHHHHHHhccc--cccHHHHHHHhcCCC-
Confidence            35889999999999999999999765533445554           2223333332222111  111233444455444 


Q ss_pred             EEEEecCC
Q 042778          249 LIVLDDVT  256 (311)
Q Consensus       249 LlVLDdV~  256 (311)
                      ||||||+.
T Consensus       181 lLviDDlg  188 (268)
T PRK08116        181 LLILDDLG  188 (268)
T ss_pred             EEEEeccc
Confidence            89999993

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.56  E-value=0.00072  Score=65.57  Aligned_cols=113  Identities=12%  Similarity=0.138  Sum_probs=67.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCc--eEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEG--SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~--~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ...+.|+|..|+|||+|++++.+.+...+..  +.++.           ...+...+...+...     ....+.+.++.
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~~  211 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVT-----------SEKFTNDFVNALRNN-----TMEEFKEKYRS  211 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHHHHHHHcC-----cHHHHHHHHhc
Confidence            4568999999999999999999997766533  33444           122233333333211     11334444443


Q ss_pred             CeEEEEEecCCCh---H-HHHHh-------hccCCC----------------------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF---R-QIKSL-------IGMLRN----------------------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~---~-~l~~l-------~~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                       --+||||||...   + ..+.+       ......                      .....++++++++.++-.+++.
T Consensus       212 -~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~  290 (450)
T PRK00149        212 -VDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILK  290 (450)
T ss_pred             -CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHH
Confidence             337888999531   1 11111       100000                      3344678999999999999999


Q ss_pred             HhhcC
Q 042778          293 RHAFK  297 (311)
Q Consensus       293 ~~af~  297 (311)
                      +++-.
T Consensus       291 ~~~~~  295 (450)
T PRK00149        291 KKAEE  295 (450)
T ss_pred             HHHHH
Confidence            98753

>PRK07261 topology modulation protein; Provisional

Probab=97.56  E-value=0.00026  Score=59.47  Aligned_cols=34  Identities=21%  Similarity=0.400  Sum_probs=25.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc---CcCceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS---NFEGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~---~F~~~~wv~  203 (311)
                      .|.|+|++|+||||||+.+......   +.|...|-.
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~   38 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQP   38 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEecc
Confidence            4899999999999999999876422   345555543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.55  E-value=0.00057  Score=66.03  Aligned_cols=113  Identities=10%  Similarity=0.114  Sum_probs=66.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRK  247 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr  247 (311)
                      ..-+.|+|..|+|||+|++++.+.+...-..+.++.           ...+...+...+...     ....++..++. .
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~-----------~~~f~~~~~~~l~~~-----~~~~f~~~~~~-~  203 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVR-----------SELFTEHLVSAIRSG-----EMQRFRQFYRN-V  203 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEee-----------HHHHHHHHHHHHhcc-----hHHHHHHHccc-C
Confidence            356889999999999999999998754433344554           122333333333211     11334444433 3


Q ss_pred             EEEEEecCCChH-------HHHHh----hccCCC----------------------cCCceEEEcCCCChHHHHHHHHHh
Q 042778          248 VLIVLDDVTCFR-------QIKSL----IGMLRN----------------------CCVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       248 ~LlVLDdV~~~~-------~l~~l----~~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                      -+|++||+....       .+-.+    ......                      ...+.++++++++.++-..++.++
T Consensus       204 dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k  283 (445)
T PRK12422        204 DALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERK  283 (445)
T ss_pred             CEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHH
Confidence            477789985321       11111    100000                      334578899999999999999887


Q ss_pred             hcC
Q 042778          295 AFK  297 (311)
Q Consensus       295 af~  297 (311)
                      +=.
T Consensus       284 ~~~  286 (445)
T PRK12422        284 AEA  286 (445)
T ss_pred             HHH
Confidence            743

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.53  E-value=0.00081  Score=65.14  Aligned_cols=114  Identities=17%  Similarity=0.255  Sum_probs=68.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC--ceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE--GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~--~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ..-+.|+|..|+|||+|++++.+.+.....  .++++.           ...+...+...+....   ..++.+++.++.
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~-----------~~~f~~~~~~~l~~~~---~~~~~~~~~~~~  206 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS-----------GDEFARKAVDILQKTH---KEIEQFKNEICQ  206 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHHHHHHHHhh---hHHHHHHHHhcc
Confidence            356889999999999999999997654322  223443           2344555554443211   112334444443


Q ss_pred             CeEEEEEecCCCh----HHHHHhh-------ccCCC----------------------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF----RQIKSLI-------GMLRN----------------------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~----~~l~~l~-------~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                       .-+|||||+...    ...+.+.       .....                      ...+-+.++++++.++-.+++.
T Consensus       207 -~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~  285 (450)
T PRK14087        207 -NDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIK  285 (450)
T ss_pred             -CCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHH
Confidence             347888999632    1122221       00000                      3345678899999999999999


Q ss_pred             Hhhc
Q 042778          293 RHAF  296 (311)
Q Consensus       293 ~~af  296 (311)
                      +++=
T Consensus       286 ~~~~  289 (450)
T PRK14087        286 KEIK  289 (450)
T ss_pred             HHHH
Confidence            8874

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.52  E-value=0.00072  Score=68.02  Aligned_cols=47  Identities=19%  Similarity=0.309  Sum_probs=38.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++++|.+..+..+.+.+..  .....+.|+|.+|+||||||+.+++..
T Consensus       153 ~~~iiGqs~~~~~l~~~ia~--~~~~~vlL~Gp~GtGKTTLAr~i~~~~  199 (615)
T TIGR02903       153 FSEIVGQERAIKALLAKVAS--PFPQHIILYGPPGVGKTTAARLALEEA  199 (615)
T ss_pred             HHhceeCcHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            46789999988888777643  235579999999999999999998864

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.52  E-value=0.00035  Score=62.08  Aligned_cols=50  Identities=12%  Similarity=0.153  Sum_probs=33.8

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +..+.+....-......+.++|.+|+|||+||.++.+.+...-..++++.
T Consensus        85 l~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it  134 (244)
T PRK07952         85 LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT  134 (244)
T ss_pred             HHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            34444444322223457889999999999999999998655444555655

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.52  E-value=0.0017  Score=60.64  Aligned_cols=49  Identities=20%  Similarity=0.255  Sum_probs=39.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+++|.+..++.+.+.+..+. -...+-++|..|+||||+|+.+.+.+.
T Consensus        13 ~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~   61 (355)
T TIGR02397        13 FEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALN   61 (355)
T ss_pred             HhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3568999999999998886432 245778999999999999999998753

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

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

Probab=97.52  E-value=0.002  Score=59.47  Aligned_cols=146  Identities=18%  Similarity=0.323  Sum_probs=89.6

Q ss_pred             CCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          145 NQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      .++=|.+..+++|.+-....           -+..+=|.+||++|.|||-||++|+++....|     +.    +..   
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtF-----Ir----vvg---  218 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATF-----IR----VVG---  218 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceE-----EE----ecc---
Confidence            34558899999988866431           12356788999999999999999999986654     43    222   


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCCHHHHHHHhC-CCeEEEEEecCCC-------------hH----HHHHhh---c--cCCC
Q 042778          214 GLGFLQQKLLSKLLQDGIVIPDIALSFRQLS-RRKVLIVLDDVTC-------------FR----QIKSLI---G--MLRN  270 (311)
Q Consensus       214 ~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~-~kr~LlVLDdV~~-------------~~----~l~~l~---~--~~~~  270 (311)
                            .+|.....++...+  +..+.+.-+ +..++|.+|.++.             .+    .++-|.   |  ..++
T Consensus       219 ------SElVqKYiGEGaRl--VRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~n  290 (406)
T COG1222         219 ------SELVQKYIGEGARL--VRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGN  290 (406)
T ss_pred             ------HHHHHHHhccchHH--HHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCC
Confidence                  12333333332200  022222222 4678999999873             11    111111   1  0111


Q ss_pred             --------------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          271 --------------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       271 --------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                                          ...++.++++.-+.+.-.++|.=|+-+=+ ...-+|+.|++
T Consensus       291 vKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~  351 (406)
T COG1222         291 VKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLAR  351 (406)
T ss_pred             eEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHH
Confidence                                34678899998888888889988876533 44567877764

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.51  E-value=0.0015  Score=60.13  Aligned_cols=49  Identities=18%  Similarity=0.175  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+...+.+..++..+ .-..++.++|.+|+||||+|+++++...
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~-~~~~~lll~G~~G~GKT~la~~l~~~~~   68 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKG-RIPNMLLHSPSPGTGKTTVAKALCNEVG   68 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcC-CCCeEEEeeCcCCCCHHHHHHHHHHHhC
Confidence            357899999999998888742 2256777799999999999999998764

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.49  E-value=0.00085  Score=65.89  Aligned_cols=52  Identities=17%  Similarity=0.245  Sum_probs=37.2

Q ss_pred             CCCccchhhhHHHHHHhhcc----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -++++|.+...+++.+++..          +....+-+.++|++|+|||+||+++++.....
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~  115 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP  115 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            56788988777666654431          11224458899999999999999999875443

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.48  E-value=0.00099  Score=65.79  Aligned_cols=50  Identities=26%  Similarity=0.321  Sum_probs=39.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..++.+...+..+. -...+.++|..|+||||+|+.+.+.+..
T Consensus        15 f~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   64 (527)
T PRK14969         15 FSELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAKSLNC   64 (527)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3568999999998888887432 1456789999999999999999987643

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.47  E-value=0.0018  Score=61.04  Aligned_cols=137  Identities=15%  Similarity=0.217  Sum_probs=79.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC--------cCceEEEecCccccCCCCCh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN--------FEGSCFLQNVREESQRPGGL  215 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~--------F~~~~wv~~~~~~s~~~~~~  215 (311)
                      -++++|.+..++.+.+.+..+ .-.+.+-++|+.|+||||+|+.+.+.+...        |...+.-.+   ... ..+.
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~-~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~---~~~-~~~~   90 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENN-HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELD---AAS-NNSV   90 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEec---ccc-CCCH
Confidence            356899999999998888643 225688899999999999999998875431        222111110   011 1222


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh----ccCCC-----------------cC
Q 042778          216 GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI----GMLRN-----------------CC  272 (311)
Q Consensus       216 ~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~----~~~~~-----------------~~  272 (311)
                      ..+. .++..+...            -..+++-+||+|+++..  ..++.+.    ..+..                 ..
T Consensus        91 ~~i~-~l~~~~~~~------------p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~s  157 (367)
T PRK14970         91 DDIR-NLIDQVRIP------------PQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILS  157 (367)
T ss_pred             HHHH-HHHHHHhhc------------cccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHh
Confidence            2222 222221100            01234457899988643  2344442    11111                 12


Q ss_pred             CceEEEcCCCChHHHHHHHHHhhcCC
Q 042778          273 VKEKYEMKELGDDHALELFSRHAFKQ  298 (311)
Q Consensus       273 ~~~~y~v~~L~~~ea~~Lf~~~af~~  298 (311)
                      ....++.++++.++....+...+-..
T Consensus       158 r~~~v~~~~~~~~~l~~~l~~~~~~~  183 (367)
T PRK14970        158 RCQIFDFKRITIKDIKEHLAGIAVKE  183 (367)
T ss_pred             cceeEecCCccHHHHHHHHHHHHHHc
Confidence            34578999999999888888766543

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.47  E-value=9.3e-05  Score=57.95  Aligned_cols=23  Identities=22%  Similarity=0.405  Sum_probs=21.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|+|.|++|+||||+|+.+.+++
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999975

...

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.47  E-value=0.00051  Score=65.50  Aligned_cols=50  Identities=18%  Similarity=0.182  Sum_probs=39.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..++.|...+..+. -...+.++|+.|+||||+|+.+++.+..
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~c   64 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4578999988888888886431 1445889999999999999999998644

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.00082  Score=62.95  Aligned_cols=143  Identities=17%  Similarity=0.139  Sum_probs=84.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC----cCceEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN----FEGSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~----F~~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      ...++|.+.....+...+..+ .-...+.|+|..|+||||+|..+.+.+-.+    +.....       .. ..+-....
T Consensus        22 ~~~l~Gh~~a~~~L~~a~~~g-rl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~-------~~-~~~~c~~c   92 (351)
T PRK09112         22 NTRLFGHEEAEAFLAQAYREG-KLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETL-------AD-PDPASPVW   92 (351)
T ss_pred             hhhccCcHHHHHHHHHHHHcC-CCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcccc-------CC-CCCCCHHH
Confidence            467899999999998888743 225578999999999999999999986442    111100       00 11111122


Q ss_pred             HHHHHH-------HhcC---CC-------CCCCHHHHHHHhC-----CCeEEEEEecCCC--hHHHHHhh----ccCCC-
Q 042778          220 QKLLSK-------LLQD---GI-------VIPDIALSFRQLS-----RRKVLIVLDDVTC--FRQIKSLI----GMLRN-  270 (311)
Q Consensus       220 ~~ll~~-------l~~~---~~-------~~~~~~~l~~~L~-----~kr~LlVLDdV~~--~~~l~~l~----~~~~~-  270 (311)
                      +.+...       +...   ..       .++++..+.+++.     +++-++|+|+++.  ....+.|+    ..+.. 
T Consensus        93 ~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~  172 (351)
T PRK09112         93 RQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARA  172 (351)
T ss_pred             HHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCc
Confidence            222111       1000   00       0111234444443     4566899999985  33444443    11111 


Q ss_pred             ----------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ----------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ----------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                      ......+.+.+|+.++..+++...+
T Consensus       173 ~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~  213 (351)
T PRK09112        173 LFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLG  213 (351)
T ss_pred             eEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhh
Confidence                            2344689999999999999998754

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.45  E-value=0.0011  Score=64.05  Aligned_cols=113  Identities=11%  Similarity=0.135  Sum_probs=66.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC--ceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE--GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~--~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ..-+.|||..|+|||+|++++++.+.....  .+.|+.           ...+...+...+...     ....+++.++.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~-----------~~~f~~~~~~~~~~~-----~~~~f~~~~~~  193 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT-----------SEKFLNDLVDSMKEG-----KLNEFREKYRK  193 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHHHHHHhcc-----cHHHHHHHHHh
Confidence            445999999999999999999998765543  234544           122333443333211     12233333333


Q ss_pred             CeEEEEEecCCCh---H----HHHHhh----ccCCC----------------------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF---R----QIKSLI----GMLRN----------------------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~---~----~l~~l~----~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                      +.-+|+|||+...   .    .+-.+.    .....                      ...+.+.++++.+.+.-..++.
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~  273 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIAR  273 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHH
Confidence            3447778888632   1    111111    00000                      2344678899999999999998


Q ss_pred             Hhhc
Q 042778          293 RHAF  296 (311)
Q Consensus       293 ~~af  296 (311)
                      +.+-
T Consensus       274 ~~~~  277 (440)
T PRK14088        274 KMLE  277 (440)
T ss_pred             HHHH
Confidence            8874

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.45  E-value=0.0013  Score=65.43  Aligned_cols=49  Identities=24%  Similarity=0.219  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+..++.+...+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~-rl~hA~Lf~GP~GvGKTTlA~~lAk~L~   63 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNN-KLTHAYIFSGPRGIGKTSIAKIFAKAIN   63 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            357899999999888887643 2246788999999999999999999864

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.44  E-value=0.00073  Score=63.28  Aligned_cols=98  Identities=17%  Similarity=0.195  Sum_probs=62.1

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc-Cce-EEEecCccccCCCCChHHHHHHHHHHHhcCCCCCC
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF-EGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIP  234 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~  234 (311)
                      +++++..-. .-..++|+|..|+|||||++.+++.+..+. +.. +|+.    +.++.....++.+.++..+.....+..
T Consensus       123 vID~l~PiG-kGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~l----IgER~~EV~df~~~i~~~Vvast~de~  197 (380)
T PRK12608        123 VVDLVAPIG-KGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLL----IDERPEEVTDMRRSVKGEVYASTFDRP  197 (380)
T ss_pred             hhhheeecC-CCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEE----ecCCCCCHHHHHHHHhhhEEeecCCCC
Confidence            666665322 234569999999999999999999876544 443 4444    333366778888888776554322111


Q ss_pred             C---H------HHHHHHh--CCCeEEEEEecCCChH
Q 042778          235 D---I------ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       235 ~---~------~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                      .   .      ..+-+++  .+++++||+|++....
T Consensus       198 ~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr~A  233 (380)
T PRK12608        198 PDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLA  233 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHHHH
Confidence            1   1      1122222  4799999999997543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0024  Score=63.57  Aligned_cols=50  Identities=26%  Similarity=0.250  Sum_probs=40.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++||.+..++.|...+..+ .-...+.++|..|+||||+|+.+++.+..
T Consensus        12 f~eivGq~~i~~~L~~~i~~~-r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   61 (584)
T PRK14952         12 FAEVVGQEHVTEPLSSALDAG-RINHAYLFSGPRGCGKTSSARILARSLNC   61 (584)
T ss_pred             HHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            357899999999999888743 12445789999999999999999987653

>COG3903 Predicted ATPase [General function prediction only]

Probab=97.43  E-value=0.00017  Score=67.47  Aligned_cols=124  Identities=20%  Similarity=0.243  Sum_probs=83.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-CCCCH-HHHHHHhC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-VIPDI-ALSFRQLS  244 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-~~~~~-~~l~~~L~  244 (311)
                      ..+.+.++|.|||||||++-.+.. +...|....|+.+..+++.     ..+.--++....+-.. .-++. ..+..++.
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~~~~~~v~~vdl~pitD-----~~~v~~~~ag~~gl~~~~g~~~~~~~~~~~~   86 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AASEYADGVAFVDLAPITD-----PALVFPTLAGALGLHVQPGDSAVDTLVRRIG   86 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-HhhhcccceeeeeccccCc-----hhHhHHHHHhhcccccccchHHHHHHHHHHh
Confidence            478999999999999999999999 8888987777776666555     2222222222122111 21222 57788889


Q ss_pred             CCeEEEEEecCCChHH-----HHHhhccCCC------------cCCceEEEcCCCChH-HHHHHHHHhhc
Q 042778          245 RRKVLIVLDDVTCFRQ-----IKSLIGMLRN------------CCVKEKYEMKELGDD-HALELFSRHAF  296 (311)
Q Consensus       245 ~kr~LlVLDdV~~~~~-----l~~l~~~~~~------------~~~~~~y~v~~L~~~-ea~~Lf~~~af  296 (311)
                      ++|.++|+||..+...     +..+.+.+..            ...+..+.++.|+.. ++.++|.-.|-
T Consensus        87 ~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~  156 (414)
T COG3903          87 DRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAV  156 (414)
T ss_pred             hhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHH
Confidence            9999999999865321     2233333222            445677888988877 79999887764

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

Probab=97.42  E-value=0.00088  Score=68.68  Aligned_cols=47  Identities=23%  Similarity=0.303  Sum_probs=38.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -+.++||+.++.++.+.|....  ..-+.++|.+|+|||+||+.+++++
T Consensus       185 ~~~liGR~~ei~~~i~iL~r~~--~~n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        185 IDPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CCcCcCCCHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHHHH
Confidence            3579999999999999887532  2234579999999999999999874

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.42  E-value=0.0019  Score=66.79  Aligned_cols=50  Identities=20%  Similarity=0.216  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++||.+..++.|...|..+. -...+.++|..|+||||+|+.+.+.+.+
T Consensus        14 f~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C   63 (824)
T PRK07764         14 FAEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNC   63 (824)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCc
Confidence            3468999988888888887432 1356789999999999999999998643

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.41  E-value=0.0049  Score=52.30  Aligned_cols=26  Identities=19%  Similarity=0.189  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+.++|..|+||||+|+.+.+.+.
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~l~   39 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKALL   39 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHc
Confidence            46789999999999999999998854

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.0015  Score=65.16  Aligned_cols=50  Identities=20%  Similarity=0.217  Sum_probs=39.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..++.|...+..+ .-...+.++|..|+||||+|+.+.+.+..
T Consensus        15 f~dIiGQe~v~~~L~~ai~~~-ri~ha~Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959         15 FAEVAGQETVKAILSRAAQEN-RVAPAYLFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             HHHhcCCHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHhccc
Confidence            356789888888888877633 12567889999999999999999988643

>PRK06696 uridine kinase; Validated

Probab=97.36  E-value=0.00027  Score=61.93  Aligned_cols=46  Identities=17%  Similarity=0.211  Sum_probs=36.4

Q ss_pred             chhhhHHHHHHhhcc-cCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          149 GVESRVEEIESLLGA-ESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .|+..+++|.+.+.. ......+|+|.|.+|.||||||+.+.+.+..
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKK   48 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            356677777777653 3445889999999999999999999987643

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.36  E-value=0.00067  Score=59.44  Aligned_cols=58  Identities=19%  Similarity=0.330  Sum_probs=35.1

Q ss_pred             CCcc-chhh-hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          145 NQLV-GVES-RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       145 ~~~v-Gr~~-~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++++ |... .+..+.++.. .....+.+.|+|..|+|||+||+++++.....=....+++
T Consensus        18 d~f~~~~~~~~~~~l~~~~~-~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~   77 (227)
T PRK08903         18 DNFVAGENAELVARLRELAA-GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLD   77 (227)
T ss_pred             cccccCCcHHHHHHHHHHHh-ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            3444 4433 3333444433 2233567889999999999999999997533222334444

>PRK06620 hypothetical protein; Validated

Probab=97.34  E-value=0.00033  Score=61.09  Aligned_cols=25  Identities=20%  Similarity=0.187  Sum_probs=21.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +.+-|||..|+|||+|++++.+...
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~   69 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSN   69 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccC
Confidence            6789999999999999999877653

>CHL00181 cbbX CbbX; Provisional

Probab=97.33  E-value=0.003  Score=57.55  Aligned_cols=48  Identities=21%  Similarity=0.262  Sum_probs=32.4

Q ss_pred             CCccchhhhHHHHHHhh---cc-------c---CCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          145 NQLVGVESRVEEIESLL---GA-------E---SKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L---~~-------~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+++|.+...++|.++.   ..       +   .+....+.++|.+|+||||+|+.+++..
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~   83 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADIL   83 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            45788776666554432   11       0   1123357889999999999999998864

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.31  E-value=0.0026  Score=63.67  Aligned_cols=51  Identities=22%  Similarity=0.339  Sum_probs=41.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+++|.+..++.|.+.+..+. -...+.++|..|+||||+|+.+++.+...
T Consensus        23 f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~   73 (598)
T PRK09111         23 FDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARALNYE   73 (598)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhhCcC
Confidence            4578999999999999887432 25578899999999999999999986543

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.30  E-value=0.0022  Score=64.37  Aligned_cols=50  Identities=18%  Similarity=0.224  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++||.+..+..|...+..+ .-...+.++|+.|+||||+|+.+.+.+..
T Consensus        15 f~eivGQe~i~~~L~~~i~~~-ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMD-RVGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcC-CCCeeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            357899998888888877632 12455889999999999999999988644

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.30  E-value=0.0023  Score=61.21  Aligned_cols=113  Identities=14%  Similarity=0.173  Sum_probs=66.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCc--eEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEG--SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~--~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ...+.|+|..|+|||+|++++++.+......  ++++.           ...+...+...+...     ....+.+.+++
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~~  199 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS-----------SEKFTNDFVNALRNN-----KMEEFKEKYRS  199 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE-----------HHHHHHHHHHHHHcC-----CHHHHHHHHHh
Confidence            3568899999999999999999987655432  34443           122333344333221     12334444433


Q ss_pred             CeEEEEEecCCCh---HH-HHHhh-------ccCCC----------------------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF---RQ-IKSLI-------GMLRN----------------------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~---~~-l~~l~-------~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                       .-+|||||+...   +. .+.+.       .....                      .....++++++.+.++-..++.
T Consensus       200 -~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~  278 (405)
T TIGR00362       200 -VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQ  278 (405)
T ss_pred             -CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHH
Confidence             237888999632   11 11111       00000                      2234578899999999999999


Q ss_pred             HhhcC
Q 042778          293 RHAFK  297 (311)
Q Consensus       293 ~~af~  297 (311)
                      +++-.
T Consensus       279 ~~~~~  283 (405)
T TIGR00362       279 KKAEE  283 (405)
T ss_pred             HHHHH
Confidence            88754

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).

>PRK07667 uridine kinase; Provisional

Probab=97.29  E-value=0.00056  Score=58.55  Aligned_cols=40  Identities=18%  Similarity=0.368  Sum_probs=31.7

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +..+.+.|........+|||.|.+|.||||+|+.+...+.
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~   42 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMK   42 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3455666655455578999999999999999999998754

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

Probab=97.29  E-value=0.00021  Score=66.60  Aligned_cols=30  Identities=27%  Similarity=0.459  Sum_probs=26.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -.+.++|||++|+|||.+|++++++....|
T Consensus       147 ~PlgllL~GPPGcGKTllAraiA~elg~~~  176 (413)
T PLN00020        147 VPLILGIWGGKGQGKSFQCELVFKKMGIEP  176 (413)
T ss_pred             CCeEEEeeCCCCCCHHHHHHHHHHHcCCCe
Confidence            378999999999999999999999976654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.28  E-value=0.0014  Score=57.52  Aligned_cols=47  Identities=15%  Similarity=0.244  Sum_probs=33.2

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC------cCceEEEe
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN------FEGSCFLQ  203 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F~~~~wv~  203 (311)
                      |..+|..+-..-.++.|+|.+|+||||||..++-.....      -..++|++
T Consensus         8 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~   60 (235)
T cd01123           8 LDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID   60 (235)
T ss_pred             hHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEe
Confidence            444554333446799999999999999999887543221      25778887

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.27  E-value=0.0046  Score=63.68  Aligned_cols=53  Identities=19%  Similarity=0.295  Sum_probs=38.9

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -.++.|.+...++|.+.+..           +-...+-+.++|.+|+|||+||+++++.....|
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~f  515 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANF  515 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCE
Confidence            35677888887777775532           111245688999999999999999999876544

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.27  E-value=0.00028  Score=65.75  Aligned_cols=51  Identities=12%  Similarity=0.253  Sum_probs=42.4

Q ss_pred             CCCccchhhhHHHHHHhhccc----CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAE----SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..++++.+.+...    ....++++|+|++|.||||||+++.+.+..
T Consensus        50 ~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             chhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            448999999999999988642    223689999999999999999999987543

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.26  E-value=0.0068  Score=59.29  Aligned_cols=49  Identities=22%  Similarity=0.236  Sum_probs=39.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+..+..+.+.+..+. -.....++|..|+||||+|+.++..+.
T Consensus        15 f~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~L~   63 (486)
T PRK14953         15 FKEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKVLN   63 (486)
T ss_pred             HHHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3568899999999998886432 245667899999999999999998754

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

Probab=97.25  E-value=0.0042  Score=63.94  Aligned_cols=50  Identities=16%  Similarity=0.335  Sum_probs=39.6

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|.+..++.+...+...      ++. ..++.++|+.|+|||+||+.++..+.
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~  509 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG  509 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc
Confidence            567889999888888877531      122 45688999999999999999998773

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

Probab=97.24  E-value=0.001  Score=59.57  Aligned_cols=37  Identities=24%  Similarity=0.205  Sum_probs=29.4

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +..-+.++|.+|+|||.||.++.+++...=-.+.|++
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~  140 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFIT  140 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEE
Confidence            4567899999999999999999999773323456666

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.22  E-value=0.00096  Score=57.37  Aligned_cols=89  Identities=13%  Similarity=0.114  Sum_probs=51.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEE-ecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCCC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL-QNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSRR  246 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv-~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~k  246 (311)
                      .+|.|+|..|.||||++.++...+.......++. .+-.+...  .+.    ..++.+... ..+.... +.++..|+..
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~--~~~----~~~i~q~~v-g~~~~~~~~~i~~aLr~~   74 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVH--ESK----RSLINQREV-GLDTLSFENALKAALRQD   74 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCccccc--cCc----cceeeeccc-CCCccCHHHHHHHHhcCC
Confidence            4789999999999999999888876554444433 21111000  000    001100000 0012223 6777778777


Q ss_pred             eEEEEEecCCChHHHHHh
Q 042778          247 KVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       247 r~LlVLDdV~~~~~l~~l  264 (311)
                      .=+|++|++.+.+.+...
T Consensus        75 pd~ii~gEird~e~~~~~   92 (198)
T cd01131          75 PDVILVGEMRDLETIRLA   92 (198)
T ss_pred             cCEEEEcCCCCHHHHHHH
Confidence            779999999887766554

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.20  E-value=0.0044  Score=62.12  Aligned_cols=49  Identities=22%  Similarity=0.293  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++||.+..++.|...+..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~   63 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVN   63 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4578999999998888886432 245678999999999999999998864

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.18  E-value=0.0097  Score=56.10  Aligned_cols=48  Identities=19%  Similarity=0.144  Sum_probs=39.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+++|.+...+.+.+.+..+ .-...+.++|+.|+||+|+|..+.+.+
T Consensus        18 ~~~iiGq~~~~~~L~~~~~~~-rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         18 TTALFGHAAAEAALLDAYRSG-RLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             hhhccChHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            467899999999898888743 125568899999999999999999875

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=97.17  E-value=0.00025  Score=57.03  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=20.6

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|+|..|+|||+||+.+++..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL   23 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999988

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

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

Probab=97.16  E-value=0.00037  Score=62.33  Aligned_cols=54  Identities=22%  Similarity=0.433  Sum_probs=43.4

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      -.++||.+...++|.-.+...   ...+-.+.++|++|.||||||..+++.+..++.
T Consensus        25 l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k   81 (332)
T COG2255          25 LDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLK   81 (332)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeE
Confidence            467999998888887766532   233778999999999999999999999876654

>PRK06921 hypothetical protein; Provisional

Probab=97.15  E-value=0.00058  Score=61.52  Aligned_cols=36  Identities=14%  Similarity=0.184  Sum_probs=29.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~  203 (311)
                      ..-+.++|..|+|||.||.++++.+..+ -..++|+.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            5678999999999999999999986654 34456666

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.15  E-value=0.0012  Score=61.21  Aligned_cols=35  Identities=14%  Similarity=0.198  Sum_probs=28.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .-+.++|..|+|||.||.++++.+...--.++|++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t  218 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRT  218 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEE
Confidence            67999999999999999999998654433456665

>PRK08181 transposase; Validated

Probab=97.15  E-value=0.0016  Score=58.71  Aligned_cols=35  Identities=23%  Similarity=0.132  Sum_probs=27.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .-+.|+|.+|+|||.||.++.+......-.+.|+.
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~  141 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR  141 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeee
Confidence            45899999999999999999998654433445555

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

Probab=97.12  E-value=0.0011  Score=60.40  Aligned_cols=78  Identities=15%  Similarity=0.301  Sum_probs=47.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh----ccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCC-CCCH-HHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI----SSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIV-IPDI-ALSFR  241 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~----~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~-~~~~-~~l~~  241 (311)
                      -|+|.++|++|.|||+|++++++++    ...|....-+.    +..     .    .|+++-..+... ...+ ..+.+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liE----ins-----h----sLFSKWFsESgKlV~kmF~kI~E  243 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIE----INS-----H----SLFSKWFSESGKLVAKMFQKIQE  243 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEE----Eeh-----h----HHHHHHHhhhhhHHHHHHHHHHH
Confidence            4789999999999999999999973    33455444454    322     2    222222222221 1112 66667


Q ss_pred             HhCCCe--EEEEEecCCCh
Q 042778          242 QLSRRK--VLIVLDDVTCF  258 (311)
Q Consensus       242 ~L~~kr--~LlVLDdV~~~  258 (311)
                      .+.++.  +++.+|.|...
T Consensus       244 Lv~d~~~lVfvLIDEVESL  262 (423)
T KOG0744|consen  244 LVEDRGNLVFVLIDEVESL  262 (423)
T ss_pred             HHhCCCcEEEEEeHHHHHH
Confidence            776655  46678888643

>COG3899 Predicted ATPase [General function prediction only]

Probab=97.11  E-value=0.0086  Score=62.49  Aligned_cols=50  Identities=16%  Similarity=0.270  Sum_probs=42.0

Q ss_pred             CccchhhhHHHHHHhhcccC-CCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          146 QLVGVESRVEEIESLLGAES-KDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++||+.+++.|...+..-. ....++.+.|..|||||+|+++|...+...
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~   51 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQ   51 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhcc
Confidence            37899999999998886543 347799999999999999999999976554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.11  E-value=0.0097  Score=57.72  Aligned_cols=49  Identities=22%  Similarity=0.314  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -++++|.+..+..+...+..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~l~   64 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKALN   64 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            4578999999998888886431 146688999999999999999998753

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

Probab=97.10  E-value=0.0021  Score=56.09  Aligned_cols=97  Identities=22%  Similarity=0.307  Sum_probs=61.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc-cCc-CceEEEecCccccCCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS-SNF-EGSCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~-~~F-~~~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      -.++||-++.++.+.-...  +.+.+-+.|.||+|+||||-+..+++.+- ..| +++.=+.    .|. ..++.-+..+
T Consensus        26 l~dIVGNe~tv~rl~via~--~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELN----ASd-eRGIDvVRn~   98 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAK--EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELN----ASD-ERGIDVVRNK   98 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHH--cCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhcc----Ccc-ccccHHHHHH
Confidence            3578999988887765444  34588899999999999999999999843 334 3333333    444 6666665555


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHh-CCCeEEEEEecCCCh
Q 042778          222 LLSKLLQDGIVIPDIALSFRQL-SRRKVLIVLDDVTCF  258 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L-~~kr~LlVLDdV~~~  258 (311)
                      |-.-....           -.| .++.=+||||..++.
T Consensus        99 IK~FAQ~k-----------v~lp~grhKIiILDEADSM  125 (333)
T KOG0991|consen   99 IKMFAQKK-----------VTLPPGRHKIIILDEADSM  125 (333)
T ss_pred             HHHHHHhh-----------ccCCCCceeEEEeeccchh
Confidence            42211110           001 245558899999874

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.08  E-value=0.0026  Score=55.56  Aligned_cols=48  Identities=19%  Similarity=0.254  Sum_probs=36.2

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|.++|..+-..-.++.|+|.+|.||||||..++......-..++|++
T Consensus        11 ~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         11 MLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            455555544344679999999999999999999887655556678887

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.08  E-value=0.00056  Score=56.20  Aligned_cols=39  Identities=23%  Similarity=0.331  Sum_probs=29.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCce-EEEecCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEGS-CFLQNVR  206 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~-~wv~~~~  206 (311)
                      ..-|+|.||+|+|||||++.+.+.++.. |... +|...++
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVR   45 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeee
Confidence            4568999999999999999999987665 6543 4444343

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

Probab=97.07  E-value=0.0017  Score=57.31  Aligned_cols=52  Identities=17%  Similarity=0.435  Sum_probs=39.2

Q ss_pred             CCCccchhhhHHHHHHhhcc--cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA--ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++++|.+...+.|.+=...  ......-+.+||..|.|||+|++++.+.....
T Consensus        26 l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   26 LDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            67899999988888752211  11235567889999999999999999986553

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

Probab=97.07  E-value=0.00071  Score=57.23  Aligned_cols=36  Identities=25%  Similarity=0.220  Sum_probs=25.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..-+.|+|..|+|||.||.++.+....+=..+.|+.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~   82 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFIT   82 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEee
Confidence            456899999999999999999998443323346666

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.07  E-value=0.011  Score=58.13  Aligned_cols=48  Identities=23%  Similarity=0.254  Sum_probs=38.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.+..++.|...+..+. -.....++|..|+||||+|+.+.+.+
T Consensus        13 fdeiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L   60 (535)
T PRK08451         13 FDELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARAL   60 (535)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHh
Confidence            3578999988898988886432 24566899999999999999998875

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.06  E-value=0.0041  Score=54.20  Aligned_cols=48  Identities=15%  Similarity=0.165  Sum_probs=34.9

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc------CceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF------EGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F------~~~~wv~  203 (311)
                      .|..+|..+-..-.++.|+|.+|+|||+||..+.......-      ..++|+.
T Consensus         7 ~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~   60 (226)
T cd01393           7 ALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID   60 (226)
T ss_pred             HHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEe
Confidence            44455553434467999999999999999999877644443      5568887

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.06  E-value=0.0007  Score=56.86  Aligned_cols=36  Identities=28%  Similarity=0.599  Sum_probs=31.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+|.|.|+.|.||||+|+.+++.+...+...+++.
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~   42 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLD   42 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            568999999999999999999999887777777774

>PRK09183 transposase/IS protein; Provisional

Probab=97.06  E-value=0.0024  Score=57.37  Aligned_cols=25  Identities=20%  Similarity=0.232  Sum_probs=21.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+.|+|..|+|||+||.++.+..
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a  126 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEA  126 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHH
Confidence            3467899999999999999998874

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.05  E-value=0.0038  Score=65.29  Aligned_cols=112  Identities=13%  Similarity=0.182  Sum_probs=65.2

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChH
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLG  216 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~  216 (311)
                      ...++|.+..++.+...+...      ++. ...+.++|..|+|||++|+.+.......-...+.+.    .+. ... .
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d----~s~-~~~-~  637 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRID----MSE-YME-K  637 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEe----chh-hcc-c
Confidence            467899999999999877542      122 457889999999999999999987654333333333    222 111 1


Q ss_pred             HHHHHHHHHHhcCCC---CCCCHHHHHHHhCC-CeEEEEEecCCC--hHHHHHhh
Q 042778          217 FLQQKLLSKLLQDGI---VIPDIALSFRQLSR-RKVLIVLDDVTC--FRQIKSLI  265 (311)
Q Consensus       217 ~l~~~ll~~l~~~~~---~~~~~~~l~~~L~~-kr~LlVLDdV~~--~~~l~~l~  265 (311)
                      .    ....+.+..+   .......+.+.++. ...+|+||+|..  ++.+..|.
T Consensus       638 ~----~~~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~~v~~~Ll  688 (852)
T TIGR03346       638 H----SVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLL  688 (852)
T ss_pred             c----hHHHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCHHHHHHHH
Confidence            1    1122222222   11111334444433 345999999984  44555443

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.

>cd01394 radB RadB

Probab=97.05  E-value=0.0052  Score=53.35  Aligned_cols=49  Identities=16%  Similarity=0.290  Sum_probs=35.7

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..|..+|..+-..-.++.|.|.+|+||||||..++.....+=..++|+.
T Consensus         6 ~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394           6 KGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             hHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3455566544344679999999999999999999887654434566776

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.05  E-value=0.012  Score=58.57  Aligned_cols=49  Identities=27%  Similarity=0.268  Sum_probs=40.3

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+++|.+..+..|...+..+ .-...+.++|..|+||||+|+.+++.+-
T Consensus        15 f~diiGqe~iv~~L~~~i~~~-~i~hayLf~Gp~G~GKTt~Ar~lAk~L~   63 (563)
T PRK06647         15 FNSLEGQDFVVETLKHSIESN-KIANAYIFSGPRGVGKTSSARAFARCLN   63 (563)
T ss_pred             HHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            357899999999999888743 2255788999999999999999999854

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=97.03  E-value=0.00049  Score=54.03  Aligned_cols=22  Identities=41%  Similarity=0.723  Sum_probs=20.3

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |+|.|+.|+||||||+.+.++.
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999884

...

>PRK06526 transposase; Provisional

Probab=97.02  E-value=0.00063  Score=60.85  Aligned_cols=26  Identities=15%  Similarity=0.100  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..-+.|+|.+|+|||+||.++.+...
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~  123 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRAC  123 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHH
Confidence            45689999999999999999988743

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.02  E-value=0.0066  Score=60.49  Aligned_cols=112  Identities=10%  Similarity=0.137  Sum_probs=67.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcC--ceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFE--GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRR  246 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~--~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~k  246 (311)
                      ..+.|||-.|+|||.|++++.+.....+.  .+.++.           ...+...+...+...     ....+++.+++-
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit-----------aeef~~el~~al~~~-----~~~~f~~~y~~~  378 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS-----------SEEFTNEFINSIRDG-----KGDSFRRRYREM  378 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee-----------HHHHHHHHHHHHHhc-----cHHHHHHHhhcC
Confidence            45899999999999999999998765432  234444           223333443333211     112344444332


Q ss_pred             eEEEEEecCCCh---HH----HHHhh----ccCCC----------------------cCCceEEEcCCCChHHHHHHHHH
Q 042778          247 KVLIVLDDVTCF---RQ----IKSLI----GMLRN----------------------CCVKEKYEMKELGDDHALELFSR  293 (311)
Q Consensus       247 r~LlVLDdV~~~---~~----l~~l~----~~~~~----------------------~~~~~~y~v~~L~~~ea~~Lf~~  293 (311)
                       =||||||+...   +.    +-.+.    .....                      ....-+++|+..+.+.-..++.+
T Consensus       379 -DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~k  457 (617)
T PRK14086        379 -DILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRK  457 (617)
T ss_pred             -CEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHH
Confidence             36788998532   11    11111    10000                      44567899999999999999998


Q ss_pred             hhcC
Q 042778          294 HAFK  297 (311)
Q Consensus       294 ~af~  297 (311)
                      ++-.
T Consensus       458 ka~~  461 (617)
T PRK14086        458 KAVQ  461 (617)
T ss_pred             HHHh
Confidence            8754

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.99  E-value=0.00062  Score=58.26  Aligned_cols=25  Identities=28%  Similarity=0.484  Sum_probs=22.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +|||.|.+|+||||+|+.+...+..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~   25 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK   25 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc
Confidence            6999999999999999999998653

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.99  E-value=0.0026  Score=54.83  Aligned_cols=44  Identities=18%  Similarity=0.241  Sum_probs=33.8

Q ss_pred             hhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          160 LLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       160 ~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +|..+-..-.++-|+|.+|.|||++|..+.......-..++|++
T Consensus         4 ~l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~   47 (209)
T TIGR02237         4 LLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID   47 (209)
T ss_pred             hhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            34333334679999999999999999998887655556788887

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.98  E-value=0.013  Score=59.54  Aligned_cols=48  Identities=19%  Similarity=0.340  Sum_probs=39.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++|.+..++.|...+..+. -.....++|+.|+||||+|+.+++.+-
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~Ln   65 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANALN   65 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhc
Confidence            468899999999988886431 255678999999999999999998753

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

Probab=96.97  E-value=0.0011  Score=64.92  Aligned_cols=53  Identities=19%  Similarity=0.290  Sum_probs=41.8

Q ss_pred             CCCccchhhhHHHHHHhhcccC----------CCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAES----------KDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~----------~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..++=|++..+.+|.+++..-.          .-.+=|.++|++|+|||.||++++++..-.|
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf  251 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPF  251 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCce
Confidence            3567789999999988775421          1256688999999999999999999976655

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.96  E-value=0.0045  Score=64.51  Aligned_cols=112  Identities=11%  Similarity=0.184  Sum_probs=65.6

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChH
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLG  216 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~  216 (311)
                      ...++|.+..++.|...+...      .+. ...+.++|+.|+|||+||+.+++.+...-...+-+. ..+... .+...
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d-~s~~~~-~~~~~  585 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLD-MSEYME-KHTVS  585 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEE-chhccc-cccHH
Confidence            578899999999998877521      122 456778999999999999999987643322222232 222111 11111


Q ss_pred             HHHHHHHHHHhcCCC---CCCCHHHHHHHhCCCe-EEEEEecCCC--hHHHHHhh
Q 042778          217 FLQQKLLSKLLQDGI---VIPDIALSFRQLSRRK-VLIVLDDVTC--FRQIKSLI  265 (311)
Q Consensus       217 ~l~~~ll~~l~~~~~---~~~~~~~l~~~L~~kr-~LlVLDdV~~--~~~l~~l~  265 (311)
                              .+.+..+   .......|.+.++.+. .+|+||+++.  ++.++.|.
T Consensus       586 --------~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka~~~v~~~Ll  632 (821)
T CHL00095        586 --------KLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLL  632 (821)
T ss_pred             --------HhcCCCCcccCcCccchHHHHHHhCCCeEEEECChhhCCHHHHHHHH
Confidence                    1222211   1222244555665544 5999999984  45555554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.94  E-value=0.0054  Score=64.13  Aligned_cols=112  Identities=15%  Similarity=0.205  Sum_probs=64.9

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChH
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLG  216 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~  216 (311)
                      ...++|.+..++.|...+...      ++. ...+.++|..|+|||+||+++++.....-...+.+.    .+. - .  
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id----~se-~-~--  638 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRID----MSE-F-M--  638 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEE----hHH-h-h--
Confidence            567899999999888877532      122 357889999999999999999987643333333333    211 1 0  


Q ss_pred             HHHHHHHHHHhcCCCC---CCCHHHHHHHhCC-CeEEEEEecCC--ChHHHHHhh
Q 042778          217 FLQQKLLSKLLQDGIV---IPDIALSFRQLSR-RKVLIVLDDVT--CFRQIKSLI  265 (311)
Q Consensus       217 ~l~~~ll~~l~~~~~~---~~~~~~l~~~L~~-kr~LlVLDdV~--~~~~l~~l~  265 (311)
                        .......+.+..+.   ......+.+.++. ..-+|+|||+.  +++.+..|.
T Consensus       639 --~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll  691 (857)
T PRK10865        639 --EKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILL  691 (857)
T ss_pred             --hhhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCCHHHHHHHH
Confidence              01122233332221   1111234444433 33599999998  455555553

>PRK06217 hypothetical protein; Validated

Probab=96.94  E-value=0.0048  Score=52.21  Aligned_cols=34  Identities=21%  Similarity=0.359  Sum_probs=25.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC-c--CceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN-F--EGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~-F--~~~~wv~  203 (311)
                      .|.|.|++|.||||||+.+.++..-. |  |...|..
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D~~~~~~   39 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTDDYFWLP   39 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcCceeecc
Confidence            58999999999999999999985432 2  4445543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.94  E-value=0.016  Score=58.36  Aligned_cols=50  Identities=22%  Similarity=0.232  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..+..|..++..+. -...+.++|..|+||||+|+.+++.+..
T Consensus        15 f~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c   64 (620)
T PRK14948         15 FDELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNC   64 (620)
T ss_pred             HhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcC
Confidence            3578999999999988887432 2456789999999999999999998644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.93  E-value=0.0028  Score=65.24  Aligned_cols=52  Identities=17%  Similarity=0.294  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -+++.|++..++++.+++...           -...+-+.++|.+|+||||||+++++.....
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~  239 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY  239 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCe
Confidence            456889999998888776321           1224668899999999999999999987544

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.

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

Probab=96.92  E-value=0.0035  Score=59.69  Aligned_cols=147  Identities=16%  Similarity=0.229  Sum_probs=95.6

Q ss_pred             CCCccchhhhHHHHHHhhcc--cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCc--eEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGA--ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEG--SCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~--~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      +..++||+.++..+.+++..  +.+..+.+-|.|-+|.|||.+...++.+.......  ++.+...   +  -....++.
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~---s--l~~~~aiF  223 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCT---S--LTEASAIF  223 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeec---c--ccchHHHH
Confidence            77899999999999998864  34557889999999999999999999986655433  2444321   1  13456677


Q ss_pred             HHHHHHHhcCCC----CCCCHHHHHHHhCCC--eEEEEEecCCChH-----------HHHHhhccC-------CC-----
Q 042778          220 QKLLSKLLQDGI----VIPDIALSFRQLSRR--KVLIVLDDVTCFR-----------QIKSLIGML-------RN-----  270 (311)
Q Consensus       220 ~~ll~~l~~~~~----~~~~~~~l~~~L~~k--r~LlVLDdV~~~~-----------~l~~l~~~~-------~~-----  270 (311)
                      ..|+..+.....    ..+-.+.+..+....  -+|+|||..+...           +|..+-+..       +.     
T Consensus       224 ~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTd  303 (529)
T KOG2227|consen  224 KKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTD  303 (529)
T ss_pred             HHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHH
Confidence            777777633222    211125666666553  5899999987432           233221110       00     


Q ss_pred             ----------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ----------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ----------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                .-......-++-+.++-.++|..+.
T Consensus       304 R~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl  338 (529)
T KOG2227|consen  304 RFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRL  338 (529)
T ss_pred             HHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHH
Confidence                      2234566678888888888888774

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.89  E-value=0.0068  Score=59.23  Aligned_cols=51  Identities=18%  Similarity=0.173  Sum_probs=35.5

Q ss_pred             CCccchhhhHHHHHHhhc---c-----cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLG---A-----ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~---~-----~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++.|.+...+.+.....   .     +-...+-|.++|++|+|||.+|+++++.....
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~  286 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLP  286 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            456788766665554221   0     11235678899999999999999999986543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.89  E-value=0.0073  Score=55.52  Aligned_cols=55  Identities=20%  Similarity=0.210  Sum_probs=35.6

Q ss_pred             chhhhHHHHHHhhcccC--CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          149 GVESRVEEIESLLGAES--KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~--~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++........+++..-.  ...+-+-|+|..|+|||.||.++++.....=..+.|+.
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~  191 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLH  191 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            34444444444554211  13457889999999999999999999654433345665

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.88  E-value=0.0061  Score=49.49  Aligned_cols=34  Identities=18%  Similarity=0.272  Sum_probs=27.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++.|+|.+|.||||++..+.......-..++|+.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            3689999999999999999888655444566665

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

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

Probab=96.88  E-value=0.0024  Score=65.88  Aligned_cols=53  Identities=17%  Similarity=0.277  Sum_probs=43.2

Q ss_pred             CCCccchhhhHHHHHHhhccc----CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE----SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+.+|.+...+.|.++|...    .....++.++|.+|+||||+|+.+.......|
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~  377 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKY  377 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            677999999999999888632    12356899999999999999999998766554

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.87  E-value=0.001  Score=57.51  Aligned_cols=27  Identities=33%  Similarity=0.559  Sum_probs=24.4

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ....+|+|.|.+|+||||||+.++..+
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999999876

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

Probab=96.83  E-value=0.0071  Score=61.59  Aligned_cols=111  Identities=16%  Similarity=0.254  Sum_probs=74.4

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChH
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLG  216 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~  216 (311)
                      ...++|.+..+..+.+.+...      ++. .......|+.|+|||.||++++..+...=+..+-+.    +|+      
T Consensus       490 ~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~D----MSE------  559 (786)
T COG0542         490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRID----MSE------  559 (786)
T ss_pred             hcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeec----hHH------
Confidence            568899999999998877431      222 567778999999999999999988654333333333    332      


Q ss_pred             HHHHH-HHHHHhcCCC---CCCCHHHHHHHhCCCeE-EEEEecCC--ChHHHHHhh
Q 042778          217 FLQQK-LLSKLLQDGI---VIPDIALSFRQLSRRKV-LIVLDDVT--CFRQIKSLI  265 (311)
Q Consensus       217 ~l~~~-ll~~l~~~~~---~~~~~~~l~~~L~~kr~-LlVLDdV~--~~~~l~~l~  265 (311)
                       .+.+ -.+.+.|..+   ..++-..|.+..+++.| +|.||+|.  +++.++-|+
T Consensus       560 -y~EkHsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilL  614 (786)
T COG0542         560 -YMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLL  614 (786)
T ss_pred             -HHHHHHHHHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHH
Confidence             2222 2445555544   22222677777888877 89999997  567676665

>PRK08233 hypothetical protein; Provisional

Probab=96.82  E-value=0.001  Score=55.76  Aligned_cols=26  Identities=19%  Similarity=0.312  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|+|.|.+|.||||||+.+...+.
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            47899999999999999999998754

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

Probab=96.82  E-value=0.013  Score=55.92  Aligned_cols=99  Identities=17%  Similarity=0.152  Sum_probs=61.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEE
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVL  249 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~L  249 (311)
                      ++.|.|+-++|||||++.+.......   .+++......    .+-..+ .+.+.             .+...-..++.+
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~---~iy~~~~d~~----~~~~~l-~d~~~-------------~~~~~~~~~~~y   97 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE---IIYINFDDLR----LDRIEL-LDLLR-------------AYIELKEREKSY   97 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcc---eEEEEecchh----cchhhH-HHHHH-------------HHHHhhccCCce
Confidence            99999999999999997776665444   4444311111    111111 11111             111111127899


Q ss_pred             EEEecCCChHHHHHhh------ccCCC------------------cCCceEEEcCCCChHHHHH
Q 042778          250 IVLDDVTCFRQIKSLI------GMLRN------------------CCVKEKYEMKELGDDHALE  289 (311)
Q Consensus       250 lVLDdV~~~~~l~~l~------~~~~~------------------~~~~~~y~v~~L~~~ea~~  289 (311)
                      |+||.|.....|+...      +..+-                  .|....+++-||+-.|-+.
T Consensus        98 ifLDEIq~v~~W~~~lk~l~d~~~~~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373          98 IFLDEIQNVPDWERALKYLYDRGNLDVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             EEEecccCchhHHHHHHHHHccccceEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            9999999988877653      11101                  4567789999999999876

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.018  Score=57.93  Aligned_cols=49  Identities=22%  Similarity=0.281  Sum_probs=39.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.+..++.|...+..+. -...+.++|..|+||||+|+.+...+.
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            3578999999999988886431 245688999999999999999888754

>PRK03839 putative kinase; Provisional

Probab=96.81  E-value=0.001  Score=56.09  Aligned_cols=26  Identities=23%  Similarity=0.480  Sum_probs=22.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .|.|.||+|+||||+|+.++++..-.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~   27 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYE   27 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCc
Confidence            48899999999999999999986443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.81  E-value=0.03  Score=55.80  Aligned_cols=49  Identities=16%  Similarity=0.182  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+..++.+.+.+..+. -...+.++|..|+||||+|+.+.+.+.
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAkal~   63 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAKAVN   63 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4578999999999998887532 255677899999999999999988753

>PRK06762 hypothetical protein; Provisional

Probab=96.81  E-value=0.0011  Score=55.02  Aligned_cols=25  Identities=28%  Similarity=0.400  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|+|+.|+||||+|+.+.+.+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999999886

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.77  E-value=0.014  Score=58.31  Aligned_cols=49  Identities=18%  Similarity=0.287  Sum_probs=39.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+..++.|...+..+ .-...+.++|..|+||||+|+.+.+.+.
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~-~~~hayLf~Gp~G~GKtt~A~~lak~l~   63 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTG-RVAHAFLFTGARGVGKTSTARILAKALN   63 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            457899998888888888643 1245678999999999999999998754

>PTZ00301 uridine kinase; Provisional

Probab=96.76  E-value=0.0012  Score=57.40  Aligned_cols=27  Identities=19%  Similarity=0.460  Sum_probs=23.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.+|||.|.+|.||||||+.+.+++..
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~~   29 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELMA   29 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHHh
Confidence            578999999999999999999877543

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.75  E-value=0.0017  Score=65.23  Aligned_cols=50  Identities=22%  Similarity=0.322  Sum_probs=41.0

Q ss_pred             CCCccchhhhHHHHHHhhcccC---CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAES---KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~---~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.+..++++..+|....   ...+++.|+|..|+||||+++.++..+.
T Consensus        83 ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~  135 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG  135 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4678999999999998886532   2356899999999999999999998753

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

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.74  E-value=0.014  Score=59.41  Aligned_cols=103  Identities=16%  Similarity=0.141  Sum_probs=67.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      +.+.|-|..    +.+.|... .+.+.+.|..+.|.|||||+...... ...=..+.|+.    ....+.+...+...++
T Consensus        18 ~~~~v~R~r----L~~~L~~~-~~~RL~li~APAGfGKttl~aq~~~~-~~~~~~v~Wls----lde~dndp~rF~~yLi   87 (894)
T COG2909          18 PDNYVVRPR----LLDRLRRA-NDYRLILISAPAGFGKTTLLAQWREL-AADGAAVAWLS----LDESDNDPARFLSYLI   87 (894)
T ss_pred             cccccccHH----HHHHHhcC-CCceEEEEeCCCCCcHHHHHHHHHHh-cCcccceeEee----cCCccCCHHHHHHHHH
Confidence            445555554    44555432 45899999999999999999998873 33335578998    4443778889999998


Q ss_pred             HHHhcCCCC-------------CCCH----HHHHHHhC--CCeEEEEEecCC
Q 042778          224 SKLLQDGIV-------------IPDI----ALSFRQLS--RRKVLIVLDDVT  256 (311)
Q Consensus       224 ~~l~~~~~~-------------~~~~----~~l~~~L~--~kr~LlVLDdV~  256 (311)
                      ..+..-.+.             ..++    ..+..-|.  .+..+|||||-.
T Consensus        88 ~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyH  139 (894)
T COG2909          88 AALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYH  139 (894)
T ss_pred             HHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEecccc
Confidence            888743221             1111    22222222  367899999975

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.74  E-value=0.0013  Score=54.65  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=23.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|+|++|+||||+|+.++++..
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999999864

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.74  E-value=0.011  Score=55.83  Aligned_cols=94  Identities=13%  Similarity=0.184  Sum_probs=54.6

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC---
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI---  231 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~---  231 (311)
                      .++..+|..+-..-.++.|.|.+|+|||||+..++......-..++|+..       ......+... ...+.....   
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~-------EEs~~qi~~R-a~rlg~~~~~l~  140 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSG-------EESPEQIKLR-ADRLGISTENLY  140 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEC-------CcCHHHHHHH-HHHcCCCcccEE
Confidence            44555565333345689999999999999999998876555445667761       1122222221 223322111   


Q ss_pred             --CCCCHHHHHHHhC-CCeEEEEEecCC
Q 042778          232 --VIPDIALSFRQLS-RRKVLIVLDDVT  256 (311)
Q Consensus       232 --~~~~~~~l~~~L~-~kr~LlVLDdV~  256 (311)
                        ...+++.+.+.+. .+.-+||+|.+.
T Consensus       141 l~~e~~le~I~~~i~~~~~~lVVIDSIq  168 (372)
T cd01121         141 LLAETNLEDILASIEELKPDLVIIDSIQ  168 (372)
T ss_pred             EEccCcHHHHHHHHHhcCCcEEEEcchH
Confidence              1122344544443 356689999974

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.72  E-value=0.0087  Score=62.50  Aligned_cols=51  Identities=16%  Similarity=0.295  Sum_probs=40.5

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++|.+..+..+.+.+...      ++. ..++.++|+.|+|||.||++++..+..
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~  622 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYG  622 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhC
Confidence            568899999999998877421      122 557899999999999999999887643

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.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=96.72  E-value=0.0013  Score=52.79  Aligned_cols=24  Identities=17%  Similarity=0.382  Sum_probs=21.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|.++|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            578999999999999999987654

...

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

Probab=96.71  E-value=0.0049  Score=56.98  Aligned_cols=48  Identities=17%  Similarity=0.194  Sum_probs=34.7

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|..+|. .+=..-+++-|+|.+|+||||||..++......-..++|++
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          42 SLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             HHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            3445554 33334678899999999999999988776554445678887

RecA couples ATP hydrolysis to DNA strand exchange.

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

Probab=96.71  E-value=0.011  Score=58.22  Aligned_cols=123  Identities=15%  Similarity=0.265  Sum_probs=72.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHH-HHHhCCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALS-FRQLSRR  246 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l-~~~L~~k  246 (311)
                      ..=|.+||++|+|||-||++|+|.-.-+|-.         +-  .       -+||...-++..  ..+..+ ++.-..-
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEag~NFis---------VK--G-------PELlNkYVGESE--rAVR~vFqRAR~sa  604 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEAGANFIS---------VK--G-------PELLNKYVGESE--RAVRQVFQRARASA  604 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhccCceEe---------ec--C-------HHHHHHHhhhHH--HHHHHHHHHhhcCC
Confidence            4457899999999999999999998777643         11  1       123333222211  001112 2222347


Q ss_pred             eEEEEEecCCCh-------------HHHHHhh----ccCCC----------------------cCCceEEEcCCCChHHH
Q 042778          247 KVLIVLDDVTCF-------------RQIKSLI----GMLRN----------------------CCVKEKYEMKELGDDHA  287 (311)
Q Consensus       247 r~LlVLDdV~~~-------------~~l~~l~----~~~~~----------------------~~~~~~y~v~~L~~~ea  287 (311)
                      .|+|.+|.++..             ..+..|+    |....                      ...+.+.-|..-+.+|-
T Consensus       605 PCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR  684 (802)
T KOG0733|consen  605 PCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEER  684 (802)
T ss_pred             CeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHH
Confidence            799999998631             1122222    11100                      23466777999999999


Q ss_pred             HHHHHHhhcCCC---CCCCcHHHhhc
Q 042778          288 LELFSRHAFKQN---NPHIGFEELSS  310 (311)
Q Consensus       288 ~~Lf~~~af~~~---~~~~~~~~l~~  310 (311)
                      ..+++...=...   .+.-+|.+|++
T Consensus       685 ~~ILK~~tkn~k~pl~~dVdl~eia~  710 (802)
T KOG0733|consen  685 VAILKTITKNTKPPLSSDVDLDEIAR  710 (802)
T ss_pred             HHHHHHHhccCCCCCCcccCHHHHhh
Confidence            999998875322   23356777764

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.70  E-value=0.003  Score=54.25  Aligned_cols=36  Identities=11%  Similarity=0.202  Sum_probs=27.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++++.++|+.|+||||.+..++.+...+=..+..++
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhccccceeec
Confidence            368999999999999999999887555433345555

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK04040 adenylate kinase; Provisional

Probab=96.69  E-value=0.0017  Score=55.40  Aligned_cols=25  Identities=20%  Similarity=0.424  Sum_probs=23.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|+|+|++|+||||+++.+.+++.
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            5899999999999999999999875

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.69  E-value=0.0051  Score=61.40  Aligned_cols=73  Identities=21%  Similarity=0.190  Sum_probs=48.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC-ceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE-GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRR  246 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~-~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~k  246 (311)
                      .+-|-|.|..|+|||+||+++++.+...-. +..++.+-  ... ...+..+|+.+-             ..+...+...
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs--~l~-~~~~e~iQk~l~-------------~vfse~~~~~  494 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCS--TLD-GSSLEKIQKFLN-------------NVFSEALWYA  494 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEech--hcc-chhHHHHHHHHH-------------HHHHHHHhhC
Confidence            457899999999999999999998764322 22333311  112 334566665542             2344556778


Q ss_pred             eEEEEEecCC
Q 042778          247 KVLIVLDDVT  256 (311)
Q Consensus       247 r~LlVLDdV~  256 (311)
                      .-+|||||++
T Consensus       495 PSiIvLDdld  504 (952)
T KOG0735|consen  495 PSIIVLDDLD  504 (952)
T ss_pred             CcEEEEcchh
Confidence            8999999997

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.69  E-value=0.0023  Score=52.83  Aligned_cols=35  Identities=23%  Similarity=0.360  Sum_probs=29.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .+|-|.|++|.||||||+++.+++...-..+.++.
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LD   37 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLD   37 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEec
Confidence            57889999999999999999999877666666664

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>TIGR00235 udk uridine kinase

Probab=96.68  E-value=0.0017  Score=56.07  Aligned_cols=27  Identities=33%  Similarity=0.553  Sum_probs=23.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+|+|.|.+|+||||||+.+.....
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            467999999999999999999988654

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.68  E-value=0.0022  Score=55.56  Aligned_cols=30  Identities=27%  Similarity=0.470  Sum_probs=26.9

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+.+|||-|.+|.||||+|+.+++.+..+
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHHhCcC
Confidence            457899999999999999999999987755

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.67  E-value=0.002  Score=63.40  Aligned_cols=52  Identities=17%  Similarity=0.226  Sum_probs=42.5

Q ss_pred             CCCccchhhhHHHHHHhhc----ccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLG----AESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~----~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+++|++..++.|.+.|.    .....-+++.++|++|+||||||+.+.+-+...
T Consensus        75 F~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~  130 (644)
T PRK15455         75 FEEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERV  130 (644)
T ss_pred             hhcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhC
Confidence            4578999999999999883    223446899999999999999999998865443

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

Probab=96.66  E-value=0.0023  Score=63.84  Aligned_cols=137  Identities=19%  Similarity=0.256  Sum_probs=86.7

Q ss_pred             CCCccchhhhHHHHHHhhccc----CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE----SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      ..+-.|.+...+.|.+.|.-.    .-.-+++.++|++|+|||.|++.+++-+...|-. +=+-.+++.++         
T Consensus       322 d~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR-~sLGGvrDEAE---------  391 (782)
T COG0466         322 DKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVR-ISLGGVRDEAE---------  391 (782)
T ss_pred             cccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEE-EecCccccHHH---------
Confidence            678899999999999988532    2235799999999999999999999998777643 22333444332         


Q ss_pred             HHHHHHHhcCCC-CCCCH--HHHH--HHhCCCeEEEEEecCCChH----------HHHHhhccCCC--------------
Q 042778          220 QKLLSKLLQDGI-VIPDI--ALSF--RQLSRRKVLIVLDDVTCFR----------QIKSLIGMLRN--------------  270 (311)
Q Consensus       220 ~~ll~~l~~~~~-~~~~~--~~l~--~~L~~kr~LlVLDdV~~~~----------~l~~l~~~~~~--------------  270 (311)
                            +-|... -+..+  ..++  ..-+.+.-|++||.|+...          -|+-|-|..+.              
T Consensus       392 ------IRGHRRTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS  465 (782)
T COG0466         392 ------IRGHRRTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLS  465 (782)
T ss_pred             ------hccccccccccCChHHHHHHHHhCCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchh
Confidence                  111111 12222  2222  1224567799999997421          12222221111              


Q ss_pred             ------------------cCCceEEEcCCCChHHHHHHHHHhhc
Q 042778          271 ------------------CCVKEKYEMKELGDDHALELFSRHAF  296 (311)
Q Consensus       271 ------------------~~~~~~y~v~~L~~~ea~~Lf~~~af  296 (311)
                                        .....++++.+-+++|-+++-++|-.
T Consensus       466 ~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~Li  509 (782)
T COG0466         466 KVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHLI  509 (782)
T ss_pred             heEEEeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhcc
Confidence                              23446788888888998888777754

>PRK00625 shikimate kinase; Provisional

Probab=96.66  E-value=0.0015  Score=54.98  Aligned_cols=26  Identities=15%  Similarity=0.289  Sum_probs=22.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .|.|+||+|+||||+++.+.++..-.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~   27 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLP   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            47899999999999999999886443

>PRK09354 recA recombinase A; Provisional

Probab=96.62  E-value=0.0067  Score=56.55  Aligned_cols=48  Identities=17%  Similarity=0.212  Sum_probs=35.1

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|..+|. .+=..-+++-|+|.+|+||||||..+.......=..++|+.
T Consensus        47 ~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId   95 (349)
T PRK09354         47 ALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   95 (349)
T ss_pred             HHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC
Confidence            4445565 33344678999999999999999987776544445678887

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.62  E-value=0.032  Score=55.35  Aligned_cols=154  Identities=16%  Similarity=0.139  Sum_probs=83.8

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCce-------EEEecCc
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGS-------CFLQNVR  206 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~-------~wv~~~~  206 (311)
                      +++=|.+....+|.+....           +-+..+-|..+|++|+||||+|+++++.-...|-.+       -|+-   
T Consensus       434 ~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~vG---  510 (693)
T KOG0730|consen  434 DDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKYVG---  510 (693)
T ss_pred             hhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHHHhcC---
Confidence            4455688777777755432           123467889999999999999999999876666432       2322   


Q ss_pred             cccCCCCChHHHHHHHHHHHhcCCC------CCC-----------CH--HHHHHHh------CCCeEEEEEecCCChHHH
Q 042778          207 EESQRPGGLGFLQQKLLSKLLQDGI------VIP-----------DI--ALSFRQL------SRRKVLIVLDDVTCFRQI  261 (311)
Q Consensus       207 ~~s~~~~~~~~l~~~ll~~l~~~~~------~~~-----------~~--~~l~~~L------~~kr~LlVLDdV~~~~~l  261 (311)
                             .-....++++++.-...+      +++           +.  ..|...|      ..++-++|+=--+.++++
T Consensus       511 -------eSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~I  583 (693)
T KOG0730|consen  511 -------ESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMI  583 (693)
T ss_pred             -------chHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhc
Confidence                   112233333333221111      000           00  1111111      123333343333334444


Q ss_pred             HHhhccCCCcCCceEEEcCCCChHHHHHHHHHhhcCCCCC-CCcHHHhhc
Q 042778          262 KSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFKQNNP-HIGFEELSS  310 (311)
Q Consensus       262 ~~l~~~~~~~~~~~~y~v~~L~~~ea~~Lf~~~af~~~~~-~~~~~~l~~  310 (311)
                      +.-+-.+  ...+.++.|+.-+.+--+++|+.++=+-+-+ .-++++|+.
T Consensus       584 D~ALlRP--GRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~  631 (693)
T KOG0730|consen  584 DPALLRP--GRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQ  631 (693)
T ss_pred             CHHHcCC--cccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHH
Confidence            4322111  2356777888888888899999998654432 336777764

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.61  E-value=0.004  Score=55.80  Aligned_cols=64  Identities=16%  Similarity=0.203  Sum_probs=39.5

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hccCc----CceEEEecCccccCCCCChHHHHHHHHHH
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISSNF----EGSCFLQNVREESQRPGGLGFLQQKLLSK  225 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~~F----~~~~wv~~~~~~s~~~~~~~~l~~~ll~~  225 (311)
                      .|.++|..+-..-.+.=|+|.+|+|||+||..++-.  +....    ..++||+    ... .+...++.+ |+..
T Consensus        26 ~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyid----Te~-~f~~~Rl~~-i~~~   95 (256)
T PF08423_consen   26 SLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYID----TEG-TFSPERLQQ-IAER   95 (256)
T ss_dssp             HHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEE----SSS-SS-HHHHHH-HHHH
T ss_pred             HHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEe----CCC-CCCHHHHHH-Hhhc
Confidence            455666433223568899999999999999877654  33222    2368887    333 566666653 4443

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.61  E-value=0.0073  Score=54.37  Aligned_cols=88  Identities=15%  Similarity=0.200  Sum_probs=55.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc----cCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-H-
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS----SNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-I-  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~----~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-~-  236 (311)
                      -..++|.|-.|+|||||+..+.++..    .+-+.++++-    +.++.....++...+...-.....     ..++ . 
T Consensus        69 GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~----IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~  144 (276)
T cd01135          69 GQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAA----MGITMEDARFFKDDFEETGALERVVLFLNLANDPTI  144 (276)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEE----eccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHH
Confidence            35689999999999999999888743    2235666666    444355666666666543211111     0111 0 


Q ss_pred             ---------HHHHHHhC---CCeEEEEEecCCChH
Q 042778          237 ---------ALSFRQLS---RRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ---------~~l~~~L~---~kr~LlVLDdV~~~~  259 (311)
                               ..+.++++   ++++|+++||+....
T Consensus       145 ~r~~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr~A  179 (276)
T cd01135         145 ERIITPRMALTTAEYLAYEKGKHVLVILTDMTNYA  179 (276)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCeEEEEEcChhHHH
Confidence                     34445543   689999999997644

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>PRK13947 shikimate kinase; Provisional

Probab=96.60  E-value=0.0017  Score=54.11  Aligned_cols=27  Identities=22%  Similarity=0.431  Sum_probs=23.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -|.|+||+|+||||+|+.+.+++.-.|
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~   29 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGF   29 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCE
Confidence            488999999999999999999875543

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.60  E-value=0.0052  Score=58.86  Aligned_cols=86  Identities=9%  Similarity=0.115  Sum_probs=50.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-H-----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-I-----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-~-----  236 (311)
                      -..++|.|..|+|||||++.+......  +..++.-    +.++.....++...++..-.....     ..++ .     
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~~~~--dv~Vi~l----IGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRGTTA--DVIVVGL----VGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccCCCC--CEEEEEE----EcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            457999999999999999998865433  4555543    333233445555554333111110     1111 0     


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           ..+.+++  +++++||++||+....
T Consensus       236 a~~~A~tiAEyfrd~G~~VLl~~DslTR~A  265 (444)
T PRK08972        236 GCETATTIAEYFRDQGLNVLLLMDSLTRYA  265 (444)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcChHHHH
Confidence                 2234444  5799999999997543

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

Probab=96.59  E-value=0.0073  Score=60.43  Aligned_cols=72  Identities=19%  Similarity=0.303  Sum_probs=47.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhC--
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLS--  244 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~--  244 (311)
                      .-+++.++|++|+||||||..++++-.  |. ++=|.    .|. ......+-..|...+....           .|.  
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaG--Ys-VvEIN----ASD-eRt~~~v~~kI~~avq~~s-----------~l~ad  385 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAG--YS-VVEIN----ASD-ERTAPMVKEKIENAVQNHS-----------VLDAD  385 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcC--ce-EEEec----ccc-cccHHHHHHHHHHHHhhcc-----------ccccC
Confidence            367999999999999999999998732  11 12222    344 5555666666655544332           121  


Q ss_pred             CCeEEEEEecCCC
Q 042778          245 RRKVLIVLDDVTC  257 (311)
Q Consensus       245 ~kr~LlVLDdV~~  257 (311)
                      .+..-||+|.++-
T Consensus       386 srP~CLViDEIDG  398 (877)
T KOG1969|consen  386 SRPVCLVIDEIDG  398 (877)
T ss_pred             CCcceEEEecccC
Confidence            4666789999984

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

Probab=96.58  E-value=0.0018  Score=45.70  Aligned_cols=23  Identities=22%  Similarity=0.445  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|+|.|..|.||||+|+.+.+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999885

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PF14516 AAA_35: AAA-like domain

Probab=96.57  E-value=0.046  Score=50.89  Aligned_cols=148  Identities=8%  Similarity=0.080  Sum_probs=90.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCC-CCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQR-PGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~-~~~~~~l~~~  221 (311)
                      .+..|.|...-+++.+.|..   .-..+.|.|.-.+|||+|...+.+.... .|.+ +++. +..+... ..+...+.+.
T Consensus        10 ~~~Yi~R~~~e~~~~~~i~~---~G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~-v~id-~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen   10 SPFYIERPPAEQECYQEIVQ---PGSYIRIKAPRQMGKTSLLLRLLERLQQQGYRC-VYID-LQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             CCcccCchHHHHHHHHHHhc---CCCEEEEECcccCCHHHHHHHHHHHHHHCCCEE-EEEE-eecCCCcccCCHHHHHHH
Confidence            45678888666667766653   1348899999999999999999888643 4444 3443 2222210 2456666666


Q ss_pred             HHHHHhcCCC-----------CCCCH----HHHHHHh---CCCeEEEEEecCCChHH--------HHHhh-------ccC
Q 042778          222 LLSKLLQDGI-----------VIPDI----ALSFRQL---SRRKVLIVLDDVTCFRQ--------IKSLI-------GML  268 (311)
Q Consensus       222 ll~~l~~~~~-----------~~~~~----~~l~~~L---~~kr~LlVLDdV~~~~~--------l~~l~-------~~~  268 (311)
                      ++..+...-.           .....    ..+.+.+   .+++.+|+||+|+..-.        +..|+       ...
T Consensus        85 ~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~  164 (331)
T PF14516_consen   85 FCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNP  164 (331)
T ss_pred             HHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCc
Confidence            6655543221           11111    4444443   25899999999984221        11111       011


Q ss_pred             CC-----------------------cCCceEEEcCCCChHHHHHHHHHhhc
Q 042778          269 RN-----------------------CCVKEKYEMKELGDDHALELFSRHAF  296 (311)
Q Consensus       269 ~~-----------------------~~~~~~y~v~~L~~~ea~~Lf~~~af  296 (311)
                      .|                       ..+...++|++++.+|...|..++-.
T Consensus       165 ~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~  215 (331)
T PF14516_consen  165 IWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGL  215 (331)
T ss_pred             ccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhc
Confidence            12                       23456788999999999999988743

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.56  E-value=0.008  Score=50.18  Aligned_cols=26  Identities=19%  Similarity=0.317  Sum_probs=22.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++.+.|++|.||||++..++......
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~   27 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            67899999999999999999876554

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=96.55  E-value=0.0018  Score=51.47  Aligned_cols=28  Identities=25%  Similarity=0.500  Sum_probs=20.7

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      |-|+|.+|+||||+|++++..+...|..
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~f~R   29 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLSFKR   29 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT--EEE
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCceeE
Confidence            6799999999999999999998888764

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.55  E-value=0.0092  Score=55.09  Aligned_cols=48  Identities=17%  Similarity=0.219  Sum_probs=34.3

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|..+|. .+=..-+++-|+|.+|+||||||..+.......=..++|++
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId   90 (321)
T TIGR02012        42 SLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   90 (321)
T ss_pred             HHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Confidence            3445554 33344679999999999999999988776544445567886

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.54  E-value=0.023  Score=52.48  Aligned_cols=59  Identities=14%  Similarity=0.173  Sum_probs=37.9

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc------CceEEEecCccccCCCCChHHHH
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF------EGSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F------~~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      .+..+|..+-..-.++-|+|.+|+|||++|..++-......      ..++|++    ... .+....+.
T Consensus        90 ~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~----te~-~f~~~rl~  154 (317)
T PRK04301         90 ELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID----TEG-TFRPERIE  154 (317)
T ss_pred             HHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe----CCC-CcCHHHHH
Confidence            34455543333467889999999999999998876532211      3678887    323 44555544

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.54  E-value=0.0021  Score=54.22  Aligned_cols=26  Identities=23%  Similarity=0.158  Sum_probs=23.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++.+|.|.|++|+||||+|+.+..+.
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            36799999999999999999998764

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.53  E-value=0.0074  Score=53.70  Aligned_cols=25  Identities=20%  Similarity=0.470  Sum_probs=21.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .|.++|++|+||||+|+.+......
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~   25 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSE   25 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999987643

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

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

Probab=96.53  E-value=0.0089  Score=61.47  Aligned_cols=50  Identities=14%  Similarity=0.254  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhccc------CCC-eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAE------SKD-VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|.+..++.|...+...      .+. ...+.++|+.|+|||+||+.++....
T Consensus       457 ~~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~  513 (758)
T PRK11034        457 KMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_pred             cceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            456899999999998877531      122 45789999999999999999988874

>PRK06547 hypothetical protein; Provisional

Probab=96.51  E-value=0.0026  Score=53.52  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=24.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ....+|+|.|++|.||||+|+.+.+..
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            458899999999999999999998874

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.51  E-value=0.0045  Score=53.93  Aligned_cols=83  Identities=16%  Similarity=0.241  Sum_probs=50.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCCH-------
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPDI-------  236 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~~-------  236 (311)
                      ..++|.|..|+|||+|+..+.+.....  ..+++.    +.++...+.++.+++...-.....     ..++.       
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~~~d--~~V~~~----iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~   89 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQDAD--VVVYAL----IGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRA   89 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHCTTT--EEEEEE----ESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhccccc--ceeeee----ccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhh
Confidence            468999999999999999998886432  335555    333134455555555333111110     11110       


Q ss_pred             --------HHHHHHhCCCeEEEEEecCCChH
Q 042778          237 --------ALSFRQLSRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 --------~~l~~~L~~kr~LlVLDdV~~~~  259 (311)
                              +.+++  +++++||++||+....
T Consensus        90 ~~~a~t~AEyfrd--~G~dVlli~Dsltr~a  118 (215)
T PF00006_consen   90 PYTALTIAEYFRD--QGKDVLLIIDSLTRWA  118 (215)
T ss_dssp             HHHHHHHHHHHHH--TTSEEEEEEETHHHHH
T ss_pred             hccchhhhHHHhh--cCCceeehhhhhHHHH
Confidence                    33333  6899999999986543

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PRK08356 hypothetical protein; Provisional

Probab=96.50  E-value=0.0086  Score=51.22  Aligned_cols=22  Identities=23%  Similarity=0.255  Sum_probs=19.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      ..+|+|+|++|+||||+|+.+-
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            3579999999999999999983

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.49  E-value=0.0094  Score=55.73  Aligned_cols=88  Identities=11%  Similarity=0.098  Sum_probs=52.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe-cCccccCCCCChHHHHHHHHHHHhcCCC-CCCCH-HHHHHHhC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ-NVREESQRPGGLGFLQQKLLSKLLQDGI-VIPDI-ALSFRQLS  244 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~-~~~~~s~~~~~~~~l~~~ll~~l~~~~~-~~~~~-~~l~~~L~  244 (311)
                      -..+.|.|..|.||||+.+++.+.+.......++.. +--+... . +.    ..++.+  .+.. ...+. ..++..|+
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~-~-~~----~~~i~q--~evg~~~~~~~~~l~~~lr  193 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVH-R-NK----RSLINQ--REVGLDTLSFANALRAALR  193 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhc-c-Cc----cceEEc--cccCCCCcCHHHHHHHhhc
Confidence            468999999999999999999988766555554432 1111000 0 00    000000  0000 11233 67777888


Q ss_pred             CCeEEEEEecCCChHHHHH
Q 042778          245 RRKVLIVLDDVTCFRQIKS  263 (311)
Q Consensus       245 ~kr~LlVLDdV~~~~~l~~  263 (311)
                      ...=.|++|.+.+.+.+..
T Consensus       194 ~~pd~i~vgEird~~~~~~  212 (343)
T TIGR01420       194 EDPDVILIGEMRDLETVEL  212 (343)
T ss_pred             cCCCEEEEeCCCCHHHHHH
Confidence            8888889999988776554

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.

>TIGR00416 sms DNA repair protein RadA

Probab=96.47  E-value=0.017  Score=56.00  Aligned_cols=52  Identities=19%  Similarity=0.222  Sum_probs=36.7

Q ss_pred             hhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          152 SRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       152 ~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .-+.++..+|..+-..-.++.|.|.+|+|||||+..+.......=..++|+.
T Consensus        78 TGi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416        78 SGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             cCcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            3445566666544344678999999999999999998777544323466776

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)).

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.46  E-value=0.019  Score=52.61  Aligned_cols=49  Identities=22%  Similarity=0.209  Sum_probs=37.4

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .++|-+.....+..+.....+....+.++|+.|+||||+|.++.+.+..
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~   50 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLC   50 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhC
Confidence            4567777777777777643333446999999999999999999998654

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

Probab=96.46  E-value=0.01  Score=56.33  Aligned_cols=115  Identities=15%  Similarity=0.162  Sum_probs=67.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRK  247 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr  247 (311)
                      -..+-|||..|.|||-|++++.+...........+.    ++.     ......++..+...     ..+..++..  .-
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y----~~s-----e~f~~~~v~a~~~~-----~~~~Fk~~y--~~  176 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVY----LTS-----EDFTNDFVKALRDN-----EMEKFKEKY--SL  176 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEe----ccH-----HHHHHHHHHHHHhh-----hHHHHHHhh--cc
Confidence            678999999999999999999999776665333333    111     22222333222221     113344444  22


Q ss_pred             EEEEEecCCCh---HH-HHHh-------hcc------------CCC----------cCCceEEEcCCCChHHHHHHHHHh
Q 042778          248 VLIVLDDVTCF---RQ-IKSL-------IGM------------LRN----------CCVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       248 ~LlVLDdV~~~---~~-l~~l-------~~~------------~~~----------~~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                      =++++||++-.   +. -+.+       ...            ..+          ...+-++++.+++.+....++.++
T Consensus       177 dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kk  256 (408)
T COG0593         177 DLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKK  256 (408)
T ss_pred             CeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHH
Confidence            36677776521   11 1111       100            000          344578999999999999999997


Q ss_pred             hcCC
Q 042778          295 AFKQ  298 (311)
Q Consensus       295 af~~  298 (311)
                      |-..
T Consensus       257 a~~~  260 (408)
T COG0593         257 AEDR  260 (408)
T ss_pred             HHhc
Confidence            7543

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.43  E-value=0.012  Score=56.98  Aligned_cols=113  Identities=16%  Similarity=0.215  Sum_probs=64.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe--cCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ--NVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLS  244 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~--~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~  244 (311)
                      ....+.+.|.+|.|||+||..++..  ..|+.+=-+.  +.-..++ .....++.                 ....+.-+
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~--S~FPFvKiiSpe~miG~sE-saKc~~i~-----------------k~F~DAYk  596 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS--SDFPFVKIISPEDMIGLSE-SAKCAHIK-----------------KIFEDAYK  596 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh--cCCCeEEEeChHHccCccH-HHHHHHHH-----------------HHHHHhhc
Confidence            4677889999999999999988854  4565322221  0000111 11111111                 22233334


Q ss_pred             CCeEEEEEecCCChHHHHHhhccCCC--------------------------------------cCCceEEEcCCCCh-H
Q 042778          245 RRKVLIVLDDVTCFRQIKSLIGMLRN--------------------------------------CCVKEKYEMKELGD-D  285 (311)
Q Consensus       245 ~kr~LlVLDdV~~~~~l~~l~~~~~~--------------------------------------~~~~~~y~v~~L~~-~  285 (311)
                      ..--.||+||+...-+|-.+.|...+                                      ..-...|.|+.|+. +
T Consensus       597 S~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~  676 (744)
T KOG0741|consen  597 SPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGE  676 (744)
T ss_pred             CcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchH
Confidence            55678899998755444433222111                                      23456788999887 7


Q ss_pred             HHHHHHHHhh-cCCC
Q 042778          286 HALELFSRHA-FKQN  299 (311)
Q Consensus       286 ea~~Lf~~~a-f~~~  299 (311)
                      +..+.++..- |...
T Consensus       677 ~~~~vl~~~n~fsd~  691 (744)
T KOG0741|consen  677 QLLEVLEELNIFSDD  691 (744)
T ss_pred             HHHHHHHHccCCCcc
Confidence            7788877754 5543

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.43  E-value=0.0051  Score=54.05  Aligned_cols=29  Identities=21%  Similarity=0.269  Sum_probs=25.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ....++||.|..|.|||||++.+...+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~   59 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQ   59 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            45889999999999999999999886543

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=96.43  E-value=0.028  Score=56.98  Aligned_cols=52  Identities=23%  Similarity=0.282  Sum_probs=34.7

Q ss_pred             CCccchhhhHHHHHHhhcccC----------CCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          145 NQLVGVESRVEEIESLLGAES----------KDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~----------~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++.|.+...+.+.+.+....          .-.+-|.|+|.+|.||||+|+.+.++....|
T Consensus       152 ~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f  213 (644)
T PRK10733        152 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPF  213 (644)
T ss_pred             HHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCE
Confidence            355677666555555432110          1133488999999999999999998865544

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

Probab=96.41  E-value=0.011  Score=52.88  Aligned_cols=86  Identities=20%  Similarity=0.146  Sum_probs=51.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEec--CccccCCCCChHHHHHHHHHHHhcCCC-------CCCC--H
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQN--VREESQRPGGLGFLQQKLLSKLLQDGI-------VIPD--I  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~--~~~~s~~~~~~~~l~~~ll~~l~~~~~-------~~~~--~  236 (311)
                      -.++||+|..|+|||||++.+..-...... .+++..  +...+  .........++|..++....       ++..  .
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L~~pt~G-~i~f~g~~i~~~~--~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGLEEPTSG-EILFEGKDITKLS--KEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcCcCCCCc-eEEEcCcchhhcc--hhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            458999999999999999999876544433 333331  11111  11233445556666553322       1111  1


Q ss_pred             --HHHHHHhCCCeEEEEEecCC
Q 042778          237 --ALSFRQLSRRKVLIVLDDVT  256 (311)
Q Consensus       237 --~~l~~~L~~kr~LlVLDdV~  256 (311)
                        -.+.+.|.-+.=|||.|.--
T Consensus       116 QRi~IARALal~P~liV~DEpv  137 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPV  137 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCch
Confidence              45667788888999999854

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.40  E-value=0.0029  Score=53.08  Aligned_cols=25  Identities=20%  Similarity=0.263  Sum_probs=22.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|.+.|++|.||||+|+.+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5799999999999999999988754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.36  E-value=0.01  Score=57.33  Aligned_cols=87  Identities=18%  Similarity=0.220  Sum_probs=54.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      -..++|.|-.|+|||||+..+.+.... +-+.++++.    +.++......+...++..-.....     ..+.  .   
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~~~~~dv~V~~l----iGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~  218 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNISKQHSGSSVFAG----VGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARM  218 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhhCCCEEEEEc----CCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHH
Confidence            457999999999999999988887653 445666665    333244555565555443211111     1111  0   


Q ss_pred             ------HHHHHHh---CCCeEEEEEecCCCh
Q 042778          237 ------ALSFRQL---SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ------~~l~~~L---~~kr~LlVLDdV~~~  258 (311)
                            ..+.+++   .++++||++|++...
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLl~~DslTR~  249 (461)
T PRK12597        219 RVVLTGLTIAEYLRDEEKEDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEeccchHH
Confidence                  3445555   379999999999654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.36  E-value=0.026  Score=54.36  Aligned_cols=29  Identities=17%  Similarity=0.227  Sum_probs=25.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ...+|.++|.+|+||||+|..++..+...
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~  122 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKK  122 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            46899999999999999999998876543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.017  Score=54.39  Aligned_cols=36  Identities=17%  Similarity=0.259  Sum_probs=27.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc--CceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF--EGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F--~~~~wv~  203 (311)
                      -.+++++|..|+||||++..+..+....+  ..+.++.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit  174 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLT  174 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            56999999999999999999998754333  3445554

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.33  E-value=0.038  Score=50.02  Aligned_cols=95  Identities=17%  Similarity=0.092  Sum_probs=57.0

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHH-HhcCCC-CCC
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSK-LLQDGI-VIP  234 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~-l~~~~~-~~~  234 (311)
                      |..+|..+-..-+++=|+|+.|.||||||..++-.....-..++||+    .-. .+++..+.. +... +..-.. ...
T Consensus        49 LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~aq~~g~~a~fID----tE~-~l~p~r~~~-l~~~~~d~l~v~~~~  122 (279)
T COG0468          49 LDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKPGGKAAFID----TEH-ALDPERAKQ-LGVDLLDNLLVSQPD  122 (279)
T ss_pred             HHHHhcCCcccceEEEEecCCCcchhhHHHHHHHHhhcCCCeEEEEe----CCC-CCCHHHHHH-HHHhhhcceeEecCC
Confidence            34445433345789999999999999999987776555555789998    333 555555433 3333 211111 222


Q ss_pred             CH-------HHHHHHhCCCeEEEEEecCCC
Q 042778          235 DI-------ALSFRQLSRRKVLIVLDDVTC  257 (311)
Q Consensus       235 ~~-------~~l~~~L~~kr~LlVLDdV~~  257 (311)
                      +.       ..+.+....+--|||+|.|-.
T Consensus       123 ~~e~q~~i~~~~~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         123 TGEQQLEIAEKLARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             CHHHHHHHHHHHHHhccCCCCEEEEecCcc
Confidence            22       333333333345999999863

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.33  E-value=0.0057  Score=52.47  Aligned_cols=37  Identities=19%  Similarity=0.201  Sum_probs=28.0

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      ....+|+|+|++|.||||||+.+...+...-...+++
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~l   58 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLL   58 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEE
Confidence            3467999999999999999999998764332233444

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=96.33  E-value=0.0043  Score=52.48  Aligned_cols=24  Identities=33%  Similarity=0.549  Sum_probs=21.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|+|.|..|.||||||+.+...+.
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~   24 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLR   24 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999988754

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=96.32  E-value=0.0032  Score=51.24  Aligned_cols=24  Identities=21%  Similarity=0.401  Sum_probs=21.2

Q ss_pred             EEEeccCcchhHHHHHHHHHhhcc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      |.|+|++|.||||+|+.+.....-
T Consensus         2 i~l~G~~GsGKstla~~la~~l~~   25 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALGL   25 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCC
Confidence            689999999999999999987643

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.32  E-value=0.003  Score=50.91  Aligned_cols=24  Identities=25%  Similarity=0.447  Sum_probs=21.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|.|.|+.|.||||+|+.+..+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~   24 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999998753

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.32  E-value=0.005  Score=51.58  Aligned_cols=27  Identities=33%  Similarity=0.443  Sum_probs=23.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+|.|.|++|.||||+|+.+......
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            458999999999999999999998643

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.32  E-value=0.0026  Score=54.47  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|||.|..|+||||||+.+...+
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998765

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.30  E-value=0.0022  Score=49.38  Aligned_cols=26  Identities=23%  Similarity=0.506  Sum_probs=21.6

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccCc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      |-|+|.+|+|||+||+.+...+..++
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~   26 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHI   26 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHh
Confidence            45899999999999999988765443

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.29  E-value=0.006  Score=55.05  Aligned_cols=26  Identities=15%  Similarity=0.152  Sum_probs=20.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.|.|+|.+|.||||+|+.+...+..
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh
Confidence            46889999999999999999887554

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.28  E-value=0.0029  Score=53.94  Aligned_cols=23  Identities=26%  Similarity=0.453  Sum_probs=21.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|+|.|.+|.||||||+.+....
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999875

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=96.27  E-value=0.014  Score=56.14  Aligned_cols=85  Identities=15%  Similarity=0.147  Sum_probs=49.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|+|||||++.+.+....  +..++..    +.++......+....+..-.....     ..++  .    
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~~--d~~v~~~----iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~  231 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNADA--DVSVIGL----IGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQ  231 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccCC--CEEEEEE----EecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHH
Confidence            457899999999999999998876543  3445443    333233444444444332211100     1111  1    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                           -.+.+++  .++++||++||+...
T Consensus       232 a~~~a~tiAEyfrd~G~~Vll~~DslTr~  260 (442)
T PRK08927        232 AAYLTLAIAEYFRDQGKDVLCLMDSVTRF  260 (442)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCcHHH
Confidence                 2334444  479999999999654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.26  E-value=0.03  Score=50.90  Aligned_cols=36  Identities=11%  Similarity=0.159  Sum_probs=27.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC--cCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN--FEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~--F~~~~wv~  203 (311)
                      .++++|+|.+|+||||++..++......  -..++.++
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            5799999999999999999998875432  12345554

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

Probab=96.26  E-value=0.0055  Score=61.18  Aligned_cols=54  Identities=24%  Similarity=0.320  Sum_probs=45.9

Q ss_pred             CCCccchhhhHHHHHHhhcc----cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          144 KNQLVGVESRVEEIESLLGA----ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      .++-.|+++..+.|.+.|.-    ++-+-+++..+|++|+|||.+|+.++.-+...|-
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFf  467 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFF  467 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceE
Confidence            67889999999999998853    3345789999999999999999999998777664

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.25  E-value=0.003  Score=53.17  Aligned_cols=23  Identities=17%  Similarity=0.190  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|.|.|++|+||||+|+.+..+.
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999999999998876

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK13946 shikimate kinase; Provisional

Probab=96.25  E-value=0.0036  Score=53.06  Aligned_cols=28  Identities=14%  Similarity=0.261  Sum_probs=24.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .+.|.+.||.|+||||+++.+.+++.-.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~   37 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLP   37 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            4579999999999999999999987443

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.24  E-value=0.023  Score=53.07  Aligned_cols=60  Identities=10%  Similarity=0.124  Sum_probs=38.7

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hccC----cCceEEEecCccccCCCCChHHHHH
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISSN----FEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~~----F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      .|-++|..+=..-.++-|+|.+|+|||+|+..++-.  ....    -..++||+    .-. .+...++.+
T Consensus       114 ~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyId----TE~-tF~peRl~~  179 (344)
T PLN03187        114 ALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYID----TEG-TFRPDRIVP  179 (344)
T ss_pred             hHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEE----cCC-CCCHHHHHH
Confidence            445556544344678889999999999999877543  2221    13568888    333 556666544

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.24  E-value=0.026  Score=52.12  Aligned_cols=61  Identities=7%  Similarity=0.163  Sum_probs=38.9

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hcc----CcCceEEEecCccccCCCCChHHHHH
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISS----NFEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~----~F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      ..|..+|..+=..-+++-|+|.+|+||||||..++-.  ...    .=..++|++    .-. .+...++.+
T Consensus        83 ~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYId----tE~-~f~~eRi~~  149 (313)
T TIGR02238        83 QALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID----TEG-TFRPDRIRA  149 (313)
T ss_pred             HHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEE----cCC-CCCHHHHHH
Confidence            3455566544344678999999999999999876542  221    113568887    333 455666543

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.23  E-value=0.11  Score=47.96  Aligned_cols=145  Identities=13%  Similarity=0.125  Sum_probs=82.7

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC---------------cCceEEEecCcccc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN---------------FEGSCFLQNVREES  209 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~---------------F~~~~wv~~~~~~s  209 (311)
                      .+++|.+..++.+...+..+ .-....-++|..|+||+++|.++.+.+-..               ++...|+.-.-...
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~-rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~   82 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQN-RIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQ   82 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhC-CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEecccccc
Confidence            46889999999888888643 115789999999999999999998874321               22334443110000


Q ss_pred             CCCCChHHHHHHHHHHHhcCCC-----CCCCHHHHHHHhC-----CCeEEEEEecCCCh--HHHHHhh----ccCCC---
Q 042778          210 QRPGGLGFLQQKLLSKLLQDGI-----VIPDIALSFRQLS-----RRKVLIVLDDVTCF--RQIKSLI----GMLRN---  270 (311)
Q Consensus       210 ~~~~~~~~l~~~ll~~l~~~~~-----~~~~~~~l~~~L~-----~kr~LlVLDdV~~~--~~l~~l~----~~~~~---  270 (311)
                      .  ...   -..-+...+....     .++.++.+.+.+.     +++=++|+|+++..  ....+|+    .++..   
T Consensus        83 g--~~~---~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~~~fI  157 (314)
T PRK07399         83 G--KLI---TASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPGNGTLI  157 (314)
T ss_pred             c--ccc---chhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCCCCeEE
Confidence            0  000   0000001110000     1111233444433     45568888988743  3344443    11122   


Q ss_pred             -------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 -------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 -------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                   ......+++++++.++..+.+.+..
T Consensus       158 Li~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~  195 (314)
T PRK07399        158 LIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLG  195 (314)
T ss_pred             EEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhh
Confidence                         3456789999999999999999874

>PRK13949 shikimate kinase; Provisional

Probab=96.23  E-value=0.0039  Score=52.23  Aligned_cols=26  Identities=19%  Similarity=0.330  Sum_probs=22.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .|.|+||.|.||||+++.+.+...-.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~   28 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLS   28 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            58899999999999999999886433

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.22  E-value=0.0038  Score=53.64  Aligned_cols=26  Identities=23%  Similarity=0.395  Sum_probs=23.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|+|-||=|+||||||+.+.+++.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC
Confidence            46899999999999999999999875

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.20  E-value=0.014  Score=56.34  Aligned_cols=88  Identities=17%  Similarity=0.246  Sum_probs=53.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC-ceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE-GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~-~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      -..++|.|-.|+|||||+..+......+.. .++++-    +.++......+.+.++..-.....     ..+.  .   
T Consensus       144 GQR~gIfa~~GvGKt~Ll~~i~~~~~~~~~~v~V~~l----iGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~  219 (463)
T PRK09280        144 GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAG----VGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARL  219 (463)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEE----eccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            457899999999999999998777554433 344443    333244556666666543211111     1111  0   


Q ss_pred             ------HHHHHHh---CCCeEEEEEecCCChH
Q 042778          237 ------ALSFRQL---SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ------~~l~~~L---~~kr~LlVLDdV~~~~  259 (311)
                            ..+.+++   +++++||++|++....
T Consensus       220 ~a~~~a~tiAEyfrd~~G~~VLll~DslTR~A  251 (463)
T PRK09280        220 RVALTGLTMAEYFRDVEGQDVLLFIDNIFRFT  251 (463)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEecchHHHH
Confidence                  3455555   5799999999997543

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

Probab=96.20  E-value=0.021  Score=51.51  Aligned_cols=51  Identities=25%  Similarity=0.395  Sum_probs=38.7

Q ss_pred             CCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++=|.++.+++|.+-....           -...+=|-+||.+|.|||-||++|+|+.+..
T Consensus       185 ~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSAT  246 (440)
T KOG0726|consen  185 ADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSAT  246 (440)
T ss_pred             cccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchh
Confidence            45668999999998865431           1225567899999999999999999975443

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.20  E-value=0.0032  Score=55.11  Aligned_cols=24  Identities=29%  Similarity=0.422  Sum_probs=21.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|||.|..|.||||||+.+...+.
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999988764

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=96.18  E-value=0.011  Score=56.96  Aligned_cols=88  Identities=15%  Similarity=0.186  Sum_probs=54.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc-cCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS-SNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~-~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      -..++|.|-.|+|||+|+..+.+... .+-+.++|+-    +.++......+.+.++..-.....     ..++  .   
T Consensus       138 GQr~~Ifg~~G~GKt~l~~~~~~~~~~~~~~v~V~~~----iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~  213 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCG----IGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARF  213 (449)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEE----eccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHH
Confidence            45789999999999999998877654 3336667765    433244555666665543111111     1111  0   


Q ss_pred             ------HHHHHHhC---CCeEEEEEecCCChH
Q 042778          237 ------ALSFRQLS---RRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ------~~l~~~L~---~kr~LlVLDdV~~~~  259 (311)
                            ..+.++++   ++++||++||+....
T Consensus       214 ~~~~~a~tiAEyfrd~~G~~VLl~~DslTR~A  245 (449)
T TIGR03305       214 RVGHTALTMAEYFRDDEKQDVLLLIDNIFRFI  245 (449)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEecChHHHH
Confidence                  34555554   589999999997543

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PRK08149 ATP synthase SpaL; Validated

Probab=96.16  E-value=0.018  Score=55.17  Aligned_cols=86  Identities=10%  Similarity=0.171  Sum_probs=51.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-------CCCC-----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-------VIPD-----  235 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-------~~~~-----  235 (311)
                      -..++|.|..|+|||||+..+......  +..++..    +..+...+..+...++........       +...     
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~~--dv~v~g~----Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSEA--DVFVIGL----IGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCCC--CeEEEEE----EeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHh
Confidence            457899999999999999988875432  2323322    222255666666666654221111       1110     


Q ss_pred             -H---HHHHHHh--CCCeEEEEEecCCChH
Q 042778          236 -I---ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       236 -~---~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                       .   ..+.+++  .+|++||++||+....
T Consensus       225 a~~~a~tiAE~fr~~G~~Vll~~DslTr~A  254 (428)
T PRK08149        225 AALVATTVAEYFRDQGKRVVLFIDSMTRYA  254 (428)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEccchHHHH
Confidence             0   2333333  4799999999997543

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.16  E-value=0.0064  Score=58.91  Aligned_cols=46  Identities=15%  Similarity=0.068  Sum_probs=37.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|++..++.+...+..+    .-|.|.|.+|+|||+||+.+.....
T Consensus        19 ~~~i~gre~vI~lll~aalag----~hVLL~GpPGTGKT~LAraLa~~~~   64 (498)
T PRK13531         19 EKGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAFQ   64 (498)
T ss_pred             hhhccCcHHHHHHHHHHHccC----CCEEEECCCChhHHHHHHHHHHHhc
Confidence            456899999999888766543    2488999999999999999998754

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

Probab=96.15  E-value=0.021  Score=51.85  Aligned_cols=139  Identities=19%  Similarity=0.269  Sum_probs=85.3

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc--CcCceEEEecCccccCCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS--NFEGSCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F~~~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      .++++|.+..++-|.+.+..  ...+....+|++|.|||+-|.++...+..  -|.+++--.|.   |. ..++.-+..+
T Consensus        35 ~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lna---Sd-erGisvvr~K  108 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNA---SD-ERGISVVREK  108 (346)
T ss_pred             HHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcc---cc-cccccchhhh
Confidence            46789999988888887764  45889999999999999999999988544  35554332222   22 2332211111


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHhC------CCe-EEEEEecCCCh--HHHHHhhccCCC---------------------c
Q 042778          222 LLSKLLQDGIVIPDIALSFRQLS------RRK-VLIVLDDVTCF--RQIKSLIGMLRN---------------------C  271 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L~------~kr-~LlVLDdV~~~--~~l~~l~~~~~~---------------------~  271 (311)
                      +           .+...+...+.      .+. =.+|||+++..  +.|.+|......                     .
T Consensus       109 i-----------k~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~  177 (346)
T KOG0989|consen  109 I-----------KNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLV  177 (346)
T ss_pred             h-----------cCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHH
Confidence            1           11111111110      122 37899999864  457777532211                     2


Q ss_pred             CCceEEEcCCCChHHHHHHHHHhhcCCC
Q 042778          272 CVKEKYEMKELGDDHALELFSRHAFKQN  299 (311)
Q Consensus       272 ~~~~~y~v~~L~~~ea~~Lf~~~af~~~  299 (311)
                      .....|.-++|.+++..+-+..-|=..+
T Consensus       178 SRC~KfrFk~L~d~~iv~rL~~Ia~~E~  205 (346)
T KOG0989|consen  178 SRCQKFRFKKLKDEDIVDRLEKIASKEG  205 (346)
T ss_pred             hhHHHhcCCCcchHHHHHHHHHHHHHhC
Confidence            3345678888998888887777765443

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=96.15  E-value=0.0092  Score=55.11  Aligned_cols=35  Identities=26%  Similarity=0.264  Sum_probs=26.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      .+++.+.|.||+||||+|.+..-........+.-+
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g~kvLlv   36 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLV   36 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcCCcEEEE
Confidence            47899999999999999999777655554434433

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.15  E-value=0.022  Score=54.42  Aligned_cols=25  Identities=20%  Similarity=0.077  Sum_probs=22.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..++.++|.+|+||||++..++...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998753

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=96.12  E-value=0.022  Score=47.71  Aligned_cols=47  Identities=21%  Similarity=0.289  Sum_probs=34.5

Q ss_pred             ccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          147 LVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       147 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +||....++++.+.+..-.....-|-|+|..|.||+.+|+.+++...
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~   47 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSP   47 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCST
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhh
Confidence            47888888888887765333334566999999999999999999643

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.11  E-value=0.004  Score=50.65  Aligned_cols=23  Identities=17%  Similarity=0.553  Sum_probs=20.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++.|+|++|+||||+|+.+.+..
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            46789999999999999998873

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.10  E-value=0.043  Score=53.18  Aligned_cols=95  Identities=13%  Similarity=0.196  Sum_probs=54.5

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC--
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI--  231 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~--  231 (311)
                      +.++..+|..+-..-.++.|.|.+|+|||||+..+......+=..++|+.    .   ......+... ...++....  
T Consensus        66 i~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs----~---Ees~~qi~~r-a~rlg~~~~~l  137 (446)
T PRK11823         66 IGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVS----G---EESASQIKLR-AERLGLPSDNL  137 (446)
T ss_pred             cHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE----c---cccHHHHHHH-HHHcCCChhcE
Confidence            44566666544334568999999999999999999887654333456766    1   1223333222 223322111  


Q ss_pred             ---CCCCHHHHHHHhCC-CeEEEEEecCC
Q 042778          232 ---VIPDIALSFRQLSR-RKVLIVLDDVT  256 (311)
Q Consensus       232 ---~~~~~~~l~~~L~~-kr~LlVLDdV~  256 (311)
                         ...++..+.+.+.. +.-+||+|.+.
T Consensus       138 ~~~~e~~l~~i~~~i~~~~~~lVVIDSIq  166 (446)
T PRK11823        138 YLLAETNLEAILATIEEEKPDLVVIDSIQ  166 (446)
T ss_pred             EEeCCCCHHHHHHHHHhhCCCEEEEechh
Confidence               11233444444433 45589999975

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.10  E-value=0.0048  Score=51.83  Aligned_cols=25  Identities=12%  Similarity=0.178  Sum_probs=21.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++.|.|+.|+|||||++.+...+.
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3789999999999999999988643

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK13948 shikimate kinase; Provisional

Probab=96.08  E-value=0.005  Score=52.22  Aligned_cols=29  Identities=14%  Similarity=0.188  Sum_probs=24.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+.|.++||.|+||||+++.+.+++...
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~~   37 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALMLH   37 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            35788999999999999999999986543

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.07  E-value=0.0086  Score=48.56  Aligned_cols=35  Identities=14%  Similarity=0.280  Sum_probs=26.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc-cCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS-SNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~-~~F~~~~wv~  203 (311)
                      ++|.|+|..|+|||||++.+.+... ..+...+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~   36 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRGYRVAVIKH   36 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcCCceEEEEE
Confidence            4799999999999999999999855 5565554554

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

Probab=96.06  E-value=0.024  Score=55.69  Aligned_cols=123  Identities=17%  Similarity=0.183  Sum_probs=69.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC-CChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP-GGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~-~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ..+.+-++|++|.|||+||+++++.....|-....-.    ...+. .......+                .......+.
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~----l~sk~vGesek~ir----------------~~F~~A~~~  334 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSE----LLSKWVGESEKNIR----------------ELFEKARKL  334 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHH----HhccccchHHHHHH----------------HHHHHHHcC
Confidence            3668999999999999999999997666654321111    00000 00011111                222223345


Q ss_pred             CeEEEEEecCCChH-------------HHHHhh----ccC-------------CC---------cCCceEEEcCCCChHH
Q 042778          246 RKVLIVLDDVTCFR-------------QIKSLI----GML-------------RN---------CCVKEKYEMKELGDDH  286 (311)
Q Consensus       246 kr~LlVLDdV~~~~-------------~l~~l~----~~~-------------~~---------~~~~~~y~v~~L~~~e  286 (311)
                      ..+.|.+|+++...             ....++    +..             .+         ...+..+.+++-+.++
T Consensus       335 ~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~  414 (494)
T COG0464         335 APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEE  414 (494)
T ss_pred             CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHH
Confidence            67888888876311             111111    000             00         1346788899999999


Q ss_pred             HHHHHHHhhcCCCCC---CCcHHHhh
Q 042778          287 ALELFSRHAFKQNNP---HIGFEELS  309 (311)
Q Consensus       287 a~~Lf~~~af~~~~~---~~~~~~l~  309 (311)
                      ..+.|..+.=+...+   ..++.+|+
T Consensus       415 r~~i~~~~~~~~~~~~~~~~~~~~l~  440 (494)
T COG0464         415 RLEIFKIHLRDKKPPLAEDVDLEELA  440 (494)
T ss_pred             HHHHHHHHhcccCCcchhhhhHHHHH
Confidence            999999987644332   34455544

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.06  E-value=0.11  Score=48.23  Aligned_cols=46  Identities=15%  Similarity=0.122  Sum_probs=34.2

Q ss_pred             Cccc-hhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVG-VESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vG-r~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++| .+..++.+...+..+ .-....-++|..|+||||+|+.+.+.+
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~-~l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKN-RLSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3566 666667777776532 125667999999999999999998874

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.05  E-value=0.032  Score=52.13  Aligned_cols=61  Identities=10%  Similarity=0.058  Sum_probs=39.0

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc--cC---c-CceEEEecCccccCCCCChHHHH
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS--SN---F-EGSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~--~~---F-~~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      ...|..+|..+-..-.++-|+|.+|+|||+||..++-...  ..   - ..++|++    .-. .+...++.
T Consensus       109 ~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyId----tE~-~f~~eRl~  175 (342)
T PLN03186        109 SRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYID----TEG-TFRPQRLI  175 (342)
T ss_pred             CHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEE----CCC-CccHHHHH
Confidence            3455566654434467889999999999999987765321  11   1 2578888    333 45555543

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.04  E-value=0.016  Score=52.33  Aligned_cols=38  Identities=16%  Similarity=0.229  Sum_probs=28.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...+++.++|++|+||||++..++......=..+..+.
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~  107 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAA  107 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEe
Confidence            34789999999999999999999877654422344443

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.

>PRK04182 cytidylate kinase; Provisional

Probab=96.04  E-value=0.0058  Score=51.06  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=22.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|.|.|+.|.||||+|+.+.+++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg   25 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            689999999999999999998853

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.02  E-value=0.01  Score=47.59  Aligned_cols=25  Identities=16%  Similarity=0.211  Sum_probs=22.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+|.+.|.-|.||||+++.+.+.+
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            4589999999999999999999874

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=96.02  E-value=0.023  Score=54.84  Aligned_cols=88  Identities=17%  Similarity=0.245  Sum_probs=53.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC-ceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE-GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~-~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      -..++|.|-.|+|||||+..+......+.. .++++-    +.++.....++...++..-.....     ..++  .   
T Consensus       143 GQr~~If~~~G~GKt~L~~~~~~~~~~~~~~v~V~al----IGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~  218 (461)
T TIGR01039       143 GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAG----VGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARM  218 (461)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHHHHhcCCCeEEEEE----ecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            457899999999999999998887544333 344443    333244556666666432111110     1111  1   


Q ss_pred             ------HHHHHHh---CCCeEEEEEecCCChH
Q 042778          237 ------ALSFRQL---SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ------~~l~~~L---~~kr~LlVLDdV~~~~  259 (311)
                            -.+.+++   +++++||++||+....
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLll~DslTR~A  250 (461)
T TIGR01039       219 RVALTGLTMAEYFRDEQGQDVLLFIDNIFRFT  250 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCeeEEEecchhHHH
Confidence                  3445555   4589999999997643

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK13975 thymidylate kinase; Provisional

Probab=96.00  E-value=0.0065  Score=51.73  Aligned_cols=26  Identities=27%  Similarity=0.341  Sum_probs=23.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..|.|.|+.|+||||+|+.+.+++..
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999998764

>PTZ00035 Rad51 protein; Provisional

Probab=96.00  E-value=0.047  Score=50.94  Aligned_cols=38  Identities=13%  Similarity=0.221  Sum_probs=28.6

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|..+|..+-..-.++.|+|..|.|||||+..++-.
T Consensus       104 ~~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~  141 (337)
T PTZ00035        104 STQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVT  141 (337)
T ss_pred             cHHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHH
Confidence            34555666544445779999999999999999887654

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.98  E-value=0.0045  Score=52.61  Aligned_cols=88  Identities=20%  Similarity=0.212  Sum_probs=52.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHh-cCC-C---CCCCH-HHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLL-QDG-I---VIPDI-ALSFR  241 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~-~~~-~---~~~~~-~~l~~  241 (311)
                      -..++|.|..|.|||||++++...+... ...+-+.+..+... .. .     ... ++. ... .   ...+. +.++.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~~~-~~~i~ied~~E~~~-~~-~-----~~~-~~~~~~~~~~~~~~~~~~~~l~~   95 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIPPD-ERIITIEDTAELQL-PH-P-----NWV-RLVTRPGNVEGSGEVTMADLLRS   95 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCCC-CCEEEECCccccCC-CC-C-----CEE-EEEEecCCCCCCCccCHHHHHHH
Confidence            4689999999999999999998876533 23333432222111 00 0     000 000 000 0   11122 66777


Q ss_pred             HhCCCeEEEEEecCCChHHHHHh
Q 042778          242 QLSRRKVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       242 ~L~~kr~LlVLDdV~~~~~l~~l  264 (311)
                      .++...=.++++.+.+.+.++.+
T Consensus        96 ~lR~~pd~i~igEir~~ea~~~~  118 (186)
T cd01130          96 ALRMRPDRIIVGEVRGGEALDLL  118 (186)
T ss_pred             HhccCCCEEEEEccCcHHHHHHH
Confidence            78888888999999998876654

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=95.98  E-value=0.0065  Score=51.00  Aligned_cols=26  Identities=19%  Similarity=0.290  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|+|+.|.||||||+.+.+...
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~   29 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcC
Confidence            34689999999999999999998754

>PRK14974 cell division protein FtsY; Provisional

Probab=95.96  E-value=0.067  Score=49.83  Aligned_cols=28  Identities=14%  Similarity=0.205  Sum_probs=24.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+|+++|+.|+||||++..++..+..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~  166 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKK  166 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3789999999999999999888876544

>PRK06936 type III secretion system ATPase; Provisional

Probab=95.95  E-value=0.021  Score=54.80  Aligned_cols=86  Identities=14%  Similarity=0.176  Sum_probs=50.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|+|||||.+.+++....  +.+++..    +.++.....++....+..-.....     ..++  .    
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~~~--dv~V~~l----iGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSAEV--DVTVLAL----IGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAK  235 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCCCC--CEEEEEE----EccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHH
Confidence            568999999999999999999987644  3445554    333233444444433322111100     1111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           ..+.+++  .++++||++||+....
T Consensus       236 a~~~a~tiAEyfrd~G~~Vll~~DslTR~A  265 (439)
T PRK06936        236 AGFVATSIAEYFRDQGKRVLLLMDSVTRFA  265 (439)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHHH
Confidence                 2233343  4799999999997543

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=95.95  E-value=0.0062  Score=50.71  Aligned_cols=25  Identities=24%  Similarity=0.319  Sum_probs=22.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .|.|+|+.|.||||+|+.+.+++.-
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~lg~   28 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQALGY   28 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5788999999999999999988643

>TIGR00763 lon ATP-dependent protease La

Probab=95.93  E-value=0.0095  Score=61.73  Aligned_cols=53  Identities=19%  Similarity=0.304  Sum_probs=41.5

Q ss_pred             CCCccchhhhHHHHHHhhcc----cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA----ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+.+|.+...+.|.+++..    ......++.++|.+|+|||++|+++++.+...|
T Consensus       319 ~~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~  375 (775)
T TIGR00763       319 DEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKF  375 (775)
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCe
Confidence            45688999888888876642    122345899999999999999999999876554

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.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.93  E-value=0.0057  Score=49.35  Aligned_cols=27  Identities=19%  Similarity=0.519  Sum_probs=22.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .+.|+|+.|+|||||++.+.......|
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~~~~   27 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFDPNF   27 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCCccc
Confidence            378999999999999999998765443

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.92  E-value=0.056  Score=49.13  Aligned_cols=33  Identities=12%  Similarity=0.216  Sum_probs=28.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      .++.++.|.|..|.|||||...+.+.+......
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~~~~  134 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMRLKDSVPC  134 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHhccCCCE
Confidence            458999999999999999999999987766543

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.91  E-value=0.0058  Score=51.29  Aligned_cols=24  Identities=21%  Similarity=0.432  Sum_probs=21.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++++|+|+.|+||||||+.+.+..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            478999999999999999999864

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.90  E-value=0.028  Score=50.35  Aligned_cols=45  Identities=18%  Similarity=0.141  Sum_probs=36.6

Q ss_pred             HhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          159 SLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       159 ~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|..+-..-+++.|+|.+|+|||++|..+..+...+...++||.
T Consensus        14 ~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          14 EILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             HHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            344433345789999999999999999999998777788899988

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.90  E-value=0.057  Score=51.98  Aligned_cols=36  Identities=11%  Similarity=0.148  Sum_probs=26.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc--cCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS--SNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~--~~F~~~~wv~  203 (311)
                      .+++.++|.+|+||||++..++....  ..-..+.+++
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            46899999999999999998887654  2223345554

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.89  E-value=0.028  Score=50.63  Aligned_cols=92  Identities=15%  Similarity=0.134  Sum_probs=51.0

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC------
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD------  235 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~------  235 (311)
                      -..++|.|-.|+|||+|| ..+.++.  +-+..+.+..+++   +......+.+.+...-.....     ..++      
T Consensus        69 GQr~~Ifg~~g~GKt~L~l~~i~~~~--~~~v~~V~~~iGe---r~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  143 (274)
T cd01132          69 GQRELIIGDRQTGKTAIAIDTIINQK--GKKVYCIYVAIGQ---KASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQY  143 (274)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHHhc--CCCeEEEEEeccc---chHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHH
Confidence            357899999999999996 5666653  2345433333333   234556666666543211100     0111      


Q ss_pred             --H---HHHHHHh--CCCeEEEEEecCCChH-HHHHh
Q 042778          236 --I---ALSFRQL--SRRKVLIVLDDVTCFR-QIKSL  264 (311)
Q Consensus       236 --~---~~l~~~L--~~kr~LlVLDdV~~~~-~l~~l  264 (311)
                        .   -.+.+++  +++.+||++||+.... .+.++
T Consensus       144 ~a~~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         144 LAPYTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHH
Confidence              0   1222222  4799999999997643 34444

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

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.88  E-value=0.0052  Score=50.75  Aligned_cols=22  Identities=27%  Similarity=0.578  Sum_probs=19.9

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|+|+.|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999886

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK14530 adenylate kinase; Provisional

Probab=95.88  E-value=0.0066  Score=52.75  Aligned_cols=23  Identities=13%  Similarity=0.239  Sum_probs=21.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|+|++|.||||+|+.+..+.
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998875

>PRK05922 type III secretion system ATPase; Validated

Probab=95.88  E-value=0.036  Score=53.22  Aligned_cols=86  Identities=10%  Similarity=0.114  Sum_probs=48.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|+|||||.+.+......  +...+.. +++.   ......+..+..........     ..++  .    
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~~~~--d~gvi~l-iGer---g~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~  230 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKGSKS--TINVIAL-IGER---GREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVI  230 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCCC--CceEEEE-eCCC---CchHHHHHHHHHhhccccceEEEEECCCCCHHHHHH
Confidence            346899999999999999998876433  2233322 1111   22334444444433222111     1111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           ..+.+++  +++++||++||+....
T Consensus       231 a~~~a~tiAEyfrd~G~~VLl~~DslTR~A  260 (434)
T PRK05922        231 AGRAAMTIAEYFRDQGHRVLFIMDSLSRWI  260 (434)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHHH
Confidence                 2344444  4799999999997643

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.88  E-value=0.25  Score=45.97  Aligned_cols=27  Identities=19%  Similarity=0.247  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+.++|+.|+||||+|+.+++.+-.
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC   48 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLC   48 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcC
Confidence            567889999999999999999987543

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.88  E-value=0.032  Score=49.04  Aligned_cols=55  Identities=20%  Similarity=0.343  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhc-c-cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          144 KNQLVGVESRVEEIESLLG-A-ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~-~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      -..++|.|...+.+.+=-. . ..-..--|.+||--|.||+.|++++.+.+....-.
T Consensus        59 L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glr  115 (287)
T COG2607          59 LADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADEGLR  115 (287)
T ss_pred             HHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhcCCe
Confidence            4578999988877765221 1 11124568899999999999999999998777655

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.88  E-value=0.016  Score=58.30  Aligned_cols=74  Identities=15%  Similarity=0.138  Sum_probs=54.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      -+.++|.+..+..|...+...    +.+.|+|.+|+||||+|+.+.+.+.. +++...|+.|-      ......+.+.+
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~np------~~~~~~~~~~v   99 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPNP------EDPNNPKIRTV   99 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeCC------CcchHHHHHHH
Confidence            456889988888877766533    36889999999999999999988644 35777888852      34555666666


Q ss_pred             HHHHh
Q 042778          223 LSKLL  227 (311)
Q Consensus       223 l~~l~  227 (311)
                      +...+
T Consensus       100 ~~~~G  104 (637)
T PRK13765        100 PAGKG  104 (637)
T ss_pred             HHhcC
Confidence            54443

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=95.87  E-value=0.0072  Score=50.52  Aligned_cols=84  Identities=21%  Similarity=0.332  Sum_probs=50.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCc-eEEEe--------cCccccCCCCChHHHHHHHHHHHhcCCC---C-C-C
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEG-SCFLQ--------NVREESQRPGGLGFLQQKLLSKLLQDGI---V-I-P  234 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~-~~wv~--------~~~~~s~~~~~~~~l~~~ll~~l~~~~~---~-~-~  234 (311)
                      +-|.++||.|.||||+.+.+++.+.-.|-. =-+|.        .+-+... ......+-..++..+....+   . - .
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D~~Ie~~~g~sI~eIF~~~G-E~~FR~~E~~vl~~l~~~~~~ViaTGGG   81 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQEIEKRTGMSIAEIFEEEG-EEGFRRLETEVLKELLEEDNAVIATGGG   81 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccchHHHHHHHCcCHHHHHHHHh-HHHHHHHHHHHHHHHhhcCCeEEECCCc
Confidence            347889999999999999999987776621 11221        0000111 33455555666666665543   1 1 1


Q ss_pred             CH--HHHHHHhCCCeEEEEEe
Q 042778          235 DI--ALSFRQLSRRKVLIVLD  253 (311)
Q Consensus       235 ~~--~~l~~~L~~kr~LlVLD  253 (311)
                      .+  +.-+++|+++-..|.||
T Consensus        82 ~v~~~enr~~l~~~g~vv~L~  102 (172)
T COG0703          82 AVLSEENRNLLKKRGIVVYLD  102 (172)
T ss_pred             cccCHHHHHHHHhCCeEEEEe
Confidence            12  77778887777666665

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.87  E-value=0.008  Score=51.67  Aligned_cols=25  Identities=28%  Similarity=0.226  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|++|+||||+|+.+..+.
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999999874

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

Probab=95.87  E-value=0.013  Score=55.83  Aligned_cols=53  Identities=17%  Similarity=0.274  Sum_probs=40.2

Q ss_pred             CCCccchhhhHHHHHHhhccc--------C----CCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE--------S----KDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--------~----~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...++|.+..++.+...+...        .    ...+.|.++|+.|+||||||+.+...+...|
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~f   78 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   78 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChh
Confidence            456889998888887766421        0    1146789999999999999999999865544

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.86  E-value=0.012  Score=56.11  Aligned_cols=53  Identities=17%  Similarity=0.283  Sum_probs=38.8

Q ss_pred             CCCccchhhhHHHHHHhhccc------------CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE------------SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...++|.+..++.+.-.+...            ....+-|.++|++|+||||||+.+...+...|
T Consensus        11 d~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~f   75 (441)
T TIGR00390        11 DKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   75 (441)
T ss_pred             hhhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            346788888777776544321            11246789999999999999999999876554

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.85  E-value=0.064  Score=50.92  Aligned_cols=27  Identities=15%  Similarity=0.133  Sum_probs=23.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++|.++|..|+||||.+..++..+.
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            367999999999999999999887654

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.85  E-value=0.018  Score=54.52  Aligned_cols=27  Identities=19%  Similarity=0.320  Sum_probs=23.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +.++|+|+|.+|+||||++..++....
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~  266 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFH  266 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHH
Confidence            368999999999999999999987754

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.85  E-value=0.01  Score=58.74  Aligned_cols=35  Identities=20%  Similarity=0.406  Sum_probs=28.1

Q ss_pred             HHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          158 ESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       158 ~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|....+++.+|||.|..|.||||||+.+...+
T Consensus        55 ~qlL~~~~~~riIIGIaGpSGSGKTTLAk~LaglL   89 (656)
T PLN02318         55 CQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLNFM   89 (656)
T ss_pred             HHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHhhC
Confidence            34444444568999999999999999999998764

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.85  E-value=0.055  Score=53.14  Aligned_cols=27  Identities=15%  Similarity=0.218  Sum_probs=23.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|+|.+|+||||++..+......
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~  376 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAA  376 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            579999999999999999998876443

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.85  E-value=0.036  Score=51.20  Aligned_cols=50  Identities=14%  Similarity=0.211  Sum_probs=34.3

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc--cCc----CceEEEe
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS--SNF----EGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~--~~F----~~~~wv~  203 (311)
                      ...|..+|..+-..-.++.|+|.+|+||||||..++....  ...    ..++|++
T Consensus        82 ~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyId  137 (316)
T TIGR02239        82 SKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYID  137 (316)
T ss_pred             CHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEE
Confidence            3455566654444578999999999999999998775321  111    2458887

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).

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.83  E-value=0.023  Score=57.22  Aligned_cols=58  Identities=21%  Similarity=0.308  Sum_probs=43.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecC
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNV  205 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~  205 (311)
                      .++++|.+..+..+...+...    +.+.++|+.|+||||+|+++.+.+... |...+.+.|.
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~----~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~n~   75 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQK----RNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNP   75 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcC----CCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEeCC
Confidence            467889998888777766643    255699999999999999999987654 4445555533

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

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.83  E-value=0.012  Score=51.80  Aligned_cols=23  Identities=22%  Similarity=0.406  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|++|+||||+|+.+.+++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998875

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=95.82  E-value=0.088  Score=46.90  Aligned_cols=50  Identities=16%  Similarity=0.301  Sum_probs=36.7

Q ss_pred             CCccchhhhHHHHHHhhcccC-----------CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGAES-----------KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~-----------~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +++=|.+..++++.+.+...-           ...+=+..||++|.|||-+|++.+.+...
T Consensus       171 sDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~a  231 (424)
T KOG0652|consen  171 SDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNA  231 (424)
T ss_pred             cccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccc
Confidence            456688889999888654211           12456888999999999999998775433

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.81  E-value=0.0086  Score=51.78  Aligned_cols=31  Identities=13%  Similarity=0.190  Sum_probs=25.2

Q ss_pred             hcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          161 LGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       161 L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +..+....+.+.|+|.+|+|||||++.+.+.
T Consensus         6 ~~~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          6 LFNKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             ccCCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            3334456789999999999999999998764

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

Probab=95.81  E-value=0.07  Score=48.03  Aligned_cols=87  Identities=9%  Similarity=0.021  Sum_probs=52.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSRR  246 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~k  246 (311)
                      -.++.|.|..|.||||+++++.+.+...-...+.+.+..+..-  .+.        .++.-....-.+. ..++..|+..
T Consensus        80 ~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~--~~~--------~q~~v~~~~~~~~~~~l~~~lR~~  149 (264)
T cd01129          80 HGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQI--PGI--------NQVQVNEKAGLTFARGLRAILRQD  149 (264)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecC--CCc--------eEEEeCCcCCcCHHHHHHHHhccC
Confidence            4589999999999999999988876542223344443222111  110        0000000001123 7788888888


Q ss_pred             eEEEEEecCCChHHHHHh
Q 042778          247 KVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       247 r~LlVLDdV~~~~~l~~l  264 (311)
                      .=.|++++|.+.+....+
T Consensus       150 PD~i~vgEiR~~e~a~~~  167 (264)
T cd01129         150 PDIIMVGEIRDAETAEIA  167 (264)
T ss_pred             CCEEEeccCCCHHHHHHH
Confidence            889999999998765543

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.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.80  E-value=0.011  Score=49.77  Aligned_cols=28  Identities=18%  Similarity=0.287  Sum_probs=24.6

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+++|+|..|+|||||++.+...+..
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~   32 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCA   32 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhh
Confidence            4679999999999999999999987654

>PRK05439 pantothenate kinase; Provisional

Probab=95.80  E-value=0.015  Score=53.51  Aligned_cols=28  Identities=29%  Similarity=0.389  Sum_probs=24.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...-+|||.|.+|+||||+|+.+...+.
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4478999999999999999998887654

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=95.80  E-value=0.01  Score=53.64  Aligned_cols=37  Identities=14%  Similarity=0.221  Sum_probs=26.4

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+.+++..   .-+-+.++|..|+|||++++....+..
T Consensus        22 ~~~ll~~l~~---~~~pvLl~G~~GtGKT~li~~~l~~l~   58 (272)
T PF12775_consen   22 YSYLLDLLLS---NGRPVLLVGPSGTGKTSLIQNFLSSLD   58 (272)
T ss_dssp             HHHHHHHHHH---CTEEEEEESSTTSSHHHHHHHHHHCST
T ss_pred             HHHHHHHHHH---cCCcEEEECCCCCchhHHHHhhhccCC
Confidence            3445554442   245678999999999999999887643

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.80  E-value=0.033  Score=51.56  Aligned_cols=86  Identities=16%  Similarity=0.193  Sum_probs=49.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|.|||||.+.+.......  ..++..    +..+...+..+....+..-.....     ..++  .    
T Consensus        69 Gqri~I~G~sG~GKTtLl~~Ia~~~~~~--~~vi~~----iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~  142 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARGTTAD--VNVIAL----IGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVK  142 (326)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCCCC--EEEEEE----EecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHH
Confidence            4578999999999999999888765432  223322    222134555555555443211100     0111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           -.+.+++  ++|.+||++||+....
T Consensus       143 ~~~~a~~~AEyfr~~g~~Vll~~Dsltr~a  172 (326)
T cd01136         143 AAYTATAIAEYFRDQGKDVLLLMDSLTRFA  172 (326)
T ss_pred             HHHHHHHHHHHHHHcCCCeEEEeccchHHH
Confidence                 2233333  4799999999987643

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.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.79  E-value=0.0063  Score=50.67  Aligned_cols=20  Identities=25%  Similarity=0.488  Sum_probs=18.6

Q ss_pred             EEEEeccCcchhHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~  189 (311)
                      .|+|.|.+|+||||+|+.+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999887

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.78  E-value=0.022  Score=54.87  Aligned_cols=86  Identities=15%  Similarity=0.179  Sum_probs=48.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC----CCCC--H-----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI----VIPD--I-----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~----~~~~--~-----  236 (311)
                      -..++|+|..|+|||||++.+...... ..+++++...    . ...+..+....+.......-    ..++  .     
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~p-d~gvv~liGe----r-grev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~  238 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADAF-DTVVIALVGE----R-GREVREFLEDTLADNLKKAVAVVATSDESPMMRRLA  238 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCC-Ceeeeeeccc----C-CccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHH
Confidence            457999999999999999888765332 2233443210    1 34455554444443321110    1111  0     


Q ss_pred             ----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 ----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                          -.+.+++  +++++||++||+....
T Consensus       239 ~~~a~~iAEyfrd~G~~Vll~~DslTr~A  267 (450)
T PRK06002        239 PLTATAIAEYFRDRGENVLLIVDSVTRFA  267 (450)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchHHHH
Confidence                2233333  4799999999997543

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.78  E-value=0.015  Score=51.62  Aligned_cols=42  Identities=19%  Similarity=0.306  Sum_probs=30.0

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++.+.|.....+..+|||.|.+|.||+||.-++...+..
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~   55 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRE   55 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhh
Confidence            344555555555556889999999999999999988776443

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.76  E-value=0.0077  Score=51.70  Aligned_cols=26  Identities=15%  Similarity=0.316  Sum_probs=23.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+|+|+|..|+||||||+.+.....
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            46899999999999999999998753

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=95.76  E-value=0.033  Score=54.25  Aligned_cols=86  Identities=23%  Similarity=0.125  Sum_probs=51.5

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCc-eEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-H---
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEG-SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-I---  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~-~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-~---  236 (311)
                      -..++|.|-.|+|||||| ..+.++..  -+. ++++.    +.++......+.+.+...-.....     ..++ .   
T Consensus       162 GQR~~Ifg~~g~GKT~Lal~~I~~q~~--~dv~~V~~~----IGeR~rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r  235 (497)
T TIGR03324       162 GQRELILGDRQTGKTAIAIDTILNQKG--RNVLCIYCA----IGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQ  235 (497)
T ss_pred             CCEEEeecCCCCCHHHHHHHHHHHhcC--CCcEEEEEE----eccCcHHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHH
Confidence            457899999999999997 47777643  344 45554    444244556666665543211111     1111 0   


Q ss_pred             -------HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -------ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -------~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                             ..+-+++  +++++|||+||+....
T Consensus       236 ~~ap~~a~aiAEyfrd~G~~VLlv~DdlTr~A  267 (497)
T TIGR03324       236 YIAPYAATSIGEHFMEQGRDVLIVYDDLTQHA  267 (497)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEEcChhHHH
Confidence                   3344444  5799999999997543

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.76  E-value=0.011  Score=49.96  Aligned_cols=36  Identities=14%  Similarity=0.255  Sum_probs=30.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .+++.|+|+.|+|||||++.+..+....|...+..+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcccccccceeec
Confidence            468899999999999999999999988886555544

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.74  E-value=0.0074  Score=51.17  Aligned_cols=25  Identities=12%  Similarity=0.198  Sum_probs=21.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++.|+|+.|.|||||++.++....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~   27 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQ   27 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCC
Confidence            3789999999999999999977643

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=95.74  E-value=0.0092  Score=49.41  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|+|.|+.|.||||+|+.+.++.
T Consensus         2 iI~i~G~~GSGKstia~~la~~l   24 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKL   24 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            78999999999999999998875

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PRK12678 transcription termination factor Rho; Provisional

Probab=95.73  E-value=0.023  Score=56.02  Aligned_cols=90  Identities=21%  Similarity=0.220  Sum_probs=50.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCC--------H-H
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPD--------I-A  237 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~--------~-~  237 (311)
                      -.-.+|+|.+|+|||||++.+.+.+.... ++.+++.-+.+-   ...+..+.+.+-..+.....+...        + -
T Consensus       416 GQR~LIvgpp~aGKTtLL~~IAn~i~~n~~~~~~ivvLIgER---peEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai  492 (672)
T PRK12678        416 GQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDER---PEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAI  492 (672)
T ss_pred             CCEeEEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCc---hhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHH
Confidence            45688999999999999999999875433 444455433332   222333333221111111111100        0 2


Q ss_pred             HHHHHh--CCCeEEEEEecCCChHH
Q 042778          238 LSFRQL--SRRKVLIVLDDVTCFRQ  260 (311)
Q Consensus       238 ~l~~~L--~~kr~LlVLDdV~~~~~  260 (311)
                      .+-++|  .++.+||+||++.....
T Consensus       493 ~~Ae~fre~G~dVlillDSlTR~Ar  517 (672)
T PRK12678        493 ERAKRLVELGKDVVVLLDSITRLGR  517 (672)
T ss_pred             HHHHHHHHcCCCEEEEEeCchHHHH
Confidence            333444  57999999999975543

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=95.72  E-value=0.054  Score=54.17  Aligned_cols=108  Identities=15%  Similarity=0.237  Sum_probs=77.4

Q ss_pred             CCCccchhhhHHHHHHhhcc--cC-CCeEEEEEeccCcchhHHHHHHHHHhhc--------cCcCceEEEecCccccCCC
Q 042778          144 KNQLVGVESRVEEIESLLGA--ES-KDVYALGIWGIGGIDRTTIARAIFNKIS--------SNFEGSCFLQNVREESQRP  212 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~--------~~F~~~~wv~~~~~~s~~~  212 (311)
                      +..+-+|+.+..+|...+..  .. ..-+.+-|.|.+|.|||..+..|.+.+.        ..|+ .+.|...+     -
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~-----l  468 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLR-----L  468 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEccee-----e
Confidence            56788999999999998864  22 2245899999999999999999998533        1243 24454322     3


Q ss_pred             CChHHHHHHHHHHHhcCCCC-CCCHHHHHHHhC-----CCeEEEEEecCCC
Q 042778          213 GGLGFLQQKLLSKLLQDGIV-IPDIALSFRQLS-----RRKVLIVLDDVTC  257 (311)
Q Consensus       213 ~~~~~l~~~ll~~l~~~~~~-~~~~~~l~~~L~-----~kr~LlVLDdV~~  257 (311)
                      .....+...|+..+.++... ...++.|..++.     .+.++|++|+++.
T Consensus       469 ~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~  519 (767)
T KOG1514|consen  469 ASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDI  519 (767)
T ss_pred             cCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHH
Confidence            45788899999998887662 223366776665     4668999999864

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.70  E-value=0.01  Score=53.33  Aligned_cols=24  Identities=25%  Similarity=0.353  Sum_probs=20.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.|.|.+|+|||+||+++++...
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~lg   46 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARKRD   46 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999998653

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

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

Probab=95.70  E-value=0.038  Score=54.07  Aligned_cols=141  Identities=16%  Similarity=0.208  Sum_probs=81.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .+++||.+..+..|...|..+.- ...-...|.-|+||||+|+.++.-+...=..         ... .++-....+.|-
T Consensus        15 F~evvGQe~v~~~L~nal~~~ri-~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~---------~~e-PC~~C~~Ck~I~   83 (515)
T COG2812          15 FDDVVGQEHVVKTLSNALENGRI-AHAYLFSGPRGVGKTTIARILAKALNCENGP---------TAE-PCGKCISCKEIN   83 (515)
T ss_pred             HHHhcccHHHHHHHHHHHHhCcc-hhhhhhcCCCCcCchhHHHHHHHHhcCCCCC---------CCC-cchhhhhhHhhh
Confidence            35679999999999988875421 4455678999999999999999874332100         111 222222222221


Q ss_pred             HH-------HhcCCC-CCCCHHHHHHHhCC-----CeEEEEEecCCC--hHHHHHhhcc----CCC--------------
Q 042778          224 SK-------LLQDGI-VIPDIALSFRQLSR-----RKVLIVLDDVTC--FRQIKSLIGM----LRN--------------  270 (311)
Q Consensus       224 ~~-------l~~~~~-~~~~~~~l~~~L~~-----kr~LlVLDdV~~--~~~l~~l~~~----~~~--------------  270 (311)
                      ..       +....+ .+++++.|.+....     +-=+.|+|+|+-  ...+.+|+..    +..              
T Consensus        84 ~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip  163 (515)
T COG2812          84 EGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIP  163 (515)
T ss_pred             cCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCc
Confidence            11       000000 22333555555432     333789999984  4567777522    111              


Q ss_pred             ---cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ---CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ---~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                         ......|..+.|+.++-...+..-+
T Consensus       164 ~TIlSRcq~f~fkri~~~~I~~~L~~i~  191 (515)
T COG2812         164 NTILSRCQRFDFKRLDLEEIAKHLAAIL  191 (515)
T ss_pred             hhhhhccccccccCCCHHHHHHHHHHHH
Confidence               4456789999999987666665544

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

Probab=95.69  E-value=0.18  Score=44.69  Aligned_cols=124  Identities=11%  Similarity=0.117  Sum_probs=74.4

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-CCCCH-----HH
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-VIPDI-----AL  238 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-~~~~~-----~~  238 (311)
                      .++-+++.++|.-|.|||++++++.....+.=-+.+.+.      ........+...++..+..... .....     ..
T Consensus        48 ~d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~------~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~  121 (269)
T COG3267          48 ADGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVID------KPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRE  121 (269)
T ss_pred             hcCCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEec------CcchhHHHHHHHHHHHhccCccchhHHHHHHHHHH
Confidence            345679999999999999999966554443222222332      2145566677777777766222 33322     22


Q ss_pred             HHHH-hCCCe-EEEEEecCCC--hHHHHHhh---cc------C-CC--------------------cCCceE-EEcCCCC
Q 042778          239 SFRQ-LSRRK-VLIVLDDVTC--FRQIKSLI---GM------L-RN--------------------CCVKEK-YEMKELG  283 (311)
Q Consensus       239 l~~~-L~~kr-~LlVLDdV~~--~~~l~~l~---~~------~-~~--------------------~~~~~~-y~v~~L~  283 (311)
                      |... -+++| +.++.||..+  .+.++.+.   +.      + ..                    .....+ |+++|++
T Consensus       122 L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~  201 (269)
T COG3267         122 LAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLT  201 (269)
T ss_pred             HHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcC
Confidence            2222 24677 9999999874  34555552   00      0 00                    112233 9999999


Q ss_pred             hHHHHHHHHHh
Q 042778          284 DDHALELFSRH  294 (311)
Q Consensus       284 ~~ea~~Lf~~~  294 (311)
                      .++.-.++.++
T Consensus       202 ~~~t~~yl~~~  212 (269)
T COG3267         202 EAETGLYLRHR  212 (269)
T ss_pred             hHHHHHHHHHH
Confidence            99887777665

>PRK04296 thymidine kinase; Provisional

Probab=95.68  E-value=0.013  Score=49.90  Aligned_cols=34  Identities=9%  Similarity=-0.152  Sum_probs=25.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      .++.|+|..|.||||+|..+..+...+-..++.+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            4678899999999999999888865443333333

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.67  E-value=0.026  Score=47.67  Aligned_cols=25  Identities=20%  Similarity=0.369  Sum_probs=22.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +|.|.|+.|+||||+++.+.+.+..
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEA   26 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999998643

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.66  E-value=0.0093  Score=49.15  Aligned_cols=26  Identities=27%  Similarity=0.475  Sum_probs=22.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +|.|-|.+|+||||+|+.+++.+.-.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~   27 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK   27 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc
Confidence            68999999999999999999985443

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=95.65  E-value=0.0085  Score=44.08  Aligned_cols=25  Identities=24%  Similarity=0.480  Sum_probs=21.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++.+.|.+|+||||++..+...++.
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4678999999999999999988654

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK15453 phosphoribulokinase; Provisional

Probab=95.64  E-value=0.017  Score=52.16  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=24.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|+|.|-+|.||||+|+.+.+.+.
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3467999999999999999999987653

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.64  E-value=0.029  Score=45.53  Aligned_cols=35  Identities=20%  Similarity=0.286  Sum_probs=26.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.+++|.|..|.|||||++.+...... ..+.+++.
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~-~~G~i~~~   60 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEP-DEGIVTWG   60 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCC-CceEEEEC
Confidence            458999999999999999998875432 24444443

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.62  E-value=0.018  Score=53.42  Aligned_cols=40  Identities=20%  Similarity=0.349  Sum_probs=30.0

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+.+.+........+|+|.|.+|+|||||+..+...+..
T Consensus        43 ~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~   82 (332)
T PRK09435         43 QELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIE   82 (332)
T ss_pred             HHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3455555433456889999999999999999988776543

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.62  E-value=0.022  Score=49.80  Aligned_cols=24  Identities=33%  Similarity=0.634  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .|+|+|-||+||||+|..+..++.
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~   25 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLL   25 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHH
Confidence            689999999999999999777643

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=95.62  E-value=0.015  Score=52.58  Aligned_cols=34  Identities=18%  Similarity=0.241  Sum_probs=28.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|+|+|.+|+|||||+..+...++... .++-+.
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~IK   35 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLSGRG-RVGTVK   35 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhCC-CEEEEE
Confidence            5799999999999999999999877665 455554

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

Probab=95.62  E-value=0.063  Score=50.72  Aligned_cols=36  Identities=11%  Similarity=0.186  Sum_probs=26.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc--cCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS--SNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~--~~F~~~~wv~  203 (311)
                      -++|.++|+.|+||||-...++.+..  ..=..+.+|+
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiIT  240 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIIT  240 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEE
Confidence            78999999999999987766666643  3334455665

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.62  E-value=0.017  Score=52.63  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=22.7

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ....+|||.|..|+||||+|+.+...+
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll   86 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALL   86 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            347899999999999999998775544

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.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=95.60  E-value=0.0091  Score=49.99  Aligned_cols=24  Identities=21%  Similarity=0.433  Sum_probs=20.3

Q ss_pred             EEEeccCcchhHHHHHHHHHhhcc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      |.|.|..|+|||||.+.+.+.++.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            679999999999999999988643

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

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

Probab=95.59  E-value=0.013  Score=51.43  Aligned_cols=23  Identities=35%  Similarity=0.466  Sum_probs=20.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.++||+|..|+|||||++.+.-
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhc
Confidence            45899999999999999999865

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.55  E-value=0.01  Score=50.11  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=20.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|.|.|.+|.||||+|+.+.++
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999998

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.54  E-value=0.047  Score=49.34  Aligned_cols=145  Identities=14%  Similarity=0.161  Sum_probs=86.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .+.++|-... +++...+......-+.+.|+|+.|+|||+-++.+++..     ...|+..   .+. .+....++..+.
T Consensus        71 ~~~~l~tkt~-r~~~~~~~~A~k~g~l~~vyg~~g~gKt~a~~~y~~s~-----p~~~l~~---~~p-~~~a~~~i~~i~  140 (297)
T COG2842          71 APDFLETKTV-RRIFFRTRPASKTGSLVVVYGYAGLGKTQAAKNYAPSN-----PNALLIE---ADP-SYTALVLILIIC  140 (297)
T ss_pred             cccccccchh-HhHhhhhhhhhhcCceEEEeccccchhHHHHHhhcccC-----ccceeec---CCh-hhHHHHHHHHHH
Confidence            4566766543 33444444333334488999999999999999888765     2344431   333 555666666666


Q ss_pred             HHHhcCCC-CCCCH-HHHHHHhCCCeEEEEEecCCC--hHHHHHhhccCCC-------cCCceEEEcCCCChHHHHHHHH
Q 042778          224 SKLLQDGI-VIPDI-ALSFRQLSRRKVLIVLDDVTC--FRQIKSLIGMLRN-------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       224 ~~l~~~~~-~~~~~-~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~~~~~-------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                      ........ ...+. ..+..++++..=+|+.|+.+.  ...++.+....+-       .|.......-.=+..+..++|.
T Consensus       141 ~~~~~~~~~~~~d~~~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d~~Gi~~vLvG~prL~~~l~~~~~~~~rl~s  220 (297)
T COG2842         141 AAAFGATDGTINDLTERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDKTGIGVVLVGMPRLFKVLRRPEDELSRLYS  220 (297)
T ss_pred             HHHhcccchhHHHHHHHHHHHHccCcceeeeehhhccChHHHHHHHHHHHhhCceEEEecChHHHhccccchHHHHHHHH
Confidence            66555443 33333 566666788888899998875  3455555432222       2222222222234567788888


Q ss_pred             HhhcCC
Q 042778          293 RHAFKQ  298 (311)
Q Consensus       293 ~~af~~  298 (311)
                      +.+|+.
T Consensus       221 rv~v~~  226 (297)
T COG2842         221 RVRVGK  226 (297)
T ss_pred             HhhhHh
Confidence            888864

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.53  E-value=0.021  Score=51.16  Aligned_cols=36  Identities=11%  Similarity=0.140  Sum_probs=27.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.++.|.|.+|.||||+|..+.......=+.+++++
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            568999999999999999987665323324556666

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.53  E-value=0.0097  Score=49.10  Aligned_cols=26  Identities=19%  Similarity=0.299  Sum_probs=22.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +++|+|..|+|||||+..+...++..
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~   26 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKAR   26 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            57899999999999999999986554

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=95.53  E-value=0.039  Score=52.81  Aligned_cols=85  Identities=13%  Similarity=0.173  Sum_probs=47.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|.|||||.+.+.+....  +..++..    +..+...+..+...++..-.....     ..++  .    
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~~~--~~~vi~~----iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~  210 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYTEA--DVVVVGL----IGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLR  210 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCC--CEEEEEE----EecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHH
Confidence            457999999999999999988876543  2333332    222123344444443322111000     1111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                           ..+.+++  +++++||++||+...
T Consensus       211 a~~~a~tiAEyfr~~G~~Vll~~Dsltr~  239 (411)
T TIGR03496       211 AAFYATAIAEYFRDQGKDVLLLMDSLTRF  239 (411)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEeChHHH
Confidence                 2333443  479999999999654

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

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

Probab=95.51  E-value=0.022  Score=56.82  Aligned_cols=51  Identities=20%  Similarity=0.298  Sum_probs=37.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++..+-|.+-.+.|.++.......-.+|.|+|+.|.||||||+.++.++..
T Consensus       368 pP~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L~~  418 (568)
T PRK05537        368 IPEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKLME  418 (568)
T ss_pred             CChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHhhh
Confidence            455566665556555554444444668999999999999999999998754

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

Probab=95.50  E-value=0.017  Score=52.30  Aligned_cols=40  Identities=20%  Similarity=0.344  Sum_probs=32.2

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.++...|.....+..+|||.|.||+||+||.-++-.++.
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~   76 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELR   76 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHH
Confidence            3456666666667789999999999999999998877643

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.49  E-value=0.01  Score=48.47  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++.|+|.+|.||||||+.+.....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999998764

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.49  E-value=0.16  Score=52.23  Aligned_cols=93  Identities=15%  Similarity=0.101  Sum_probs=53.2

Q ss_pred             HHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-
Q 042778          154 VEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-  231 (311)
Q Consensus       154 ~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-  231 (311)
                      +..|..+|. .+=..-+++-|+|..|+||||||..+.......=..++|+.    ... ..+.     ..+.+++.... 
T Consensus        45 i~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId----~E~-t~~~-----~~A~~lGvDl~~  114 (790)
T PRK09519         45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFID----AEH-ALDP-----DYAKKLGVDTDS  114 (790)
T ss_pred             cHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC----Ccc-chhH-----HHHHHcCCChhH
Confidence            345556665 33344678889999999999999876655333335568887    222 2332     23334432211 


Q ss_pred             ----CCCCH----HHHHHHhCC-CeEEEEEecCC
Q 042778          232 ----VIPDI----ALSFRQLSR-RKVLIVLDDVT  256 (311)
Q Consensus       232 ----~~~~~----~~l~~~L~~-kr~LlVLDdV~  256 (311)
                          .....    ..+...++. +--|||+|-|-
T Consensus       115 llv~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        115 LLVSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCeEEEEcchh
Confidence                11121    344444444 45589999975

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.47  E-value=0.051  Score=52.90  Aligned_cols=47  Identities=26%  Similarity=0.337  Sum_probs=33.8

Q ss_pred             CCCccchhhh---HHHHHHhhcccC------CC-eEEEEEeccCcchhHHHHHHHHH
Q 042778          144 KNQLVGVESR---VEEIESLLGAES------KD-VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       144 ~~~~vGr~~~---~~~l~~~L~~~~------~~-~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .++.-|.|+.   +++|.+.|....      ++ .+=|.++|++|.|||-||++++-
T Consensus       303 F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAG  359 (752)
T KOG0734|consen  303 FEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAG  359 (752)
T ss_pred             cccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhc
Confidence            4567788764   555566665421      12 56788999999999999999854

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

Probab=95.45  E-value=0.021  Score=54.69  Aligned_cols=50  Identities=12%  Similarity=0.168  Sum_probs=35.1

Q ss_pred             CCCccchhhhHHHHHHhhc-------cc-C--C----CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLG-------AE-S--K----DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~-------~~-~--~----~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|.+..++.+...+.       .. .  +    ..+.+.++|.+|+|||+||+.++....
T Consensus        70 ~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~  133 (412)
T PRK05342         70 DQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILD  133 (412)
T ss_pred             hhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhC
Confidence            3467899888777754331       10 0  0    135689999999999999999987643

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=95.45  E-value=0.033  Score=53.66  Aligned_cols=86  Identities=13%  Similarity=0.129  Sum_probs=48.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|+|..|.|||||++.+.....  .+..++..    +..+......+...++..-.....     ..++  .    
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~~~--~dv~V~g~----Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~  241 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRFTE--ADIIVVGL----IGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLR  241 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC--CCEEEEEE----eCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHH
Confidence            45799999999999999998876432  23333322    222134455555554433211111     1111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           ..+.+++  +++++||++||+....
T Consensus       242 a~~~a~aiAEyfrd~G~~VLl~~DslTR~A  271 (451)
T PRK05688        242 AAMYCTRIAEYFRDKGKNVLLLMDSLTRFA  271 (451)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEecchhHHH
Confidence                 2233444  5799999999997543

>PLN02924 thymidylate kinase

Probab=95.44  E-value=0.066  Score=46.85  Aligned_cols=28  Identities=7%  Similarity=0.041  Sum_probs=24.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -..|.|-|.-|.||||+|+.+.+.+...
T Consensus        16 g~~IviEGiDGsGKsTq~~~L~~~l~~~   43 (220)
T PLN02924         16 GALIVLEGLDRSGKSTQCAKLVSFLKGL   43 (220)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            5689999999999999999999986554

>PRK13768 GTPase; Provisional

Probab=95.44  E-value=0.021  Score=51.11  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..++.|.|.||+||||++..+....
T Consensus         2 ~~~i~v~G~~G~GKTt~~~~~~~~l   26 (253)
T PRK13768          2 MYIVFFLGTAGSGKTTLTKALSDWL   26 (253)
T ss_pred             cEEEEEECCCCccHHHHHHHHHHHH
Confidence            3578999999999999998877654

>TIGR01287 nifH nitrogenase iron protein

Probab=95.41  E-value=0.011  Score=53.32  Aligned_cols=24  Identities=29%  Similarity=0.596  Sum_probs=20.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.|+|+|=||+||||+|..++.-+
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~L   24 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAAL   24 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHH
Confidence            478999999999999999887754

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.41  E-value=0.031  Score=51.28  Aligned_cols=87  Identities=20%  Similarity=0.157  Sum_probs=53.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCc--CceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNF--EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSR  245 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F--~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~  245 (311)
                      +.+.|+|..|.||||+++++.+.+....  ...+-+.+..+..-...+...        +. ......+. ..++..|+.
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~--------~~-~~~~~~~~~~~l~~aLR~  203 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQ--------LR-TSDDAISMTRLLKATLRL  203 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEE--------EE-ecCCCCCHHHHHHHHhcC
Confidence            4577999999999999999998876532  223334433332110001000        00 00112244 778888888


Q ss_pred             CeEEEEEecCCChHHHHHh
Q 042778          246 RKVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       246 kr~LlVLDdV~~~~~l~~l  264 (311)
                      ..=.||+..|.+.+.++.+
T Consensus       204 ~pD~iivGEiR~~ea~~~l  222 (299)
T TIGR02782       204 RPDRIIVGEVRGGEALDLL  222 (299)
T ss_pred             CCCEEEEeccCCHHHHHHH
Confidence            8888999999998876654

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.

>PRK13695 putative NTPase; Provisional

Probab=95.41  E-value=0.017  Score=48.35  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=21.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|.|.+|+|||||++.+++...
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~   25 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLK   25 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999988754

>PLN02200 adenylate kinase family protein

Probab=95.40  E-value=0.014  Score=51.52  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=22.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|++|+||||+|+.+.++.
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999998765

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.39  E-value=0.018  Score=51.50  Aligned_cols=32  Identities=13%  Similarity=0.200  Sum_probs=27.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      ...+|.++||+|.||||..+.++..+...+..
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~p   49 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLHAKKTP   49 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHhhccCC
Confidence            46788899999999999999999887766653

>PRK10867 signal recognition particle protein; Provisional

Probab=95.38  E-value=0.11  Score=49.95  Aligned_cols=29  Identities=17%  Similarity=0.235  Sum_probs=24.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ...+|.++|.+|+||||+|..++..+...
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~  127 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            36899999999999999998887765444

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

Probab=95.38  E-value=0.02  Score=50.67  Aligned_cols=52  Identities=19%  Similarity=0.349  Sum_probs=37.9

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++=|.+-..+++.+....           +-+..+-|.++|++|.|||.||++|++.....|
T Consensus       155 ~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~f  217 (408)
T KOG0727|consen  155 ADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  217 (408)
T ss_pred             cccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchhe
Confidence            3455777777777664432           123467789999999999999999999765544

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.37  E-value=0.12  Score=48.78  Aligned_cols=94  Identities=16%  Similarity=0.217  Sum_probs=55.7

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC--
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI--  231 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~--  231 (311)
                      +.++...|-.+--.-.+|.|=|-+|||||||...+..++...- .+.+|+.       ......+. --..+++....  
T Consensus        79 ~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVsG-------EES~~Qik-lRA~RL~~~~~~l  149 (456)
T COG1066          79 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVSG-------EESLQQIK-LRADRLGLPTNNL  149 (456)
T ss_pred             hHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEeC-------CcCHHHHH-HHHHHhCCCccce
Confidence            3445555543222346899999999999999999999987766 6677761       22222221 11233332112  


Q ss_pred             ---CCCCHHHHHHHhCC-CeEEEEEecCC
Q 042778          232 ---VIPDIALSFRQLSR-RKVLIVLDDVT  256 (311)
Q Consensus       232 ---~~~~~~~l~~~L~~-kr~LlVLDdV~  256 (311)
                         ...+++.+.+.+.. +.-|+|+|-+-
T Consensus       150 ~l~aEt~~e~I~~~l~~~~p~lvVIDSIQ  178 (456)
T COG1066         150 YLLAETNLEDIIAELEQEKPDLVVIDSIQ  178 (456)
T ss_pred             EEehhcCHHHHHHHHHhcCCCEEEEeccc
Confidence               12233555555554 66799999874

>PRK06761 hypothetical protein; Provisional

Probab=95.37  E-value=0.015  Score=52.77  Aligned_cols=34  Identities=26%  Similarity=0.380  Sum_probs=26.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC-cCceEEE
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFL  202 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv  202 (311)
                      ++|.|.|++|+||||+++.+++.+... ++..++.
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~g~~v~~~~   38 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQNGIEVELYL   38 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcCceEEEEEe
Confidence            579999999999999999999986543 3433433

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.37  E-value=0.19  Score=41.56  Aligned_cols=24  Identities=17%  Similarity=0.144  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..|-|++-.|-||||+|..+.-+.
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra   26 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRA   26 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            467788888999999999888873

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=95.36  E-value=0.014  Score=50.25  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ..+|||+|+.|+||||.|+.+-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            36899999999999999997765

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=95.36  E-value=0.013  Score=49.62  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=20.1

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|.|++|+||||+|+.+..+.
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999998874

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.36  E-value=0.014  Score=48.32  Aligned_cols=21  Identities=24%  Similarity=0.253  Sum_probs=17.9

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |+|.|-.|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999987

>PLN02348 phosphoribulokinase

Probab=95.35  E-value=0.023  Score=53.70  Aligned_cols=30  Identities=13%  Similarity=0.269  Sum_probs=26.1

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+...+|||.|.+|.||||+|+.+.+.+..
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~~Lg~   75 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTSVFGG   75 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            345889999999999999999999987653

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.35  E-value=0.073  Score=51.11  Aligned_cols=28  Identities=14%  Similarity=0.145  Sum_probs=23.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+|.++|..|+||||+|..++..++.
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~  126 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQR  126 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3689999999999999999988875443

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.

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=95.34  E-value=0.049  Score=52.74  Aligned_cols=87  Identities=17%  Similarity=0.210  Sum_probs=52.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc--Cc-C-ceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS--NF-E-GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F-~-~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~  236 (311)
                      -..++|.|-.|+|||||+..+.+....  .+ + .++++.    +.++......+...++..-.....     ..++  .
T Consensus       141 GQR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~----iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~  216 (458)
T TIGR01041       141 GQKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAA----MGITYEEANFFMKDFEETGALERAVVFLNLADDPAV  216 (458)
T ss_pred             CCEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEE----ccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHH
Confidence            357899999999999999999886432  11 1 334444    333245566666666533211111     0111  0


Q ss_pred             ---------HHHHHHhC---CCeEEEEEecCCCh
Q 042778          237 ---------ALSFRQLS---RRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ---------~~l~~~L~---~kr~LlVLDdV~~~  258 (311)
                               ..+.++++   ++++||++||+...
T Consensus       217 ~R~~a~~~a~tiAEyfr~d~G~~VLli~DslTR~  250 (458)
T TIGR01041       217 ERIVTPRMALTAAEYLAFEKDMHVLVILTDMTNY  250 (458)
T ss_pred             HHHHHHHHHHHHHHHHHHccCCcEEEEEcChhHH
Confidence                     34556665   68899999999754

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.34  E-value=0.073  Score=50.23  Aligned_cols=37  Identities=14%  Similarity=0.171  Sum_probs=28.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+++.|+|..|+||||++..++.....+=..+.+++
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lIt  241 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFIT  241 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3689999999999999999999876533323345555

>PRK14527 adenylate kinase; Provisional

Probab=95.31  E-value=0.015  Score=49.52  Aligned_cols=26  Identities=15%  Similarity=0.153  Sum_probs=23.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|.|.|.+|.||||+|+.+.++.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            35789999999999999999998775

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.31  E-value=0.039  Score=52.81  Aligned_cols=86  Identities=16%  Similarity=0.191  Sum_probs=48.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|..|+|||||++.+....... ...+.+.     .++...+.++....+..-.....     ..++  .    
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~~~~~-~gvi~~i-----Ger~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~  213 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARNTDAD-VVVIALV-----GERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQ  213 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCCCC-EEEEEEE-----eeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHH
Confidence            4579999999999999999888765432 2222222     11133344444444332211111     1111  0    


Q ss_pred             -----HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                           ..+.+++  +++++||++||+....
T Consensus       214 a~~~a~~iAEyfrd~G~~Vll~~DslTr~A  243 (418)
T TIGR03498       214 AAYTATAIAEYFRDQGKDVLLLMDSVTRFA  243 (418)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHHH
Confidence                 2344444  4799999999997543

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=95.31  E-value=0.016  Score=48.92  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=22.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++|+|..|.|||||++.+.....
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~   28 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFS   28 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4789999999999999999998754

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.30  E-value=0.012  Score=49.54  Aligned_cols=21  Identities=24%  Similarity=0.390  Sum_probs=19.4

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +|+|.|+.|+||||+|+.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999876

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.29  E-value=0.038  Score=48.30  Aligned_cols=48  Identities=13%  Similarity=0.131  Sum_probs=33.2

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|.++|..+=..-..+.|.|.+|.||||||..+.......-+.++|+.
T Consensus         8 ~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881         8 GLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             hHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            444555433334678999999999999999987665333335667776

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>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=95.28  E-value=0.017  Score=51.85  Aligned_cols=110  Identities=16%  Similarity=0.123  Sum_probs=62.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLS  224 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~  224 (311)
                      +++.-.....+.+.++|...-...+.|.|.|..|.||||++.++...+...-...+-+.+..+..-...+          
T Consensus       104 e~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~~~~----------  173 (270)
T PF00437_consen  104 EDLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLPGPN----------  173 (270)
T ss_dssp             CCCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--SCSS----------
T ss_pred             hhccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeecccc----------
Confidence            3444344445566666654323467899999999999999999998876661222333322221000000          


Q ss_pred             HHhcCC-CCCCCH-HHHHHHhCCCeEEEEEecCCChHHHHHh
Q 042778          225 KLLQDG-IVIPDI-ALSFRQLSRRKVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       225 ~l~~~~-~~~~~~-~~l~~~L~~kr~LlVLDdV~~~~~l~~l  264 (311)
                      .+.... ....+. +.++..|+...=.||++++.+.+.+..+
T Consensus       174 ~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~~e~~~~~  215 (270)
T PF00437_consen  174 QIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIRDPEAAEAI  215 (270)
T ss_dssp             EEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-SCHHHHHH
T ss_pred             eEEEEeecCcccHHHHHHHHhcCCCCcccccccCCHhHHHHH
Confidence            000000 011223 7788888887788999999988877664

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 ....

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.28  E-value=0.072  Score=47.03  Aligned_cols=49  Identities=8%  Similarity=0.078  Sum_probs=34.1

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..|-++|..+=..-.++.|.|.+|.|||+||..+...-...=+.++|+.
T Consensus         8 ~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877         8 PGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             HhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            3455566544445679999999999999999886655323345567776

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

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

Probab=95.27  E-value=0.0092  Score=48.01  Aligned_cols=47  Identities=21%  Similarity=0.249  Sum_probs=33.1

Q ss_pred             cchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ||.-..++++.+.+..-......|.|+|..|.||+++|+.++..-..
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~   47 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGR   47 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCc
Confidence            46666677777766543344556789999999999999999886443

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.27  E-value=0.074  Score=47.50  Aligned_cols=92  Identities=18%  Similarity=0.385  Sum_probs=54.0

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      .+.=|-...+++|.+....           +-+..+=|.++|++|.|||-+|++|+|+..     .||+.    +-.   
T Consensus       177 ~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtd-----acfir----vig---  244 (435)
T KOG0729|consen  177 SDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTD-----ACFIR----VIG---  244 (435)
T ss_pred             ccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccC-----ceEEe----ehh---
Confidence            3445666677766654321           113356688999999999999999999874     35665    211   


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC-CeEEEEEecCC
Q 042778          214 GLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR-RKVLIVLDDVT  256 (311)
Q Consensus       214 ~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~-kr~LlVLDdV~  256 (311)
                       -     +|.....++..  .-+..|.+.-+. |-|+|.+|.|+
T Consensus       245 -s-----elvqkyvgega--rmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 -S-----ELVQKYVGEGA--RMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             -H-----HHHHHHhhhhH--HHHHHHHHHhcccceEEEEeeccc
Confidence             1     12222222211  001344444444 56899999886

>PRK01184 hypothetical protein; Provisional

Probab=95.25  E-value=0.015  Score=49.02  Aligned_cols=22  Identities=18%  Similarity=0.439  Sum_probs=18.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+|+|+|++|.||||+|+ ++.+
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~~   23 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IARE   23 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHH
Confidence            479999999999999987 4443

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.25  E-value=0.062  Score=47.21  Aligned_cols=47  Identities=13%  Similarity=0.132  Sum_probs=33.0

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh-hccCcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK-ISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~-~~~~F~~~~wv~  203 (311)
                      .|.++|..+-..-.++.|+|.+|.||||||..+... ... =..++|+.
T Consensus        13 ~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~-g~~~~y~~   60 (234)
T PRK06067         13 ELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQ-GKKVYVIT   60 (234)
T ss_pred             HHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhC-CCEEEEEE
Confidence            445555544344678999999999999999998654 433 34566766

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.24  E-value=0.016  Score=44.82  Aligned_cols=21  Identities=19%  Similarity=0.461  Sum_probs=19.4

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|..|+|||||.+.+...
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~   22 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGG   22 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            789999999999999999875

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.23  E-value=0.045  Score=45.95  Aligned_cols=33  Identities=18%  Similarity=0.080  Sum_probs=24.8

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +.|.|.+|+|||+||..+.......=..++|+.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            678999999999999988776433324456765

A related protein is found in archaea.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.23  E-value=0.019  Score=50.86  Aligned_cols=23  Identities=26%  Similarity=0.429  Sum_probs=19.1

Q ss_pred             EeccCcchhHHHHHHHHHhhccC
Q 042778          173 IWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       173 I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      |+||+|.||||+++.+.+-....
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~   23 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESN   23 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhc
Confidence            68999999999999999875444

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.23  E-value=0.037  Score=51.19  Aligned_cols=29  Identities=17%  Similarity=0.389  Sum_probs=24.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ...+++++|++|+||||++..++..+...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~  141 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQ  141 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            46899999999999999999998875543

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=95.23  E-value=0.055  Score=52.65  Aligned_cols=88  Identities=16%  Similarity=0.165  Sum_probs=53.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHHHHHHhc-CC-------C----CCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQ-DG-------I----VIP  234 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~-~~-------~----~~~  234 (311)
                      -..++|.|-.|+|||||+..+...+... =+.++++-    +.++.....++...++..-.. ..       .    ..+
T Consensus       161 GQR~gIfgg~GvGKs~L~~~~~~~~~~~~~dv~V~~l----IGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd  236 (494)
T CHL00060        161 GGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGG----VGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMN  236 (494)
T ss_pred             CCEEeeecCCCCChhHHHHHHHHHHHHhcCCeEEEEE----eccCchHHHHHHHHHHhcCccccCcccccceEEEEECCC
Confidence            4579999999999999999887764322 25566665    433244556666666552110 10       0    001


Q ss_pred             -C-H---------HHHHHHhCC---CeEEEEEecCCChH
Q 042778          235 -D-I---------ALSFRQLSR---RKVLIVLDDVTCFR  259 (311)
Q Consensus       235 -~-~---------~~l~~~L~~---kr~LlVLDdV~~~~  259 (311)
                       . .         ..+.+++++   +++||++||+....
T Consensus       237 ~p~~~R~~a~~~A~tiAEyfrd~g~~~VLll~DslTR~A  275 (494)
T CHL00060        237 EPPGARMRVGLTALTMAEYFRDVNKQDVLLFIDNIFRFV  275 (494)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHcCCCCEEEEcccchHHH
Confidence             1 0         446666643   49999999997543

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.22  E-value=0.062  Score=55.02  Aligned_cols=48  Identities=21%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..++|....++.+.+.+..-...-.-|.|+|..|+|||++|+++++.-
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s  423 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS  423 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            468999988888887776433344578899999999999999999864

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

Probab=95.21  E-value=0.084  Score=47.93  Aligned_cols=51  Identities=18%  Similarity=0.301  Sum_probs=38.5

Q ss_pred             CCccchhhhHHHHHHhhcc---------c-CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLGA---------E-SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~---------~-~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++.-|.+...+.|.+....         + ....+-|.++|++|.||+.||++|+..-...
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnST  193 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANST  193 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCCc
Confidence            5678999888888764321         1 1227889999999999999999999875433

>PRK14532 adenylate kinase; Provisional

Probab=95.20  E-value=0.016  Score=49.11  Aligned_cols=22  Identities=18%  Similarity=0.265  Sum_probs=19.9

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|.|++|.||||+|+.+.++.
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6789999999999999998765

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.19  E-value=0.054  Score=45.94  Aligned_cols=26  Identities=27%  Similarity=0.284  Sum_probs=23.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..|.|.|..|+||||+|+.+.+.+..
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~   29 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQE   29 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57999999999999999999988654

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.19  E-value=0.02  Score=49.47  Aligned_cols=28  Identities=14%  Similarity=0.325  Sum_probs=24.9

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|+++|..|.|||||...+.+...
T Consensus        20 ~~~~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        20 HGLVVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             cCcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4699999999999999999999887743

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=95.19  E-value=0.13  Score=46.63  Aligned_cols=44  Identities=20%  Similarity=0.306  Sum_probs=30.3

Q ss_pred             cchhhhHHHHHHhhcccC---------CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          148 VGVESRVEEIESLLGAES---------KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~---------~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|.+..++.+.+++....         .....++|+|++|+|||||...+.++
T Consensus        89 ~gi~~L~~~i~~~~~~~~~~~~~~~~~~~~~~~~~vG~~nvGKSslin~l~~~  141 (276)
T TIGR03596        89 KGVKKIIKAAKKLLKEKNEKLKAKGLKNRPIRAMIVGIPNVGKSTLINRLAGK  141 (276)
T ss_pred             ccHHHHHHHHHHHHHHhhhhhhhccCCCCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            455655555655553221         12456899999999999999998764

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.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=95.18  E-value=0.028  Score=51.76  Aligned_cols=28  Identities=14%  Similarity=0.401  Sum_probs=24.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +.-..|+|+||.|.||||+++.+..++.
T Consensus       131 ~~~~~I~l~G~~GsGKStvg~~La~~Lg  158 (309)
T PRK08154        131 ARRRRIALIGLRGAGKSTLGRMLAARLG  158 (309)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3466899999999999999999998763

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.17  E-value=0.033  Score=46.64  Aligned_cols=36  Identities=22%  Similarity=0.206  Sum_probs=28.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      ...+|=+.|++|.||||||.+++.++...--.+.-+
T Consensus        22 ~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~L   57 (197)
T COG0529          22 KGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLL   57 (197)
T ss_pred             CCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            356888889999999999999999976654444433

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=95.17  E-value=0.037  Score=53.14  Aligned_cols=26  Identities=19%  Similarity=0.367  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -..++|.|..|.|||||++.+.+...
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~~  180 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAPD  180 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCCC
Confidence            45889999999999999998887643

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.16  E-value=0.14  Score=49.02  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=22.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.+++++|..|+||||+...+..+
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~  214 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAAR  214 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3579999999999999999988765

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=95.16  E-value=0.03  Score=43.85  Aligned_cols=25  Identities=32%  Similarity=0.542  Sum_probs=22.0

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccC
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      |.+.|.||+||||++..+.+.+...
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~   26 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEK   26 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            7899999999999999999886553

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>cd04159 Arl10_like Arl10-like subfamily

Probab=95.15  E-value=0.097  Score=41.85  Aligned_cols=21  Identities=19%  Similarity=0.335  Sum_probs=19.1

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |+|+|..|+|||||.+.+...
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            789999999999999988775

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=95.14  E-value=0.016  Score=50.19  Aligned_cols=25  Identities=24%  Similarity=0.571  Sum_probs=21.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|+|.|-||+||||++..++.-+.
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~la   25 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAALA   25 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHHHH
Confidence            4789999999999999988877543

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=95.14  E-value=0.014  Score=50.32  Aligned_cols=23  Identities=22%  Similarity=0.560  Sum_probs=21.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|+|+|++|+|||||+..+.+.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~   28 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGD   28 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcC
Confidence            57899999999999999998876

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.12  E-value=0.041  Score=47.47  Aligned_cols=50  Identities=14%  Similarity=0.158  Sum_probs=28.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc-------cCcCceEEEecCccccCCCCChHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS-------SNFEGSCFLQNVREESQRPGGLGFLQQKLLS  224 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~-------~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~  224 (311)
                      +..|+|++|.||||++..+...+.       ..-...+-++    ... +..+..+...+..
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~----~~s-N~avd~~~~~l~~   75 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVV----SPS-NAAVDNILERLKK   75 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEE----ESS-HHHHHHHHHHHHC
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceee----cCC-chhHHHHHHHHHh
Confidence            788999999999987777666651       2333334443    222 3445555555554

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.12  E-value=0.03  Score=51.37  Aligned_cols=36  Identities=17%  Similarity=0.231  Sum_probs=27.2

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.+-+........+|+|.|.+|+|||||+..+....
T Consensus        23 ~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~   58 (300)
T TIGR00750        23 LLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMEL   58 (300)
T ss_pred             HHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            333343333458899999999999999999987753

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

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=95.10  E-value=0.053  Score=52.62  Aligned_cols=85  Identities=16%  Similarity=0.121  Sum_probs=48.9

Q ss_pred             eEEEEEeccCcchhHHHHH-HHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H--
Q 042778          168 VYALGIWGIGGIDRTTIAR-AIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I--  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~-~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~--  236 (311)
                      -..++|.|-.|+||||||. .+.++.  .-+.. +++.    +.++......+.+.+...-.....     ..++  .  
T Consensus       141 GQR~~I~g~~g~GKt~Lal~~I~~q~--~~dv~cV~~~----IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r  214 (485)
T CHL00059        141 GQRELIIGDRQTGKTAVATDTILNQK--GQNVICVYVA----IGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQ  214 (485)
T ss_pred             CCEEEeecCCCCCHHHHHHHHHHhcc--cCCeEEEEEE----ecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHH
Confidence            3578999999999999965 566653  33444 4444    333245566666665543211111     1111  0  


Q ss_pred             -------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 -------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                             ..+.+++  +++++|||+||+...
T Consensus       215 ~~ap~~a~aiAEyfr~~G~~VLlv~DdlTr~  245 (485)
T CHL00059        215 YLAPYTGAALAEYFMYRGRHTLIIYDDLSKQ  245 (485)
T ss_pred             HHHHHHHhhHHHHHHHcCCCEEEEEcChhHH
Confidence                   2233333  479999999999754

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=95.08  E-value=0.018  Score=47.75  Aligned_cols=35  Identities=20%  Similarity=0.238  Sum_probs=27.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      .++++|+|..|.|||||...+..+++.+--.++-|
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G~rVa~i   36 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARGYRVATV   36 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCCcEEEEE
Confidence            46899999999999999999988765543333333

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=95.08  E-value=0.019  Score=52.29  Aligned_cols=24  Identities=25%  Similarity=0.225  Sum_probs=21.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|.+.|.+|+||||+|+.+.++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHC
Confidence            578889999999999999998875

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

Probab=95.07  E-value=0.02  Score=44.13  Aligned_cols=22  Identities=27%  Similarity=0.326  Sum_probs=20.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      -..++|.|..|.|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4689999999999999999976

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

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

Probab=95.06  E-value=0.061  Score=42.66  Aligned_cols=59  Identities=24%  Similarity=0.380  Sum_probs=50.8

Q ss_pred             EEecCccccCCCChHHHHHHHHHhCCCcEEe-eCCCCCCCcchHHHHHHHHhccceeeeeccC
Q 042778           21 VFQSFRGEDNRDNFTGHLYSALSQKGIETFI-DDQLNRGDEISQSLVDAIEASAISLIIFSEA   82 (311)
Q Consensus        21 vFis~~g~D~~~~f~~~L~~~L~~~gi~~f~-d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~~   82 (311)
                      |||.|. .|.  .....+..-|+..|+.+.+ .+....|..+...+.+.+.++..+|++++|+
T Consensus         2 VFIvhg-~~~--~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpD   61 (125)
T PF10137_consen    2 VFIVHG-RDL--AAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPD   61 (125)
T ss_pred             EEEEeC-CCH--HHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEccc
Confidence            899988 553  5888999999988988875 3466889999999999999999999999985

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

>PRK14531 adenylate kinase; Provisional

Probab=95.06  E-value=0.022  Score=48.19  Aligned_cols=24  Identities=21%  Similarity=0.119  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.|.|+|++|.||||+|+.+.++.
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358899999999999999998875

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

Probab=95.06  E-value=0.017  Score=55.05  Aligned_cols=26  Identities=19%  Similarity=0.207  Sum_probs=23.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -++.|+|+|..|.|||||++++++..
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~~  243 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANIF  243 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999998764

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

Probab=95.04  E-value=0.038  Score=52.87  Aligned_cols=50  Identities=12%  Similarity=0.175  Sum_probs=36.1

Q ss_pred             CCCccchhhhHHHHHHhhc-------c---cC--CC----eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLG-------A---ES--KD----VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~-------~---~~--~~----~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|.+..++.+...+.       .   ..  ++    ...+.++|+.|+|||+||+.++..+.
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~  141 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILN  141 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcC
Confidence            4567899988887754441       1   11  11    25789999999999999999987654

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=95.04  E-value=0.059  Score=51.82  Aligned_cols=25  Identities=12%  Similarity=0.193  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -..++|.|..|+|||||++.+....
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~~  179 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRYT  179 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhccc
Confidence            5689999999999999999887754

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

Probab=95.03  E-value=0.029  Score=57.23  Aligned_cols=48  Identities=17%  Similarity=0.346  Sum_probs=37.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -+.++||+.+++.+++.|.....+-  -.++|-+|+|||+++.-++.++.
T Consensus       169 lDPvIGRd~EI~r~iqIL~RR~KNN--PvLiGEpGVGKTAIvEGLA~rIv  216 (786)
T COG0542         169 LDPVIGRDEEIRRTIQILSRRTKNN--PVLVGEPGVGKTAIVEGLAQRIV  216 (786)
T ss_pred             CCCCcChHHHHHHHHHHHhccCCCC--CeEecCCCCCHHHHHHHHHHHHh
Confidence            4678999999999999887543221  13568999999999999999843

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.03  E-value=0.026  Score=47.69  Aligned_cols=25  Identities=16%  Similarity=0.345  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.++.|.|+.|+|||||+++++++.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4578899999999999999999987

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.02  E-value=0.019  Score=46.67  Aligned_cols=24  Identities=21%  Similarity=0.271  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+-|.|.|.+|+||||||..++..
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~   30 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEK   30 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHH
Confidence            456889999999999999999865

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=95.02  E-value=0.017  Score=46.05  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=21.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++|+|..|.|||||.+.+.....
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~~~   36 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGLLP   36 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTSSH
T ss_pred             CEEEEEccCCCccccceeeeccccc
Confidence            4899999999999999999877543

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.01  E-value=0.27  Score=44.04  Aligned_cols=53  Identities=11%  Similarity=-0.024  Sum_probs=36.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKLLSKLL  227 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~  227 (311)
                      -.++.|.|.+|+||||++..+......+ =..++|+.    .   ......+...++..+.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS----~---E~~~~~~~~r~~~~~~   83 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS----L---EEPVVRTARRLLGQYA   83 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE----c---ccCHHHHHHHHHHHHh
Confidence            4588899999999999999988775433 24466766    2   2344556666655443

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.00  E-value=0.14  Score=42.91  Aligned_cols=77  Identities=8%  Similarity=0.031  Sum_probs=43.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCC------CCH-HHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVI------PDI-ALSFRQ  242 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~------~~~-~~l~~~  242 (311)
                      ++.|.|.+|.||||+|..+..+...   ...++.    ..  ...-.+.++.+-.+........      .++ +.+...
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~---~~~~ia----t~--~~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~   73 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGL---QVLYIA----TA--QPFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRAD   73 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCC---CcEeCc----CC--CCChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhh
Confidence            6889999999999999999876432   123333    11  2223445555544443322221      223 444443


Q ss_pred             hCCCeEEEEEecCC
Q 042778          243 LSRRKVLIVLDDVT  256 (311)
Q Consensus       243 L~~kr~LlVLDdV~  256 (311)
                      ..+.. ++++|.+.
T Consensus        74 ~~~~~-~VlID~Lt   86 (170)
T PRK05800         74 AAPGR-CVLVDCLT   86 (170)
T ss_pred             cCCCC-EEEehhHH
Confidence            43333 78888874

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=94.99  E-value=0.033  Score=51.26  Aligned_cols=23  Identities=35%  Similarity=0.381  Sum_probs=20.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +++-+.|-||+||||+|.+++-.
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~   24 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALA   24 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHH
Confidence            57889999999999999877664

...

>PRK14737 gmk guanylate kinase; Provisional

Probab=94.98  E-value=0.024  Score=48.26  Aligned_cols=25  Identities=20%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|.|+|++|+|||||++.+..+.
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            5789999999999999999998875

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=94.97  E-value=0.038  Score=45.78  Aligned_cols=27  Identities=22%  Similarity=0.436  Sum_probs=23.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++++|+|..|+|||||+..+.......
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l~~~   28 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPALSAR   28 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999886544

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=94.97  E-value=0.048  Score=50.82  Aligned_cols=98  Identities=18%  Similarity=0.338  Sum_probs=60.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-------
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-------  235 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-------  235 (311)
                      -..||+.|-.|+|||-|.+++-+.+..+..+...+..+++-   ...-.++..++...-.....     ++.+       
T Consensus       147 GgKiGLFGGAGVGKTVl~~ELI~Nia~~h~g~SVFaGvGER---tREGndLy~Em~es~vl~ktalv~gQMNEpPGaR~R  223 (468)
T COG0055         147 GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGER---TREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMR  223 (468)
T ss_pred             CceeeeeccCCccceeeHHHHHHHHHHHcCCeEEEEecccc---ccchHHHHHHHHhcCCCCceeEEEeecCCCCcceee
Confidence            45799999999999999999999988777776555555553   33445566665544211111     1111       


Q ss_pred             --H--HHHHHHh---CCCeEEEEEecCCChHH----HHHhhccC
Q 042778          236 --I--ALSFRQL---SRRKVLIVLDDVTCFRQ----IKSLIGML  268 (311)
Q Consensus       236 --~--~~l~~~L---~~kr~LlVLDdV~~~~~----l~~l~~~~  268 (311)
                        +  -.+.+++   .++.+|+.+||+...-|    .-.|+|.-
T Consensus       224 ValtGlT~AEyfRD~~gqdVLlFIDNIfRftQAGsEVSalLGr~  267 (468)
T COG0055         224 VALTGLTMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRM  267 (468)
T ss_pred             ehhhhhhHHHHhhcccCCeEEEEehhhhHHhhcchHHHHHhccC
Confidence              0  1223333   36899999999976544    44555443

>smart00072 GuKc Guanylate kinase homologues

Probab=94.95  E-value=0.023  Score=48.08  Aligned_cols=30  Identities=20%  Similarity=0.398  Sum_probs=25.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      .+.+.|+|+.|+||+||+..+.+.....|.
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~~~~~~   31 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEIPDAFE   31 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcCCcceE
Confidence            368999999999999999999888654443

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PLN02796 D-glycerate 3-kinase

Probab=94.94  E-value=0.022  Score=53.02  Aligned_cols=28  Identities=21%  Similarity=0.268  Sum_probs=24.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..-+|||.|..|.|||||++.+...+..
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~lL~~  126 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYLFNA  126 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHhcc
Confidence            4678999999999999999999887644

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

Probab=94.94  E-value=0.039  Score=51.19  Aligned_cols=50  Identities=26%  Similarity=0.218  Sum_probs=37.8

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      ..++|.+..+..+...+..+    +.+-+.|.+|+|||+||+.+...+...|-.
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~----~~vll~G~PG~gKT~la~~lA~~l~~~~~~   73 (329)
T COG0714          24 KVVVGDEEVIELALLALLAG----GHVLLEGPPGVGKTLLARALARALGLPFVR   73 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcC----CCEEEECCCCccHHHHHHHHHHHhCCCeEE
Confidence            34888877777666555432    357889999999999999999988755543

>PHA02244 ATPase-like protein

Probab=94.94  E-value=0.027  Score=52.86  Aligned_cols=26  Identities=19%  Similarity=0.243  Sum_probs=22.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -|.|+|..|+|||+||+++++.....
T Consensus       121 PVLL~GppGtGKTtLA~aLA~~lg~p  146 (383)
T PHA02244        121 PVFLKGGAGSGKNHIAEQIAEALDLD  146 (383)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            46779999999999999999986443

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

Probab=94.94  E-value=0.032  Score=49.66  Aligned_cols=57  Identities=18%  Similarity=0.220  Sum_probs=41.5

Q ss_pred             CCCCCCCccchhhhHHH---HHHhhcc----cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          140 PCSNKNQLVGVESRVEE---IESLLGA----ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       140 ~~l~~~~~vGr~~~~~~---l~~~L~~----~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      +.+..++.||.+....+   |.+.|..    +....+-|..+|++|.|||.+|+++++..+..|
T Consensus       116 ~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp~  179 (368)
T COG1223         116 SDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPL  179 (368)
T ss_pred             ccccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCce
Confidence            33336788999876543   3445543    234488999999999999999999999865543

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=94.93  E-value=0.073  Score=51.34  Aligned_cols=26  Identities=19%  Similarity=0.302  Sum_probs=22.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -..++|.|-.|+|||||+..+.++..
T Consensus       141 GQRigIfagsGvGKs~L~~~i~~~~~  166 (466)
T TIGR01040       141 GQKIPIFSAAGLPHNEIAAQICRQAG  166 (466)
T ss_pred             CCeeeeecCCCCCHHHHHHHHHHhhc
Confidence            45789999999999999999888753

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

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

Probab=94.92  E-value=0.047  Score=43.24  Aligned_cols=48  Identities=19%  Similarity=0.331  Sum_probs=34.4

Q ss_pred             CCCccchhhhHHHHHHhh----cc-cCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          144 KNQLVGVESRVEEIESLL----GA-ESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L----~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..+++|..-..+.|.+.|    .. .+++.-|++.+|..|+|||.+++.+++.
T Consensus        24 ~~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   24 QRNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            346777765555555444    33 3455889999999999999988877775

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

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=94.91  E-value=0.1  Score=50.37  Aligned_cols=27  Identities=22%  Similarity=0.354  Sum_probs=23.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .-..++|.|..|.|||||++.+.....
T Consensus       157 ~Gq~i~I~G~sG~GKStLl~~I~~~~~  183 (438)
T PRK07721        157 KGQRVGIFAGSGVGKSTLMGMIARNTS  183 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcccC
Confidence            356899999999999999998887644

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=94.90  E-value=0.026  Score=52.42  Aligned_cols=47  Identities=17%  Similarity=0.138  Sum_probs=38.6

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..++|....++++.+.+..-...-.-|.|+|-.|+||+++|+.++..
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            46899999999998887654444456889999999999999999865

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=94.90  E-value=0.06  Score=51.74  Aligned_cols=26  Identities=23%  Similarity=0.344  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -..++|.|..|+|||||++.+.....
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~~~  182 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKGCL  182 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhccC
Confidence            45889999999999999999987543

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=94.89  E-value=0.02  Score=46.49  Aligned_cols=22  Identities=14%  Similarity=0.412  Sum_probs=19.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|+++|.+|+|||||...+.+.
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988764

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>PRK00698 tmk thymidylate kinase; Validated

Probab=94.89  E-value=0.072  Score=45.44  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=22.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|.|.|+.|+||||+++.+.+.+.
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~l~   28 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKELLE   28 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5899999999999999999998754

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=94.89  E-value=0.067  Score=52.17  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=30.4

Q ss_pred             hHHHHHHhhc-----ccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          153 RVEEIESLLG-----AESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       153 ~~~~l~~~L~-----~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.++..||.     ...-+.+++.|+|+.|+||||..+.+....
T Consensus        90 KI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel  134 (634)
T KOG1970|consen   90 KISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL  134 (634)
T ss_pred             hHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh
Confidence            4556666766     222346799999999999999999888863

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=94.88  E-value=0.079  Score=50.75  Aligned_cols=28  Identities=18%  Similarity=0.322  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .-..++|.|..|.|||||.+.+.+....
T Consensus       136 ~Gqri~I~G~sG~GKTtLl~~i~~~~~~  163 (413)
T TIGR03497       136 KGQRVGIFAGSGVGKSTLLGMIARNAKA  163 (413)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            3568999999999999999988876543

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK12338 hypothetical protein; Provisional

Probab=94.86  E-value=0.025  Score=52.10  Aligned_cols=25  Identities=28%  Similarity=0.425  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|.+|+||||+|+.+..+.
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l   28 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTL   28 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHC
Confidence            5789999999999999999999874

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=94.85  E-value=0.023  Score=51.45  Aligned_cols=24  Identities=25%  Similarity=0.448  Sum_probs=20.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++|+|+|=||+||||+|..++.-+
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~L   25 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAAL   25 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            478899999999999999887754

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.85  E-value=0.05  Score=51.14  Aligned_cols=90  Identities=13%  Similarity=0.055  Sum_probs=52.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC---ceEEEecCccccCCCCChHHHHH--HHHHHHhcCCCCCCCH-HHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE---GSCFLQNVREESQRPGGLGFLQQ--KLLSKLLQDGIVIPDI-ALSFR  241 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~---~~~wv~~~~~~s~~~~~~~~l~~--~ll~~l~~~~~~~~~~-~~l~~  241 (311)
                      -..|.|+|..|.||||+++++.+.+....+   .++.+.+.-+..     +..+..  ..+.+... ..+..+. ..++.
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE~~-----~~~~~~~~~~v~Q~~v-~~~~~~~~~~l~~  207 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIEFV-----YDEIETISASVCQSEI-PRHLNNFAAGVRN  207 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCceEe-----ccccccccceeeeeec-cccccCHHHHHHH
Confidence            479999999999999999999887754433   223333222111     111100  00001000 0012233 67777


Q ss_pred             HhCCCeEEEEEecCCChHHHHH
Q 042778          242 QLSRRKVLIVLDDVTCFRQIKS  263 (311)
Q Consensus       242 ~L~~kr~LlVLDdV~~~~~l~~  263 (311)
                      .|+...-.+++..+.+.+..+.
T Consensus       208 aLR~~Pd~i~vGEiRd~et~~~  229 (358)
T TIGR02524       208 ALRRKPHAILVGEARDAETISA  229 (358)
T ss_pred             HhccCCCEEeeeeeCCHHHHHH
Confidence            8888888888999988876653

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.

>TIGR00017 cmk cytidylate kinase

Probab=94.85  E-value=0.026  Score=49.27  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=22.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|+|.|+.|.||||+|+.++.++.
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~~~   27 (217)
T TIGR00017         3 MIIAIDGPSGAGKSTVAKAVAEKLG   27 (217)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999998754

This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.

>PRK14490 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional

Probab=94.84  E-value=0.028  Score=53.07  Aligned_cols=29  Identities=24%  Similarity=0.553  Sum_probs=25.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+|+|+|..|.|||||+..+...++..+
T Consensus         5 ~~~i~i~G~~gsGKTTl~~~l~~~l~~~~   33 (369)
T PRK14490          5 PFEIAFCGYSGSGKTTLITALVRRLSERF   33 (369)
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHhhCc
Confidence            56899999999999999999999876553

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.84  E-value=0.043  Score=50.48  Aligned_cols=92  Identities=16%  Similarity=0.092  Sum_probs=53.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSRR  246 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~k  246 (311)
                      -..+.|.|..|.|||||++++...+.... ..+.+.+..+..-...+...+    ...-.......-+. +.++..|+..
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~~~~~-~iv~ied~~El~~~~~~~~~l----~~~~~~~~~~~~~~~~~l~~~Lr~~  218 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEIPKDE-RIITIEDTREIFLPHPNYVHL----FYSKGGQGLAKVTPKDLLQSCLRMR  218 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccCCccc-cEEEEcCccccCCCCCCEEEE----EecCCCCCcCccCHHHHHHHHhcCC
Confidence            46899999999999999999988764432 334444433322100010000    00000000011122 6777778888


Q ss_pred             eEEEEEecCCChHHHHHh
Q 042778          247 KVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       247 r~LlVLDdV~~~~~l~~l  264 (311)
                      .=.||+|.+...+.++.+
T Consensus       219 pd~ii~gE~r~~e~~~~l  236 (308)
T TIGR02788       219 PDRIILGELRGDEAFDFI  236 (308)
T ss_pred             CCeEEEeccCCHHHHHHH
Confidence            888999999987766544

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=94.82  E-value=0.12  Score=47.56  Aligned_cols=59  Identities=14%  Similarity=0.167  Sum_probs=38.1

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC------cCceEEEecCccccCCCCChHHHH
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN------FEGSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F~~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      .+..+|..+-..-.++-|+|.+|+||||||..++......      =..++||+    .-. .+...++.
T Consensus        83 ~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~----te~-~f~~~rl~  147 (310)
T TIGR02236        83 ELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID----TEN-TFRPERIM  147 (310)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE----CCC-CCCHHHHH
Confidence            3445555333346788999999999999999887664321      12678887    322 44555543

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.

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=94.81  E-value=0.032  Score=53.77  Aligned_cols=26  Identities=8%  Similarity=0.239  Sum_probs=22.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -..++|.|..|+|||||.+.+.....
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~~~  200 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARYTQ  200 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCCCC
Confidence            45799999999999999998887653

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=94.80  E-value=0.028  Score=47.45  Aligned_cols=27  Identities=26%  Similarity=0.370  Sum_probs=23.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++.|.|.+|.||||+|+.+.....
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~   43 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLE   43 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999999998754

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.78  E-value=0.029  Score=46.54  Aligned_cols=25  Identities=20%  Similarity=0.407  Sum_probs=21.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+++.|+|.+|+||||+.+.+-...
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l   28 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL   28 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH
Confidence            5789999999999999998776665

>cd03114 ArgK-like The function of this protein family is unkown

Probab=94.78  E-value=0.035  Score=45.38  Aligned_cols=25  Identities=24%  Similarity=0.566  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++++.|.+|+||||++..+......
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~~~~   25 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITALRA   25 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHH
Confidence            3789999999999999999887533

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=94.78  E-value=0.044  Score=54.04  Aligned_cols=55  Identities=25%  Similarity=0.329  Sum_probs=40.1

Q ss_pred             CccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          146 QLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      +++--...++++..||...   ....+++.+.|++|+||||.++.+++...  |+..=|.
T Consensus        20 eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg--~~v~Ew~   77 (519)
T PF03215_consen   20 ELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG--FEVQEWI   77 (519)
T ss_pred             HhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC--CeeEEec
Confidence            3444456788888888642   23367999999999999999999999752  3444454

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.77  E-value=0.035  Score=55.00  Aligned_cols=45  Identities=20%  Similarity=0.457  Sum_probs=36.2

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ++++|.+..++.+...+...  ....+-|+|..|+||||+|+.+++.
T Consensus        65 ~~iiGqs~~i~~l~~al~~~--~~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGP--NPQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHH
Confidence            46899999998888766432  2345678999999999999999875

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.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=94.76  E-value=0.14  Score=42.80  Aligned_cols=77  Identities=6%  Similarity=-0.012  Sum_probs=44.0

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCC---CCHHHHHHHhCC--
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVI---PDIALSFRQLSR--  245 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~---~~~~~l~~~L~~--  245 (311)
                      +.|.|..|.|||++|..+...   .-...+++.    ..+ ..+. .+++.+...........   +....+.+.+..  
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~---~~~~~~y~a----t~~-~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~   72 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE---LGGPVTYIA----TAE-AFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELD   72 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh---cCCCeEEEE----ccC-cCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcC
Confidence            678999999999999988765   223455665    333 3433 35555544333222222   112445555522  


Q ss_pred             CeEEEEEecCC
Q 042778          246 RKVLIVLDDVT  256 (311)
Q Consensus       246 kr~LlVLDdV~  256 (311)
                      +.-.|++|.+.
T Consensus        73 ~~~~VLIDclt   83 (169)
T cd00544          73 PGDVVLIDCLT   83 (169)
T ss_pred             CCCEEEEEcHh
Confidence            23379999874

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK14529 adenylate kinase; Provisional

Probab=94.76  E-value=0.14  Score=44.83  Aligned_cols=23  Identities=22%  Similarity=0.289  Sum_probs=20.7

Q ss_pred             EEEeccCcchhHHHHHHHHHhhc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      |.|.|++|+||||+|+.+..++.
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~   25 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYD   25 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
Confidence            77899999999999999988754

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=94.76  E-value=0.024  Score=49.17  Aligned_cols=25  Identities=16%  Similarity=0.064  Sum_probs=22.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||++.++.-.
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~Gl~   54 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGGLD   54 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCCc
Confidence            4589999999999999999998753

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>PRK06820 type III secretion system ATPase; Validated

Probab=94.74  E-value=0.11  Score=49.94  Aligned_cols=25  Identities=16%  Similarity=0.380  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -..++|.|..|+|||||++.+....
T Consensus       163 Gqri~I~G~sG~GKStLl~~I~~~~  187 (440)
T PRK06820        163 GQRIGIFAAAGVGKSTLLGMLCADS  187 (440)
T ss_pred             CCEEEEECCCCCChHHHHHHHhccC
Confidence            3478999999999999999887754

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=94.74  E-value=0.13  Score=47.23  Aligned_cols=44  Identities=9%  Similarity=0.371  Sum_probs=35.4

Q ss_pred             hhHHHHHHhhcccC-CCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          152 SRVEEIESLLGAES-KDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       152 ~~~~~l~~~L~~~~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .-.+.|.+.|...+ +...+|||.|.=|+||||+.+.+.+++...
T Consensus         3 ~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen    3 PYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             HHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            34566777776543 568999999999999999999999987666

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=94.74  E-value=0.024  Score=50.24  Aligned_cols=24  Identities=21%  Similarity=0.368  Sum_probs=20.6

Q ss_pred             EEEEEecc-CcchhHHHHHHHHHhh
Q 042778          169 YALGIWGI-GGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~Gm-gGiGKTtLA~~v~~~~  192 (311)
                      ++|+|+|+ ||+|||||+.++..-+
T Consensus         2 ~~iai~s~kGGvG~TTltAnLA~aL   26 (243)
T PF06564_consen    2 KVIAIVSPKGGVGKTTLTANLAWAL   26 (243)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHH
Confidence            47889988 8999999999988753

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=94.73  E-value=0.034  Score=49.90  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|+|.|-.|.||||+|+++.+.+.
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~   24 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFA   24 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999887654

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=94.73  E-value=0.024  Score=50.74  Aligned_cols=25  Identities=24%  Similarity=0.565  Sum_probs=21.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|+|.|-||+||||+|..++.-+.
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~La   26 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAALA   26 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHHHH
Confidence            4678889999999999998887644

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.71  E-value=0.16  Score=49.54  Aligned_cols=25  Identities=16%  Similarity=0.246  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+++++|..|+||||++..++...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~  280 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARC  280 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHH
Confidence            4799999999999999999998865

>PRK09099 type III secretion system ATPase; Provisional

Probab=94.71  E-value=0.062  Score=51.79  Aligned_cols=87  Identities=15%  Similarity=0.179  Sum_probs=48.4

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      .-..++|.|..|.|||||++.+....... .+++...     .++......+.+.++..-.....     ..+.  .   
T Consensus       162 ~Gq~~~I~G~sG~GKTtLl~~ia~~~~~d-~~vi~~i-----Ger~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~  235 (441)
T PRK09099        162 EGQRMGIFAPAGVGKSTLMGMFARGTQCD-VNVIALI-----GERGREVREFIELILGEDGMARSVVVCATSDRSSIERA  235 (441)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCCC-eEEEEEE-----ccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHH
Confidence            35689999999999999999988754332 1233322     11133444444444332111000     0111  0   


Q ss_pred             ------HHHHHHh--CCCeEEEEEecCCChH
Q 042778          237 ------ALSFRQL--SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 ------~~l~~~L--~~kr~LlVLDdV~~~~  259 (311)
                            ..+.+++  +++++||++||+....
T Consensus       236 ~a~~~a~tiAEyfrd~G~~VLl~~DslTr~A  266 (441)
T PRK09099        236 KAAYVATAIAEYFRDRGLRVLLMMDSLTRFA  266 (441)
T ss_pred             HHHHHHHHHHHHHHHcCCCEEEeccchhHHH
Confidence                  2333444  4789999999997643

>PRK02496 adk adenylate kinase; Provisional

Probab=94.70  E-value=0.03  Score=47.18  Aligned_cols=23  Identities=22%  Similarity=0.219  Sum_probs=20.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.|.|++|.||||+|+.+....
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47889999999999999998875

>PF13614 AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ_A 3KB1_B 1ION_A 3LA6_H 3BFV_B 3CIO_D

Probab=94.69  E-value=0.048  Score=44.41  Aligned_cols=35  Identities=17%  Similarity=0.440  Sum_probs=28.3

Q ss_pred             EEEEEec-cCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWG-IGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~G-mgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|+||| .||+||||+|..++..+...-..++.++
T Consensus         1 k~i~v~s~~~g~G~t~~a~~lA~~la~~~~~Vllid   36 (157)
T PF13614_consen    1 KVIAVWSPKGGVGKTTLALNLAAALARKGKKVLLID   36 (157)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHHHHHTTT-EEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHhcCCCeEEEE
Confidence            5899999 7899999999999998766654466665

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.69  E-value=0.098  Score=48.33  Aligned_cols=94  Identities=15%  Similarity=0.085  Sum_probs=51.8

Q ss_pred             HHHHHhhcc-cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC--
Q 042778          155 EEIESLLGA-ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI--  231 (311)
Q Consensus       155 ~~l~~~L~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~--  231 (311)
                      ..|...|.. +-..-+++-|+|..|+||||||..+.......-..++|++    ... ..+.     ..+..++-..+  
T Consensus        39 ~~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~~q~~g~~~a~ID----~e~-~ld~-----~~a~~lGvdl~rl  108 (322)
T PF00154_consen   39 PALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKQGGICAFID----AEH-ALDP-----EYAESLGVDLDRL  108 (322)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEE----SSS----H-----HHHHHTT--GGGE
T ss_pred             cccchhhccCccccCceEEEeCCCCCchhhhHHHHHHhhhcccceeEEec----Ccc-cchh-----hHHHhcCccccce
Confidence            344445542 2123569999999999999999988887655555678988    333 3332     33333332211  


Q ss_pred             ---CCCCH----HHHHHHhCC-CeEEEEEecCCCh
Q 042778          232 ---VIPDI----ALSFRQLSR-RKVLIVLDDVTCF  258 (311)
Q Consensus       232 ---~~~~~----~~l~~~L~~-kr~LlVLDdV~~~  258 (311)
                         ..+..    ..+...++. .--++|+|-|-..
T Consensus       109 lv~~P~~~E~al~~~e~lirsg~~~lVVvDSv~al  143 (322)
T PF00154_consen  109 LVVQPDTGEQALWIAEQLIRSGAVDLVVVDSVAAL  143 (322)
T ss_dssp             EEEE-SSHHHHHHHHHHHHHTTSESEEEEE-CTT-
T ss_pred             EEecCCcHHHHHHHHHHHhhcccccEEEEecCccc
Confidence               11221    444444544 3459999998753

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase

Probab=94.69  E-value=0.13  Score=50.70  Aligned_cols=26  Identities=12%  Similarity=0.221  Sum_probs=23.4

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....+|.++|.+|.||||+|+.++..
T Consensus       367 ~~p~LVil~G~pGSGKST~A~~l~~~  392 (526)
T TIGR01663       367 APCEMVIAVGFPGAGKSHFCKKFFQP  392 (526)
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999999998875

Note that the EC number for the kinase function is: 2.7.1.78

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=94.68  E-value=0.024  Score=51.09  Aligned_cols=24  Identities=25%  Similarity=0.581  Sum_probs=20.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++|+|+|=||+||||+|..+..-+
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~~L   25 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAAL   25 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            478888999999999998887754

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=94.68  E-value=0.07  Score=52.28  Aligned_cols=85  Identities=18%  Similarity=0.155  Sum_probs=50.1

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H--
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I--  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~--  236 (311)
                      -..++|.|-.|+|||||| ..+.++.  ..+.. +++.    +.++.....++.+.+...-.....     ..++  .  
T Consensus       161 GQr~~I~g~~g~GKt~Lal~~i~~~~--~~dv~~V~~~----IGer~rev~e~~~~~~~~~~l~~tvvV~atsd~p~~~r  234 (501)
T TIGR00962       161 GQRELIIGDRQTGKTAVAIDTIINQK--DSDVYCVYVA----IGQKASTVAQVVRKLEEHGAMDYTIVVAATASDSASLQ  234 (501)
T ss_pred             CCEEEeecCCCCCccHHHHHHHHhhc--CCCeEEEEEE----ccCChHHHHHHHHHHHhcCccceeEEEEecCCCCHHHH
Confidence            457899999999999996 5676664  33554 5554    333244556666665543211111     1111  0  


Q ss_pred             -------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 -------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                             ..+.+++  +++++|||+||+...
T Consensus       235 ~~a~~~a~aiAEyfrd~G~~VLlv~Ddltr~  265 (501)
T TIGR00962       235 YLAPYTGCTMAEYFRDNGKHALIIYDDLSKH  265 (501)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEecchHHH
Confidence                   2233333  369999999999754

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>PF00142 Fer4_NifH: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family; InterPro: IPR000392 This entry represents members of the NifH/BchL/ChlL family

Probab=94.67  E-value=0.027  Score=50.25  Aligned_cols=27  Identities=26%  Similarity=0.497  Sum_probs=22.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +.|+|+|-|||||+|.+..+.--+...
T Consensus         1 r~IAiYGKGGIGKST~~~Nlsaala~~   27 (273)
T PF00142_consen    1 RKIAIYGKGGIGKSTTASNLSAALAEM   27 (273)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CeEEEEcCCCcccChhhhHHHHHHHhc
Confidence            568999999999999999887654443

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [, , ]. The nitrogenase enzyme complex consists of two components: Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits. Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene []. Component II has 2 ATP-binding domains and one 4Fe-4S cluster per homodimer: it supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component I for the reduction of molecular nitrogen to ammonia []. There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) IPR001687 from INTERPRO and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster. Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL is present as a homodimer, and binds one 4Fe-4S cluster per dimer. The conserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases []. ; GO: 0005524 ATP binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1CP2_A 2AFI_F 1N2C_F 1FP6_C 2AFK_G 1M34_M 1XD8_A 1NIP_A 1M1Y_N 1G21_H ....

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.66  E-value=0.026  Score=48.64  Aligned_cols=25  Identities=20%  Similarity=0.167  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||++.++...
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G~~   51 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNGLL   51 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC
Confidence            4589999999999999999998753

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK00279 adk adenylate kinase; Reviewed

Probab=94.64  E-value=0.029  Score=48.66  Aligned_cols=23  Identities=30%  Similarity=0.283  Sum_probs=20.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|++|+||||+|+.+..+.
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998775

>TIGR01351 adk adenylate kinases

Probab=94.64  E-value=0.027  Score=48.73  Aligned_cols=22  Identities=32%  Similarity=0.333  Sum_probs=19.8

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|.|++|+||||+|+.+..+.
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6789999999999999998764

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PLN02165 adenylate isopentenyltransferase

Probab=94.63  E-value=0.03  Score=51.85  Aligned_cols=26  Identities=12%  Similarity=0.219  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+++|+|+.|+||||||..++..+.
T Consensus        43 g~iivIiGPTGSGKStLA~~LA~~l~   68 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVDLATRFP   68 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHcC
Confidence            55899999999999999999988754

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=94.63  E-value=0.069  Score=51.83  Aligned_cols=87  Identities=17%  Similarity=0.177  Sum_probs=52.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC---cC-ceEEEecCccccCCCCChHHHHHHHHHHHhcCCC----CCC-C--H
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN---FE-GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI----VIP-D--I  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~---F~-~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~----~~~-~--~  236 (311)
                      -..++|.|-.|+|||||+..+.+....+   =+ .++++.    +.++...+.++.+.++..-.....    ... .  .
T Consensus       143 GQR~gIfgg~G~GKs~L~~~ia~~~~~d~~~~~~v~V~~~----iGeRgrEv~e~~~~~~~~~~l~rtvvV~atsd~p~~  218 (460)
T PRK04196        143 GQKLPIFSGSGLPHNELAAQIARQAKVLGEEENFAVVFAA----MGITFEEANFFMEDFEETGALERSVVFLNLADDPAI  218 (460)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHhhhhccCCCceEEEEEE----eccccHHHHHHHHHHHhcCCcceEEEEEEcCCCCHH
Confidence            3568999999999999999988874321   11 334444    333345566666666553211111    011 0  0


Q ss_pred             ---------HHHHHHhC---CCeEEEEEecCCCh
Q 042778          237 ---------ALSFRQLS---RRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ---------~~l~~~L~---~kr~LlVLDdV~~~  258 (311)
                               ..+.++++   ++++||++||+...
T Consensus       219 ~R~~a~~~a~tiAEyfr~d~G~~VLli~DslTR~  252 (460)
T PRK04196        219 ERILTPRMALTAAEYLAFEKGMHVLVILTDMTNY  252 (460)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcEEEEEcChHHH
Confidence                     45566665   49999999999653

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

Probab=94.61  E-value=0.065  Score=50.12  Aligned_cols=56  Identities=25%  Similarity=0.246  Sum_probs=38.4

Q ss_pred             CCCccchhhhHHH---HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCce
Q 042778          144 KNQLVGVESRVEE---IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGS  199 (311)
Q Consensus       144 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~  199 (311)
                      ...+||.....+.   +.+++..+.-.-+.|.|.|++|.|||+||.++.+.+....+.+
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~   81 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFV   81 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EE
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCee
Confidence            5689998765553   4455554433367889999999999999999999988766543

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.

>PRK10536 hypothetical protein; Provisional

Probab=94.61  E-value=0.076  Score=47.42  Aligned_cols=53  Identities=9%  Similarity=0.062  Sum_probs=38.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh-h-ccCcCceEE
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK-I-SSNFEGSCF  201 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~-~-~~~F~~~~w  201 (311)
                      ..+.++......+...|..    ..++.+.|..|.|||+||.++..+ + ...|+..+.
T Consensus        55 ~~i~p~n~~Q~~~l~al~~----~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES----KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc----CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            3456677777777776653    248999999999999999998885 3 445554443

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.59  E-value=0.057  Score=50.26  Aligned_cols=92  Identities=18%  Similarity=0.077  Sum_probs=53.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCC-CCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQR-PGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~-~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~  245 (311)
                      .+.|.|+|..|.||||+.+++.+.+... +..+-+.+..+..-. .++...    ++..-.+.....-+. ..++..|+.
T Consensus       160 ~~nili~G~tgSGKTTll~aL~~~ip~~-~ri~tiEd~~El~l~~~~n~~~----~~~~~~~~~~~~~~~~~ll~~~LR~  234 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFTNAALREIPAI-ERLITVEDAREIVLSNHPNRVH----LLASKGGQGRAKVTTQDLIEACLRL  234 (332)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHhhCCCC-CeEEEecCCCccccccCCCEEE----EEecCCCCCcCcCcHHHHHHHHhcc
Confidence            4579999999999999999998876553 223333332222110 011100    000000000011123 778888888


Q ss_pred             CeEEEEEecCCChHHHHHh
Q 042778          246 RKVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       246 kr~LlVLDdV~~~~~l~~l  264 (311)
                      ..=.||++.|.+.+.+..+
T Consensus       235 ~PD~IivGEiR~~ea~~~l  253 (332)
T PRK13900        235 RPDRIIVGELRGAEAFSFL  253 (332)
T ss_pred             CCCeEEEEecCCHHHHHHH
Confidence            8889999999998877655

>PRK07429 phosphoribulokinase; Provisional

Probab=94.58  E-value=0.051  Score=50.43  Aligned_cols=30  Identities=23%  Similarity=0.364  Sum_probs=25.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+.+|||.|..|.||||+++.+...+...
T Consensus         6 ~~~~IIgI~G~SGSGKSTla~~L~~ll~~~   35 (327)
T PRK07429          6 DRPVLLGVAGDSGCGKTTFLRGLADLLGEE   35 (327)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHhHhccC
Confidence            457899999999999999999998775533

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=94.58  E-value=0.028  Score=43.46  Aligned_cols=21  Identities=24%  Similarity=0.419  Sum_probs=19.6

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |+|.|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>PTZ00185 ATPase alpha subunit; Provisional

Probab=94.58  E-value=0.1  Score=51.04  Aligned_cols=86  Identities=20%  Similarity=0.132  Sum_probs=47.1

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhc-------cCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC------CC
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKIS-------SNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI------VI  233 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~-------~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~------~~  233 (311)
                      -..++|.|-.|+|||||| -.+.++..       .+-+.++++.    +.++......+.+. |.+-+.-+.      ..
T Consensus       189 GQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~Vyva----IGeR~rEV~ei~~~-L~e~GaL~~TvVV~AtA  263 (574)
T PTZ00185        189 GQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVS----IGQRCSNVARIHRL-LRSYGALRYTTVMAATA  263 (574)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEE----eccchHHHHHHHHH-HHhcCCccceEEEEECC
Confidence            356899999999999997 55666531       2334456665    44423333332222 222221001      11


Q ss_pred             CC---H--------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          234 PD---I--------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       234 ~~---~--------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                      ++   .        ..+-+++  +++.+|||+||+...
T Consensus       264 dep~~~r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        264 AEPAGLQYLAPYSGVTMGEYFMNRGRHCLCVYDDLSKQ  301 (574)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEcCchHH
Confidence            11   0        2333333  479999999999753

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=94.57  E-value=0.028  Score=48.71  Aligned_cols=25  Identities=16%  Similarity=0.141  Sum_probs=22.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||++.+..-.
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl~   53 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGIE   53 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4589999999999999999998753

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=94.57  E-value=0.082  Score=42.57  Aligned_cols=22  Identities=18%  Similarity=0.531  Sum_probs=19.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+.++|++|+|||||...+..+
T Consensus        85 ~~~~~G~~~vGKstlin~l~~~  106 (141)
T cd01857          85 TIGLVGYPNVGKSSLINALVGK  106 (141)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            6889999999999999888754

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.

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=94.56  E-value=0.031  Score=47.89  Aligned_cols=23  Identities=13%  Similarity=0.202  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ++|+|+|+.|.||||+|+.+.+.
T Consensus         2 ~~i~itG~~gsGKst~~~~l~~~   24 (195)
T PRK14730          2 RRIGLTGGIASGKSTVGNYLAQQ   24 (195)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999988775

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=94.56  E-value=0.089  Score=51.56  Aligned_cols=91  Identities=19%  Similarity=0.127  Sum_probs=50.3

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H--
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I--  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~--  236 (311)
                      -..++|.|-.|+|||||| ..+.++.  .-+.. +++.    +.++......+...+...-.....     ..++  .  
T Consensus       162 GQr~~Ifg~~g~GKt~lal~~i~~~~--~~dv~~V~~~----IGer~~ev~e~~~~~~~~~~l~~tvvv~atsd~p~~~r  235 (502)
T PRK09281        162 GQRELIIGDRQTGKTAIAIDTIINQK--GKDVICIYVA----IGQKASTVAQVVRKLEEHGAMEYTIVVAATASDPAPLQ  235 (502)
T ss_pred             CcEEEeecCCCCCchHHHHHHHHHhc--CCCeEEEEEE----ecCChHHHHHHHHHHhhcCCccceEEEEeCCCCCHHHH
Confidence            457899999999999996 4555544  33443 4444    333234455555555443111111     1111  0  


Q ss_pred             -------HHHHHHh--CCCeEEEEEecCCChH-HHHHh
Q 042778          237 -------ALSFRQL--SRRKVLIVLDDVTCFR-QIKSL  264 (311)
Q Consensus       237 -------~~l~~~L--~~kr~LlVLDdV~~~~-~l~~l  264 (311)
                             ..+.+++  +++++|||+||+.... .+..+
T Consensus       236 ~~a~~~a~tiAEyfrd~G~~VLli~DdlTr~A~A~REi  273 (502)
T PRK09281        236 YLAPYAGCAMGEYFMDNGKDALIVYDDLSKQAVAYRQL  273 (502)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEecCchHHHHHHHHH
Confidence                   2223333  3799999999997543 34443

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.56  E-value=0.026  Score=48.49  Aligned_cols=27  Identities=19%  Similarity=0.279  Sum_probs=22.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +.|-+.|.+|+||||+|+++.+.++..
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            467789999999999999999865543

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.55  E-value=0.094  Score=50.66  Aligned_cols=26  Identities=19%  Similarity=0.342  Sum_probs=22.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -..++|.|..|.|||||.+.+.....
T Consensus       163 Gq~~~I~G~sG~GKStLl~~I~~~~~  188 (440)
T TIGR01026       163 GQRIGIFAGSGVGKSTLLGMIARNTE  188 (440)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45789999999999999998887643

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>TIGR00959 ffh signal recognition particle protein

Probab=94.55  E-value=0.65  Score=44.74  Aligned_cols=26  Identities=15%  Similarity=0.183  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++.++|.+|+||||+|..++....
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            67999999999999999998888754

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.

>cd01858 NGP_1 NGP-1

Probab=94.54  E-value=0.054  Score=44.42  Aligned_cols=44  Identities=18%  Similarity=0.315  Sum_probs=30.8

Q ss_pred             cchhhhHHHHHHhhcccC-CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          148 VGVESRVEEIESLLGAES-KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~-~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|.+..++.+.+++.... .....|+++|++|+|||||...+..+
T Consensus        81 ~~~~~L~~~l~~~~~~~~~~~~~~v~~~G~~nvGKStliN~l~~~  125 (157)
T cd01858          81 FGKGSLIQLLRQFSKLHSDKKQISVGFIGYPNVGKSSIINTLRSK  125 (157)
T ss_pred             ccHHHHHHHHHHHHhhhccccceEEEEEeCCCCChHHHHHHHhcC
Confidence            456666666666553221 22456789999999999999998764

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.

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=94.54  E-value=0.025  Score=51.16  Aligned_cols=24  Identities=21%  Similarity=0.394  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|||.|..|+|||||++.+...+.
T Consensus         1 iigI~G~sGsGKSTl~~~L~~ll~   24 (273)
T cd02026           1 IIGVAGDSGCGKSTFLRRLTSLFG   24 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhhC
Confidence            589999999999999999987654

This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=94.53  E-value=0.073  Score=52.04  Aligned_cols=85  Identities=19%  Similarity=0.151  Sum_probs=49.0

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC---H-
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD---I-  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~---~-  236 (311)
                      -..++|.|-.|+|||||| ..+.++.  .-+.. +++.    +.++......+...+...-.....     ..++   . 
T Consensus       162 GQR~~I~g~~g~GKt~Lal~~i~~~~--~~dv~~V~~~----IGer~rev~e~~~~l~~~~~l~~tvvV~atsd~~~~~r  235 (502)
T PRK13343        162 GQRELIIGDRQTGKTAIAIDAIINQK--DSDVICVYVA----IGQKASAVARVIETLREHGALEYTTVVVAEASDPPGLQ  235 (502)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHhhc--CCCEEEEEEE----eccChHHHHHHHHHHHhcCccceeEEEEecccccHHHH
Confidence            457899999999999996 5666653  23443 4444    333234455555555443211111     0111   0 


Q ss_pred             -------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 -------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                             ..+-+++  +++++|||+||+...
T Consensus       236 ~~ap~~a~aiAEyfrd~G~~VLlv~DdlTr~  266 (502)
T PRK13343        236 YLAPFAGCAIAEYFRDQGQDALIVYDDLSKH  266 (502)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEecchHHH
Confidence                   2334444  479999999999754

>cd01862 Rab7 Rab7 subfamily

Probab=94.53  E-value=0.026  Score=46.34  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=19.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|+|+|.+|+|||||+..+.+.
T Consensus         2 ki~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           2 KVIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999988765

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.52  E-value=0.046  Score=48.11  Aligned_cols=45  Identities=9%  Similarity=0.093  Sum_probs=28.8

Q ss_pred             HHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh-ccCcCceEEEe
Q 042778          158 ESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI-SSNFEGSCFLQ  203 (311)
Q Consensus       158 ~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~-~~~F~~~~wv~  203 (311)
                      .+.|..+-..-.++.|.|..|.||||||..+.... ... ..+++++
T Consensus        14 d~~l~ggi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g-~~~~yi~   59 (230)
T PRK08533         14 HKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNG-YSVSYVS   59 (230)
T ss_pred             ehhhCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCC-CcEEEEe
Confidence            33443332335699999999999999986655543 333 3445555

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=94.52  E-value=0.03  Score=47.52  Aligned_cols=25  Identities=16%  Similarity=0.254  Sum_probs=21.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||.+.+....
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G~~   42 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNGLL   42 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4589999999999999999988753

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=94.52  E-value=0.031  Score=46.99  Aligned_cols=35  Identities=20%  Similarity=0.250  Sum_probs=26.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.+++|.|..|.|||||++.+..... ...+.+.+.
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~~-~~~G~i~~~   60 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGLEE-PDSGSILID   60 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC-CCceEEEEC
Confidence            45899999999999999999986532 234445443

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR00101 ureG urease accessory protein UreG

Probab=94.52  E-value=0.047  Score=46.96  Aligned_cols=28  Identities=18%  Similarity=0.405  Sum_probs=23.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..|+|.|..|.|||||.+.+.+.+...+
T Consensus         2 ~~i~i~G~~GsGKTTll~~l~~~l~~~~   29 (199)
T TIGR00101         2 LKIGVAGPVGSGKTALIEALTRALRQKY   29 (199)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhhCcCC
Confidence            3689999999999999999998765543

This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.51  E-value=0.19  Score=51.51  Aligned_cols=25  Identities=20%  Similarity=0.251  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++++++|..|+||||++..+....
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            4799999999999999999888764

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.49  E-value=0.13  Score=52.17  Aligned_cols=93  Identities=23%  Similarity=0.338  Sum_probs=56.9

Q ss_pred             CCccchhhhHHHHHHhhccc-------CCC---eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCC
Q 042778          145 NQLVGVESRVEEIESLLGAE-------SKD---VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGG  214 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~-------~~~---~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~  214 (311)
                      +++=|.+....+|.+-+...       +.+   ..=|.+||++|.|||-||++|+...+-.|     +.    +-    +
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL~F-----lS----VK----G  738 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSLNF-----LS----VK----G  738 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhceeeE-----Ee----ec----C
Confidence            45667888888887765431       122   34578899999999999999998765443     33    21    1


Q ss_pred             hHHHHHHHHHHHhcCCCCCCCHHHHHHHh-CCCeEEEEEecCCC
Q 042778          215 LGFLQQKLLSKLLQDGIVIPDIALSFRQL-SRRKVLIVLDDVTC  257 (311)
Q Consensus       215 ~~~l~~~ll~~l~~~~~~~~~~~~l~~~L-~~kr~LlVLDdV~~  257 (311)
                      .     +|+.-..|+.  ..+++.+.++- ..+.|.|.||.+++
T Consensus       739 P-----ELLNMYVGqS--E~NVR~VFerAR~A~PCVIFFDELDS  775 (953)
T KOG0736|consen  739 P-----ELLNMYVGQS--EENVREVFERARSAAPCVIFFDELDS  775 (953)
T ss_pred             H-----HHHHHHhcch--HHHHHHHHHHhhccCCeEEEeccccc
Confidence            1     2333222221  12223333333 34889999999874

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=94.48  E-value=0.057  Score=50.34  Aligned_cols=46  Identities=15%  Similarity=0.161  Sum_probs=34.3

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+||.+..+..+.-.+..  ....-+.|.|..|.|||||++.+..-+
T Consensus         4 ~~ivgq~~~~~al~~~~~~--~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVID--PKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             cccccHHHHHHHHHHHhcC--CCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            4678998888776544432  224457799999999999999998754

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.48  E-value=0.056  Score=51.51  Aligned_cols=25  Identities=16%  Similarity=0.308  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      |=-.++|++|.|||++..+++|.+.
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L~  260 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYLN  260 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhcC
Confidence            4456899999999999999998763

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=94.46  E-value=0.03  Score=45.62  Aligned_cols=21  Identities=14%  Similarity=0.253  Sum_probs=19.1

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.++|.+|+|||||...+.++
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998775

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=94.44  E-value=0.045  Score=49.33  Aligned_cols=26  Identities=23%  Similarity=0.475  Sum_probs=22.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++|+|.|=||+||||+|..+..-+..
T Consensus         3 ~vIav~~KGGVGKTT~a~nLA~~La~   28 (275)
T PRK13233          3 RKIAIYGKGGIGKSTTTQNTAAAMAY   28 (275)
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            68888899999999999988777653

>PRK02118 V-type ATP synthase subunit B; Provisional

Probab=94.44  E-value=0.12  Score=49.54  Aligned_cols=86  Identities=15%  Similarity=0.177  Sum_probs=51.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H----
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~----  236 (311)
                      -..++|.|-.|+|||+|+..+.++...  +.++|..    +.++......+...+...-.....     ..++  .    
T Consensus       140 GQkigIF~gaGvgk~~L~~~ia~~~~~--~v~Vfa~----iGeR~rE~~ef~~~~~~~~~l~rtvlv~~~adep~~~R~~  213 (436)
T PRK02118        140 SQKIPIFSVSGEPYNALLARIALQAEA--DIIILGG----MGLTFDDYLFFKDTFENAGALDRTVMFIHTASDPPVECLL  213 (436)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHhhCC--CeEEEEE----eccchhHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHH
Confidence            346899999999999999998877543  4456665    444234455555544433111110     1111  0    


Q ss_pred             -----HHHHHHh---CCCeEEEEEecCCChH
Q 042778          237 -----ALSFRQL---SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       237 -----~~l~~~L---~~kr~LlVLDdV~~~~  259 (311)
                           -.+.+++   .++++||++||+-...
T Consensus       214 ~~~~AltiAEyfrd~g~~~VLli~DdlTr~a  244 (436)
T PRK02118        214 VPDMALAVAEKFALEGKKKVLVLLTDMTNFA  244 (436)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEeccCchHHH
Confidence                 2333444   3489999999997643

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=94.44  E-value=0.064  Score=46.26  Aligned_cols=43  Identities=23%  Similarity=0.252  Sum_probs=30.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|.+..+..+.-...    +..-+.+.|..|+|||+||+.+-.-
T Consensus         3 ~dI~GQe~aKrAL~iAAa----G~h~lLl~GppGtGKTmlA~~l~~l   45 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAA----GGHHLLLIGPPGTGKTMLARRLPSL   45 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHH----CC--EEEES-CCCTHHHHHHHHHHC
T ss_pred             hhhcCcHHHHHHHHHHHc----CCCCeEEECCCCCCHHHHHHHHHHh
Confidence            467888876666554333    2357889999999999999998763

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=94.43  E-value=0.032  Score=48.08  Aligned_cols=25  Identities=32%  Similarity=0.438  Sum_probs=22.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||++.+.-..
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~~   50 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGII   50 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            4589999999999999999998753

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK07165 F0F1 ATP synthase subunit alpha; Validated

Probab=94.43  E-value=0.11  Score=50.82  Aligned_cols=86  Identities=22%  Similarity=0.194  Sum_probs=49.0

Q ss_pred             eEEEEEeccCcchhHHHH-HHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCCH-----
Q 042778          168 VYALGIWGIGGIDRTTIA-RAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPDI-----  236 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~~-----  236 (311)
                      -..++|.|-.|+|||||| ..+.++....+. ++++.    +.++......+.+.+...-.....     ..+..     
T Consensus       143 GQR~~Ifg~~gtGKT~lal~~I~~q~~~dv~-~V~~~----IGer~~ev~~~~~~l~~~gal~~tvvV~atsd~~~~r~~  217 (507)
T PRK07165        143 GQRELIIGDRQTGKTHIALNTIINQKNTNVK-CIYVA----IGQKRENLSRIYETLKEHDALKNTIIIDAPSTSPYEQYL  217 (507)
T ss_pred             CCEEEeecCCCCCccHHHHHHHHHhcCCCeE-EEEEE----ccCChHHHHHHHHHhhhcCceeeeEEEEeCCCCHHHHHH
Confidence            457899999999999996 467776443332 24554    333244556666666543111100     00110     


Q ss_pred             -----HHHHHHhC-CCeEEEEEecCCCh
Q 042778          237 -----ALSFRQLS-RRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -----~~l~~~L~-~kr~LlVLDdV~~~  258 (311)
                           ..+.++++ .+.+|||+||+...
T Consensus       218 ap~~a~tiAEyfrd~~dVLlv~DdLTr~  245 (507)
T PRK07165        218 APYVAMAHAENISYNDDVLIVFDDLTKH  245 (507)
T ss_pred             HHHHHHHHHHHHHhcCceEEEEcChHHH
Confidence                 22333332 18999999999754

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=94.42  E-value=0.032  Score=48.19  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=21.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|..|.|||||++.+..-.
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~Gl~   52 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYGAL   52 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4589999999999999999987753

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=94.41  E-value=0.032  Score=49.05  Aligned_cols=24  Identities=29%  Similarity=0.327  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+..-
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~   49 (235)
T cd03261          26 GEILAIIGPSGSGKSTLLRLIVGL   49 (235)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999864

The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=94.39  E-value=0.032  Score=45.27  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +.|-++|..|.|||||++++-..
T Consensus         2 krimliG~~g~GKTTL~q~L~~~   24 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGE   24 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCC
Confidence            35788999999999999999775

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.38  E-value=0.062  Score=53.34  Aligned_cols=50  Identities=14%  Similarity=0.233  Sum_probs=40.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|....++++.+.+..-...-..|.|+|..|+|||++|+.+++...
T Consensus       195 ~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~  244 (534)
T TIGR01817       195 EDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSP  244 (534)
T ss_pred             cCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCC
Confidence            56789999999999888765433344677999999999999999998743

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.

>PRK14528 adenylate kinase; Provisional

Probab=94.38  E-value=0.037  Score=46.96  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=21.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.|.|.|++|.||||+|+.+....
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            458899999999999999998765

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=94.38  E-value=0.032  Score=49.08  Aligned_cols=24  Identities=17%  Similarity=0.235  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (241)
T cd03256          27 GEFVALIGPSGAGKSTLLRCLNGL   50 (241)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999764

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=94.37  E-value=0.033  Score=48.09  Aligned_cols=24  Identities=29%  Similarity=0.295  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||++.+...
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G~   49 (213)
T cd03259          26 GEFLALLGPSGCGKTTLLRLIAGL   49 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999874

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=94.37  E-value=0.03  Score=45.67  Aligned_cols=20  Identities=25%  Similarity=0.345  Sum_probs=18.5

Q ss_pred             EeccCcchhHHHHHHHHHhh
Q 042778          173 IWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       173 I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|.+|+||||+|+.++++.
T Consensus         1 i~G~PgsGK~t~~~~la~~~   20 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRY   20 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHhc
Confidence            68999999999999999875

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=94.37  E-value=0.041  Score=45.10  Aligned_cols=29  Identities=24%  Similarity=0.577  Sum_probs=25.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -.++.|.|..|.||||+++++..+++..|
T Consensus        12 k~~i~vmGvsGsGKSTigk~L~~~l~~~F   40 (191)
T KOG3354|consen   12 KYVIVVMGVSGSGKSTIGKALSEELGLKF   40 (191)
T ss_pred             ceeEEEEecCCCChhhHHHHHHHHhCCcc
Confidence            34889999999999999999999987766

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=94.36  E-value=0.036  Score=50.58  Aligned_cols=25  Identities=24%  Similarity=0.335  Sum_probs=23.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .-+|.|.|.+|+||||+|..+++++
T Consensus        92 p~iIlI~G~sgsGKStlA~~La~~l  116 (301)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRL  116 (301)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999999999999999886

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	311
3jrn_A	176	Crystal Structure Of Tir Domain From Arabidopsis Th		2e-18
3ozi_A	204	Crystal Structure Of The Tir Domain From The Flax D		9e-17

>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana Length = 176

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 57/141 (40%), Positives = 68/141 (48%), Gaps = 31/141 (21%)
Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISL 76
           KYDVF SFRG D R NF   LY  L ++ I TF DD +L  G   S  L   IE S  ++
Sbjct: 8   KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAV 67
Query: 77  IIFSEAYASSRWCLDELVKILTRE-------------------------LEEMFK----- 106
           ++ SE YA+S WCLDELV I+  E                         L E FK     
Sbjct: 68  VVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR 127
Query: 107 ENSEKLQTWRNALKEAAGLSG 127
           E+ EK+  WR AL   A LSG
Sbjct: 128 EDPEKVLKWRQALTNFAQLSG 148

>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease Resistance Protein L6 Length = 204

Iteration: 1
 Score = 84.3 bits (207), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 51/144 (35%), Positives = 76/144 (52%), Gaps = 32/144 (22%)
Query: 18  KYDVFQSFRGEDNRDNFTGHLYSALSQKGIETF-IDDQLNRGDEISQSLVDAIEASAISL 76
           +Y+VF SFRG D R+ FT  LY +L +  I TF  DD+L +G EI  +L+ AI+ S I +
Sbjct: 35  EYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYV 94
Query: 77  IIFSEAYASSRWCLDELVKILTRELEE--------------------------MFKENSE 110
            I S  YA S+WCL EL +I+ R+ E+                           F++++ 
Sbjct: 95  PIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHAN 154
Query: 111 K-----LQTWRNALKEAAGLSGFH 129
           K     +Q W++ALK+   L G+H
Sbjct: 155 KFDGQTIQNWKDALKKVGDLKGWH 178

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	311
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	1e-60
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	2e-58
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	1e-47
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-18
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	7e-13
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	4e-12
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	4e-11
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	2e-06
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	3e-05
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	5e-05

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum} Length = 204

 Score =  191 bits (487), Expect = 1e-60
 Identities = 53/166 (31%), Positives = 80/166 (48%), Gaps = 32/166 (19%)

Query: 1   MAAYSSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGD 59
           + A S S +   S  + +Y+VF SFRG D R+ FT  LY +L +  I TF DD  L +G 
Sbjct: 18  VDAISDSTNPSGSFPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGK 77

Query: 60  EISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKIL---------------------- 97
           EI  +L+ AI+ S I + I S  YA S+WCL EL +I+                      
Sbjct: 78  EIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSD 137

Query: 98  ----TRELEEMFKE-----NSEKLQTWRNALKEAAGLSGFHSQNIR 134
               T   ++ F++     + + +Q W++ALK+   L G+H     
Sbjct: 138 VRHQTGCYKKAFRKHANKFDGQTIQNWKDALKKVGDLKGWHIGKND 183

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana} Length = 176

 Score =  184 bits (470), Expect = 2e-58
 Identities = 59/152 (38%), Positives = 72/152 (47%), Gaps = 31/152 (20%)

Query: 12  SSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIE 70
           SS    KYDVF SFRG D R NF   LY  L ++ I TF DD+ L  G   S  L   IE
Sbjct: 2   SSHTATKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIE 61

Query: 71  ASAISLIIFSEAYASSRWCLDELVKIL-------------------------TRELEEMF 105
            S  ++++ SE YA+S WCLDELV I+                         T  L E F
Sbjct: 62  VSRFAVVVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQF 121

Query: 106 -----KENSEKLQTWRNALKEAAGLSGFHSQN 132
                +E+ EK+  WR AL   A LSG  S +
Sbjct: 122 KKHASREDPEKVLKWRQALTNFAQLSGDCSGD 153

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222} Length = 154

 Score =  155 bits (395), Expect = 1e-47
 Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 2/103 (1%)

Query: 1   MAAYSSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGD 59
           M   +   ++        +D+F S   ED + +F   L   L   G E + DD  L  GD
Sbjct: 3   MKPTAGPTTNADLTSAPPHDIFISHAWED-KADFVEALAHTLRAAGAEVWYDDFSLRPGD 61

Query: 60  EISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELE 102
            + +S+   + +S   +++ S  +    W   EL  +   E  
Sbjct: 62  SLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESS 104

>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 = 83.4 bits (205), Expect = 6e-18
 Identities = 57/326 (17%), Positives = 115/326 (35%), Gaps = 79/326 (24%)

Query: 16  NHKY-DVFQSFRGEDNRDNFTGH-----LYSALSQKGIETFIDDQLNRGDEISQSLVDAI 69
            ++Y D+   F  +   DNF          S LS++  E  ID  +   D +S +L    
Sbjct: 15  QYQYKDILSVFE-DAFVDNFDCKDVQDMPKSILSKE--E--IDHIIMSKDAVSGTLR--- 66

Query: 70  EASAISLIIFSEAYASSRWCL-DELVKILTRELEEMFKENSEKLQT-WRNALKEAAGLSG 127
                   +F        W L  +  +++ + +EE+ + N + L +  +   ++ + ++ 
Sbjct: 67  --------LF--------WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR 110

Query: 128 FHSQNIRLAEVSPCSNKNQLVG---VESRVEEIESLLGA--ESKDVYALGIWGIGGIDRT 182
            + +     +     N NQ+     V SR++    L  A  E +    + I G+ G  +T
Sbjct: 111 MYIE-----QRDRLYNDNQVFAKYNV-SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164

Query: 183 TIARAIFN--KISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSF 240
            +A  +    K+    +   F  N++     P  +  + QKLL ++  +     D + + 
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNC-NSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 241 RQ--------LSR-------RKVLIVLDDV------------------TCFRQIKSLIGM 267
           +         L R          L+VL +V                  T F+Q+   +  
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283

Query: 268 LRNCCVKEKYEMKELGDDHALELFSR 293
                +   +    L  D    L  +
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLK 309

>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 = 2e-04
 Identities = 46/352 (13%), Positives = 95/352 (26%), Gaps = 101/352 (28%)

Query: 15  RNHKYDVFQSFR------GEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDA 68
            ++K      F+         N       +   L  +     ID       + S ++   
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ-----IDPNWTSRSDHSSNIKLR 226

Query: 69  IEA--SAISLIIFSEAYASSRWCLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLS 126
           I +  + +  ++ S+ Y +    L   V+    +    F  + + L T R   +    LS
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLN-VQ--NAKAWNAFNLSCKILLTTRFK-QVTDFLS 282

Query: 127 GFHSQNIRLAEVSPCSNKNQLVGVESRVEEIE-SLLGAESKDVYALGIWGIG-----GID 180
              + +I L   S     +++  +  +  +     L  E        +  I      G+ 
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342

Query: 181 R-------------TTIAR-----------------AIFN---KISSNFEGSCFLQNVRE 207
                         T I                   ++F     I +      +   ++ 
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402

Query: 208 ESQRPGGLGFLQQKLLSKLLQDG------IVIPDIALSFR-QLSRRKVL--IVLDDVTCF 258
           +         +  KL    L +       I IP I L  + +L     L   ++D    +
Sbjct: 403 DVMV------VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD---HY 453

Query: 259 RQIKSL-----------------IGMLRNCCVKEKYEMKELGDDHALELFSR 293
              K+                  IG          + +K +     + LF  
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIG----------HHLKNIEHPERMTLFRM 495

>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 = 40.6 bits (94), Expect = 6e-04
 Identities = 48/270 (17%), Positives = 86/270 (31%), Gaps = 67/270 (24%)

Query: 41  ALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRE 100
            LS   I   I D L   D       D +  + I               L+ L     R+
Sbjct: 329 RLSI--IAESIRDGLATWDNWKHVNCDKLT-TIIES------------SLNVLEPAEYRK 373

Query: 101 LEE---MFKEN----SEKLQT-WRNALKEAAG--LSGFHSQNIRLAEVSPCSNKNQLVGV 150
           + +   +F  +    +  L   W + +K      ++  H     L E      K   + +
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY--SLVE---KQPKESTISI 428

Query: 151 ESRVEEIESLLGAESKDVYAL--GIWGIGGIDRTTIARAI-FNKISSNFEGSCF------ 201
            S    I   L  + ++ YAL   I     +D   I +    + +   +    F      
Sbjct: 429 PS----IYLELKVKLENEYALHRSI-----VDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479

Query: 202 -LQNVREESQRPGG-------LGFLQQKLL---SKLLQDGIVIPDIALSFRQLSRRKVLI 250
            L+N+ E  +R            FL+QK+    +     G ++  +     QL   K  I
Sbjct: 480 HLKNI-EHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQ----QLKFYKPYI 534

Query: 251 VLDDVTCFRQIKSLIGMLRNC---CVKEKY 277
             +D    R + +++  L       +  KY
Sbjct: 535 CDNDPKYERLVNAILDFLPKIEENLICSKY 564

>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 = 67.9 bits (166), Expect = 7e-13
 Identities = 41/239 (17%), Positives = 75/239 (31%), Gaps = 35/239 (14%)

Query: 101 LEEMFKENSEKLQTWRNALKEAAGLSGFHSQNIRLAEVSPCSNKNQL----VGVESRVEE 156
           L E +K+ +  L      +  ++G          +  V       Q     V  +  V  
Sbjct: 76  LHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNA 135

Query: 157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFN---KISSNFEGSCFLQNVREESQRPG 213
           I+  L     +   + I G+ G  ++ +A         +   F G     +V  +  + G
Sbjct: 136 IQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSV-GKQDKSG 194

Query: 214 GLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRR----------KVLIVLDDV---TCFRQ 260
            L  L Q L ++L QD      + L+  +   R          + L++LDDV      + 
Sbjct: 195 LLMKL-QNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA 253

Query: 261 IKS----LI-----GMLRNCC--VKEKYEMKELGDDHALELFSRHAFKQNN--PHIGFE 306
             S    L+      +  +             LG +  LE+ S     +    P     
Sbjct: 254 FDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHS 312

>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 = 62.0 bits (151), Expect = 4e-12
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 7/99 (7%)

Query: 8   PSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSAL--SQKGIETFIDDQ-LNRGDEISQS 64
           P S    +   YDV      ED        L S L  S   +  F+  +    G  I   
Sbjct: 2   PGSSRWSK--DYDVCVCHSEED--LVAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSE 57

Query: 65  LVDAIEASAISLIIFSEAYASSRWCLDELVKILTRELEE 103
           L  A+ +S   +++ +  +    WC  ++++ LT     
Sbjct: 58  LCQALSSSHCRVLLITPGFLQDPWCKYQMLQALTEAPGA 96

>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 = 62.7 bits (152), Expect = 4e-11
 Identities = 34/245 (13%), Positives = 68/245 (27%), Gaps = 33/245 (13%)

Query: 89  CLDELVKILTRELEEMFKENSEKLQTWRNALKEAAGLSGFHSQNI-RLAEVSPCSNKNQL 147
            +D         L +  ++  +      + L+       F  Q + R   +     +   
Sbjct: 71  LIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTC 130

Query: 148 VGVESRVEEI-ESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK---ISSNFEGSCFLQ 203
              E  V+ + + L      D + L + G  G  ++ IA    +K   +      S    
Sbjct: 131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWL 190

Query: 204 NVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIA----------LSFRQLSRRKVLIVLD 253
                + +     F    L+ K   D +  P +           +    + R   L V D
Sbjct: 191 KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFD 250

Query: 254 DV------TCFRQIKSLIGML---RN-------CCVKEKYEMKELGDDHALELFSRHAFK 297
           DV         ++++     L   R+           E  E+  L  D   +    +   
Sbjct: 251 DVVQEETIRWAQELRLRC--LVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMP 308

Query: 298 QNNPH 302
                
Sbjct: 309 MPVGE 313

>2j67_A TOLL like receptor 10; TIR, IL-1, TLR10, membrane, innate immunity, immune response, leucine-rich repeat, glycoprotein, transmembrane; 2.20A {Homo sapiens} PDB: 1fyv_A Length = 178

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 4/93 (4%)

Query: 14  PRNHKYDVFQSFRGEDNRDNFTGHLYSAL--SQKGIETFIDDQ-LNRGDEISQSLVDAIE 70
            RN ++  F S+   D        L   L      I   + +   + G  IS+++V  IE
Sbjct: 31  KRNVRFHAFISYSEHD-SLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIE 89

Query: 71  ASAISLIIFSEAYASSRWCLDELVKILTRELEE 103
            S  S+ + S  +  + WC  E          E
Sbjct: 90  KSYKSIFVLSPNFVQNEWCHYEFYFAHHNLFHE 122

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 44.8 bits (106), Expect = 3e-05
 Identities = 26/139 (18%), Positives = 52/139 (37%), Gaps = 18/139 (12%)

Query: 148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAI---FNKISSNFEGSCFLQN 204
           V  +  V  I+  L   + +   + I+G+ G  ++ +A       + +   F G     +
Sbjct: 127 VTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS 186

Query: 205 VREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRR----------KVLIVLDD 254
           + +  Q   GL    Q L  +L Q+      + L+  +   R          + L++LDD
Sbjct: 187 IGK--QDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD 244

Query: 255 VTCFRQIKSLIGMLRNCCV 273
           V     +K+       C +
Sbjct: 245 VWDPWVLKAF---DNQCQI 260

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens} Length = 159

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 18/99 (18%), Positives = 32/99 (32%), Gaps = 13/99 (13%)

Query: 18  KYDVFQSFRGEDNR---------DNFTGHLYSAL--SQKGIETFIDD-QLNRGDEISQSL 65
            YD + S+   D           + F   +   +     G + FI D  L       + +
Sbjct: 2   DYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDV 61

Query: 66  VDAIEASAISLIIFSEAYA-SSRWCLDELVKILTRELEE 103
              ++ S   +I+ +  Y     W + EL   L   L  
Sbjct: 62  ARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVT 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	311
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	100.0
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	100.0
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.92
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	99.91
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	99.86
1fyx_A	149	TOLL-like receptor 2; beta-alpha-beta fold, signal	99.82
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	99.81
2js7_A	160	Myeloid differentiation primary response protein M	99.81
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.8
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	99.8
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.78
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.73
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.42
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.19
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.18
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.06
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.01
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.88
2fna_A	357	Conserved hypothetical protein; structural genomic	98.84
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.84
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.78
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.75
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.67
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.55
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.55
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.48
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.42
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.31
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.26
3pvs_A	447	Replication-associated recombination protein A; ma	98.21
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.21
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.19
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.14
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.14
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.12
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.12
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.08
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.05
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.05
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.03
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.97
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.95
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.93
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.93
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.88
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.87
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.85
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.84
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.82
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.82
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.81
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.8
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.8
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.78
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.77
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.77
3bos_A	242	Putative DNA replication factor; P-loop containing	97.76
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.74
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.74
3co5_A	143	Putative two-component system transcriptional RES	97.73
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.68
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.61
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.6
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.59
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.57
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.55
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.54
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.5
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.5
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.48
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.48
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.43
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.4
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.35
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.35
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.34
2qgz_A	308	Helicase loader, putative primosome component; str	97.29
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.25
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.22
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.1
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.09
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.07
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.07
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.06
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.02
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.01
1eiw_A	111	Hypothetical protein MTH538; CHEY-like fold, flavo	96.96
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.92
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.87
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.84
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.84
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.82
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.78
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.77
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.75
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.72
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.71
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.69
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.68
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.66
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.66
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.63
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.58
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.51
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.5
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.5
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.47
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.45
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.44
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.42
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.41
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.4
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.38
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.38
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.35
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.35
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.34
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	96.33
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.32
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.32
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.32
1via_A	175	Shikimate kinase; structural genomics, transferase	96.31
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.31
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.31
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.28
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.27
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.26
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.25
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.23
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.22
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.22
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.21
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.2
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.2
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.19
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.19
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.18
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.17
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.17
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.14
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.14
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.13
3ice_A	422	Transcription termination factor RHO; transcriptio	96.13
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.12
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.11
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.1
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.09
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.09
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.07
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.07
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.05
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.04
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.03
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.03
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.03
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.02
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.01
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.98
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.98
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.97
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.97
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.95
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.94
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.94
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.93
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.91
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.91
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.89
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.88
3fwy_A	314	Light-independent protochlorophyllide reductase I	95.87
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.87
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.87
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.86
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.81
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.77
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.74
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.74
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.73
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.72
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.72
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.72
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.69
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.67
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.66
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.65
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.65
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.65
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.63
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.62
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.61
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.58
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	95.57
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.56
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.55
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.54
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.53
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.53
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.53
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.51
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.51
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.51
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.49
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.46
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.46
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.45
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.43
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.42
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.42
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.4
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.36
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.35
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.31
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.28
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.28
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.27
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.26
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.25
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.25
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.24
3io5_A	333	Recombination and repair protein; storage dimer, i	95.23
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.23
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.23
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.23
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.21
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.17
2xxa_A	433	Signal recognition particle protein; protein trans	95.15
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.14
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.13
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.12
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.11
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.11
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.09
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.08
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.07
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.04
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.02
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.02
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.02
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.01
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.0
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.98
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.94
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.82
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.82
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	94.79
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.78
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.78
2z43_A	324	DNA repair and recombination protein RADA; archaea	94.77
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.75
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.72
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.71
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.7
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.69
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.68
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.66
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.65
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	94.63
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.59
2og2_A	359	Putative signal recognition particle receptor; nuc	94.58
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.56
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.54
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.53
3end_A	307	Light-independent protochlorophyllide reductase ir	94.52
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.52
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.49
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.48
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.48
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	94.47
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.46
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.44
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.44
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.44
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.43
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.43
1g6h_A	257	High-affinity branched-chain amino acid transport	94.42
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.41
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.41
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	94.4
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.39
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.39
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.38
3hyn_A	189	Putative signal transduction protein; DUF1863 fami	94.37
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.37
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	94.36
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.36
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.33
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.32
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	94.32
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.32
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.29
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.27
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.25
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.23
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.23
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.22
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.22
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	94.21
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.2
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.18
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.16
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	94.14
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	94.13
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	94.13
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	94.12
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	94.1
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.1
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.1
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.09
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.09
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.08
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	94.07
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.06
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.06
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.06
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.05
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	94.02
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.01
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.99
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.96
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.96
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.94
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	93.93
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.93
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	93.9
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.86
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	93.85
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.85
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.84
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.83
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.75
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.73
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	93.73
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	93.7
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	93.7
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.69
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.64
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.63
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.6
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.6
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.58
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.57
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.54
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.54
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.53
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.51
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.51
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.44
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.43
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.43
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.38
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	93.37
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.35
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	93.34
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.33
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.33
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.32
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.32
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.31
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.31
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	93.3
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.28
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.28
1nrj_B	218	SR-beta, signal recognition particle receptor beta	93.26
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.25
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.24
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.23
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	93.21
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.14
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.13
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.12
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	93.11
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.11
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.08
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.07
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	93.07
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.06
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	93.05
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.04
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.04
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.03
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.02
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.02
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.02
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.02
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	93.01
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.0
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.0
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	92.97
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	92.97
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.96
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.95
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	92.94
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.93
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	92.91
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	92.9
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	92.9
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	92.89
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.88
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.88
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	92.85
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	92.84
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.82
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	92.82
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	92.81
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.79
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	92.78
3cwq_A	209	Para family chromosome partitioning protein; alpha	92.78
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.72
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.71
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.68
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.67
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.67
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.66
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.66
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	92.64
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	92.63
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.63
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	92.61
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.61
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.6
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.6
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.59
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.59
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.56
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.53
1p9r_A	418	General secretion pathway protein E; bacterial typ	92.5
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	92.47
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.47
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	92.47
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	92.45
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	92.43
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.43
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	92.43
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.42
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.41
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.39
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	92.39
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.36
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	92.29
3llu_A	196	RAS-related GTP-binding protein C; structural geno	92.28
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	92.27
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	92.26
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	92.26
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.25
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.23
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	92.2
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	92.14
2fh5_B	214	SR-beta, signal recognition particle receptor beta	92.14
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	92.12
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	92.1
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.1
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.1
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.09
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.09
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	92.08
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	92.07
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	92.06
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.05
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	92.03
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	92.03
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.02
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	91.98
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	91.95
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.95
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	91.85
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	91.83
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	91.83
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	91.82
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	91.81
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	91.78
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	91.77
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.76
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	91.75
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.72
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.72
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.7
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	91.7
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	91.63
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.62
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.62
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	91.6
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.59
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	91.58
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	91.54
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	91.53
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	91.52
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	91.48
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	91.48
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.48
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	91.45
1wcv_1	257	SOJ, segregation protein; ATPase, bacterial, chrom	91.45
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	91.45
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	91.44
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	91.44
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.43
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	91.43
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	91.41
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	91.4
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	91.39

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum}

Probab=100.00  E-value=9e-41  Score=282.83  Aligned_cols=130  Identities=40%  Similarity=0.721  Sum_probs=113.9

Q ss_pred             CCCCCCCCCCCCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCc
Q 042778            5 SSSPSSPSSPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAY   83 (311)
Q Consensus         5 ~~~~~~s~~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y   83 (311)
                      |+|+++|++.+.++|||||||||+|+|++|++||+.+|+++||++|+|+ ++++|+.|.++|.+||++|+++|+|||+||
T Consensus        22 ~~s~~~s~~~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~GI~~f~D~~el~~G~~I~~~l~~aIe~Sri~IvV~S~nY  101 (204)
T 3ozi_A           22 SDSTNPSGSFPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGY  101 (204)
T ss_dssp             ------------CCCCEEEEECHHHHTTTHHHHHHHHHHHTTCCEEEEETTTCCGGGTTTTHHHHHHHCSEEEEEECTTG
T ss_pred             ccCCCCcCCCCCcCCeEEEeccccCCCHHHHHHHHHHHHHCCCcEEEeCCccCCCCchHHHHHHHHHhCcEeeEEEEccc
Confidence            3455666677789999999999999999999999999999999999998 999999999999999999999999999999


Q ss_pred             ccccchHHHHHHHHhhH--------------------------hHHHHhHhH-----HHHHHHHHHHHHHhhhcCCccCC
Q 042778           84 ASSRWCLDELVKILTRE--------------------------LEEMFKENS-----EKLQTWRNALKEAAGLSGFHSQN  132 (311)
Q Consensus        84 ~~S~wcl~El~~i~e~~--------------------------~~~~~~~~~-----~~v~~w~~~l~~~~~~~g~~~~~  132 (311)
                      ++|.|||+||++|++|.                          ||++|.+|+     +++++||.||+++++++||++.+
T Consensus       102 a~S~WCl~EL~~I~e~~~~~~~~~ViPIFY~VdPs~Vr~q~g~fg~af~~~~~~~~~~~v~~Wr~AL~~va~lsG~~~~~  181 (204)
T 3ozi_A          102 ADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDGQTIQNWKDALKKVGDLKGWHIGK  181 (204)
T ss_dssp             GGCHHHHHHHHHHHHHHHHCTTSEECCEEESSCHHHHHHTCTTHHHHHHHHTTTSCHHHHHHHHHHHHHHHTSCBEEECT
T ss_pred             ccCcHHHHHHHHHHHHHHhcCCeeeEEEEeecCHHHHHhccccHHHHHHHHHHhhCHHHHHHHHHHHHHHhccCceecCC
Confidence            99999999999999985                          999999988     68999999999999999999887


Q ss_pred             CC
Q 042778          133 IR  134 (311)
Q Consensus       133 ~~  134 (311)
                      ..
T Consensus       182 ~~  183 (204)
T 3ozi_A          182 ND  183 (204)
T ss_dssp             TS
T ss_pred             CC
Confidence            64

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana}

Probab=100.00  E-value=1.7e-38  Score=264.60  Aligned_cols=119  Identities=49%  Similarity=0.787  Sum_probs=97.8

Q ss_pred             CCCCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccchHH
Q 042778           13 SPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLD   91 (311)
Q Consensus        13 ~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~   91 (311)
                      ++.+++|||||||||+|+|++|++||+.+|+++||++|+|+ ++++|+.|.++|.+||++|+++|+|||+||++|.||++
T Consensus         3 ss~~~~yDVFiSfrg~D~r~~Fv~~L~~~L~~~gi~~f~D~~~l~~G~~i~~~l~~aIe~Sri~IvV~S~ny~~S~WCl~   82 (176)
T 3jrn_A            3 SHTATKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLD   82 (176)
T ss_dssp             ----CCEEEEEEECHHHHTTTHHHHHHHHHHHTTCCEECCCC--------------CCTTEEEEEEEECTTTTTCHHHHH
T ss_pred             CCCCCCCeEEEECcCcccChHHHHHHHHHHHHCCCEEEEEcccccCCCchHHHHHHHHHhCCEEEEEecCCcCCChhHHH
Confidence            34568999999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             HHHHHHhhH-------------------------hHHHHhHhH-----HHHHHHHHHHHHHhhhcCCccC
Q 042778           92 ELVKILTRE-------------------------LEEMFKENS-----EKLQTWRNALKEAAGLSGFHSQ  131 (311)
Q Consensus        92 El~~i~e~~-------------------------~~~~~~~~~-----~~v~~w~~~l~~~~~~~g~~~~  131 (311)
                      ||++|++|.                         ||++|.+|+     +++++||.||+++++++||++.
T Consensus        83 EL~~i~~~~~~~~~~ViPIfy~V~ps~Vr~q~g~fg~af~~~~~~~~~~~~~~Wr~AL~~va~~~G~~~~  152 (176)
T 3jrn_A           83 ELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASREDPEKVLKWRQALTNFAQLSGDCSG  152 (176)
T ss_dssp             HHHHHHHHHHTTSCEEEEEECSSCHHHHHHTCTHHHHHHHHHHTTSCHHHHHHHHHHHHHHTTSCCEECC
T ss_pred             HHHHHHhhhccCCCEEEEEEecCCHHHhhhccCcHHHHHHHHHhccCHHHHHHHHHHHHHHhcccceecC
Confidence            999999996                         999999998     7899999999999999999874

>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=99.92  E-value=2.7e-24  Score=211.08  Aligned_cols=155  Identities=20%  Similarity=0.195  Sum_probs=123.1

Q ss_pred             cchhhhHHHHHHhhccc-CCCeEEEEEeccCcchhHHHHHHHHH----hhccCcCceEEEecCccccCCCC--ChHHHHH
Q 042778          148 VGVESRVEEIESLLGAE-SKDVYALGIWGIGGIDRTTIARAIFN----KISSNFEGSCFLQNVREESQRPG--GLGFLQQ  220 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~-~~~~~vi~I~GmgGiGKTtLA~~v~~----~~~~~F~~~~wv~~~~~~s~~~~--~~~~l~~  220 (311)
                      +||+.++++|.++|... ..++++|+|+||||+||||||+.+|+    +++.+|++++|++    +++ ..  ++..++.
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~----vs~-~~~~~~~~~~~  205 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK----DSG-TAPKSTFDLFT  205 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE----CCC-CSTTHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEE----ECC-CCCCCHHHHHH
Confidence            69999999999999755 34589999999999999999999997    6899999999997    665 53  7899999


Q ss_pred             HHHHHHhcCCC-----CCCC-----H-HHHHHHhCCC-eEEEEEecCCChHHHHHhhccCCC--------------cC-C
Q 042778          221 KLLSKLLQDGI-----VIPD-----I-ALSFRQLSRR-KVLIVLDDVTCFRQIKSLIGMLRN--------------CC-V  273 (311)
Q Consensus       221 ~ll~~l~~~~~-----~~~~-----~-~~l~~~L~~k-r~LlVLDdV~~~~~l~~l~~~~~~--------------~~-~  273 (311)
                      .|+.++.....     ....     + ..+++.|.++ ||||||||||+.+++ .+.+..++              ++ .
T Consensus       206 ~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~~~gs~ilvTTR~~~v~~~~~~~  284 (549)
T 2a5y_B          206 DILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQELRLRCLVTTRDVEISNAASQT  284 (549)
T ss_dssp             HHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHHHTTCEEEEEESBGGGGGGCCSC
T ss_pred             HHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccccCCCEEEEEcCCHHHHHHcCCC
Confidence            99999986521     1211     2 7889999996 999999999999876 33222222              22 3


Q ss_pred             ceEEEcCCCChHHHHHHHHHhhcCCCCCCCcHHHhh
Q 042778          274 KEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELS  309 (311)
Q Consensus       274 ~~~y~v~~L~~~ea~~Lf~~~af~~~~~~~~~~~l~  309 (311)
                      ..+|+|++|+.+|||+||+++||.... ++++++++
T Consensus       285 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~-~~~~~~~~  319 (549)
T 2a5y_B          285 CEFIEVTSLEIDECYDFLEAYGMPMPV-GEKEEDVL  319 (549)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHHH
T ss_pred             CeEEECCCCCHHHHHHHHHHHhcCCCC-chhHHHHH
Confidence            468999999999999999999998643 35666554

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222}

Probab=99.91  E-value=6.4e-26  Score=186.69  Aligned_cols=86  Identities=24%  Similarity=0.426  Sum_probs=79.4

Q ss_pred             CCCCCcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccchHH
Q 042778           13 SPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLD   91 (311)
Q Consensus        13 ~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~   91 (311)
                      ..+.++|||||||+++| +..|++||+.+|+++|+++|+|+ ++.+|+.|.++|.++|++|+++|+|+||||++|.||++
T Consensus        15 ~~~~~~~dvFISy~~~D-~~~~~~~L~~~L~~~gi~v~~D~~~l~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wc~~   93 (154)
T 3h16_A           15 LTSAPPHDIFISHAWED-KADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQK   93 (154)
T ss_dssp             ---CCSEEEEEEEEGGG-TTTTHHHHHHHHHHHTCCEECGGGEECTTCCHHHHHHHHHTSEEEEEEEEEHHHHTTCCCHH
T ss_pred             cCCCCCceEEEECcccC-hHHHHHHHHHHHHHCCCcEEEcHHhCCCccHHHHHHHHHHHhCcEEEEEeCcchhcChHHHH
Confidence            56789999999999999 56799999999999999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHhh
Q 042778           92 ELVKILTR   99 (311)
Q Consensus        92 El~~i~e~   99 (311)
                      ||.++++|
T Consensus        94 El~~~~~~  101 (154)
T 3h16_A           94 ELDGLFQL  101 (154)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHHHHH
Confidence            99888764

>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=99.86  E-value=1.4e-23  Score=170.77  Aligned_cols=86  Identities=22%  Similarity=0.388  Sum_probs=66.0

Q ss_pred             CCCCCcccEEecCccccCCCChHHHHHHHHHh--CCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccch
Q 042778           13 SPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQ--KGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWC   89 (311)
Q Consensus        13 ~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~--~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wc   89 (311)
                      ....+.|||||||+++|+  .|+.||+.+|++  +|+++|+++ ++.+|+.+.++|.+||++|+++|+||||||++|.||
T Consensus         5 ~r~~k~YDvFISy~~~D~--~~v~~L~~~Le~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~I~VlS~~y~~S~wc   82 (146)
T 3ub2_A            5 SRWSKDYDVCVCHSEEDL--VAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDPWC   82 (146)
T ss_dssp             CTTSSSEEEEEECCGGGH--HHHHHHHHHHHC------------------CCCEEECCTTCCEEEEEEEECHHHHHCHHH
T ss_pred             CCCCCcceEEEeCChhhH--HHHHHHHHHHhCcCCCeEEEEECccccccccHHHHHHHHHHhCCEEEEEECcccccCHHH
Confidence            455679999999999997  489999999998  699999998 999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhH
Q 042778           90 LDELVKILTRE  100 (311)
Q Consensus        90 l~El~~i~e~~  100 (311)
                      +.||..++.+.
T Consensus        83 ~~El~~al~~~   93 (146)
T 3ub2_A           83 KYQMLQALTEA   93 (146)
T ss_dssp             HHHHHHHHHTS
T ss_pred             HHHHHHHHHHH
Confidence            99999998763

>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=99.82  E-value=1.3e-21  Score=159.81  Aligned_cols=82  Identities=24%  Similarity=0.397  Sum_probs=76.5

Q ss_pred             CCCcccEEecCccccCCCChHHH-HHHHHHhC--CCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccchH
Q 042778           15 RNHKYDVFQSFRGEDNRDNFTGH-LYSALSQK--GIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCL   90 (311)
Q Consensus        15 ~~~~~dvFis~~g~D~~~~f~~~-L~~~L~~~--gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl   90 (311)
                      .++.|||||||+++|+  .|+.+ |+.+|+++  |+++|+|+ ++.+|+.+.++|.++|++|+++|+|+||||++|.||+
T Consensus         2 ~~~~yDvFiSy~~~D~--~~v~~~L~~~Le~~~~g~~~~~~~rd~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~S~wc~   79 (149)
T 1fyx_A            2 RNIXYDAFVSYSERDA--YWVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWXK   79 (149)
T ss_dssp             CSCCEEEEEECCGGGH--HHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCccceEEEECCcccH--HHHHHHHHHHHhcCCCCeEEeeccccCCCchhHHHHHHHHHHHcCEEEEEeCcchhccchHH
Confidence            3578999999999997  69997 99999987  99999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q 042778           91 DELVKILT   98 (311)
Q Consensus        91 ~El~~i~e   98 (311)
                      .||..++.
T Consensus        80 ~El~~a~~   87 (149)
T 1fyx_A           80 YELDFSHF   87 (149)
T ss_dssp             HHSCCSCC
T ss_pred             HHHHHHHH
Confidence            99977653

>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=99.81  E-value=4.1e-21  Score=161.14  Aligned_cols=85  Identities=24%  Similarity=0.420  Sum_probs=77.7

Q ss_pred             CCCCCCcccEEecCccccCCCChHHH-HHHHHHh--CCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCccccc
Q 042778           12 SSPRNHKYDVFQSFRGEDNRDNFTGH-LYSALSQ--KGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSR   87 (311)
Q Consensus        12 ~~~~~~~~dvFis~~g~D~~~~f~~~-L~~~L~~--~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~   87 (311)
                      ....++.|||||||+++|+  +|+.+ |+.+|++  +|+++|+|+ ++.+|+.+.++|.++|++|+++|+|+||||++|.
T Consensus        29 ~~~~~~~yDvFISys~~D~--~fv~~~L~~~LE~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~IvVlS~~yl~S~  106 (178)
T 2j67_A           29 QLKRNVRFHAFISYSEHDS--LWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKSYKSIFVLSPNFVQNE  106 (178)
T ss_dssp             -CCCSCCEEEEEECCGGGH--HHHHHTHHHHHTTCC-CCCEEEHHHHCCTTSCHHHHHHHHHHTEEEEEEEECHHHHHHT
T ss_pred             ccCCCccceEEEECCCCCH--HHHHHHHHHHHhcccCCeEEEEecccCCCCccHHHHHHHHHHhCCEEEEEecccccccc
Confidence            3556789999999999996  79985 9999998  899999999 9999999999999999999999999999999999


Q ss_pred             chHHHHHHHHh
Q 042778           88 WCLDELVKILT   98 (311)
Q Consensus        88 wcl~El~~i~e   98 (311)
                      ||+.||..++.
T Consensus       107 wc~~El~~a~~  117 (178)
T 2j67_A          107 WCHYEFYFAHH  117 (178)
T ss_dssp             GGGTHHHHTTC
T ss_pred             hHHHHHHHHHH
Confidence            99999987764

>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=99.81  E-value=5.7e-21  Score=157.76  Aligned_cols=85  Identities=18%  Similarity=0.264  Sum_probs=77.7

Q ss_pred             CCCCCcccEEecCccccCCCChHHHHHHHHHhC--CCcEEeeC-CCCCCCcchHHHHHHHH-hccceeeeeccCcccccc
Q 042778           13 SPRNHKYDVFQSFRGEDNRDNFTGHLYSALSQK--GIETFIDD-QLNRGDEISQSLVDAIE-ASAISLIIFSEAYASSRW   88 (311)
Q Consensus        13 ~~~~~~~dvFis~~g~D~~~~f~~~L~~~L~~~--gi~~f~d~-~~~~G~~~~~~i~~ai~-~s~~~i~v~S~~y~~S~w   88 (311)
                      .+.++.|||||||+++|.  +|+.+|+.+|+++  |+++|+|+ ++.+|+.+.++|.++|+ +|+++|+|+||||++|.|
T Consensus        11 ~~~~~~yDvFISys~~D~--~fv~~L~~~Le~~~~g~~~~~~~rd~~~G~~i~~~i~~~I~~~Sr~~IvVlS~~y~~S~w   88 (160)
T 2js7_A           11 GHMPERFDAFICYCPSDI--QFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKE   88 (160)
T ss_dssp             SCCTTCEEEEEECCGGGH--HHHHHHHHHHHTSSSCCCCEESCCSSSSSCSCCCCCGGGHHHHEEEEEEECCHHHHHSHH
T ss_pred             CCCCcceEEEEEcccccH--HHHHHHHHHHhcCCCceEEEEeCCCCCCCCcHHHHHHHHHHHhCCEEEEEECcchhcCHH
Confidence            344678999999999994  7999999999985  69999998 99999999999999999 799999999999999999


Q ss_pred             hHHHHHHHHhh
Q 042778           89 CLDELVKILTR   99 (311)
Q Consensus        89 cl~El~~i~e~   99 (311)
                      |+.||..++++
T Consensus        89 c~~El~~a~~~   99 (160)
T 2js7_A           89 CDFQTKFALSL   99 (160)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887753

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.80  E-value=2.6e-19  Score=189.44  Aligned_cols=150  Identities=20%  Similarity=0.219  Sum_probs=112.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh---hccCcC-ceEEEecCccccCCCC--ChHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK---ISSNFE-GSCFLQNVREESQRPG--GLGF  217 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~---~~~~F~-~~~wv~~~~~~s~~~~--~~~~  217 (311)
                      +..||||+.++++|.++|....+++++|+|+||||+||||||+++|++   ...+|. .++|+.    +++ ..  ++..
T Consensus       123 ~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~----~~~-~~~~~~~~  197 (1249)
T 3sfz_A          123 PVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS----IGK-QDKSGLLM  197 (1249)
T ss_dssp             CSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEE----CCS-CCHHHHHH
T ss_pred             CceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEE----ECC-cCchHHHH
Confidence            567999999999999999766667999999999999999999999997   455565 455777    444 32  2344


Q ss_pred             HHHHHHHHHhcCCC----CCCCH----HHHHHHhCCC--eEEEEEecCCChHHHHHhhccCCC-------------cCCc
Q 042778          218 LQQKLLSKLLQDGI----VIPDI----ALSFRQLSRR--KVLIVLDDVTCFRQIKSLIGMLRN-------------CCVK  274 (311)
Q Consensus       218 l~~~ll~~l~~~~~----~~~~~----~~l~~~L~~k--r~LlVLDdV~~~~~l~~l~~~~~~-------------~~~~  274 (311)
                      .+..++..+.....    ...+.    ..++..|.++  |+||||||||+.++|+.+.+...-             .+..
T Consensus       198 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~~~~~~ilvTtR~~~~~~~~~~~~  277 (1249)
T 3sfz_A          198 KLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPK  277 (1249)
T ss_dssp             HHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTTCSSCEEEEEESSTTTTTTCCSCB
T ss_pred             HHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhhcCCCEEEEEcCCHHHHHhhcCCc
Confidence            45566666655432    11222    6677777766  999999999999999987432211             3456


Q ss_pred             eEEEcCC-CChHHHHHHHHHhhcCC
Q 042778          275 EKYEMKE-LGDDHALELFSRHAFKQ  298 (311)
Q Consensus       275 ~~y~v~~-L~~~ea~~Lf~~~af~~  298 (311)
                      ..|++++ |+.+||++||+++++..
T Consensus       278 ~~~~~~~~l~~~~a~~l~~~~~~~~  302 (1249)
T 3sfz_A          278 HVVPVESGLGREKGLEILSLFVNMK  302 (1249)
T ss_dssp             CCEECCSSCCHHHHHHHHHHHHTSC
T ss_pred             eEEEecCCCCHHHHHHHHHHhhCCC
Confidence            7899996 99999999999999654

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens}

Probab=99.80  E-value=1.5e-20  Score=155.11  Aligned_cols=82  Identities=22%  Similarity=0.416  Sum_probs=73.9

Q ss_pred             CcccEEecCccccC---------CCChHHHHHH-HHH-hCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcc
Q 042778           17 HKYDVFQSFRGEDN---------RDNFTGHLYS-ALS-QKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYA   84 (311)
Q Consensus        17 ~~~dvFis~~g~D~---------~~~f~~~L~~-~L~-~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~   84 (311)
                      +.|||||||+++|+         +.+|+.+|.. .|+ ++|+++|+|+ |+.+|+.+.++|.++|++|+++|+|+||||+
T Consensus         1 k~yDaFISy~~~D~~wv~~~~~~~~~fv~~ll~~~LE~~~g~~l~~~~rD~~~G~~i~~~i~~~I~~Sr~~IvVlS~~y~   80 (159)
T 1t3g_A            1 KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYV   80 (159)
T ss_dssp             CCBSEEEECCCCC-------CCSHHHHHHTHHHHHHHHTSCCCEECHHHHCCCCTTHHHHHHHHHHTBSEEEEEECHHHH
T ss_pred             CCceEEEeCccccchhhhccchhhHHHHHHHHHHHHcCCCCeEEEEEcccccCccchHHHHHHHHHHcCEEEEEEccchh
Confidence            46999999999997         3579999665 699 7999999998 9999999999999999999999999999997


Q ss_pred             -cccchHHHHHHHHh
Q 042778           85 -SSRWCLDELVKILT   98 (311)
Q Consensus        85 -~S~wcl~El~~i~e   98 (311)
                       .|.||+.|+..++.
T Consensus        81 ~~S~wc~~El~~a~~   95 (159)
T 1t3g_A           81 VRRGWSIFELETRLR   95 (159)
T ss_dssp             HTTTTHHHHHSHHHH
T ss_pred             hcChHHHHHHHHHHH
Confidence             99999999987765

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.78  E-value=4.7e-19  Score=180.90  Aligned_cols=145  Identities=15%  Similarity=0.056  Sum_probs=109.7

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hccCcCc-eEEEecCccccCCCCChHHHHHHH
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISSNFEG-SCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~~F~~-~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      ..|||+..+++|.++|... +++++|+|+||||+||||||+.+|++  ++.+|+. ++|++    +++ .++...++..|
T Consensus       129 ~~VGRe~eLeeL~elL~~~-d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVs----Vs~-~~d~~~IL~~L  202 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN----LKN-CNSPETVLEML  202 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHC-CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEE----CCC-SSSHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhcc-CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEE----eCC-CCCHHHHHHHH
Confidence            3599999999999999743 34899999999999999999999974  7889997 78888    666 77787877777


Q ss_pred             HHHHhcCC---C-CCC---C-------H-HHHHHHh---CCCeEEEEEecCCChHHHHHhhccCCC------------cC
Q 042778          223 LSKLLQDG---I-VIP---D-------I-ALSFRQL---SRRKVLIVLDDVTCFRQIKSLIGMLRN------------CC  272 (311)
Q Consensus       223 l~~l~~~~---~-~~~---~-------~-~~l~~~L---~~kr~LlVLDdV~~~~~l~~l~~~~~~------------~~  272 (311)
                      +..+....   . ...   +       + ..+++.|   .++|+||||||||+.++|+.+.+....            +.
T Consensus       203 l~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~pGSRILVTTRd~~Va~~l~  282 (1221)
T 1vt4_I          203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLS  282 (1221)
T ss_dssp             HHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHHSSCCEEEECSCSHHHHHHH
T ss_pred             HHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhCCCeEEEEeccChHHHHhcC
Confidence            66543211   1 111   1       1 4566655   689999999999999999988532211            12


Q ss_pred             CceEEEcC------CCChHHHHHHHHHhhcC
Q 042778          273 VKEKYEMK------ELGDDHALELFSRHAFK  297 (311)
Q Consensus       273 ~~~~y~v~------~L~~~ea~~Lf~~~af~  297 (311)
                      ...+|+|+      +|+.+||++||+++ |.
T Consensus       283 g~~vy~LeL~d~dL~LS~eEA~eLF~~~-~g  312 (1221)
T 1vt4_I          283 AATTTHISLDHHSMTLTPDEVKSLLLKY-LD  312 (1221)
T ss_dssp             HHSSCEEEECSSSSCCCHHHHHHHHHHH-HC
T ss_pred             CCeEEEecCccccCCcCHHHHHHHHHHH-cC
Confidence            22367777      99999999999998 44

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.73  E-value=1.2e-17  Score=164.69  Aligned_cols=148  Identities=21%  Similarity=0.219  Sum_probs=106.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh---ccCcC-ceEEEecCccccCCCCChHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI---SSNFE-GSCFLQNVREESQRPGGLGFLQ  219 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~---~~~F~-~~~wv~~~~~~s~~~~~~~~l~  219 (311)
                      +..+|||+.++.+|.++|....++.++|+|+||||+||||||+.+|++.   ..+|+ +++|+.    ++. . +...+.
T Consensus       123 ~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~----~~~-~-~~~~~~  196 (591)
T 1z6t_A          123 PVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVS----VGK-Q-DKSGLL  196 (591)
T ss_dssp             CSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEE----EES-C-CHHHHH
T ss_pred             CCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEE----CCC-C-chHHHH
Confidence            6789999999999999998655568999999999999999999999864   77895 688887    444 3 233333


Q ss_pred             HHH---HHHHhcCCC----CCCCH----HHHHHHhCC--CeEEEEEecCCChHHHHHhhccCCC-----------cCCce
Q 042778          220 QKL---LSKLLQDGI----VIPDI----ALSFRQLSR--RKVLIVLDDVTCFRQIKSLIGMLRN-----------CCVKE  275 (311)
Q Consensus       220 ~~l---l~~l~~~~~----~~~~~----~~l~~~L~~--kr~LlVLDdV~~~~~l~~l~~~~~~-----------~~~~~  275 (311)
                      ..+   +..+.....    ...+.    ..++..|.+  +++||||||||+..+++.+.+....           .....
T Consensus       197 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l~~~~~ilvTsR~~~~~~~~~~~  276 (591)
T 1z6t_A          197 MKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGP  276 (591)
T ss_dssp             HHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTTCSSCEEEEEESCGGGGTTCCSC
T ss_pred             HHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHhcCCCeEEEECCCcHHHHhcCCC
Confidence            333   333332111    22232    556666655  7899999999999998876322111           11245


Q ss_pred             EEEc---CCCChHHHHHHHHHhhcC
Q 042778          276 KYEM---KELGDDHALELFSRHAFK  297 (311)
Q Consensus       276 ~y~v---~~L~~~ea~~Lf~~~af~  297 (311)
                      .|++   ++|+.+||++||+..++.
T Consensus       277 ~~~v~~l~~L~~~ea~~L~~~~~~~  301 (591)
T 1z6t_A          277 KYVVPVESSLGKEKGLEILSLFVNM  301 (591)
T ss_dssp             EEEEECCSSCCHHHHHHHHHHHHTS
T ss_pred             ceEeecCCCCCHHHHHHHHHHHhCC
Confidence            6666   489999999999999986

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.42  E-value=9.3e-14  Score=142.54  Aligned_cols=83  Identities=20%  Similarity=0.396  Sum_probs=75.5

Q ss_pred             CCCCcccEEecCccccCCCChH-HHHHHHHHh-----CCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccc
Q 042778           14 PRNHKYDVFQSFRGEDNRDNFT-GHLYSALSQ-----KGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASS   86 (311)
Q Consensus        14 ~~~~~~dvFis~~g~D~~~~f~-~~L~~~L~~-----~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S   86 (311)
                      ...+.|||||||+++|.  .|+ .+|...|++     +|+++++++ |+.+|+.+.++|.++|++||.+|+|+|++|+.|
T Consensus       666 ~~~~~yd~fisy~~~d~--~~v~~~l~~~Le~~~~~~~~~~~~~~~rd~~~G~~~~~~i~~~i~~sr~~i~vls~~~~~s  743 (844)
T 3j0a_A          666 PDMYKYDAYLCFSSKDF--TWVQNALLKHLDTQYSDQNRFNLCFEERDFVPGENRIANIQDAIWNSRKIVCLVSRHFLRD  743 (844)
T ss_dssp             SSCCCCSEEEECCSTTH--HHHHHTHHHHHHSTTTTTTCSCEECSSSSCCSSSCHHHHHHHHHHHSSEEEEEECTTHHHH
T ss_pred             ccceeccEEEEeeCCcH--HHHHHHHHHHHhhccccCCceEEEEEccccCCCchHHHHHHHHHHHhCeEEEEeccccccC
Confidence            45689999999999996  588 779999984     689999999 999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHh
Q 042778           87 RWCLDELVKILT   98 (311)
Q Consensus        87 ~wcl~El~~i~e   98 (311)
                      .||..|+..++.
T Consensus       744 ~wc~~e~~~a~~  755 (844)
T 3j0a_A          744 GWCLEAFSYAQG  755 (844)
T ss_dssp             TSTTHHHHHHHS
T ss_pred             hHHHHHHHHHHH
Confidence            999999876543

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.19  E-value=3.2e-10  Score=105.24  Aligned_cols=147  Identities=14%  Similarity=0.158  Sum_probs=102.2

Q ss_pred             CCCccchhhhHHHHHHhhcc--cCCCeEEEEEeccCcchhHHHHHHHHHhhccC------c--CceEEEecCccccCCCC
Q 042778          144 KNQLVGVESRVEEIESLLGA--ESKDVYALGIWGIGGIDRTTIARAIFNKISSN------F--EGSCFLQNVREESQRPG  213 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F--~~~~wv~~~~~~s~~~~  213 (311)
                      +..++||+..++++..+|..  .....+.+.|+|++|+||||||+.+++.....      +  ...+|+.    ... ..
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~----~~~-~~   93 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN----CRE-VG   93 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE----HHH-HC
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE----Ccc-CC
Confidence            67899999999999988864  23346789999999999999999999986433      2  2335554    222 33


Q ss_pred             -ChHHHHHHHHHHHhcCCC---C--CCCH-HHHHHHhCCCeEEEEEecCCChH------H-HHHhhccCCC---------
Q 042778          214 -GLGFLQQKLLSKLLQDGI---V--IPDI-ALSFRQLSRRKVLIVLDDVTCFR------Q-IKSLIGMLRN---------  270 (311)
Q Consensus       214 -~~~~l~~~ll~~l~~~~~---~--~~~~-~~l~~~L~~kr~LlVLDdV~~~~------~-l~~l~~~~~~---------  270 (311)
                       +...+...++..+.+...   .  .... ..+.+.+..++.+|||||++...      . +..+......         
T Consensus        94 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~  173 (384)
T 2qby_B           94 GTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISND  173 (384)
T ss_dssp             SCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSS
T ss_pred             CCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECC
Confidence             677788888888754332   1  1122 66777787777799999997643      2 3344322111         


Q ss_pred             ------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                  ......+++++++.++..++|..++
T Consensus       174 ~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~  210 (384)
T 2qby_B          174 INVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYA  210 (384)
T ss_dssp             TTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHH
T ss_pred             CchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHH
Confidence                        1112489999999999999999873

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.18  E-value=2.5e-10  Score=106.79  Aligned_cols=146  Identities=12%  Similarity=0.142  Sum_probs=97.5

Q ss_pred             CCCccchhhhHHHHHHhh-ccc--C--CCeEEEEE--eccCcchhHHHHHHHHHhhccC-----cCc-eEEEecCccccC
Q 042778          144 KNQLVGVESRVEEIESLL-GAE--S--KDVYALGI--WGIGGIDRTTIARAIFNKISSN-----FEG-SCFLQNVREESQ  210 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L-~~~--~--~~~~vi~I--~GmgGiGKTtLA~~v~~~~~~~-----F~~-~~wv~~~~~~s~  210 (311)
                      +..++||+.++++|...| ...  .  ...+.+.|  +|++|+||||||+.+++.....     +.. .+|+.    ...
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~----~~~   96 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN----AFN   96 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE----GGG
T ss_pred             CCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE----CCC
Confidence            578999999999999988 421  1  23445555  9999999999999999986542     222 35665    334


Q ss_pred             CCCChHHHHHHHHHHHhcCCCC-CCCH----HHHHHHhC--CCeEEEEEecCCCh--------HHHHHhh----ccC--C
Q 042778          211 RPGGLGFLQQKLLSKLLQDGIV-IPDI----ALSFRQLS--RRKVLIVLDDVTCF--------RQIKSLI----GML--R  269 (311)
Q Consensus       211 ~~~~~~~l~~~ll~~l~~~~~~-~~~~----~~l~~~L~--~kr~LlVLDdV~~~--------~~l~~l~----~~~--~  269 (311)
                       ..+...+...++..+...... ..+.    ..+.+.|.  +++++|||||++..        +.+..+.    ...  +
T Consensus        97 -~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~  175 (412)
T 1w5s_A           97 -APNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRD  175 (412)
T ss_dssp             -CCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTT
T ss_pred             -CCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCC
Confidence             567788888988888654321 1112    55555554  67999999999763        3333321    111  1


Q ss_pred             --C-------c------------------CCceEEEcCCCChHHHHHHHHHh
Q 042778          270 --N-------C------------------CVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       270 --~-------~------------------~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                        .       .                  .....+++++|+.++++++|..+
T Consensus       176 ~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~  227 (412)
T 1w5s_A          176 GVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQR  227 (412)
T ss_dssp             SCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             CCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHH
Confidence              1       0                  01233899999999999999754

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.06  E-value=2.5e-09  Score=98.81  Aligned_cols=147  Identities=10%  Similarity=0.151  Sum_probs=99.6

Q ss_pred             CCCccchhhhHHHHHHhhccc--CCCeEEEEEeccCcchhHHHHHHHHHhhccCc-----C-ceEEEecCccccCCCCCh
Q 042778          144 KNQLVGVESRVEEIESLLGAE--SKDVYALGIWGIGGIDRTTIARAIFNKISSNF-----E-GSCFLQNVREESQRPGGL  215 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-----~-~~~wv~~~~~~s~~~~~~  215 (311)
                      +..++||+..++++..+|...  ....+.+.|+|++|+||||||+.+++.....+     . ..+++.    ... ..+.
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~----~~~-~~~~   92 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN----ARH-RETP   92 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE----TTT-SCSH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE----CCc-CCCH
Confidence            578999999999999988543  34467899999999999999999999864431     2 234554    333 5567


Q ss_pred             HHHHHHHHHHHhcCCCC-CCCH----HHHHHHh--CCCeEEEEEecCCChH----H---HHHhhc-------cCCC----
Q 042778          216 GFLQQKLLSKLLQDGIV-IPDI----ALSFRQL--SRRKVLIVLDDVTCFR----Q---IKSLIG-------MLRN----  270 (311)
Q Consensus       216 ~~l~~~ll~~l~~~~~~-~~~~----~~l~~~L--~~kr~LlVLDdV~~~~----~---l~~l~~-------~~~~----  270 (311)
                      ..+...++..+...... ..+.    ..+...+  .+++++|||||++...    .   +..+..       ....    
T Consensus        93 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~  172 (387)
T 2v1u_A           93 YRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVG  172 (387)
T ss_dssp             HHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEE
T ss_pred             HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEE
Confidence            77888888887543331 1112    4555565  3468999999998643    1   222221       1111    


Q ss_pred             ----------------cCCc-eEEEcCCCChHHHHHHHHHhh
Q 042778          271 ----------------CCVK-EKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ----------------~~~~-~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                      .... ..+.+++++.++..+++..++
T Consensus       173 ~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~  214 (387)
T 2v1u_A          173 ITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRA  214 (387)
T ss_dssp             ECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHH
T ss_pred             EECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHH
Confidence                            0111 578999999999999999873

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.01  E-value=7.7e-10  Score=102.19  Aligned_cols=147  Identities=17%  Similarity=0.250  Sum_probs=96.1

Q ss_pred             CCCccchhhhHHHHHHhhccc--CCCeEEEEEeccCcchhHHHHHHHHHhhccCcC---ceEEEecCccccCCCCChHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE--SKDVYALGIWGIGGIDRTTIARAIFNKISSNFE---GSCFLQNVREESQRPGGLGFL  218 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~---~~~wv~~~~~~s~~~~~~~~l  218 (311)
                      +..++||+.+++.+.++|...  ....+.+.|+|++|+||||||+.+++.....+.   ..+|+.    ... ......+
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~----~~~-~~~~~~~   93 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN----TRQ-IDTPYRV   93 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE----HHH-HCSHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE----CCC-CCCHHHH
Confidence            678999999999999988742  344678999999999999999999998765542   345554    222 3455566


Q ss_pred             HHHHHHHHhcCCC-CCCCH----HHHHHHhC--CCeEEEEEecCCCh------HHHHHhhc------cCCC---------
Q 042778          219 QQKLLSKLLQDGI-VIPDI----ALSFRQLS--RRKVLIVLDDVTCF------RQIKSLIG------MLRN---------  270 (311)
Q Consensus       219 ~~~ll~~l~~~~~-~~~~~----~~l~~~L~--~kr~LlVLDdV~~~------~~l~~l~~------~~~~---------  270 (311)
                      ...++..+..... ...+.    ..+.+.+.  +++.+||||+++..      +.+..+..      ..+.         
T Consensus        94 ~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~  173 (386)
T 2qby_A           94 LADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDV  173 (386)
T ss_dssp             HHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCG
T ss_pred             HHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCC
Confidence            6666655533221 11112    44444543  45899999999653      23333321      1111         


Q ss_pred             ------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                  .-....+.+++|+.++..+++..++
T Consensus       174 ~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~  210 (386)
T 2qby_A          174 KFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRA  210 (386)
T ss_dssp             GGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHH
T ss_pred             ChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHH
Confidence                        0012589999999999999999863

>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=98.88  E-value=3.6e-08  Score=91.22  Aligned_cols=147  Identities=15%  Similarity=0.141  Sum_probs=98.1

Q ss_pred             CCCccchhhhHHHHHHhhccc----CCCeEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEecCccccCCCCChHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE----SKDVYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQNVREESQRPGGLGFL  218 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~~~~~~s~~~~~~~~l  218 (311)
                      ++.++||+..++++...|...    ....+.+.|+|.+|+||||||+.+++...... ...+++.    .+. ......+
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~----~~~-~~~~~~~   90 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN----GFI-YRNFTAI   90 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE----TTT-CCSHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe----Ccc-CCCHHHH
Confidence            578999999999999988642    12234899999999999999999999876542 2345554    233 4556777


Q ss_pred             HHHHHHHHhcCCCC-CCCH----HHHHHHhC--CCeEEEEEecCCC--hHHHHHhhcc---------CCC------c---
Q 042778          219 QQKLLSKLLQDGIV-IPDI----ALSFRQLS--RRKVLIVLDDVTC--FRQIKSLIGM---------LRN------C---  271 (311)
Q Consensus       219 ~~~ll~~l~~~~~~-~~~~----~~l~~~L~--~kr~LlVLDdV~~--~~~l~~l~~~---------~~~------~---  271 (311)
                      ...++..+...... ....    ..+...+.  +++.+|||||++.  .+.+..|...         .+.      .   
T Consensus        91 ~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~  170 (389)
T 1fnn_A           91 IGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDA  170 (389)
T ss_dssp             HHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH
T ss_pred             HHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCch
Confidence            88887777543221 1122    34444443  5688999999975  3444444211         111      0   


Q ss_pred             ------------CCceEEEcCCCChHHHHHHHHHhh
Q 042778          272 ------------CVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       272 ------------~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                  -....+.+++++.++..+++...+
T Consensus       171 ~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~  206 (389)
T 1fnn_A          171 VLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  206 (389)
T ss_dssp             HHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             HHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHH
Confidence                        012368999999999999998874

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.84  E-value=2.1e-08  Score=91.50  Aligned_cols=51  Identities=16%  Similarity=0.303  Sum_probs=43.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +..++||+.+++.|.+ +..     +++.|+|++|+|||||++.+.++....   .+|+.
T Consensus        12 ~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~~~~~---~~~~~   62 (357)
T 2fna_A           12 RKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINELNLP---YIYLD   62 (357)
T ss_dssp             GGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHHHTCC---EEEEE
T ss_pred             HHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHhcCCC---EEEEE
Confidence            5679999999999999 763     599999999999999999999886532   46665

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.84  E-value=5.2e-09  Score=95.36  Aligned_cols=141  Identities=13%  Similarity=0.145  Sum_probs=87.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCcccc--CCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREES--QRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s--~~~~~~~~l~~~  221 (311)
                      +..++||+.+++.|.+++..+    +++.|+|++|+|||||++.++++..     .+|+.. ....  ........+...
T Consensus        11 ~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~~-----~~~~~~-~~~~~~~~~~~~~~~~~~   80 (350)
T 2qen_A           11 REDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNERP-----GILIDC-RELYAERGHITREELIKE   80 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHSS-----EEEEEH-HHHHHTTTCBCHHHHHHH
T ss_pred             hHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHcC-----cEEEEe-ecccccccCCCHHHHHHH
Confidence            567999999999999988742    6899999999999999999998752     566652 1110  001134455555


Q ss_pred             HHHHHhc----------------CCC--CCCCH----HHHHHHhCC-CeEEEEEecCCChH---------HHHHhh---c
Q 042778          222 LLSKLLQ----------------DGI--VIPDI----ALSFRQLSR-RKVLIVLDDVTCFR---------QIKSLI---G  266 (311)
Q Consensus       222 ll~~l~~----------------~~~--~~~~~----~~l~~~L~~-kr~LlVLDdV~~~~---------~l~~l~---~  266 (311)
                      +...+..                ...  .....    ..+.+.+.. ++++|||||++...         .+..+.   .
T Consensus        81 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~~  160 (350)
T 2qen_A           81 LQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAYD  160 (350)
T ss_dssp             HHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHHH
Confidence            5443321                000  11233    334443332 48999999997632         122221   0


Q ss_pred             c-CCC-------------------------c-CCceEEEcCCCChHHHHHHHHHh
Q 042778          267 M-LRN-------------------------C-CVKEKYEMKELGDDHALELFSRH  294 (311)
Q Consensus       267 ~-~~~-------------------------~-~~~~~y~v~~L~~~ea~~Lf~~~  294 (311)
                      . .+.                         . .....+++.+|+.+|+.+++...
T Consensus       161 ~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~  215 (350)
T 2qen_A          161 SLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRG  215 (350)
T ss_dssp             HCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHH
T ss_pred             hcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHH
Confidence            0 000                         0 11247899999999999999764

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.78  E-value=5.8e-08  Score=83.05  Aligned_cols=141  Identities=14%  Similarity=0.090  Sum_probs=82.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEec---------------Cccc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQN---------------VREE  208 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~---------------~~~~  208 (311)
                      ..+++|++..++.+...+..+. ..+.+.|+|++|+||||||+.+++.....+......+.               +...
T Consensus        22 ~~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (250)
T 1njg_A           22 FADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEI  100 (250)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEE
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEe
Confidence            3568999999999999887532 23578999999999999999999986543321100000               0000


Q ss_pred             cCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhhc---c-CCC------------
Q 042778          209 SQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLIG---M-LRN------------  270 (311)
Q Consensus       209 s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~---~-~~~------------  270 (311)
                      .............++..+...            ...+++.+|||||++.  ...++.+..   . ...            
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~  168 (250)
T 1njg_A          101 DAASRTKVEDTRDLLDNVQYA------------PARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQK  168 (250)
T ss_dssp             ETTCGGGHHHHHHHHHSCCCS------------CSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGG
T ss_pred             cCcccccHHHHHHHHHHhhhc------------hhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHh
Confidence            000000011111111111000            0134679999999964  445555431   1 111            


Q ss_pred             -----cCCceEEEcCCCChHHHHHHHHHhhcC
Q 042778          271 -----CCVKEKYEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       271 -----~~~~~~y~v~~L~~~ea~~Lf~~~af~  297 (311)
                           ......+++++|+.++..+++...+..
T Consensus       169 ~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~  200 (250)
T 1njg_A          169 LPVTILSRCLQFHLKALDVEQIRHQLEHILNE  200 (250)
T ss_dssp             SCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhhhccCCCCCHHHHHHHHHHHHHh
Confidence                 122468999999999999999988764

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.75  E-value=6.8e-08  Score=81.65  Aligned_cols=136  Identities=13%  Similarity=0.180  Sum_probs=83.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCce-EEEecCccccCCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEGS-CFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~-~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      ..+++|++..++.+..++....  .+.+.|+|.+|+||||||+.+++.+... +... +.+.    .+. ..+...+...
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~----~~~-~~~~~~~~~~   88 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN----ASD-ERGIDVVRHK   88 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEE----TTC-TTCHHHHHHH
T ss_pred             HHHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEec----ccc-ccChHHHHHH
Confidence            3578999999999999887542  3348999999999999999999986433 3222 2222    112 2333333222


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh---cc--CCC----------------cCCceEEE
Q 042778          222 LLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI---GM--LRN----------------CCVKEKYE  278 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~---~~--~~~----------------~~~~~~y~  278 (311)
                      + ........          ....++.+|||||++..  ..++.+.   ..  ...                ......++
T Consensus        89 ~-~~~~~~~~----------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~  157 (226)
T 2chg_A           89 I-KEFARTAP----------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFR  157 (226)
T ss_dssp             H-HHHHTSCC----------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEE
T ss_pred             H-HHHhcccC----------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceee
Confidence            2 22111100          01257889999999753  3333332   11  111                12234889


Q ss_pred             cCCCChHHHHHHHHHhhcC
Q 042778          279 MKELGDDHALELFSRHAFK  297 (311)
Q Consensus       279 v~~L~~~ea~~Lf~~~af~  297 (311)
                      +++++.++..+++.+.+..
T Consensus       158 ~~~~~~~~~~~~l~~~~~~  176 (226)
T 2chg_A          158 FKPVPKEAMKKRLLEICEK  176 (226)
T ss_dssp             CCCCCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHH
Confidence            9999999999999987653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.67  E-value=1.5e-07  Score=85.49  Aligned_cols=145  Identities=8%  Similarity=0.069  Sum_probs=94.3

Q ss_pred             CccchhhhHHHHHHhhcc--cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc-----Cc--eEEEecCccccCCCCChH
Q 042778          146 QLVGVESRVEEIESLLGA--ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF-----EG--SCFLQNVREESQRPGGLG  216 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-----~~--~~wv~~~~~~s~~~~~~~  216 (311)
                      .+.||+.++.+|...|..  .......+-|+|++|.|||++++.+++++....     ..  .+.+.+.    . -.+..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~----~-~~t~~   95 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDAL----E-LAGMD   95 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETT----C-CC--H
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEecc----c-cCCHH
Confidence            378999999999988864  234577889999999999999999999864321     11  2344421    1 34567


Q ss_pred             HHHHHHHHHHhcCCCC-CCCHHHHHHH---h---CCCeEEEEEecCCCh---HHHHHhhc----cCCC------------
Q 042778          217 FLQQKLLSKLLQDGIV-IPDIALSFRQ---L---SRRKVLIVLDDVTCF---RQIKSLIG----MLRN------------  270 (311)
Q Consensus       217 ~l~~~ll~~l~~~~~~-~~~~~~l~~~---L---~~kr~LlVLDdV~~~---~~l~~l~~----~~~~------------  270 (311)
                      .+...|+.++.+.... ......+.+.   +   .++.++|+||+++..   +.+-.+..    ....            
T Consensus        96 ~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~  175 (318)
T 3te6_A           96 ALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVT  175 (318)
T ss_dssp             HHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCC
T ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCccc
Confidence            7888888888765432 1222333333   2   357899999999864   33333321    0000            


Q ss_pred             ----c------CC-ceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ----C------CV-KEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ----~------~~-~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                          .      .. ...+..++++.+|-.+++.+++
T Consensus       176 ~~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl  211 (318)
T 3te6_A          176 IREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRL  211 (318)
T ss_dssp             CHHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHH
T ss_pred             chhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHH
Confidence                0      11 2568899999999999998875

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.55  E-value=2.3e-07  Score=76.41  Aligned_cols=48  Identities=15%  Similarity=0.273  Sum_probs=40.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|++..++++.+.+...  ..+.+.|+|.+|+||||||+.+++.+.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            457999999999999988753  345678999999999999999999854

>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=98.55  E-value=3.4e-07  Score=82.43  Aligned_cols=134  Identities=14%  Similarity=0.236  Sum_probs=83.8

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCc-eEEEecCccccCCCCChHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEG-SCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~-~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      .+++|++..++.+..++..+  ..+.+.|+|++|+||||+|+.+++.+... +.. .+.+.    .+. ..+...+ +.+
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~----~~~-~~~~~~i-~~~   92 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDG--NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN----ASD-DRGIDVV-RNQ   92 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC----TTS-CCSHHHH-HTH
T ss_pred             HHHHCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEec----Ccc-ccChHHH-HHH
Confidence            57899999999999988743  23338999999999999999999986432 222 23333    122 2233322 222


Q ss_pred             HHHHhcCCCCCCCHHHHHHHh-CCCeEEEEEecCCC--hHHHHHhh-----ccCCC----------------cCCceEEE
Q 042778          223 LSKLLQDGIVIPDIALSFRQL-SRRKVLIVLDDVTC--FRQIKSLI-----GMLRN----------------CCVKEKYE  278 (311)
Q Consensus       223 l~~l~~~~~~~~~~~~l~~~L-~~kr~LlVLDdV~~--~~~l~~l~-----~~~~~----------------~~~~~~y~  278 (311)
                      +..+....          ..+ .+++.+||+||++.  ...++.|.     +....                ......++
T Consensus        93 ~~~~~~~~----------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~  162 (323)
T 1sxj_B           93 IKHFAQKK----------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILR  162 (323)
T ss_dssp             HHHHHHBC----------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEE
T ss_pred             HHHHHhcc----------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEe
Confidence            22222100          011 34688999999975  33344332     11111                22345899


Q ss_pred             cCCCChHHHHHHHHHhhc
Q 042778          279 MKELGDDHALELFSRHAF  296 (311)
Q Consensus       279 v~~L~~~ea~~Lf~~~af  296 (311)
                      +++++.++..+++...+.
T Consensus       163 ~~~~~~~~~~~~l~~~~~  180 (323)
T 1sxj_B          163 YSKLSDEDVLKRLLQIIK  180 (323)
T ss_dssp             CCCCCHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHH
Confidence            999999999999998764

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.48  E-value=6.2e-07  Score=79.66  Aligned_cols=146  Identities=17%  Similarity=0.259  Sum_probs=86.4

Q ss_pred             CCCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC
Q 042778          144 KNQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP  212 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~  212 (311)
                      .++++|++..+++|.+.+...           ....+.+.|+|.+|+||||||+++++.....|-.   +. ..+.....
T Consensus        16 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~---v~-~~~~~~~~   91 (285)
T 3h4m_A           16 YEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIR---VV-GSELVKKF   91 (285)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEE---EE-GGGGCCCS
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEE---Ee-hHHHHHhc
Confidence            567899999999998877431           1235568999999999999999999986543321   22 11111101


Q ss_pred             CC-hHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh----------------HHHHHhhc------cCC
Q 042778          213 GG-LGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF----------------RQIKSLIG------MLR  269 (311)
Q Consensus       213 ~~-~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~----------------~~l~~l~~------~~~  269 (311)
                      .+ .......+                +......+..+|+|||++..                ..+..+..      ...
T Consensus        92 ~~~~~~~~~~~----------------~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~  155 (285)
T 3h4m_A           92 IGEGASLVKDI----------------FKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARG  155 (285)
T ss_dssp             TTHHHHHHHHH----------------HHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSS
T ss_pred             cchHHHHHHHH----------------HHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCC
Confidence            11 11111111                12222345689999999653                11222211      100


Q ss_pred             C------------------c--CCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhh
Q 042778          270 N------------------C--CVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELS  309 (311)
Q Consensus       270 ~------------------~--~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~  309 (311)
                      .                  .  .....+.++.++.++..++|..++.... .+..++..|+
T Consensus       156 ~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~  216 (285)
T 3h4m_A          156 DVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIA  216 (285)
T ss_dssp             SEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHH
T ss_pred             CEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHH
Confidence            1                  1  2345789999999999999998876533 2334555554

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.42  E-value=5.5e-07  Score=74.04  Aligned_cols=49  Identities=16%  Similarity=0.270  Sum_probs=40.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|++..++.+.+.+...  ..+.+.|+|.+|+||||||+.+++....
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~--~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRR--TKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSS--SSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             cchhhcchHHHHHHHHHHhCC--CCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            457899999999999988642  3456789999999999999999998643

>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=98.31  E-value=1.4e-06  Score=78.55  Aligned_cols=136  Identities=15%  Similarity=0.146  Sum_probs=81.3

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc-Cc-eEEEecCccccCCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF-EG-SCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~-~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      ..+++|++..++.+..++..+  ..+.+.|+|++|+||||+|+.+++.+.... .. ...+.    .+. ..+...+. .
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~----~~~-~~~~~~~~-~   95 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELN----ASD-ERGINVIR-E   95 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE----TTC-HHHHHTTH-H
T ss_pred             HHHhhCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEee----ccc-cCchHHHH-H
Confidence            457899999999999988754  333489999999999999999999864332 11 12222    111 00111111 1


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh-----ccCCC----------------cCCceEEE
Q 042778          222 LLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI-----GMLRN----------------CCVKEKYE  278 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~-----~~~~~----------------~~~~~~y~  278 (311)
                      .+.......          .....++.+||+||++..  +.++.|.     +....                ......++
T Consensus        96 ~~~~~~~~~----------~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~  165 (327)
T 1iqp_A           96 KVKEFARTK----------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFR  165 (327)
T ss_dssp             HHHHHHHSC----------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEE
T ss_pred             HHHHHHhhC----------CcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEE
Confidence            111111000          001256789999999753  4444443     11111                11234789


Q ss_pred             cCCCChHHHHHHHHHhhcC
Q 042778          279 MKELGDDHALELFSRHAFK  297 (311)
Q Consensus       279 v~~L~~~ea~~Lf~~~af~  297 (311)
                      +++++.++..+++...+-.
T Consensus       166 ~~~l~~~~~~~~l~~~~~~  184 (327)
T 1iqp_A          166 FRPLRDEDIAKRLRYIAEN  184 (327)
T ss_dssp             CCCCCHHHHHHHHHHHHHT
T ss_pred             ecCCCHHHHHHHHHHHHHh
Confidence            9999999999999887654

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.26  E-value=5.2e-06  Score=74.39  Aligned_cols=135  Identities=12%  Similarity=0.151  Sum_probs=80.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-CcCc-eEEEecCccccCCCCChHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-NFEG-SCFLQNVREESQRPGGLGFLQQK  221 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~-~~wv~~~~~~s~~~~~~~~l~~~  221 (311)
                      ..+++|++..++.+.+++..+  ..+.+.|+|.+|+||||+|+.+++.+.. .+.. .+.+. ...... ...+..+...
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~   91 (319)
T 2chq_A           16 LDEVVGQDEVIQRLKGYVERK--NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN-ASDERG-IDVVRHKIKE   91 (319)
T ss_dssp             GGGSCSCHHHHHHHHTTTTTT--CCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEE-TTSTTC-TTTSSHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHhCC--CCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEe-CccccC-hHHHHHHHHH
Confidence            356899999999999888753  3334899999999999999999998532 2221 12222 111000 1111111111


Q ss_pred             HHHHHhcCCCCCCCHHHHHHHh-CCCeEEEEEecCCCh--HHHHHhhccCC----C-----------------cCCceEE
Q 042778          222 LLSKLLQDGIVIPDIALSFRQL-SRRKVLIVLDDVTCF--RQIKSLIGMLR----N-----------------CCVKEKY  277 (311)
Q Consensus       222 ll~~l~~~~~~~~~~~~l~~~L-~~kr~LlVLDdV~~~--~~l~~l~~~~~----~-----------------~~~~~~y  277 (311)
                      +...               ..+ .+++.+||+||++..  +..+.|.....    .                 ......+
T Consensus        92 ~~~~---------------~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i  156 (319)
T 2chq_A           92 FART---------------APIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVF  156 (319)
T ss_dssp             HHHS---------------CCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEE
T ss_pred             HHhc---------------CCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEE
Confidence            1100               001 256789999999753  34444432111    1                 1234589


Q ss_pred             EcCCCChHHHHHHHHHhhcC
Q 042778          278 EMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       278 ~v~~L~~~ea~~Lf~~~af~  297 (311)
                      ++.+++.++..+++...+-.
T Consensus       157 ~~~~~~~~~~~~~l~~~~~~  176 (319)
T 2chq_A          157 RFKPVPKEAMKKRLLEICEK  176 (319)
T ss_dssp             ECCCCCHHHHHHHHHHHHHT
T ss_pred             EecCCCHHHHHHHHHHHHHH
Confidence            99999999999999877644

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.21  E-value=5e-06  Score=79.09  Aligned_cols=130  Identities=15%  Similarity=0.312  Sum_probs=80.7

Q ss_pred             CCCccchhhhH---HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHH
Q 042778          144 KNQLVGVESRV---EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~vGr~~~~---~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      ..+++|.+..+   ..+...+..+  ....+.|||.+|+||||||+.+++.....|..   +.     .. ..+...+..
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~--~~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~---l~-----a~-~~~~~~ir~   93 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAG--HLHSMILWGPPGTGKTTLAEVIARYANADVER---IS-----AV-TSGVKEIRE   93 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHT--CCCEEEEECSTTSSHHHHHHHHHHHTTCEEEE---EE-----TT-TCCHHHHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcC--CCcEEEEECCCCCcHHHHHHHHHHHhCCCeEE---EE-----ec-cCCHHHHHH
Confidence            45789998777   6666666643  35789999999999999999999987554422   11     11 233333322


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhhccC-------------CC--------cCCceEE
Q 042778          221 KLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLIGML-------------RN--------CCVKEKY  277 (311)
Q Consensus       221 ~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~~~~-------------~~--------~~~~~~y  277 (311)
                       ++...            .......++.+|+||+++..  .+.+.|++..             +.        .....++
T Consensus        94 -~~~~a------------~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~~v~lI~att~n~~~~l~~aL~sR~~v~  160 (447)
T 3pvs_A           94 -AIERA------------RQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVY  160 (447)
T ss_dssp             -HHHHH------------HHHHHTTCCEEEEEETTTCC------CCHHHHHTTSCEEEEEESSCGGGSSCHHHHTTEEEE
T ss_pred             -HHHHH------------HHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhcCceEEEecCCCCcccccCHHHhCceeEE
Confidence             22211            11122467889999999853  3333332110             00        2334588


Q ss_pred             EcCCCChHHHHHHHHHhhcC
Q 042778          278 EMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       278 ~v~~L~~~ea~~Lf~~~af~  297 (311)
                      .+++++.++..+++.+.+-.
T Consensus       161 ~l~~l~~edi~~il~~~l~~  180 (447)
T 3pvs_A          161 LLKSLSTEDIEQVLTQAMED  180 (447)
T ss_dssp             ECCCCCHHHHHHHHHHHHHC
T ss_pred             eeCCcCHHHHHHHHHHHHHH
Confidence            99999999999999887543

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.21  E-value=1.5e-05  Score=69.53  Aligned_cols=52  Identities=15%  Similarity=0.174  Sum_probs=39.1

Q ss_pred             CCCccchhhhHHHHHHhhccc----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAE----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+..++.+.+++..-          ....+-+.|+|.+|+|||+||+++++.....
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~   66 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVP   66 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCC
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            457899998888887765321          0224568899999999999999999986543

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.19  E-value=5.6e-06  Score=80.19  Aligned_cols=144  Identities=15%  Similarity=0.153  Sum_probs=84.0

Q ss_pred             CCCccchhhhHHHHHHhhcccC---------------CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccc
Q 042778          144 KNQLVGVESRVEEIESLLGAES---------------KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREE  208 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~---------------~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~  208 (311)
                      ..+++|++..++++..+|....               ...+.+.|+|++|+||||||+++++...  +. .+.+.    .
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~--~~-~i~in----~  110 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG--YD-ILEQN----A  110 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT--CE-EEEEC----T
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC--CC-EEEEe----C
Confidence            4578999999999999986410               1247899999999999999999999873  22 12222    1


Q ss_pred             cCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHH--hCCCeEEEEEecCCCh--------HHHHHhhccCCC-------
Q 042778          209 SQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQ--LSRRKVLIVLDDVTCF--------RQIKSLIGMLRN-------  270 (311)
Q Consensus       209 s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~--L~~kr~LlVLDdV~~~--------~~l~~l~~~~~~-------  270 (311)
                      +. .... .+....+....... .+... ....+.  ...++.+|+||+|+..        ..+..+......       
T Consensus       111 s~-~~~~-~~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~~~~iIli~~  187 (516)
T 1sxj_A          111 SD-VRSK-TLLNAGVKNALDNM-SVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICN  187 (516)
T ss_dssp             TS-CCCH-HHHHHTGGGGTTBC-CSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEES
T ss_pred             CC-cchH-HHHHHHHHHHhccc-cHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhcCCCEEEEEc
Confidence            22 2222 22222222211111 11111 111111  2357789999999743        233333211111       


Q ss_pred             ----------cCCceEEEcCCCChHHHHHHHHHhhcC
Q 042778          271 ----------CCVKEKYEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       271 ----------~~~~~~y~v~~L~~~ea~~Lf~~~af~  297 (311)
                                ......+++++++.++..+++.+.+..
T Consensus       188 ~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~  224 (516)
T 1sxj_A          188 ERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIR  224 (516)
T ss_dssp             CTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHH
Confidence                      223457899999999999999887654

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.14  E-value=2.8e-05  Score=71.30  Aligned_cols=141  Identities=14%  Similarity=0.138  Sum_probs=81.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      ..+++|++..++.+...+..+. -...+.|+|..|+||||+|+.+++.+.......         .. ..+...-...+.
T Consensus        15 ~~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~---------~~-~~~~~~~~~~~~   83 (373)
T 1jr3_A           15 FADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT---------AT-PCGVCDNCREIE   83 (373)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSC---------SS-CCSSSHHHHHHH
T ss_pred             hhhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCC---------CC-CCcccHHHHHHh
Confidence            3569999999999999886432 245788999999999999999998764432110         00 000000000110


Q ss_pred             HH-------HhcCC-CCCCCHHHHHHHh-----CCCeEEEEEecCCC--hHHHHHhh----ccCCC--------------
Q 042778          224 SK-------LLQDG-IVIPDIALSFRQL-----SRRKVLIVLDDVTC--FRQIKSLI----GMLRN--------------  270 (311)
Q Consensus       224 ~~-------l~~~~-~~~~~~~~l~~~L-----~~kr~LlVLDdV~~--~~~l~~l~----~~~~~--------------  270 (311)
                      ..       +.... .....+..+.+.+     .+++.+||+||++.  ...++.|.    .....              
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~  163 (373)
T 1jr3_A           84 QGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLP  163 (373)
T ss_dssp             TSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSC
T ss_pred             ccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCc
Confidence            00       00000 0122233333333     24678999999974  33444442    11111              


Q ss_pred             ---cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ---CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ---~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                         ......+++.+++.++..+++...+
T Consensus       164 ~~l~sr~~~i~~~~l~~~~~~~~l~~~~  191 (373)
T 1jr3_A          164 VTILSRCLQFHLKALDVEQIRHQLEHIL  191 (373)
T ss_dssp             HHHHTTSEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHhheeEeeCCCCCHHHHHHHHHHHH
Confidence               2234688999999999999998765

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=98.14  E-value=5.7e-05  Score=67.79  Aligned_cols=50  Identities=22%  Similarity=0.288  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+++|.+..+++|.+.+..           +-...+.+.|+|.+|+||||||+++++...
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~   74 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ   74 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhC
Confidence            45789999988888877642           113356789999999999999999999875

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.12  E-value=1.3e-05  Score=71.73  Aligned_cols=49  Identities=16%  Similarity=0.247  Sum_probs=37.6

Q ss_pred             CccchhhhHHHHHHhhccc-------------CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          146 QLVGVESRVEEIESLLGAE-------------SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~-------------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +++|.+..++.|.+++..-             ......+.|+|.+|+|||+||+++++.+..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   93 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR   93 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            5889888888887665421             233557899999999999999999987543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.12  E-value=8.4e-06  Score=68.49  Aligned_cols=59  Identities=15%  Similarity=0.149  Sum_probs=39.0

Q ss_pred             CCccchh----hhHHHHHHhhcccCCC--eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          145 NQLVGVE----SRVEEIESLLGAESKD--VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       145 ~~~vGr~----~~~~~l~~~L~~~~~~--~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +++++..    ..++.+..++......  .+.+.|+|.+|+||||||+++++.........+++.
T Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           25 SDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             TSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             hhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            4556543    2344445555433221  268899999999999999999998765544556665

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=98.08  E-value=1.4e-05  Score=72.53  Aligned_cols=52  Identities=17%  Similarity=0.300  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhcc----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+..++.|.+.+..          .....+-+.|+|.+|+|||+||+++++.....
T Consensus        17 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~   78 (322)
T 3eie_A           17 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST   78 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCE
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCC
Confidence            45789999999999887721          11124578999999999999999999986543

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.05  E-value=2.3e-05  Score=70.61  Aligned_cols=51  Identities=22%  Similarity=0.373  Sum_probs=41.0

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|++..+..+..++...   ......+.|+|++|+||||||+++++....
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~   64 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV   64 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTC
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCC
Confidence            467999999999888877531   223467889999999999999999998753

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=98.05  E-value=4.2e-05  Score=70.42  Aligned_cols=51  Identities=18%  Similarity=0.219  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhcc----------cCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGA----------ESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|.+..++.|.+.+..          .....+.+.|+|.+|+|||+||+++++....
T Consensus        83 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~  143 (357)
T 3d8b_A           83 WEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGA  143 (357)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTC
T ss_pred             HHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCC
Confidence            45789999999999887742          1123567899999999999999999988643

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.03  E-value=9.1e-05  Score=67.21  Aligned_cols=49  Identities=14%  Similarity=0.241  Sum_probs=38.5

Q ss_pred             CCCccchhhhHHHHHHhhcc---------c-CCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGA---------E-SKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---------~-~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -++++|.+..++.|.+.+..         + ....+-+.|+|++|+|||+||+++++..
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc
Confidence            45789999888888876531         1 1124678999999999999999999986

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.97  E-value=7.9e-05  Score=68.32  Aligned_cols=52  Identities=17%  Similarity=0.173  Sum_probs=39.1

Q ss_pred             CCCccchhhhHHHHHHh---hcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESL---LGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~---L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++++|++..++.+..+   +..+....+.+.|+|.+|+|||+||+++++.....
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~   97 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPD   97 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSS
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            45799999887765443   33332224689999999999999999999987643

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.95  E-value=7.3e-05  Score=67.56  Aligned_cols=136  Identities=13%  Similarity=0.101  Sum_probs=74.0

Q ss_pred             CCCcc-chhh--hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHH
Q 042778          144 KNQLV-GVES--RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~v-Gr~~--~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      .++++ |...  ....+..++.........+.|+|.+|+||||||+.+++.....-...+++.           ...+..
T Consensus        10 f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~-----------~~~~~~   78 (324)
T 1l8q_A           10 LENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQ   78 (324)
T ss_dssp             SSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHH
T ss_pred             cccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE-----------HHHHHH
Confidence            34555 5332  233344444432223567899999999999999999998644311223443           122233


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH----HHHHhh-------ccCCC-------------------
Q 042778          221 KLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR----QIKSLI-------GMLRN-------------------  270 (311)
Q Consensus       221 ~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~----~l~~l~-------~~~~~-------------------  270 (311)
                      .+...+...     ....+...+. +..+|+|||+....    ..+.+.       .....                   
T Consensus        79 ~~~~~~~~~-----~~~~~~~~~~-~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L  152 (324)
T 1l8q_A           79 AMVEHLKKG-----TINEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRL  152 (324)
T ss_dssp             HHHHHHHHT-----CHHHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHH
T ss_pred             HHHHHHHcC-----cHHHHHHHhc-CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHh
Confidence            333333211     1122233332 35689999996432    112211       00000                   


Q ss_pred             ---cCCceEEEcCCCChHHHHHHHHHhhcC
Q 042778          271 ---CCVKEKYEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       271 ---~~~~~~y~v~~L~~~ea~~Lf~~~af~  297 (311)
                         .....++++++ +.++..+++.+++-.
T Consensus       153 ~sR~~~~~~i~l~~-~~~e~~~il~~~~~~  181 (324)
T 1l8q_A          153 VSRFEGGILVEIEL-DNKTRFKIIKEKLKE  181 (324)
T ss_dssp             HHHHHTSEEEECCC-CHHHHHHHHHHHHHH
T ss_pred             hhcccCceEEEeCC-CHHHHHHHHHHHHHh
Confidence               12336789999 999999999988753

>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=97.93  E-value=1.5e-05  Score=75.72  Aligned_cols=113  Identities=12%  Similarity=0.123  Sum_probs=69.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCce--EEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGS--CFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDIALSFRQLSR  245 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~--~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~  245 (311)
                      ...+.|+|.+|+||||||+++++.+...+...  +++.           ...+...+...+...     ....+...+..
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~~  193 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT-----------SEKFLNDLVDSMKEG-----KLNEFREKYRK  193 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEE-----------HHHHHHHHHHHHHTT-----CHHHHHHHHTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee-----------HHHHHHHHHHHHHcc-----cHHHHHHHhcC
Confidence            66789999999999999999999876655332  3333           122333444333321     12344455554


Q ss_pred             CeEEEEEecCCCh----HHHHHhhc------cCCC-----------------------cCCceEEEcCCCChHHHHHHHH
Q 042778          246 RKVLIVLDDVTCF----RQIKSLIG------MLRN-----------------------CCVKEKYEMKELGDDHALELFS  292 (311)
Q Consensus       246 kr~LlVLDdV~~~----~~l~~l~~------~~~~-----------------------~~~~~~y~v~~L~~~ea~~Lf~  292 (311)
                      +.-+|+|||++..    ...+.+..      ..+.                       ...+.++.+++++.++-.+++.
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~  273 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIAR  273 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHH
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHH
Confidence            6678999999632    12222210      0000                       1123578899999999999998


Q ss_pred             Hhhc
Q 042778          293 RHAF  296 (311)
Q Consensus       293 ~~af  296 (311)
                      +.+-
T Consensus       274 ~~~~  277 (440)
T 2z4s_A          274 KMLE  277 (440)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8764

>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=97.93  E-value=3.7e-05  Score=69.94  Aligned_cols=145  Identities=12%  Similarity=0.128  Sum_probs=81.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc--CcCce-EEEecCccccCCCCChHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS--NFEGS-CFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F~~~-~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      ..+++|++..++.+...+..+.  ...+.|+|.+|+||||+|+.+++.+..  .+... ..+.    .+. ..+...+..
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~----~~~-~~~~~~~~~  108 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN----ASD-ERGISIVRE  108 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC----SSS-CCCHHHHTT
T ss_pred             HHHhhCCHHHHHHHHHHHhcCC--CCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEc----ccc-ccchHHHHH
Confidence            4678999999999999887542  233899999999999999999988542  12222 1222    111 223333222


Q ss_pred             HHHHHHhcCCC-CCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhh---c--cCCC----------------cCCceE
Q 042778          221 KLLSKLLQDGI-VIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLI---G--MLRN----------------CCVKEK  276 (311)
Q Consensus       221 ~ll~~l~~~~~-~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~---~--~~~~----------------~~~~~~  276 (311)
                       .+........ .... ......-..+.-+|++|+++.  ......|.   .  ....                ......
T Consensus       109 -~~~~~~~~~~~~~~~-~~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~  186 (353)
T 1sxj_D          109 -KVKNFARLTVSKPSK-HDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSK  186 (353)
T ss_dssp             -HHHHHHHSCCCCCCT-THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEE
T ss_pred             -HHHHHhhhcccccch-hhcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCce
Confidence             2222211100 0000 001111124557899999864  23333332   1  1110                112347


Q ss_pred             EEcCCCChHHHHHHHHHhhcC
Q 042778          277 YEMKELGDDHALELFSRHAFK  297 (311)
Q Consensus       277 y~v~~L~~~ea~~Lf~~~af~  297 (311)
                      +++++++.++..+.+...+-.
T Consensus       187 i~~~~~~~~~~~~~l~~~~~~  207 (353)
T 1sxj_D          187 FRFKALDASNAIDRLRFISEQ  207 (353)
T ss_dssp             EECCCCCHHHHHHHHHHHHHT
T ss_pred             EEeCCCCHHHHHHHHHHHHHH
Confidence            899999999999999887643

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.88  E-value=9.1e-05  Score=75.96  Aligned_cols=48  Identities=15%  Similarity=0.298  Sum_probs=40.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.++|++..+..+...|....  ...+.|+|.+|+||||||+.+++.+.
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~~l~  216 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQRIV  216 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHHh
Confidence            4678999999999999886432  33468999999999999999999863

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.87  E-value=7.3e-05  Score=70.96  Aligned_cols=49  Identities=14%  Similarity=0.241  Sum_probs=39.2

Q ss_pred             CCCccchhhhHHHHHHhhcc---------c-CCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGA---------E-SKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---------~-~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.+..++.|.+.+..         + ....+-+.|+|++|+|||+||+++++..
T Consensus       133 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          133 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             GGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            46789999998888876631         1 1225678999999999999999999986

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.85  E-value=0.0004  Score=64.78  Aligned_cols=146  Identities=17%  Similarity=0.255  Sum_probs=85.9

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      +++.|.+..+++|.+.+..           +-...+=|.++|++|.|||.||+++++.....|-.   +. ..+...+..
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~---v~-~s~l~sk~v  223 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIR---VS-GAELVQKYI  223 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEE---EE-GGGGSCSST
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceE---EE-hHHhhcccc
Confidence            5678999988888875532           11235678899999999999999999987665421   22 111111011


Q ss_pred             C-hHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH----------------HHHHhh----ccCCC--
Q 042778          214 G-LGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR----------------QIKSLI----GMLRN--  270 (311)
Q Consensus       214 ~-~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~----------------~l~~l~----~~~~~--  270 (311)
                      + -....+.++...                -....++|.+|+++..-                .+..++    +....  
T Consensus       224 Gese~~vr~lF~~A----------------r~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~  287 (405)
T 4b4t_J          224 GEGSRMVRELFVMA----------------REHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKN  287 (405)
T ss_dssp             THHHHHHHHHHHHH----------------HHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCC
T ss_pred             chHHHHHHHHHHHH----------------HHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCC
Confidence            1 112222222211                13467899999987310                111121    11110  


Q ss_pred             --------------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          271 --------------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       271 --------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                                          ...+..++++..+.++-.++|..+.=+-+ .+..++.+|++
T Consensus       288 V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~  348 (405)
T 4b4t_J          288 IKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAE  348 (405)
T ss_dssp             EEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHH
T ss_pred             eEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHH
Confidence                                24567899999999999999987753322 23346777664

>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=97.84  E-value=5.1e-05  Score=66.84  Aligned_cols=51  Identities=12%  Similarity=0.078  Sum_probs=37.5

Q ss_pred             CCCccchhhhHHHHHH-------hhcc-cCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIES-------LLGA-ESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~-------~L~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++|....++++..       .+.. .....+.+.|+|.+|+|||+||+++++....
T Consensus        32 ~~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~   90 (272)
T 1d2n_A           32 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNF   90 (272)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             hcCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            4567888777666665       2321 1334778999999999999999999998543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.82  E-value=0.0001  Score=68.58  Aligned_cols=51  Identities=14%  Similarity=0.247  Sum_probs=40.4

Q ss_pred             CCCccchhhhHHHHHHhhccc----------CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAE----------SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|.+..++.|..++...          ....+-+.|+|..|+|||+||+++++....
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~  174 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNA  174 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTC
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcC
Confidence            467899999999998877321          112467899999999999999999988643

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.82  E-value=6.8e-05  Score=66.76  Aligned_cols=52  Identities=17%  Similarity=0.265  Sum_probs=40.9

Q ss_pred             CCCccchhhhHHHHHHhhccc----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAE----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+..++.+.+.+...          ....+.+.|+|.+|+||||||+++++.....
T Consensus        20 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~   81 (297)
T 3b9p_A           20 WTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSAT   81 (297)
T ss_dssp             GGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCE
T ss_pred             HHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC
Confidence            457899999999998877421          1124678999999999999999999986543

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.81  E-value=6.6e-05  Score=69.11  Aligned_cols=52  Identities=17%  Similarity=0.291  Sum_probs=39.9

Q ss_pred             CCCccchhhhHHHHHHhhccc----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAE----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+..++.|.+.+...          ....+-|.|+|.+|+|||+||+++++.....
T Consensus        50 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~  111 (355)
T 2qp9_X           50 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST  111 (355)
T ss_dssp             GGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCE
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            457899999999998876311          1123468899999999999999999987543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.80  E-value=0.00043  Score=65.32  Aligned_cols=147  Identities=18%  Similarity=0.296  Sum_probs=85.7

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP  212 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~  212 (311)
                      -+++.|.+..+++|.+.+..           +-.-.+=|.++|++|.|||+||+++++.....|-   .+. ..++..+.
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~---~v~-~s~l~sk~  255 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFI---FSP-ASGIVDKY  255 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEE---EEE-GGGTCCSS
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEE---EEe-hhhhcccc
Confidence            35678999988888775532           1123577899999999999999999998765542   222 11111101


Q ss_pred             CCh-HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh-------------H---HHHHhh----ccCC--
Q 042778          213 GGL-GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF-------------R---QIKSLI----GMLR--  269 (311)
Q Consensus       213 ~~~-~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~-------------~---~l~~l~----~~~~--  269 (311)
                      .+- ....+.++..                .-....++|.+|+++..             .   .+..|+    +...  
T Consensus       256 ~Gese~~ir~~F~~----------------A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~  319 (437)
T 4b4t_L          256 IGESARIIREMFAY----------------AKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLG  319 (437)
T ss_dssp             SSHHHHHHHHHHHH----------------HHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTT
T ss_pred             chHHHHHHHHHHHH----------------HHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCC
Confidence            111 1122222111                11356789999998731             0   111121    1111  


Q ss_pred             C--------------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          270 N--------------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       270 ~--------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                      .                    ...+..++++..+.++-.++|..+.-+-. .+..++..|++
T Consensus       320 ~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~  381 (437)
T 4b4t_L          320 QTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVK  381 (437)
T ss_dssp             SSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHH
T ss_pred             CeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHH
Confidence            0                    12467788999999999999987764432 34456777664

>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=97.80  E-value=0.00016  Score=65.28  Aligned_cols=124  Identities=14%  Similarity=0.155  Sum_probs=74.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .++++|.+..++.+..++..+. -..++.+.|.+|+||||+|+++.+.+...   .+.+.    . . ..+...+.. ++
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~l~~~---~~~i~----~-~-~~~~~~i~~-~~   93 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHDVNAD---MMFVN----G-S-DCKIDFVRG-PL   93 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHHTTEE---EEEEE----T-T-TCCHHHHHT-HH
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHHhCCC---EEEEc----c-c-ccCHHHHHH-HH
Confidence            4678999999999999887432 24577888999999999999999887422   22232    1 1 233333322 22


Q ss_pred             HHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH---HHHHhhc-----cCCC----------------cCCceEEEc
Q 042778          224 SKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR---QIKSLIG-----MLRN----------------CCVKEKYEM  279 (311)
Q Consensus       224 ~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~---~l~~l~~-----~~~~----------------~~~~~~y~v  279 (311)
                      .......           .+.+++.+|+|||++...   ..+.|..     ....                .....++++
T Consensus        94 ~~~~~~~-----------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~  162 (324)
T 3u61_B           94 TNFASAA-----------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITF  162 (324)
T ss_dssp             HHHHHBC-----------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEEC
T ss_pred             HHHHhhc-----------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEe
Confidence            2211110           012477899999998753   3444421     0011                112357899


Q ss_pred             CCCChHHHHH
Q 042778          280 KELGDDHALE  289 (311)
Q Consensus       280 ~~L~~~ea~~  289 (311)
                      ++++.++-.+
T Consensus       163 ~~~~~~e~~~  172 (324)
T 3u61_B          163 GQPTDEDKIE  172 (324)
T ss_dssp             CCCCHHHHHH
T ss_pred             CCCCHHHHHH
Confidence            9999887433

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.78  E-value=7.6e-05  Score=61.42  Aligned_cols=43  Identities=19%  Similarity=0.228  Sum_probs=29.9

Q ss_pred             hhhHHHHHHhhcccC-CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          151 ESRVEEIESLLGAES-KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       151 ~~~~~~l~~~L~~~~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++.+.+++..-. .....+.|+|..|+||||||+++++.+.
T Consensus        20 ~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           20 NRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             HHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            334444444443211 2256899999999999999999999864

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.77  E-value=0.00063  Score=64.42  Aligned_cols=146  Identities=18%  Similarity=0.257  Sum_probs=86.0

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      .++.|.+..+++|.+.+..           +-.-.+-|.++|++|.|||+||+++++.....|-.   +. ..++..+..
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~---vs-~s~L~sk~v  284 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIR---VI-GSELVQKYV  284 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEE---EE-GGGGCCCSS
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEE---EE-hHHhhcccC
Confidence            5788999988888875432           11336778999999999999999999987655421   22 111111011


Q ss_pred             Ch-HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH----------------H----HHHhhccCCC--
Q 042778          214 GL-GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR----------------Q----IKSLIGMLRN--  270 (311)
Q Consensus       214 ~~-~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~----------------~----l~~l~~~~~~--  270 (311)
                      +- ....+.++..                .-....++|++|+++..-                .    +..+-+....  
T Consensus       285 Gesek~ir~lF~~----------------Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~  348 (467)
T 4b4t_H          285 GEGARMVRELFEM----------------ARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGN  348 (467)
T ss_dssp             SHHHHHHHHHHHH----------------HHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTT
T ss_pred             CHHHHHHHHHHHH----------------HHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCc
Confidence            11 1222222221                123467899999987310                1    1111111110  


Q ss_pred             --------------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          271 --------------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       271 --------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                                          ...+..++++..+.++-.++|..+.=+-. ...-++..|++
T Consensus       349 ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~  409 (467)
T 4b4t_H          349 IKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISR  409 (467)
T ss_dssp             EEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHH
T ss_pred             EEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHH
Confidence                                24577899999999999999987764322 23345666653

>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=97.77  E-value=0.00024  Score=68.28  Aligned_cols=51  Identities=22%  Similarity=0.370  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|.+..+++|.+++...           ....+-|.|+|.+|+|||+||+++++....
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~  264 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA  264 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSS
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCC
Confidence            346899999999998877532           233556899999999999999999988643

>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=97.76  E-value=1.4e-05  Score=68.30  Aligned_cols=58  Identities=16%  Similarity=0.203  Sum_probs=38.8

Q ss_pred             CCCccchh---hhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          144 KNQLVGVE---SRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       144 ~~~~vGr~---~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .++++|.+   ..+..+..++...  ..+.+.|+|.+|+||||||+.+++..........++.
T Consensus        27 ~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~   87 (242)
T 3bos_A           27 FTSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIP   87 (242)
T ss_dssp             TTTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             hhhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            35677633   4455555555432  3567899999999999999999998655433445555

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.74  E-value=0.00022  Score=72.09  Aligned_cols=48  Identities=23%  Similarity=0.289  Sum_probs=40.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.++|++..++.+.+.|...  ...-+.|+|.+|+||||||+.+++.+.
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~--~~~~vlL~G~~GtGKT~la~~la~~l~  232 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhcc--CCCCeEEEcCCCCCHHHHHHHHHHHHH
Confidence            467899999999999988743  234568999999999999999999753

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.74  E-value=0.00014  Score=66.21  Aligned_cols=47  Identities=26%  Similarity=0.291  Sum_probs=37.8

Q ss_pred             CCCccchhhhHHHHHHhh-cccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLL-GAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L-~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+++|.+..++.+.+.+ ..+  ....+.|+|..|+||||+|+.++..+
T Consensus        13 ~~~~vg~~~~~~~l~~~~~~~~--~~~~~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E           13 LNALSHNEELTNFLKSLSDQPR--DLPHLLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTT--CCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHhhCC--CCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            356899999999888888 433  22238999999999999999999864

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.73  E-value=1.4e-05  Score=63.64  Aligned_cols=48  Identities=19%  Similarity=0.220  Sum_probs=35.0

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +++|.+..++++.+.+..-.....-|.|+|..|+|||++|+++++...
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~   52 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT   52 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC
Confidence            578999888888887754222233477999999999999999988654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.68  E-value=0.00021  Score=68.30  Aligned_cols=49  Identities=16%  Similarity=0.317  Sum_probs=40.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+.+||++..++.+...|....  ..-+.|+|.+|+|||+||+.+++.+..
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~~--~~~~LL~G~pG~GKT~la~~la~~l~~  227 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQQIIN  227 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             CCCccCcHHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHHHHHh
Confidence            4579999999999999886432  334579999999999999999998644

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=97.61  E-value=0.0004  Score=60.32  Aligned_cols=50  Identities=20%  Similarity=0.291  Sum_probs=35.4

Q ss_pred             CCCccchhhhHHHHHHhhccc-C---------CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAE-S---------KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-~---------~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.+....++.++...- .         .-.+-+.|+|..|+||||||++++....
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~   74 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   74 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            457888887776666544310 0         0012389999999999999999998765

>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=97.60  E-value=0.00077  Score=64.38  Aligned_cols=52  Identities=19%  Similarity=0.295  Sum_probs=38.3

Q ss_pred             CCCccchhhhHHHHHHhhcc--c--------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA--E--------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~--------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+++|.+..++++.+++..  .        ..-.+-+.|+|++|+||||||++++++....
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~   76 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVP   76 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCC
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            45789999888777775532  1        0113348899999999999999999986543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.59  E-value=0.00033  Score=66.09  Aligned_cols=53  Identities=19%  Similarity=0.305  Sum_probs=40.8

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -.++.|.+..+++|.+.+..           +-...+-|.++|++|.|||+||+++++.....|
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f  243 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATF  243 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEE
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCE
Confidence            35778999998888875432           112366789999999999999999999876544

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.57  E-value=0.00014  Score=63.43  Aligned_cols=52  Identities=21%  Similarity=0.235  Sum_probs=38.0

Q ss_pred             CCCccchhhhHHHHHHhhcc---c-------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA---E-------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---~-------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -++++|.+..++++.+++..   .       ..-.+-+.|+|..|+||||||+++++.....
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~   72 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP   72 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCC
Confidence            45789999888777665432   1       0113458899999999999999999986443

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.55  E-value=0.00059  Score=69.10  Aligned_cols=147  Identities=16%  Similarity=0.241  Sum_probs=85.1

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP  212 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~  212 (311)
                      -+++.|.+..+++|.+++..           +-...+-|.++|++|+|||+||++++++...+|   +.+....-++. .
T Consensus       203 ~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~---~~v~~~~l~sk-~  278 (806)
T 3cf2_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFF---FLINGPEIMSK-L  278 (806)
T ss_dssp             GGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEE---EEEEHHHHHSS-C
T ss_pred             hhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeE---EEEEhHHhhcc-c
Confidence            45678999888888876532           112256799999999999999999999875543   22221000111 1


Q ss_pred             CC-hHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH-------------HHHHhh----c---cC---
Q 042778          213 GG-LGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR-------------QIKSLI----G---ML---  268 (311)
Q Consensus       213 ~~-~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~-------------~l~~l~----~---~~---  268 (311)
                      .+ .....+.                ..........++|+||+++..-             .+..|+    +   ..   
T Consensus       279 ~gese~~lr~----------------lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~  342 (806)
T 3cf2_A          279 AGESESNLRK----------------AFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVI  342 (806)
T ss_dssp             TTHHHHHHHH----------------HHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEE
T ss_pred             chHHHHHHHH----------------HHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEE
Confidence            11 1111111                1222234678899999986310             111111    0   00   


Q ss_pred             -----C---C--------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          269 -----R---N--------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       269 -----~---~--------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                           +   .        ...+..+++...+.++-.++|..+.-+.. ....++.+|++
T Consensus       343 VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~  401 (806)
T 3cf2_A          343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVAN  401 (806)
T ss_dssp             EEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHH
T ss_pred             EEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHH
Confidence                 0   0        13567889999999999999987753322 23445666653

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.54  E-value=5e-05  Score=60.54  Aligned_cols=47  Identities=23%  Similarity=0.250  Sum_probs=36.5

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +++|....++++.+.+..-.....-|.|+|..|+|||++|+++++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC
Confidence            57899999999988775433333457899999999999999999874

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.50  E-value=0.0007  Score=59.71  Aligned_cols=50  Identities=20%  Similarity=0.291  Sum_probs=36.5

Q ss_pred             CCCccchhhhHHHHHHhhccc-C---------CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAE-S---------KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-~---------~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.+..+.++.++...- .         .-.+-+.|+|..|+||||||++++....
T Consensus        39 ~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~   98 (278)
T 1iy2_A           39 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   98 (278)
T ss_dssp             GGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC
Confidence            567899988777776654321 0         0012289999999999999999998865

>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=97.50  E-value=0.00055  Score=62.25  Aligned_cols=134  Identities=13%  Similarity=0.224  Sum_probs=76.0

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHHH
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .+++|.+..++.|...+..+  ....+.++|..|+||||+|+.+++.+... +...+.-.+   .+. ..+...+.. ++
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g--~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~---~~~-~~~~~~ir~-~i   97 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN---ASD-DRGIDVVRN-QI   97 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC---TTS-CCSHHHHHT-HH
T ss_pred             HHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEc---Ccc-cccHHHHHH-HH
Confidence            45788888888888777643  33348999999999999999999985432 221111111   122 233333322 22


Q ss_pred             HHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhhc---cC-CC-----------------cCCceEEEcC
Q 042778          224 SKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLIG---ML-RN-----------------CCVKEKYEMK  280 (311)
Q Consensus       224 ~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~---~~-~~-----------------~~~~~~y~v~  280 (311)
                      ........          .+...+-++|+|+++.  .+..+.|..   .+ ..                 ......+.+.
T Consensus        98 ~~~~~~~~----------~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~  167 (340)
T 1sxj_C           98 KDFASTRQ----------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQ  167 (340)
T ss_dssp             HHHHHBCC----------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECC
T ss_pred             HHHHhhcc----------cCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEecc
Confidence            22211000          0123467888998864  233333321   10 00                 1223478899


Q ss_pred             CCChHHHHHHHHHhh
Q 042778          281 ELGDDHALELFSRHA  295 (311)
Q Consensus       281 ~L~~~ea~~Lf~~~a  295 (311)
                      +++.++..+.+...+
T Consensus       168 ~l~~~~~~~~l~~~~  182 (340)
T 1sxj_C          168 PLPQEAIERRIANVL  182 (340)
T ss_dssp             CCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999888877655

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.48  E-value=0.00097  Score=62.58  Aligned_cols=53  Identities=26%  Similarity=0.428  Sum_probs=40.6

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -+++.|.+..+++|.+.+..           +-.-.+=|.++|++|.|||.||+++++.....|
T Consensus       181 ~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~f  244 (437)
T 4b4t_I          181 YSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATF  244 (437)
T ss_dssp             GGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEE
T ss_pred             ceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCE
Confidence            35677899988888775532           112256799999999999999999999876554

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.48  E-value=0.00022  Score=63.63  Aligned_cols=51  Identities=12%  Similarity=0.315  Sum_probs=39.8

Q ss_pred             CCccchhhhHHHHHHhhcccC------CC-eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLGAES------KD-VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~------~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..++|.+..++.+...+....      +. ...+.|+|..|+||||+|+.+++.....
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~   74 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT   74 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC
Confidence            467899988888887775421      11 4689999999999999999999986443

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.43  E-value=0.01  Score=52.23  Aligned_cols=51  Identities=20%  Similarity=0.155  Sum_probs=34.5

Q ss_pred             CCCccchhhhHHHHHHhhcc--c--------C-CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGA--E--------S-KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~--~--------~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.++.|.+..+++|.+.+..  .        + .-.+-++|+|.+|.||||||++++.....
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~   70 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGL   70 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTC
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCC
Confidence            35678888887777764321  0        0 11122999999999999999999987644

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.40  E-value=9.2e-05  Score=67.15  Aligned_cols=53  Identities=23%  Similarity=0.325  Sum_probs=42.7

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+++|++..++.+..++...   ......+.|+|.+|+|||+||+++++.....|
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~   83 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSANI   83 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCE
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCe
Confidence            457899999999999888642   23356789999999999999999998865443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.40  E-value=0.00076  Score=68.16  Aligned_cols=48  Identities=17%  Similarity=0.317  Sum_probs=40.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.+||++..++.+...|....  ..-+.++|.+|+|||++|+.+++.+.
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~--~~~vLL~G~pGtGKT~la~~la~~l~  226 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQQII  226 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCC--CCCeEEECCCCCCHHHHHHHHHHHHh
Confidence            4579999999999999886432  33478999999999999999999863

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.35  E-value=0.00022  Score=63.75  Aligned_cols=30  Identities=30%  Similarity=0.485  Sum_probs=25.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+.+.++|++|+|||+||+++++.....|
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~~~~   64 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMGINP   64 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHTCCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            356889999999999999999999875443

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.35  E-value=0.00054  Score=65.11  Aligned_cols=52  Identities=25%  Similarity=0.274  Sum_probs=39.4

Q ss_pred             CCCccchhhhHHHHHHhhc---ccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLG---AESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .++++|.+..++.+..++.   .+....+-+.++|++|+|||+||+++++.....
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~   90 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSK   90 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTT
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCC
Confidence            4689999988776655443   222224568899999999999999999987643

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.34  E-value=0.0026  Score=61.08  Aligned_cols=51  Identities=20%  Similarity=0.309  Sum_probs=37.8

Q ss_pred             CCCCccchhhhHHHHHHhhcc--cC--------CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          143 NKNQLVGVESRVEEIESLLGA--ES--------KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       143 ~~~~~vGr~~~~~~l~~~L~~--~~--------~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+++|.+..+.++.++...  ..        .-.+-+.|+|.+|+||||||++++....
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~   89 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   89 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            367899999887777765432  10        0123389999999999999999998865

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.29  E-value=0.00058  Score=61.50  Aligned_cols=51  Identities=16%  Similarity=0.225  Sum_probs=33.9

Q ss_pred             hHHHHHHhhcccCC-CeEEEEEeccCcchhHHHHHHHHHhhc-cCcCceEEEe
Q 042778          153 RVEEIESLLGAESK-DVYALGIWGIGGIDRTTIARAIFNKIS-SNFEGSCFLQ  203 (311)
Q Consensus       153 ~~~~l~~~L~~~~~-~~~vi~I~GmgGiGKTtLA~~v~~~~~-~~F~~~~wv~  203 (311)
                      .+..+.+++..... ....+.|+|..|+|||+||.++++... ..-..+.++.
T Consensus       136 ~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          136 AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             HHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             HHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            34444455543222 246788999999999999999999865 4433344554

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.25  E-value=0.0028  Score=56.93  Aligned_cols=127  Identities=6%  Similarity=0.033  Sum_probs=74.9

Q ss_pred             chhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh---ccCcCceEEEecCccccCCCCChHHHHHHHHHH
Q 042778          149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI---SSNFEGSCFLQNVREESQRPGGLGFLQQKLLSK  225 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~---~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~  225 (311)
                      |.+..++.|...+..+.  .+...++|+.|.||||+|+.+.+..   .........+.    .+....++..+. .++..
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~----~~~~~~~id~ir-~li~~   73 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEID----PEGENIGIDDIR-TIKDF   73 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEEC----CSSSCBCHHHHH-HHHHH
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEc----CCcCCCCHHHHH-HHHHH
Confidence            44556677777776443  6789999999999999999998752   11122334443    111023333332 34433


Q ss_pred             HhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhh----ccCCC----------------cCCceEEEcCCCC
Q 042778          226 LLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLI----GMLRN----------------CCVKEKYEMKELG  283 (311)
Q Consensus       226 l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~----~~~~~----------------~~~~~~y~v~~L~  283 (311)
                      +....            ..+++-++|+|+++.  ....+.|+    .++..                .... ++++++|+
T Consensus        74 ~~~~p------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~l~  140 (305)
T 2gno_A           74 LNYSP------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVVNV  140 (305)
T ss_dssp             HTSCC------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEECCC
T ss_pred             Hhhcc------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCCCC
Confidence            32111            124566888999974  34455553    11111                1223 89999999


Q ss_pred             hHHHHHHHHHhh
Q 042778          284 DDHALELFSRHA  295 (311)
Q Consensus       284 ~~ea~~Lf~~~a  295 (311)
                      +++..+.+.+.+
T Consensus       141 ~~~i~~~L~~~~  152 (305)
T 2gno_A          141 PKEFRDLVKEKI  152 (305)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999988775

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.22  E-value=0.0046  Score=56.05  Aligned_cols=43  Identities=16%  Similarity=0.162  Sum_probs=30.6

Q ss_pred             hhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          151 ESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       151 ~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +...+.+...+..+ .-...+.++|..|+||||+|+.+.+.+..
T Consensus         8 ~~~~~~l~~~i~~~-~~~~a~L~~G~~G~GKt~~a~~la~~l~~   50 (334)
T 1a5t_A            8 RPDFEKLVASYQAG-RGHHALLIQALPGMGDDALIYALSRYLLC   50 (334)
T ss_dssp             HHHHHHHHHHHHTT-CCCSEEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcC-CcceeEEEECCCCchHHHHHHHHHHHHhC
Confidence            34455555555432 22457899999999999999999998543

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.09  E-value=0.0028  Score=53.23  Aligned_cols=33  Identities=12%  Similarity=0.011  Sum_probs=25.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.++.|+|.+|+||||||..+..  . .-..++|+.
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~--~-~~~~v~~i~   52 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL--L-SGKKVAYVD   52 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH--H-HCSEEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--H-cCCcEEEEE
Confidence            45899999999999999999887  2 123456666

>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=97.07  E-value=0.00034  Score=63.67  Aligned_cols=51  Identities=22%  Similarity=0.346  Sum_probs=39.0

Q ss_pred             CCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..++|.+..++.+...+..+   ......+.|+|..|+||||||+.+++.+...
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~   78 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN   78 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            46788887777777666532   2234679999999999999999999987543

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.07  E-value=0.00024  Score=62.17  Aligned_cols=53  Identities=21%  Similarity=0.261  Sum_probs=39.2

Q ss_pred             CCCccchhhhHHHHHHhhcc----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+++|.+..++.+.+++..          +....+-+.|+|.+|+|||+||+++++.....|
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~   72 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPF   72 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCC
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCE
Confidence            46789999888888776542          111123477999999999999999999865443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=97.06  E-value=0.00034  Score=62.20  Aligned_cols=51  Identities=16%  Similarity=0.246  Sum_probs=39.5

Q ss_pred             CCCccchhhhHHHHHHhhcc------------cCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGA------------ESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~------------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++|.+..++.+...+..            .......+.|+|.+|+|||+||+.+++....
T Consensus        14 ~~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   76 (310)
T 1ofh_A           14 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (310)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            35689999999888877753            0122456789999999999999999998743

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.02  E-value=0.0006  Score=59.58  Aligned_cols=49  Identities=18%  Similarity=0.134  Sum_probs=35.3

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++++|.+..+..+.+.+..-......|.|+|..|+|||+||+.+++...
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSS   54 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTST
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcC
Confidence            4688999888888876654222234677999999999999999998754

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.01  E-value=0.00073  Score=61.15  Aligned_cols=24  Identities=17%  Similarity=0.145  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -+++.|+|++|+||||||..+...
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            356789999999999999999876

>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=96.96  E-value=0.00039  Score=52.90  Aligned_cols=62  Identities=10%  Similarity=0.010  Sum_probs=45.7

Q ss_pred             CcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeCCCCCCCcchHHHHHHHHhccceeeeeccCcccccchHHHHHHH
Q 042778           17 HKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKI   96 (311)
Q Consensus        17 ~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i   96 (311)
                      ..|.+||||..+|.    .+.|...|.+.|+..- |              +.|+.|.+.|++.+++-.+|.||..|+..+
T Consensus         3 ~~~~lFISh~~~d~----~~~L~~~l~~~~f~~~-~--------------~~I~~~~~vIvL~G~~t~~s~wv~~EI~~A   63 (111)
T 1eiw_A            3 AEIRLYITEGEVED----YRVFLERLEQSGLEWR-P--------------ATPEDADAVIVLAGLWGTRRDEILGAVDLA   63 (111)
T ss_dssp             CCEEEEECCCCSHH----HHHHHHHHHHHCSCEE-E--------------CCSSSCSEEEEEGGGTTTSHHHHHHHHHHH
T ss_pred             ceEEEEEecccHhH----HHHHHHHHhCCCCeee-c--------------CccccCCEEEEEeCCCcCCChHHHHHHHHH
Confidence            57999999999993    3344444445555332 3              557889999999999999999999998544


Q ss_pred             H
Q 042778           97 L   97 (311)
Q Consensus        97 ~   97 (311)
                      .
T Consensus        64 ~   64 (111)
T 1eiw_A           64 R   64 (111)
T ss_dssp             T
T ss_pred             H
Confidence            3

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=96.92  E-value=0.00045  Score=56.37  Aligned_cols=26  Identities=12%  Similarity=0.161  Sum_probs=23.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+|.|.|++|+||||+|+.+.++...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~   29 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPE   29 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            47899999999999999999987643

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.87  E-value=0.0011  Score=55.50  Aligned_cols=44  Identities=20%  Similarity=0.291  Sum_probs=33.4

Q ss_pred             hhhhHHHHHHhhccc-CCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          150 VESRVEEIESLLGAE-SKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       150 r~~~~~~l~~~L~~~-~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++..++++.+.+... .....+|+|.|..|.|||||++.+...+.
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            455667777666532 23468999999999999999999987653

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.84  E-value=0.0011  Score=55.78  Aligned_cols=41  Identities=12%  Similarity=0.193  Sum_probs=30.5

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++|.+.+........+|+|.|..|.|||||++.+...+.
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            44455555543334578999999999999999999887654

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.84  E-value=0.00061  Score=55.02  Aligned_cols=25  Identities=12%  Similarity=0.086  Sum_probs=22.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|.|.|+.|+||||+|+.+.++..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999988764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.82  E-value=0.0009  Score=63.00  Aligned_cols=53  Identities=17%  Similarity=0.294  Sum_probs=40.7

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -.++.|.+..+++|.+.+..           +-.-.+-|.++|++|+|||+||+++++.....|
T Consensus       171 ~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~  234 (428)
T 4b4t_K          171 YADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAF  234 (428)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEE
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            35778999988888775532           112356789999999999999999999876544

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=96.78  E-value=0.0011  Score=60.91  Aligned_cols=47  Identities=13%  Similarity=0.133  Sum_probs=35.8

Q ss_pred             CccchhhhHHHHHHhhcc-------------cCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVGVESRVEEIESLLGA-------------ESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~-------------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|.+..++.+...+..             .......+.++|.+|+|||++|+++++..
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            468888888888776620             01124568999999999999999998865

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.77  E-value=0.00061  Score=54.86  Aligned_cols=23  Identities=17%  Similarity=0.302  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|+|.|++|+||||+|+.+ .+.
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HHT
T ss_pred             cEEEEECCCCCCHHHHHHHH-HHC
Confidence            47899999999999999999 543

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.75  E-value=0.0011  Score=60.86  Aligned_cols=49  Identities=20%  Similarity=0.313  Sum_probs=36.8

Q ss_pred             cchhhhHHHHHHhhcc--cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          148 VGVESRVEEIESLLGA--ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~--~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      |+.+..++++.+.|..  ..+....|.|+|+.|.||||+++.++..+...|
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~~~f   52 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINEKY   52 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            5556666777766643  234577899999999999999999998865554

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.72  E-value=0.00081  Score=55.23  Aligned_cols=26  Identities=12%  Similarity=0.256  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.|.|+|+.|+||||+|+.+.++..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35788999999999999999998764

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.71  E-value=0.00082  Score=56.18  Aligned_cols=26  Identities=23%  Similarity=0.349  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|+|+.|+||||+|+.+...+.
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            45899999999999999999998763

>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=96.69  E-value=0.014  Score=53.52  Aligned_cols=50  Identities=16%  Similarity=0.127  Sum_probs=34.8

Q ss_pred             HHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          154 VEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...|..+|. .+-..-.++.|+|.+|+||||||..+.......=..++|+.
T Consensus        46 ~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId   96 (356)
T 3hr8_A           46 SLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFID   96 (356)
T ss_dssp             CHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            345555565 22233579999999999999999999887543323456776

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.68  E-value=0.00094  Score=59.96  Aligned_cols=48  Identities=15%  Similarity=0.239  Sum_probs=38.1

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.++|....+.++.+.+..-......|.|+|..|+|||++|+++++..
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            468999999999988876433333457799999999999999999864

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.66  E-value=0.0016  Score=58.69  Aligned_cols=49  Identities=12%  Similarity=0.198  Sum_probs=39.0

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...++|++..+..+...+..+    .-+.++|.+|+|||+||+.+.+.....|
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~~----~~vll~G~pGtGKT~la~~la~~~~~~~   74 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICTG----GHILLEGVPGLAKTLSVNTLAKTMDLDF   74 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHT----CCEEEESCCCHHHHHHHHHHHHHTTCCE
T ss_pred             ccceeCcHHHHHHHHHHHHcC----CeEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            357899998888887776543    2588999999999999999999765443

>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=96.66  E-value=0.011  Score=54.07  Aligned_cols=50  Identities=16%  Similarity=0.176  Sum_probs=34.0

Q ss_pred             HHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          154 VEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...|..+|. .+-..-.++.|+|.+|+||||||..+.......=..++|+.
T Consensus        46 ~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~   96 (349)
T 2zr9_A           46 SISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFID   96 (349)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            334555554 22223568999999999999999998876543323567776

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.63  E-value=0.017  Score=53.23  Aligned_cols=50  Identities=20%  Similarity=0.184  Sum_probs=33.8

Q ss_pred             HHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          154 VEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...|..+|. .+-..-.++.|+|.+|+||||||..+.......=..++|+.
T Consensus        59 ~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~  109 (366)
T 1xp8_A           59 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID  109 (366)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEE
Confidence            344555554 22122457888999999999999988877543334577887

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.58  E-value=0.0024  Score=57.03  Aligned_cols=29  Identities=17%  Similarity=0.172  Sum_probs=24.8

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .....+|+|.|..|+||||||+.+...+.
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            34578999999999999999998887654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.51  E-value=0.0015  Score=53.09  Aligned_cols=22  Identities=23%  Similarity=0.238  Sum_probs=20.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5789999999999999999987

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.50  E-value=0.0014  Score=52.94  Aligned_cols=26  Identities=15%  Similarity=0.249  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|+|.|+.|+||||+|+.+.+++.
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHhC
Confidence            56899999999999999999998754

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.50  E-value=0.0011  Score=53.67  Aligned_cols=25  Identities=20%  Similarity=0.324  Sum_probs=22.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|+|+|+.|+|||||++.+.....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4699999999999999999998754

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.47  E-value=0.0014  Score=53.94  Aligned_cols=24  Identities=33%  Similarity=0.271  Sum_probs=21.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|+.|.|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999876

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.45  E-value=0.0022  Score=53.55  Aligned_cols=25  Identities=24%  Similarity=0.425  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|.|+.|.|||||++.+....
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhh
Confidence            5689999999999999999998876

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=96.44  E-value=0.0012  Score=54.10  Aligned_cols=25  Identities=20%  Similarity=0.359  Sum_probs=22.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.|.|+|+.|+||||+|+.+.++.
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            4578899999999999999998875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.42  E-value=0.0018  Score=53.17  Aligned_cols=26  Identities=15%  Similarity=0.220  Sum_probs=23.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+|.|.|+.|+||||+|+.+.+++..
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            47899999999999999999998653

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.41  E-value=0.016  Score=52.80  Aligned_cols=48  Identities=15%  Similarity=0.178  Sum_probs=33.1

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc------CcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS------NFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~------~F~~~~wv~  203 (311)
                      .|..+|..+-..-.++.|+|.+|+||||||..+......      .=..++|+.
T Consensus       110 ~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~  163 (343)
T 1v5w_A          110 EFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID  163 (343)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             hHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            344555433234679999999999999999998876322      123567877

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=96.40  E-value=0.0026  Score=58.52  Aligned_cols=51  Identities=14%  Similarity=0.158  Sum_probs=37.5

Q ss_pred             CCCccchhhhHHHHHHhhc----c------------------------cCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLG----A------------------------ESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~----~------------------------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++|.+..++.|...+.    .                        .......+.++|.+|+|||+||+.+++....
T Consensus        20 ~~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~   98 (376)
T 1um8_A           20 DNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDI   98 (376)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             hhHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3467899888887776652    0                        0112346889999999999999999998743

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.38  E-value=0.0021  Score=52.93  Aligned_cols=25  Identities=16%  Similarity=0.185  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|+.|+||||+|+.+.++.
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            5689999999999999999998876

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.38  E-value=0.0017  Score=53.83  Aligned_cols=24  Identities=29%  Similarity=0.538  Sum_probs=21.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .|+|.|+.|+||||+|+.+.+.+.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999998764

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=96.35  E-value=0.0037  Score=54.02  Aligned_cols=41  Identities=15%  Similarity=0.047  Sum_probs=29.6

Q ss_pred             hhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          152 SRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       152 ~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+.++...+.........|+|.|+.|+||||+|+.+.++.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           13 DLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             HHHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34444444333333457789999999999999999998765

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=96.35  E-value=0.0014  Score=53.66  Aligned_cols=25  Identities=20%  Similarity=0.325  Sum_probs=21.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|.|.|+.|+||||+|+.+..+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            3589999999999999999988753

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.34  E-value=0.0022  Score=53.58  Aligned_cols=27  Identities=19%  Similarity=0.272  Sum_probs=24.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+|+|.|+.|.||||||+.+...+.
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            467999999999999999999998865

>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=96.33  E-value=0.0038  Score=60.60  Aligned_cols=53  Identities=25%  Similarity=0.345  Sum_probs=38.5

Q ss_pred             CCCccchhhhHHHHHHhhcc----cCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGA----ESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+.+|.+.....+.+.+..    .......+.|+|.+|+||||||+.++......|
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~  136 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRKF  136 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCEE
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCCe
Confidence            34578888777776554432    112356899999999999999999999875443

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.32  E-value=0.0017  Score=53.18  Aligned_cols=25  Identities=16%  Similarity=0.332  Sum_probs=22.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|.|.|+.|+||||+|+.+.++..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4799999999999999999998765

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.32  E-value=0.0017  Score=54.12  Aligned_cols=25  Identities=16%  Similarity=0.336  Sum_probs=22.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|.|+.|.||||||+.+...+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999998875

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.32  E-value=0.0023  Score=55.82  Aligned_cols=25  Identities=20%  Similarity=0.145  Sum_probs=22.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|.|+|+.|+||||||+.++.+..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999988753

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.31  E-value=0.0018  Score=52.67  Aligned_cols=24  Identities=25%  Similarity=0.439  Sum_probs=21.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .|.|.|+.|.||||+|+.+..+..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcC
Confidence            589999999999999999998754

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.31  E-value=0.0018  Score=53.19  Aligned_cols=26  Identities=23%  Similarity=0.359  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -++++|+|+.|+|||||++.+.....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            35899999999999999999988654

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.31  E-value=0.0024  Score=51.91  Aligned_cols=25  Identities=12%  Similarity=0.333  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|+.|.||||+++.+....
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998764

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.28  E-value=0.0037  Score=51.34  Aligned_cols=27  Identities=22%  Similarity=0.284  Sum_probs=23.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+|.|.|+.|.||||+++.+......
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            578999999999999999999987643

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.27  E-value=0.0017  Score=53.02  Aligned_cols=26  Identities=19%  Similarity=0.262  Sum_probs=18.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|+.|+||||+|+.+.+++.
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            35799999999999999999988754

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.26  E-value=0.003  Score=52.61  Aligned_cols=27  Identities=15%  Similarity=0.194  Sum_probs=23.8

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ....+|+|.|+.|+||||+|+.+.++.
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            346799999999999999999998875

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.25  E-value=0.0027  Score=52.63  Aligned_cols=26  Identities=27%  Similarity=0.281  Sum_probs=23.3

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +...+|+|.|+.|+||||+|+.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            34789999999999999999999875

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.23  E-value=0.0028  Score=55.01  Aligned_cols=28  Identities=11%  Similarity=0.322  Sum_probs=24.0

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|+|.|+.|.||||+|+.+...+.
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3467999999999999999999988754

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=96.22  E-value=0.0024  Score=52.64  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|+.|+||||+|+.+.++
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999999887

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.22  E-value=0.0028  Score=52.06  Aligned_cols=25  Identities=20%  Similarity=0.171  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|.|+.|+||||+|+.+.+..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998865

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.21  E-value=0.0027  Score=51.99  Aligned_cols=25  Identities=20%  Similarity=0.166  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...|+|.|+.|+||||+|+.+.++.
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998875

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.20  E-value=0.0028  Score=50.94  Aligned_cols=24  Identities=8%  Similarity=0.177  Sum_probs=21.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .|+|.|+.|+||||+|+.+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999988753

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=96.20  E-value=0.0019  Score=52.18  Aligned_cols=25  Identities=20%  Similarity=0.278  Sum_probs=22.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|.|.|+.|+||||+|+.+.++..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999998753

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.19  E-value=0.0028  Score=52.16  Aligned_cols=23  Identities=17%  Similarity=0.254  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|.|+.|.|||||++.+...
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~~   25 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAAQ   25 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhcc
Confidence            47899999999999999999863

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.19  E-value=0.0037  Score=49.93  Aligned_cols=37  Identities=11%  Similarity=0.280  Sum_probs=27.4

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .-..++|+|..|.|||||++.++......=...+++.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            3458999999999999999999997644201145554

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.18  E-value=0.0023  Score=52.75  Aligned_cols=25  Identities=20%  Similarity=0.153  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|+.|+||||+|+.+.+..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998875

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.17  E-value=0.0066  Score=57.63  Aligned_cols=34  Identities=21%  Similarity=0.492  Sum_probs=26.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCc-CceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~  203 (311)
                      .++|+|..|+|||||+..+......++ +.++++.
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~~  187 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFAG  187 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEEE
T ss_pred             EEEEECCCCCCccHHHHHHHhhhhhccCcEEEEee
Confidence            589999999999999999988765544 3344443

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.17  E-value=0.0051  Score=51.19  Aligned_cols=28  Identities=18%  Similarity=0.191  Sum_probs=24.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+|.|.|+.|+||||+|+.+.+++...
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            3589999999999999999999986543

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.14  E-value=0.0025  Score=52.66  Aligned_cols=26  Identities=19%  Similarity=0.152  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|+|.|+.|+||||+|+.+.++..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35899999999999999999998763

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=96.13  E-value=0.0028  Score=52.85  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=20.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .+|+|.|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999987

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.13  E-value=0.0018  Score=60.00  Aligned_cols=27  Identities=15%  Similarity=-0.064  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -..++|+|..|+|||||++.+.+.+..
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i~~  200 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSIAY  200 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHHhh
Confidence            358899999999999999999887544

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=96.12  E-value=0.0034  Score=52.53  Aligned_cols=26  Identities=23%  Similarity=0.538  Sum_probs=22.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|+|+|+.|.||||||+.+....
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999988754

>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=96.11  E-value=0.054  Score=51.02  Aligned_cols=27  Identities=22%  Similarity=0.196  Sum_probs=23.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+|.++|.+|+||||++..++..+..
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~  126 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQK  126 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHH
Confidence            689999999999999999998876443

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=96.10  E-value=0.013  Score=55.76  Aligned_cols=88  Identities=16%  Similarity=0.198  Sum_probs=55.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHHHHHhcC-------CC-----CCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQD-------GI-----VIP  234 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~-------~~-----~~~  234 (311)
                      -..++|.|-.|+|||+|+..+.+.+.. +-+.++|+-    +.++.....++.+.+...-...       ..     ..+
T Consensus       165 Gqr~gIfgg~GvGKT~L~~~l~~~~a~~~~~v~V~~~----iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d  240 (498)
T 1fx0_B          165 GGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGG----VGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMN  240 (498)
T ss_dssp             TCCEEEEECSSSSHHHHHHHHHHHTTTTCSSCEEEEE----ESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTT
T ss_pred             CCeEEeecCCCCCchHHHHHHHHHHHhhCCCEEEEEE----cccCcHHHHHHHHhhhcccccccccccccceEEEEeCCC
Confidence            346899999999999999999988643 446667775    4443445666666665431111       00     111


Q ss_pred             C--------H---HHHHHHhC---CCeEEEEEecCCChH
Q 042778          235 D--------I---ALSFRQLS---RRKVLIVLDDVTCFR  259 (311)
Q Consensus       235 ~--------~---~~l~~~L~---~kr~LlVLDdV~~~~  259 (311)
                      +        .   -.+.++++   ++.+||++||+....
T Consensus       241 ~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~DsitR~A  279 (498)
T 1fx0_B          241 EPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFRFV  279 (498)
T ss_dssp             SCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHHHH
Confidence            1        0   23445554   589999999996543

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=96.09  E-value=0.0032  Score=56.88  Aligned_cols=48  Identities=17%  Similarity=0.171  Sum_probs=33.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|.+..+..+...+....  ..-+.|+|.+|+|||+||+.+++...
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             chhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHHhCc
Confidence            3468898875554433332111  22388999999999999999999754

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.09  E-value=0.0035  Score=51.38  Aligned_cols=26  Identities=15%  Similarity=0.123  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|+|.|+.|+||||+|+.+.++..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999988753

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.07  E-value=0.0032  Score=53.26  Aligned_cols=24  Identities=21%  Similarity=0.332  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|+|.|+.|+||||+|+.+...+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999987753

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.07  E-value=0.0025  Score=53.42  Aligned_cols=26  Identities=15%  Similarity=0.441  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|.|+|+.|+|||||++.+.....
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            56899999999999999999988763

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=96.05  E-value=0.0036  Score=52.09  Aligned_cols=26  Identities=19%  Similarity=0.194  Sum_probs=23.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|+.|+||||+|+.+.....
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999988753

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=96.04  E-value=0.0023  Score=53.24  Aligned_cols=29  Identities=21%  Similarity=0.435  Sum_probs=24.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      |.|.|+|+.|+|||||++.+..+....|.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~~~   30 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDSFG   30 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCCeE
Confidence            45789999999999999999887655553

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.03  E-value=0.0034  Score=52.19  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|.|+.|+|||||++.+....
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3589999999999999999998764

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=96.03  E-value=0.0034  Score=52.41  Aligned_cols=22  Identities=36%  Similarity=0.477  Sum_probs=20.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .+|+|.|+.|.||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=96.03  E-value=0.0035  Score=52.72  Aligned_cols=27  Identities=19%  Similarity=0.354  Sum_probs=23.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++|+|+.|+|||||++.+......
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            568999999999999999999987654

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.02  E-value=0.0037  Score=51.32  Aligned_cols=24  Identities=25%  Similarity=0.480  Sum_probs=21.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|+|.|+.|+||||+|+.+.+++.
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~   25 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLK   25 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999998764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.01  E-value=0.0035  Score=52.09  Aligned_cols=25  Identities=20%  Similarity=0.364  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+++|+|+.|+|||||++.+....
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3589999999999999999998875

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=95.98  E-value=0.0053  Score=57.98  Aligned_cols=53  Identities=17%  Similarity=0.275  Sum_probs=38.7

Q ss_pred             CCCccchhhhHHHHHHhhccc------------CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE------------SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...++|.+..++.+...+...            ....+-|.++|++|+||||+|++++......|
T Consensus        14 d~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~   78 (444)
T 1g41_A           14 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   78 (444)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCc
Confidence            356889888887776655211            01245688999999999999999999865544

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=95.98  E-value=0.0036  Score=52.96  Aligned_cols=26  Identities=15%  Similarity=0.188  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|.|+.|+||||+|+.+.+++.
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            35789999999999999999988763

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=95.97  E-value=0.0052  Score=51.35  Aligned_cols=28  Identities=11%  Similarity=0.201  Sum_probs=24.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+|+|.|+.|+||||+|+.+.+++...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~   36 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCAA   36 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            4689999999999999999999886543

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=95.97  E-value=0.0041  Score=54.32  Aligned_cols=25  Identities=12%  Similarity=0.403  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|.|.|++|+||||+|+.+...+
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999874

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.95  E-value=0.0074  Score=52.38  Aligned_cols=26  Identities=27%  Similarity=0.276  Sum_probs=23.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|++|.||||+|+.+.....
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            67899999999999999999988764

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.94  E-value=0.0045  Score=51.69  Aligned_cols=26  Identities=23%  Similarity=0.374  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|+|.|+.|+||||+|+.+.+..
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            36799999999999999999998763

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.94  E-value=0.007  Score=53.77  Aligned_cols=26  Identities=27%  Similarity=0.350  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|.|.|++|+||||+|+.+..+.
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            36789999999999999999998865

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.93  E-value=0.0045  Score=51.81  Aligned_cols=27  Identities=26%  Similarity=0.426  Sum_probs=23.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+|+|.|..|.|||||++.+...+.
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999888654

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=95.91  E-value=0.0064  Score=49.76  Aligned_cols=29  Identities=10%  Similarity=0.081  Sum_probs=24.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..++++|.|..|.|||||+..+...+...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~~   31 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVRE   31 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHhc
Confidence            36789999999999999999999876543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.91  E-value=0.0034  Score=51.15  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=19.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      -.+++|+|..|.|||||++.++
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHc
Confidence            4689999999999999999644

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.89  E-value=0.019  Score=54.53  Aligned_cols=88  Identities=15%  Similarity=0.236  Sum_probs=53.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEecCccccCCCCChHHHHHHHHHHHhcC------CC-----CCCC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQD------GI-----VIPD  235 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~------~~-----~~~~  235 (311)
                      -..++|.|-.|+|||+|+..+.+.+.. +-+.++++-    +.++.....++.+.+...-...      ..     ..+.
T Consensus       153 GQr~~Ifgg~G~GKT~L~~~i~~~~~~~~~~v~V~~~----iGER~rEv~e~~~~~~~~~~l~~~~~~~rtvvV~~t~d~  228 (482)
T 2ck3_D          153 GGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG----VGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNE  228 (482)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHTTTTCSSEEEEEE----ESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTS
T ss_pred             CCeeeeecCCCCChHHHHHHHHHhhHhhCCCEEEEEE----CCCcchHHHHHHHHhhhccccccccCCceEEEEEECCCC
Confidence            347899999999999999999887643 335566655    4332344566666665432111      10     1111


Q ss_pred             --H---------HHHHHHh---CCCeEEEEEecCCChH
Q 042778          236 --I---------ALSFRQL---SRRKVLIVLDDVTCFR  259 (311)
Q Consensus       236 --~---------~~l~~~L---~~kr~LlVLDdV~~~~  259 (311)
                        .         -.+-+++   +++.+||++||+....
T Consensus       229 p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~DsitR~A  266 (482)
T 2ck3_D          229 PPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFT  266 (482)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHHHH
Confidence              0         2222333   4699999999996543

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.88  E-value=0.0044  Score=53.45  Aligned_cols=25  Identities=20%  Similarity=0.270  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|+|+.|.|||||++.+.+++
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999999999999999764

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=95.87  E-value=0.0046  Score=55.79  Aligned_cols=29  Identities=21%  Similarity=0.429  Sum_probs=23.8

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++.++|+|.|=||+||||.|..+.--+..
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~   74 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSI   74 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHH
Confidence            35899999999999999999887775433

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.87  E-value=0.0053  Score=58.95  Aligned_cols=45  Identities=16%  Similarity=0.061  Sum_probs=36.7

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++|.+..++.+...+..+    .-|.|+|.+|+|||+||+++++...
T Consensus        22 ~~ivGq~~~i~~l~~al~~~----~~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHT----CEEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             hhhHHHHHHHHHHHHHHhcC----CeeEeecCchHHHHHHHHHHHHHHh
Confidence            46889998888777766543    3688999999999999999998763

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.87  E-value=0.0039  Score=52.06  Aligned_cols=27  Identities=7%  Similarity=0.104  Sum_probs=23.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+|+|.|+.|+||||+|+.+.+++..
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~   36 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKN   36 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999999999987544

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.86  E-value=0.0043  Score=53.92  Aligned_cols=25  Identities=16%  Similarity=0.319  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|.|+.|.|||||++.+.+++
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998654

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.81  E-value=0.0047  Score=50.90  Aligned_cols=24  Identities=25%  Similarity=0.477  Sum_probs=21.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|+|..|+|||||++.+...+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999988653

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.77  E-value=0.0034  Score=52.58  Aligned_cols=24  Identities=17%  Similarity=0.365  Sum_probs=21.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|+|.|..|+||||+|+.+...+.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999988753

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.74  E-value=0.0039  Score=54.41  Aligned_cols=25  Identities=16%  Similarity=0.345  Sum_probs=22.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..|+|+|+.|.||||+++.+...+.
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4799999999999999999998654

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=95.73  E-value=0.006  Score=50.68  Aligned_cols=24  Identities=17%  Similarity=0.286  Sum_probs=21.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +|+|.|+.|+||||+|+.+.....
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            799999999999999999988653

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.72  E-value=0.0051  Score=52.33  Aligned_cols=25  Identities=20%  Similarity=0.271  Sum_probs=22.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...|.|.|+.|+||||+|+.+.++.
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4579999999999999999998875

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.72  E-value=0.0057  Score=51.37  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=20.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|+|.|+.|+||||+|+.+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=95.72  E-value=0.02  Score=52.39  Aligned_cols=39  Identities=21%  Similarity=0.308  Sum_probs=29.1

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..++...+........+|+|+|.+|+|||||+..+....
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            334444444344568899999999999999999987654

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.69  E-value=0.0067  Score=49.42  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=22.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+|+|.|+.|.||||+++.+...+
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4688999999999999999998875

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=95.67  E-value=0.0056  Score=50.76  Aligned_cols=25  Identities=20%  Similarity=0.150  Sum_probs=22.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...|+|.|+.|+||||+++.+.+++
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3579999999999999999999876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.66  E-value=0.01  Score=53.60  Aligned_cols=28  Identities=29%  Similarity=0.413  Sum_probs=24.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|||.|..|+||||||+.+...+.
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3477999999999999999999877654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=95.65  E-value=0.014  Score=49.08  Aligned_cols=36  Identities=11%  Similarity=0.114  Sum_probs=27.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc------CcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS------NFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~------~F~~~~wv~  203 (311)
                      -.+++|+|..|+|||||++.+......      .-...+|+.
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~   66 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   66 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEE
Confidence            569999999999999999999874322      123466766

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=95.65  E-value=0.0063  Score=51.18  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=20.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|+|.|+.|+||||+|+.+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998765

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.65  E-value=0.018  Score=51.96  Aligned_cols=28  Identities=18%  Similarity=0.245  Sum_probs=24.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+++|+|.+|+||||++..++..+..
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~  131 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAE  131 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3679999999999999999998886544

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.63  E-value=0.0071  Score=50.82  Aligned_cols=26  Identities=12%  Similarity=0.224  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|+.|.||||+|+.+...+.
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            56899999999999999999988754

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=95.62  E-value=0.018  Score=52.14  Aligned_cols=28  Identities=21%  Similarity=0.324  Sum_probs=24.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+++|+|..|+||||+++.+...+..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~  155 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKN  155 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4689999999999999999998876443

>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=95.61  E-value=0.04  Score=51.85  Aligned_cols=26  Identities=19%  Similarity=0.244  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.++|.+|+||||++..++..+.
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~  122 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYK  122 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            68999999999999999999887643

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.58  E-value=0.011  Score=58.14  Aligned_cols=49  Identities=18%  Similarity=0.300  Sum_probs=39.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...++|.+..++.+...+..+    ..+.|+|..|+||||||+.++.......
T Consensus        40 l~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~l~~~~   88 (604)
T 3k1j_A           40 IDQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAELLPTET   88 (604)
T ss_dssp             HHHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHTSCCSS
T ss_pred             cceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhccCCccc
Confidence            346789988888777777643    4789999999999999999999765544

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=95.57  E-value=0.0082  Score=56.67  Aligned_cols=85  Identities=16%  Similarity=0.190  Sum_probs=50.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcC----ceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H--
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFE----GSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I--  236 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~----~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~--  236 (311)
                      .++|.|-.|+|||+|+..+.+....+-+    .++++-    +.++......+.+.+...-.....     ..++  .  
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~----iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r  228 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAA----IGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIER  228 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEE----EEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHH
T ss_pred             EEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEE----ecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHH
Confidence            4789999999999999999988654333    344544    333234455566655442111000     0111  1  


Q ss_pred             -------HHHHHHhC---CCeEEEEEecCCCh
Q 042778          237 -------ALSFRQLS---RRKVLIVLDDVTCF  258 (311)
Q Consensus       237 -------~~l~~~L~---~kr~LlVLDdV~~~  258 (311)
                             -.+.++++   ++.+||++||+...
T Consensus       229 ~~a~~~a~tiAEyfrd~~G~~VLl~~DslTr~  260 (465)
T 3vr4_D          229 IATPRMALTAAEYLAYEKGMHVLVIMTDMTNY  260 (465)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEEcChHHH
Confidence                   23444443   68999999998643

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.56  E-value=0.0069  Score=50.84  Aligned_cols=27  Identities=22%  Similarity=0.389  Sum_probs=23.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .++++|+|+.|+|||||++.+......
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~~   45 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNPE   45 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCCc
Confidence            568999999999999999999987543

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.55  E-value=0.033  Score=49.98  Aligned_cols=36  Identities=14%  Similarity=-0.025  Sum_probs=27.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.++.|.|.+|+||||||..++.....+-..++|+.
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            458899999999999999998876443325566665

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.54  E-value=0.0054  Score=51.24  Aligned_cols=24  Identities=17%  Similarity=0.375  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++++|+|+.|.|||||++.+....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            578999999999999999988754

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=95.53  E-value=0.028  Score=47.64  Aligned_cols=48  Identities=13%  Similarity=0.144  Sum_probs=32.3

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc------CcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS------NFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~------~F~~~~wv~  203 (311)
                      .|..+|..+-..-.+++|+|.+|+|||||+..+......      .-..++|+.
T Consensus        12 ~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~   65 (243)
T 1n0w_A           12 ELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYID   65 (243)
T ss_dssp             HHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE
T ss_pred             HHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEE
Confidence            344555322223458999999999999999998885322      124567776

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.53  E-value=0.022  Score=51.10  Aligned_cols=29  Identities=14%  Similarity=0.289  Sum_probs=24.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ...+++|+|.+|+||||++..++..+...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~  131 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDE  131 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhc
Confidence            36799999999999999999998876543

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.53  E-value=0.0078  Score=53.24  Aligned_cols=24  Identities=33%  Similarity=0.709  Sum_probs=21.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHH
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999883

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.51  E-value=0.0063  Score=51.49  Aligned_cols=26  Identities=19%  Similarity=0.074  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|.|+.|+||||+|+.+.+++.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35789999999999999999998764

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.51  E-value=0.007  Score=50.73  Aligned_cols=25  Identities=16%  Similarity=0.313  Sum_probs=22.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|..|.|||||++.+..-.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4589999999999999999988764

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.51  E-value=0.0079  Score=50.66  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ..+|+|.|+.|.||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.49  E-value=0.018  Score=58.15  Aligned_cols=51  Identities=20%  Similarity=0.345  Sum_probs=39.7

Q ss_pred             CCCccchhhhHHHHHHhhcccC------C-CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAES------K-DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~------~-~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...++|.+..++.+...+....      + ....+.++|.+|+|||+||+++++....
T Consensus       490 ~~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~  547 (758)
T 3pxi_A          490 HSRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFG  547 (758)
T ss_dssp             HTTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHS
T ss_pred             hCcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4678999998888887775321      1 1347999999999999999999998633

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.46  E-value=0.0092  Score=51.44  Aligned_cols=26  Identities=15%  Similarity=0.364  Sum_probs=22.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|||.|..|.|||||++.+...+
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            35689999999999999999988754

>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=95.46  E-value=0.042  Score=51.33  Aligned_cols=26  Identities=12%  Similarity=0.132  Sum_probs=23.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|.|+|++|.||||+|+.+..+.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999998765

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.45  E-value=0.0086  Score=53.93  Aligned_cols=28  Identities=18%  Similarity=0.336  Sum_probs=24.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|+|.|..|.|||||++.+..-+.
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            3467999999999999999999887644

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.43  E-value=0.014  Score=49.13  Aligned_cols=38  Identities=18%  Similarity=0.328  Sum_probs=28.0

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+.+..++.  ......|.|+|.+|+|||||+..+....
T Consensus        25 ~a~~~r~~~~--~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           25 LADKNRKLLN--KHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHH--HTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH--hCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3444444443  2347889999999999999999988764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.42  E-value=0.014  Score=49.24  Aligned_cols=41  Identities=12%  Similarity=0.160  Sum_probs=29.8

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -+..+..++..- .....+.|+|++|.||||+|.++++.+..
T Consensus        44 f~~~l~~~~~~i-Pkkn~ili~GPPGtGKTt~a~ala~~l~g   84 (212)
T 1tue_A           44 FLGALKSFLKGT-PKKNCLVFCGPANTGKSYFGMSFIHFIQG   84 (212)
T ss_dssp             HHHHHHHHHHTC-TTCSEEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhcC-CcccEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            355566666532 22346899999999999999999998643

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.42  E-value=0.018  Score=48.20  Aligned_cols=45  Identities=18%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             chhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +.+.....+...+..  ...++|.|+|.+|+|||||+..+.......
T Consensus        13 ~~~~~~~~~~~~~~~--~~~~~i~i~G~~g~GKTTl~~~l~~~~~~~   57 (221)
T 2wsm_A           13 ENKRLAEKNREALRE--SGTVAVNIMGAIGSGKTLLIERTIERIGNE   57 (221)
T ss_dssp             HHHHHHHHHHHHHHH--HTCEEEEEEECTTSCHHHHHHHHHHHHTTT
T ss_pred             hcHHHHHHHHHhhcc--cCceEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            334455555555432  347899999999999999999988775433

>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=95.40  E-value=0.0095  Score=53.20  Aligned_cols=27  Identities=15%  Similarity=0.131  Sum_probs=23.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+++|+|.+|+||||++..++....
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356999999999999999999887654

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.36  E-value=0.024  Score=50.61  Aligned_cols=27  Identities=22%  Similarity=0.295  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++++|.+|+||||++..++.....
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~  124 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKK  124 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            679999999999999999998876543

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.35  E-value=0.0084  Score=50.64  Aligned_cols=24  Identities=21%  Similarity=0.140  Sum_probs=21.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..|.|.|+.|+||||+|+.+.+++
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999999998876

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.31  E-value=0.01  Score=54.05  Aligned_cols=25  Identities=16%  Similarity=0.266  Sum_probs=22.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+|+|.|+.|+||||||+.++.++.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            5899999999999999999998754

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.28  E-value=0.014  Score=49.11  Aligned_cols=36  Identities=11%  Similarity=0.153  Sum_probs=26.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.+++|.|.+|+|||||++.+.......=..+.|+.
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            358999999999999999999876433222345554

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=95.28  E-value=0.0094  Score=50.94  Aligned_cols=26  Identities=15%  Similarity=0.097  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|.|+.|+||||+|+.+.+++.
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998764

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=95.27  E-value=0.0096  Score=51.32  Aligned_cols=26  Identities=12%  Similarity=0.368  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|+.|.||||+|+.+..++.
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999987753

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.26  E-value=0.012  Score=50.07  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=24.2

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...++|.|.|++|+||||.|+.+.+++
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            358899999999999999999998875

>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=95.25  E-value=0.0036  Score=57.47  Aligned_cols=27  Identities=15%  Similarity=0.169  Sum_probs=23.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|.|..|.|||||.+.+...+..
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g~~~~  149 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLDYLNN  149 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccC
Confidence            349999999999999999998876543

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=95.25  E-value=0.011  Score=49.83  Aligned_cols=23  Identities=22%  Similarity=0.187  Sum_probs=20.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|+.|+||||+|+.+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998875

>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=95.24  E-value=0.016  Score=51.96  Aligned_cols=28  Identities=14%  Similarity=0.178  Sum_probs=24.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+++|+|.+|+|||||++.++.....
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~  128 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQN  128 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            3579999999999999999999876543

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=95.23  E-value=0.098  Score=47.13  Aligned_cols=34  Identities=9%  Similarity=0.094  Sum_probs=26.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCc--CceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNF--EGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F--~~~~wv~  203 (311)
                      ++-|+|.+|+||||||..+.......+  ..++|++
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            789999999999999998877654432  3467887

>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=95.23  E-value=0.018  Score=46.34  Aligned_cols=26  Identities=23%  Similarity=0.321  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .-.+++|.|..|.|||||.+.+..-+
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            35689999999999999999998865

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.23  E-value=0.0084  Score=50.88  Aligned_cols=25  Identities=28%  Similarity=0.644  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|..|.|||||++.+....
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4589999999999999999988755

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.21  E-value=0.011  Score=50.29  Aligned_cols=23  Identities=22%  Similarity=0.310  Sum_probs=21.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|+.|+||||+|+.+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998876

>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=95.17  E-value=0.019  Score=53.12  Aligned_cols=37  Identities=14%  Similarity=-0.019  Sum_probs=27.2

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.+-+...-....+++|+|+.|.|||||++.+....
T Consensus       157 ~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          157 DFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             HHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3333333333445699999999999999999999764

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.15  E-value=0.018  Score=54.18  Aligned_cols=28  Identities=14%  Similarity=0.103  Sum_probs=24.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++|.|+|.||+||||++..++..+..
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~  126 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLRE  126 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4789999999999999999999877544

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.14  E-value=0.0086  Score=49.01  Aligned_cols=26  Identities=19%  Similarity=0.291  Sum_probs=22.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+++|+|..|.|||||++.+..-+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            57999999999999999998876543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.13  E-value=0.01  Score=53.60  Aligned_cols=26  Identities=19%  Similarity=0.210  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|.|+|+.|+||||||+.++.+..
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            35899999999999999999998753

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=95.12  E-value=0.012  Score=52.03  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=21.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+|.|.|++|.||||+|+.+.++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999874

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.11  E-value=0.061  Score=49.83  Aligned_cols=37  Identities=22%  Similarity=0.087  Sum_probs=26.9

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +++.|..- ..-..++|+|..|+|||+|++.+.+.+..
T Consensus       165 aID~l~Pi-grGQR~lIfg~~g~GKT~Ll~~Ia~~i~~  201 (427)
T 3l0o_A          165 LIDLFAPI-GKGQRGMIVAPPKAGKTTILKEIANGIAE  201 (427)
T ss_dssp             HHHHHSCC-BTTCEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             hhhhcccc-cCCceEEEecCCCCChhHHHHHHHHHHhh
Confidence            44555431 12347899999999999999999987553

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.11  E-value=0.016  Score=50.71  Aligned_cols=36  Identities=11%  Similarity=0.086  Sum_probs=26.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      .-.+++|+|..|.|||||.+.+...+...+.+.+.+
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~   59 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIIT   59 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEE
Confidence            356899999999999999999887654333344433

>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=95.09  E-value=0.014  Score=58.87  Aligned_cols=50  Identities=14%  Similarity=0.242  Sum_probs=39.1

Q ss_pred             CCCccchhhhHHHHHHhhcccC------C-CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGAES------K-DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~------~-~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|.+..++.+...+....      + ....+.++|.+|+|||+||+.+++...
T Consensus       457 ~~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~  513 (758)
T 1r6b_X          457 KMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             HhhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc
Confidence            4678999988888877664321      1 245789999999999999999999873

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.08  E-value=0.017  Score=49.07  Aligned_cols=36  Identities=11%  Similarity=0.026  Sum_probs=26.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.++.|.|.+|+||||||..+.......=..++|+.
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            458999999999999999888766433323456665

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.07  E-value=0.0075  Score=53.68  Aligned_cols=27  Identities=11%  Similarity=0.151  Sum_probs=20.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...+|+|.|..|.||||+|+.+.+...
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            356899999999999999999887643

>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=95.04  E-value=0.033  Score=51.00  Aligned_cols=50  Identities=14%  Similarity=0.182  Sum_probs=34.2

Q ss_pred             HHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          154 VEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       154 ~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...|..+|. .+-..-+++.|.|.+|+||||||..+.......=..++|+.
T Consensus        48 ~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid   98 (356)
T 1u94_A           48 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   98 (356)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            344555554 22223458999999999999999998877543333567877

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.02  E-value=0.011  Score=53.82  Aligned_cols=26  Identities=12%  Similarity=0.201  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|.|+|+.|+||||||..+++++.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHCC
Confidence            46899999999999999999999754

>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=95.02  E-value=0.014  Score=52.20  Aligned_cols=28  Identities=25%  Similarity=0.347  Sum_probs=24.2

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....+|||.|..|.|||||++.+...+.
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3467999999999999999999887654

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.02  E-value=0.011  Score=49.26  Aligned_cols=23  Identities=17%  Similarity=0.228  Sum_probs=20.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +++|+|..|+|||||.+.+....
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            68999999999999999988754

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.01  E-value=0.013  Score=50.07  Aligned_cols=26  Identities=19%  Similarity=0.297  Sum_probs=22.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|+|.|+.|.||||+++.+..++
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            36789999999999999999998754

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.00  E-value=0.0084  Score=51.09  Aligned_cols=25  Identities=20%  Similarity=0.227  Sum_probs=16.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHH-Hhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIF-NKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~-~~~  192 (311)
                      -.+++|+|..|+|||||++.+. ...
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3589999999999999999998 543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=94.98  E-value=0.012  Score=50.06  Aligned_cols=26  Identities=8%  Similarity=0.116  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.+++|+|+.|+|||||.+.+.....
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46899999999999999999988765

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.94  E-value=0.023  Score=50.87  Aligned_cols=26  Identities=19%  Similarity=0.254  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|+|..|+|||||++.++..+.
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999999887654

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=94.82  E-value=0.039  Score=52.73  Aligned_cols=35  Identities=17%  Similarity=0.350  Sum_probs=27.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+++|+|..|+|||||++.+...+... .+.+++.
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll~~~-~G~V~l~  327 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQFEQQ-GKSVMLA  327 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHhhhc-CCeEEEe
Confidence            5799999999999999999998865433 3444443

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.82  E-value=0.015  Score=47.65  Aligned_cols=26  Identities=15%  Similarity=0.295  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++++|.|..|+|||||+..+...+.
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            57899999999999999999988754

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=94.79  E-value=0.016  Score=54.84  Aligned_cols=86  Identities=17%  Similarity=0.193  Sum_probs=50.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCc----CceEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H-
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNF----EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I-  236 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F----~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~-  236 (311)
                      ..++|.|-.|+|||+|+..+++....+-    +.++++-    +.++......+.+.+...-.....     ..++  . 
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~----iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~  228 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAA----MGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVE  228 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEE----EEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEE----ccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHH
Confidence            4578889999999999999998754321    2344544    333233456666666543111110     1111  0 


Q ss_pred             --------HHHHHHhC---CCeEEEEEecCCCh
Q 042778          237 --------ALSFRQLS---RRKVLIVLDDVTCF  258 (311)
Q Consensus       237 --------~~l~~~L~---~kr~LlVLDdV~~~  258 (311)
                              -.+.++++   ++.+||++||+...
T Consensus       229 r~~~~~~a~tiAEyfrdd~G~dVLl~~DsltR~  261 (469)
T 2c61_A          229 RIVTPRMALTAAEYLAYEHGMHVLVILTDITNY  261 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCeEEEEEeCHHHH
Confidence                    23444444   69999999997543

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.78  E-value=0.013  Score=49.49  Aligned_cols=23  Identities=22%  Similarity=0.034  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|.|||||.+.+.--
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999988764

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=94.78  E-value=0.039  Score=47.14  Aligned_cols=28  Identities=14%  Similarity=0.267  Sum_probs=24.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .-..|.|.|+.|+||||+++.+.+.+..
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3568999999999999999999998754

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=94.77  E-value=0.056  Score=48.61  Aligned_cols=96  Identities=15%  Similarity=0.098  Sum_probs=53.3

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC------cCceEEEecCccccCCCCChHHHHHHHHHHHhcC
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN------FEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQD  229 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~  229 (311)
                      .|..+|..+-..-.++.|+|.+|+||||||..+.......      =..++|+.    ... .++...+.. ++..+...
T Consensus        95 ~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~----~e~-~~~~~~l~~-~~~~~g~~  168 (324)
T 2z43_A           95 ALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYID----TEG-TFRWERIEN-MAKALGLD  168 (324)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE----SSS-CCCHHHHHH-HHHHTTCC
T ss_pred             hHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEE----CCC-CCCHHHHHH-HHHHhCCC
Confidence            3444553221224589999999999999999988764322      23567877    222 334444443 23333211


Q ss_pred             C-----C----CCCCH-------HHHHHHhC--CCeEEEEEecCCC
Q 042778          230 G-----I----VIPDI-------ALSFRQLS--RRKVLIVLDDVTC  257 (311)
Q Consensus       230 ~-----~----~~~~~-------~~l~~~L~--~kr~LlVLDdV~~  257 (311)
                      .     .    ...+.       ..+...+.  .+--+||+|.+..
T Consensus       169 ~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          169 IDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHhccEEEEeCCCHHHHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence            0     0    11121       34444443  4566999999864

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.75  E-value=0.016  Score=50.12  Aligned_cols=25  Identities=12%  Similarity=0.041  Sum_probs=22.2

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .. .+++|+|..|.|||||.+.+.--
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCC
Confidence            45 78999999999999999998864

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=94.72  E-value=0.024  Score=50.11  Aligned_cols=36  Identities=8%  Similarity=0.016  Sum_probs=27.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC-ceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE-GSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~-~~~wv~  203 (311)
                      -.+++|.|.+|+|||||++.++..+...-. .++|+.
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            458999999999999999998887554322 344554

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.71  E-value=0.015  Score=49.97  Aligned_cols=24  Identities=21%  Similarity=0.122  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            458999999999999999998763

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.70  E-value=0.013  Score=50.00  Aligned_cols=24  Identities=17%  Similarity=0.077  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            348999999999999999998764

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.69  E-value=0.033  Score=47.97  Aligned_cols=26  Identities=15%  Similarity=0.174  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++.+.|.||+|||||+..+.....
T Consensus        14 ~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           14 SMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            67899999999999999999987654

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=94.68  E-value=0.02  Score=53.89  Aligned_cols=26  Identities=27%  Similarity=0.280  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++|.|+|.+|+||||++..+.....
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~  124 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQ  124 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            56899999999999999999888644

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=94.66  E-value=0.029  Score=49.96  Aligned_cols=28  Identities=21%  Similarity=0.138  Sum_probs=23.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ...+++|+|.+|+||||++..++.....
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~  124 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKG  124 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3579999999999999999998876543

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=94.63  E-value=0.033  Score=48.30  Aligned_cols=27  Identities=22%  Similarity=0.495  Sum_probs=22.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++|+|.|-||+||||+|..++..+...
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~   28 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAM   28 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTT
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHC
Confidence            578889999999999999998876543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.59  E-value=0.078  Score=44.17  Aligned_cols=34  Identities=12%  Similarity=0.127  Sum_probs=26.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|.|=|.-|+||||.++.+++.+...-..+.+..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~tr   35 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKR   35 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            4778899999999999999998765543444444

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.58  E-value=0.031  Score=51.32  Aligned_cols=26  Identities=19%  Similarity=0.254  Sum_probs=23.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++|+|..|+|||||++.++..+.
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag~l~  182 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAHRLK  182 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHhhcc
Confidence            57999999999999999999988654

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.56  E-value=0.019  Score=49.91  Aligned_cols=23  Identities=13%  Similarity=0.312  Sum_probs=21.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|.|||||.+.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998874

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=94.54  E-value=0.019  Score=49.85  Aligned_cols=25  Identities=20%  Similarity=0.235  Sum_probs=21.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+++|+|..|.|||||.+.+.--+.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            4899999999999999999877544

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.53  E-value=0.016  Score=49.95  Aligned_cols=25  Identities=12%  Similarity=0.279  Sum_probs=21.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|..|.|||||.+.+..-+
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3589999999999999999987753

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=94.52  E-value=0.054  Score=49.18  Aligned_cols=29  Identities=21%  Similarity=0.255  Sum_probs=24.2

Q ss_pred             cCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          164 ESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       164 ~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ......+|+|+|.+|.|||||+..+....
T Consensus        52 ~~~~~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           52 YCGNTLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             GCSCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ccCCCEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            33557899999999999999999987653

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=94.49  E-value=0.022  Score=51.21  Aligned_cols=25  Identities=12%  Similarity=0.202  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|.|.|+.|+||||||..++.+.
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhC
Confidence            3588999999999999999999874

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.48  E-value=0.016  Score=50.68  Aligned_cols=24  Identities=25%  Similarity=0.237  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.48  E-value=0.086  Score=47.90  Aligned_cols=51  Identities=12%  Similarity=0.008  Sum_probs=34.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSK  225 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~  225 (311)
                      -.++.|.|.+|+||||||..++.....+=..++|+.    .   .-....+...++..
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS----l---Ems~~ql~~Rlls~   96 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS----L---EMSAEQLALRALSD   96 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE----S---SSCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe----C---CCCHHHHHHHHHHH
Confidence            458889999999999999998887544223345554    1   33455566665443

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=94.47  E-value=0.027  Score=53.08  Aligned_cols=25  Identities=24%  Similarity=0.301  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++|.|-.|+|||+|+..+.+...
T Consensus       148 Qr~~Ifgg~G~GKt~L~~~Ia~~~~  172 (464)
T 3gqb_B          148 QKLPIFSGSGLPANEIAAQIARQAT  172 (464)
T ss_dssp             CBCCEEEETTSCHHHHHHHHHHHCB
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHH
Confidence            3578899999999999999988754

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.46  E-value=0.024  Score=44.44  Aligned_cols=23  Identities=13%  Similarity=0.265  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +.|.|+|.+|+|||||...+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998764

>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=94.44  E-value=0.02  Score=50.23  Aligned_cols=24  Identities=17%  Similarity=0.268  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.++--
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998874

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.44  E-value=0.055  Score=51.58  Aligned_cols=84  Identities=17%  Similarity=0.117  Sum_probs=47.5

Q ss_pred             EEEEEeccCcchhHHHH-HHHHHhhccCcCc-eEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC-H----
Q 042778          169 YALGIWGIGGIDRTTIA-RAIFNKISSNFEG-SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD-I----  236 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~-~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~-~----  236 (311)
                      ..++|.|-.|+|||+|| ..+.++.  +-+. ++++-    +.++......+.+.+...-.....     ..++ .    
T Consensus       163 QR~~Ifg~~g~GKT~l~l~~I~n~~--~~dv~~V~~~----IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~  236 (513)
T 3oaa_A          163 QRELIIGDRQTGKTALAIDAIINQR--DSGIKCIYVA----IGQKASTISNVVRKLEEHGALANTIVVVATASESAALQY  236 (513)
T ss_dssp             CBCEEEESSSSSHHHHHHHHHHTTS--SSSCEEEEEE----ESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHH
T ss_pred             CEEEeecCCCCCcchHHHHHHHhhc--cCCceEEEEE----ecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHH
Confidence            46789999999999997 5677753  2343 34554    333234455566654432111111     1111 0    


Q ss_pred             ------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 ------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                            ..+-+++  +++.+||++||+...
T Consensus       237 ~a~~~a~tiAEyfrd~G~dVLli~Dsltr~  266 (513)
T 3oaa_A          237 LAPYAGCAMGEYFRDRGEDALIIYDDLSKQ  266 (513)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEecChHHH
Confidence                  1222232  579999999998653

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=94.44  E-value=0.034  Score=53.38  Aligned_cols=46  Identities=9%  Similarity=0.090  Sum_probs=31.4

Q ss_pred             chhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .+.+..+.+.+..........+|.+.|+.|.||||+|+++.+++..
T Consensus       376 ~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          376 SYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             SCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            3333344444433222233578999999999999999999999753

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=94.43  E-value=0.056  Score=45.17  Aligned_cols=121  Identities=15%  Similarity=0.133  Sum_probs=61.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh-ccCcCceEEEecCccccCCCCChHHHHHHHHHHHh--cCCCCCC--C-------
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI-SSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLL--QDGIVIP--D-------  235 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~-~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~--~~~~~~~--~-------  235 (311)
                      -..|-|++-.|-||||+|-.+.-+. ...+. ++++.-+.. .. ..+...+...+--.+.  +......  +       
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~r-V~~vQF~Kg-~~-~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~  104 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKN-VGVVQFIKG-TW-PNGERNLLEPHGVEFQVMATGFTWETQNREADTAA  104 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCC-EEEEESSCC-SS-CCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCe-EEEEEeeCC-CC-CccHHHHHHhCCcEEEEcccccccCCCCcHHHHHH
Confidence            3456666666799999999988873 33343 334431111 01 2333344333300000  0000000  0       


Q ss_pred             ----HHHHHHHhCCCeE-EEEEecCCChHHHHHhhccCCCcCCceEEEcCCCChHHHHHHHHHhhcC------CCCCCCc
Q 042778          236 ----IALSFRQLSRRKV-LIVLDDVTCFRQIKSLIGMLRNCCVKEKYEMKELGDDHALELFSRHAFK------QNNPHIG  304 (311)
Q Consensus       236 ----~~~l~~~L~~kr~-LlVLDdV~~~~~l~~l~~~~~~~~~~~~y~v~~L~~~ea~~Lf~~~af~------~~~~~~~  304 (311)
                          ...+++.+.+.+| |||||++...                  ....-|+.++-++++..+.-.      .+.+++.
T Consensus       105 a~~~l~~a~~~l~~~~yDlvILDEi~~a------------------l~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~  166 (196)
T 1g5t_A          105 CMAVWQHGKRMLADPLLDMVVLDELTYM------------------VAYDYLPLEEVISALNARPGHQTVIITGRGCHRD  166 (196)
T ss_dssp             HHHHHHHHHHHTTCTTCSEEEEETHHHH------------------HHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHH
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEeCCCcc------------------ccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHH
Confidence                0667777777776 9999987321                  123445566666666554332      2345555


Q ss_pred             HHHhh
Q 042778          305 FEELS  309 (311)
Q Consensus       305 ~~~l~  309 (311)
                      +.+++
T Consensus       167 l~e~A  171 (196)
T 1g5t_A          167 ILDLA  171 (196)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            55543

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.43  E-value=0.017  Score=49.80  Aligned_cols=24  Identities=25%  Similarity=0.225  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.++--
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            348999999999999999998763

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.42  E-value=0.017  Score=50.34  Aligned_cols=24  Identities=21%  Similarity=0.111  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998764

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.41  E-value=0.02  Score=50.62  Aligned_cols=23  Identities=17%  Similarity=0.245  Sum_probs=20.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|.|||||.+.+.--
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            48999999999999999998763

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.41  E-value=0.018  Score=48.32  Aligned_cols=24  Identities=17%  Similarity=0.350  Sum_probs=21.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|+|.|+.|+||||+|+.+....
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            468999999999999999988764

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=94.40  E-value=0.024  Score=47.78  Aligned_cols=23  Identities=22%  Similarity=0.228  Sum_probs=20.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|.|.|++|+||+|+|+.+.++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            57889999999999999998875

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.39  E-value=0.045  Score=52.20  Aligned_cols=84  Identities=18%  Similarity=0.107  Sum_probs=47.6

Q ss_pred             EEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          169 YALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      ..++|.|-.|+|||+|| ..+.+...  -+.. +++-    +.++......+.+.+...-.....     ..++  .   
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~~~--~dv~~V~~~----iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~  236 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQKG--QDVICIYVA----IGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLY  236 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGGGS--CSEEEEEEE----ESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHhhc--CCcEEEEEE----CCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHH
Confidence            46799999999999996 47777653  3433 4444    333233455555555432111111     1111  0   


Q ss_pred             ------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 ------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                            -.+-+++  .++.+||++||+...
T Consensus       237 ~a~~~a~tiAEyfrd~G~dVLl~~Dsltr~  266 (502)
T 2qe7_A          237 LAPYAGCAMGEYFMYKGKHALVVYDDLSKQ  266 (502)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcEEEEEecHHHH
Confidence                  1233333  479999999998654

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.39  E-value=0.026  Score=48.32  Aligned_cols=26  Identities=15%  Similarity=0.174  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...|.|.|+.|+||||+++.+.+.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999998764

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.38  E-value=0.023  Score=46.70  Aligned_cols=24  Identities=8%  Similarity=0.340  Sum_probs=21.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            568999999999999999998875

>3hyn_A Putative signal transduction protein; DUF1863 family protein, nucleotide-binding protein, structur genomics; HET: MSE; 1.20A {Eubacterium rectale atcc 33656}

Probab=94.37  E-value=0.08  Score=43.39  Aligned_cols=64  Identities=16%  Similarity=0.120  Sum_probs=48.6

Q ss_pred             hHHHHHHHHHhCCCcEEeeC-CCC----C----CCcchHHHHHHHHhccceeeeeccCcccccchHHHHHHHH
Q 042778           34 FTGHLYSALSQKGIETFIDD-QLN----R----GDEISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKIL   97 (311)
Q Consensus        34 f~~~L~~~L~~~gi~~f~d~-~~~----~----G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i~   97 (311)
                      ....|..--....+..|.|. ++.    -    -..|.+.|.+.|..|+..|+++|++...|.|-..|+..++
T Consensus        33 yy~lL~aWk~n~n~F~F~D~Hd~~y~vrDsS~~e~tIKrrLReRI~~Sk~vIllIs~~T~~s~~v~wEIe~Ai  105 (189)
T 3hyn_A           33 YYNMLRMWKGEDNSFPFNDAHDKTYNVRDGSDWEKTLKPRLHTRLDNSKNIILFLSSITANSRALREEMNYGI  105 (189)
T ss_dssp             HHHHHHHHHHHCTTSSCCBTTTTCCCTTSCCCTTTTHHHHHHHHHHTEEEEEEECCTTCCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCceeecchhhccccccccccHHHHHHHHHHHHHHhcCcEEEEEecCccccchhHHHHHHHH
Confidence            45555555556666677786 552    2    2358889999999999999999999999999888876554

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.37  E-value=0.04  Score=52.86  Aligned_cols=27  Identities=15%  Similarity=0.153  Sum_probs=22.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..++|.|+|.+|+||||++..+.....
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~  126 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQ  126 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            377999999999999999999886543

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=94.36  E-value=0.025  Score=47.33  Aligned_cols=28  Identities=11%  Similarity=0.014  Sum_probs=24.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..+|.|.|+.|+||||+|+.+++++.-.
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~~lg~~   33 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAEHYNIP   33 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHTTCC
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHhCcC
Confidence            3589999999999999999999975433

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.36  E-value=0.02  Score=50.24  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            358999999999999999998763

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=94.33  E-value=0.08  Score=44.72  Aligned_cols=31  Identities=13%  Similarity=0.131  Sum_probs=25.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC-cCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN-FEG  198 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~  198 (311)
                      -..|.|-|+.|.||||+++.+.+.+... +..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v   37 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEV   37 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTTTCCE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHcCCCc
Confidence            4688999999999999999999986543 443

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.32  E-value=0.019  Score=49.18  Aligned_cols=25  Identities=20%  Similarity=0.312  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|..|.|||||.+.+..-+
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3489999999999999999998754

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=94.32  E-value=0.037  Score=52.89  Aligned_cols=86  Identities=17%  Similarity=0.110  Sum_probs=48.6

Q ss_pred             EEEEEeccCcchhHHHH-HHHHHhhcc------CcCc-eEEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC
Q 042778          169 YALGIWGIGGIDRTTIA-RAIFNKISS------NFEG-SCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD  235 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA-~~v~~~~~~------~F~~-~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~  235 (311)
                      ..++|.|-.|+|||+|| ..+.++...      +-+. ++++-    +.++......+.+.+...-.....     ..++
T Consensus       163 QR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~----IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~  238 (510)
T 2ck3_A          163 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVA----IGQKRSTVAQLVKRLTDADAMKYTIVVSATASD  238 (510)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEE----ESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTS
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEE----CCCCcHHHHHHHHHHHhcCCcccceEEEECCCC
Confidence            46799999999999995 577777552      2454 44544    333233455555555432111000     1111


Q ss_pred             --H---------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          236 --I---------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       236 --~---------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                        .         -.+-+++  .++.+||++||+...
T Consensus       239 p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dsltr~  274 (510)
T 2ck3_A          239 AAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQ  274 (510)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHHHH
Confidence              0         2233333  479999999998653

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.32  E-value=0.019  Score=50.39  Aligned_cols=24  Identities=17%  Similarity=0.134  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcC
Confidence            358999999999999999998764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.29  E-value=0.021  Score=49.34  Aligned_cols=24  Identities=17%  Similarity=0.076  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999998764

>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=94.27  E-value=0.044  Score=48.10  Aligned_cols=37  Identities=16%  Similarity=0.133  Sum_probs=28.2

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-+..+|.........+.++|++|.|||++|.++++.
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            3456666643233456999999999999999999985

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.25  E-value=0.02  Score=49.68  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            348999999999999999998764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=94.23  E-value=0.028  Score=50.50  Aligned_cols=25  Identities=16%  Similarity=0.126  Sum_probs=22.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|.|.|+.|+||||||..++++.
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhC
Confidence            5789999999999999999999874

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.23  E-value=0.017  Score=49.09  Aligned_cols=23  Identities=26%  Similarity=0.413  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|.|||||.+.++.-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47999999999999999998764

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=94.22  E-value=0.044  Score=52.31  Aligned_cols=84  Identities=20%  Similarity=0.132  Sum_probs=47.9

Q ss_pred             EEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhcCCC-----CCCC--H---
Q 042778          169 YALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQDGI-----VIPD--I---  236 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~-----~~~~--~---  236 (311)
                      ..++|.|-.|+|||+|| ..+.+...  -+.. +++-    +.++......+.+.+...-.....     ..++  .   
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~~--~dv~~V~~~----IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~  249 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQKG--QGVYCIYVA----IGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQY  249 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTTT--TTEEEEEEE----ESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHH
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhhc--CCcEEEEEE----cCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHH
Confidence            46899999999999996 47777653  3433 4444    333233455555555432111100     1111  0   


Q ss_pred             ------HHHHHHh--CCCeEEEEEecCCCh
Q 042778          237 ------ALSFRQL--SRRKVLIVLDDVTCF  258 (311)
Q Consensus       237 ------~~l~~~L--~~kr~LlVLDdV~~~  258 (311)
                            -.+-+++  .++.+||++||+...
T Consensus       250 ~a~~~a~tiAEyfrd~G~dVLli~DslTr~  279 (515)
T 2r9v_A          250 IAPYAGCAMGEYFAYSGRDALVVYDDLSKH  279 (515)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcEEEEeccHHHH
Confidence                  2233333  479999999998654

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.22  E-value=0.085  Score=58.28  Aligned_cols=48  Identities=15%  Similarity=0.216  Sum_probs=33.3

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|..+|. .+-...+.+-|+|++|+||||||.++......+=..+.|+.
T Consensus      1414 ~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~ 1462 (2050)
T 3cmu_A         1414 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID 1462 (2050)
T ss_dssp             HHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             HHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            3555554 22233678999999999999999999887443323456776

>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=94.21  E-value=0.02  Score=49.92  Aligned_cols=24  Identities=29%  Similarity=0.314  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998764

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.20  E-value=0.089  Score=49.64  Aligned_cols=54  Identities=9%  Similarity=0.186  Sum_probs=34.2

Q ss_pred             chhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcC-ceEEEe
Q 042778          149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFE-GSCFLQ  203 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~-~~~wv~  203 (311)
                      |...-...|..++ .+-..-.++.|.|.+|+||||||..+.......-. .++|+.
T Consensus       185 ~i~tG~~~LD~~~-gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          185 GIPTGFTELDRMT-SGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             SBCCSCHHHHHHH-SSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCCCcHHHHhhc-CCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3333334444444 22223458999999999999999999887543222 456655

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.18  E-value=0.021  Score=49.94  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -.+++|+|..|.|||||.+.+..-+
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC
Confidence            3589999999999999999987654

>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=94.16  E-value=0.056  Score=55.26  Aligned_cols=50  Identities=12%  Similarity=0.320  Sum_probs=38.6

Q ss_pred             CCccchhhhHHHHHHhhccc------CC-CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGAE------SK-DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~------~~-~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++|.+..++.+...+...      .+ ....+.|+|..|+|||+||+++++....
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~  614 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFD  614 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHS
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            35789998888887776432      11 1468999999999999999999998643

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=94.14  E-value=0.043  Score=53.26  Aligned_cols=27  Identities=22%  Similarity=0.442  Sum_probs=24.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|+|+.|.|||||++.+...+..
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhcc
Confidence            468999999999999999999998754

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=94.13  E-value=0.021  Score=50.18  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998764

>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=94.13  E-value=0.19  Score=44.37  Aligned_cols=117  Identities=15%  Similarity=0.235  Sum_probs=60.4

Q ss_pred             chHHHHHHHHhccceeeeeccCcccccchHHHHHHHHhhH-hHHHHhH--h--HHHHHHHHHHHHHHhhhcCCccCCCCc
Q 042778           61 ISQSLVDAIEASAISLIIFSEAYASSRWCLDELVKILTRE-LEEMFKE--N--SEKLQTWRNALKEAAGLSGFHSQNIRL  135 (311)
Q Consensus        61 ~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl~El~~i~e~~-~~~~~~~--~--~~~v~~w~~~l~~~~~~~g~~~~~~~e  135 (311)
                      ...++.+.++++++.|.|+.-.-..+..| .++.+++..+ .--.+.+  +  .+.++.|.+.+.+    .|+..-    
T Consensus        13 a~~~~~~~l~~aDvVl~VvDAr~p~~~~~-~~l~~~l~~kp~ilVlNK~DL~~~~~~~~~~~~~~~----~g~~~i----   83 (282)
T 1puj_A           13 ARREVTEKLKLIDIVYELVDARIPMSSRN-PMIEDILKNKPRIMLLNKADKADAAVTQQWKEHFEN----QGIRSL----   83 (282)
T ss_dssp             HHHHHHHHGGGCSEEEEEEETTSTTTTSC-HHHHHHCSSSCEEEEEECGGGSCHHHHHHHHHHHHT----TTCCEE----
T ss_pred             HHHHHHHHHhhCCEEEEEEeCCCCCccCC-HHHHHHHCCCCEEEEEECcccCCHHHHHHHHHHHHh----cCCcEE----
Confidence            34567777778888877776554444444 1233322111 0000000  0  1345667665532    122110    


Q ss_pred             ccccCCCCCCCccchhhhHHHHHHhhccc---------CCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          136 AEVSPCSNKNQLVGVESRVEEIESLLGAE---------SKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       136 ~~i~~~l~~~~~vGr~~~~~~l~~~L~~~---------~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                       .+    ....-.|.+...+.+.+++...         ......++|+|.+|+|||||...+..+
T Consensus        84 -~i----SA~~~~gi~~L~~~i~~~l~~~~~~~~~~~~~~~~~~v~~vG~~nvGKSsliN~l~~~  143 (282)
T 1puj_A           84 -SI----NSVNGQGLNQIVPASKEILQEKFDRMRAKGVKPRAIRALIIGIPNVGKSTLINRLAKK  143 (282)
T ss_dssp             -EC----CTTTCTTGGGHHHHHHHHHHHHHHHHHHTTCCCCCEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             -EE----ECCCcccHHHHHHHHHHHHHHHHHHHHhcCCCCCCceEEEEecCCCchHHHHHHHhcC
Confidence             00    1223345555555555555311         123457899999999999999988764

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=94.12  E-value=0.022  Score=49.98  Aligned_cols=24  Identities=17%  Similarity=0.131  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.++--
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            358999999999999999998764

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=94.10  E-value=0.043  Score=48.26  Aligned_cols=27  Identities=22%  Similarity=0.528  Sum_probs=22.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .++|+|.|-||+||||+|..++..+..
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~   28 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAE   28 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHH
Confidence            367888999999999999998886543

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.10  E-value=0.029  Score=46.21  Aligned_cols=24  Identities=8%  Similarity=0.340  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999998875

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.10  E-value=0.028  Score=44.78  Aligned_cols=23  Identities=22%  Similarity=0.453  Sum_probs=20.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999998763

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=94.09  E-value=0.025  Score=49.57  Aligned_cols=26  Identities=15%  Similarity=0.190  Sum_probs=22.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      -.++.|+|.+|+|||||+..+...+.
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            35899999999999999998887543

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=94.09  E-value=0.045  Score=52.74  Aligned_cols=30  Identities=10%  Similarity=0.049  Sum_probs=24.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...+|.++|++|.||||+|+.+...+...|
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~~~~   63 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLNWIG   63 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcC
Confidence            357899999999999999999988764433

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=94.08  E-value=0.026  Score=44.19  Aligned_cols=22  Identities=18%  Similarity=0.514  Sum_probs=19.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|.|+|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998764

>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=94.07  E-value=0.1  Score=46.66  Aligned_cols=37  Identities=22%  Similarity=0.267  Sum_probs=26.9

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|..+|..+-..-.++.|+|.+|+||||||..+...
T Consensus        85 ~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           85 SELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             HHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3444555422223568999999999999999988865

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.06  E-value=0.08  Score=47.98  Aligned_cols=36  Identities=17%  Similarity=0.290  Sum_probs=27.0

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.+-+...-....+++|+|..|+|||||.+.+....
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            333333333457899999999999999999988643

>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=94.06  E-value=0.028  Score=50.33  Aligned_cols=26  Identities=8%  Similarity=0.216  Sum_probs=22.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .-.+++|+|..|.|||||++.+..-+
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            35689999999999999999987653

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.06  E-value=0.023  Score=50.30  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~Gl   70 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNAY   70 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            348999999999999999998764

>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=94.05  E-value=0.035  Score=50.68  Aligned_cols=47  Identities=19%  Similarity=0.325  Sum_probs=32.0

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc--Cc---Cce-EEEe
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS--NF---EGS-CFLQ  203 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F---~~~-~wv~  203 (311)
                      |..+|..+-..-.++.|+|..|+|||||+..+......  ..   .+. +|+.
T Consensus       120 LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~  172 (349)
T 1pzn_A          120 LDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID  172 (349)
T ss_dssp             HHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEe
Confidence            33444432234679999999999999999998876532  12   233 7887

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=94.02  E-value=0.024  Score=49.38  Aligned_cols=23  Identities=17%  Similarity=0.348  Sum_probs=20.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|.|||||.+.++.-
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998764

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.01  E-value=0.096  Score=49.27  Aligned_cols=71  Identities=14%  Similarity=0.078  Sum_probs=42.8

Q ss_pred             cchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEecCccccCCCCChHHHHHHHHHHH
Q 042778          148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQNVREESQRPGGLGFLQQKLLSKL  226 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l  226 (311)
                      .|...-...|..++ .+-..-.++.|.|.+|+||||||..++....... ..++|+.    .   ......+...++...
T Consensus       181 ~~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~s----l---E~~~~~l~~R~~~~~  252 (444)
T 2q6t_A          181 AGVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYS----L---EMPAAQLTLRMMCSE  252 (444)
T ss_dssp             --CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE----S---SSCHHHHHHHHHHHH
T ss_pred             CcccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE----C---CCCHHHHHHHHHHHH
Confidence            34444444555555 2322345889999999999999999888754322 2456655    1   334556666665443

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=93.99  E-value=0.019  Score=48.95  Aligned_cols=25  Identities=20%  Similarity=0.098  Sum_probs=22.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.+|+|.|..|.|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            3579999999999999999988775

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.96  E-value=0.034  Score=45.29  Aligned_cols=25  Identities=12%  Similarity=0.037  Sum_probs=21.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3568899999999999999988775

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=93.96  E-value=0.032  Score=46.82  Aligned_cols=24  Identities=17%  Similarity=0.237  Sum_probs=21.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.|.|.|..|+||||||.++..+.
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            568899999999999999998874

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=93.94  E-value=0.032  Score=52.18  Aligned_cols=35  Identities=14%  Similarity=0.233  Sum_probs=26.9

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .+.+.|....+...+++|+|..|+|||||.+.+..
T Consensus        57 ~i~~~L~~~~~~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           57 AISDALKEIDSSVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             HHHHHHHHHHHCCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             hhhhhhhhcccCCeEEEEECCCCCcHHHHHHHHhC
Confidence            34444443334567999999999999999999987

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=93.93  E-value=0.079  Score=51.11  Aligned_cols=49  Identities=10%  Similarity=0.052  Sum_probs=33.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      -..++|.|..|+|||+|++.+.+...  -+.++++-    +.++.....++.+.+
T Consensus       227 Gqr~~I~g~~g~GKT~L~~~ia~~~~--~~~~V~~~----iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          227 GGTAAIPGPAGSGKTVTQHQLAKWSD--AQVVIYIG----CGERGNEMTDVLEEF  275 (588)
T ss_dssp             TCEEEECSCCSHHHHHHHHHHHHHSS--CSEEEEEE----CCSSSSHHHHHHHHT
T ss_pred             CCeEEeecCCCCCHHHHHHHHHhccC--CCEEEEEE----ecccHHHHHHHHHHH
Confidence            34789999999999999999887532  24566665    444244555555554

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=93.93  E-value=0.042  Score=43.29  Aligned_cols=24  Identities=8%  Similarity=0.274  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456889999999999999998875

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=93.90  E-value=0.03  Score=45.48  Aligned_cols=23  Identities=22%  Similarity=0.605  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.|.|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999998875

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.86  E-value=0.093  Score=44.73  Aligned_cols=34  Identities=18%  Similarity=0.220  Sum_probs=27.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc--CcCceE
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS--NFEGSC  200 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~--~F~~~~  200 (311)
                      ....|.|.|+.|+||||+++.+.+.+..  .++..+
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            3678999999999999999999998654  444443

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=93.85  E-value=0.032  Score=47.88  Aligned_cols=25  Identities=28%  Similarity=0.232  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+||.|++|+||||+|+.+.+++
T Consensus         8 ~~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            8 HMRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             -CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccceeeECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999998875

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=93.85  E-value=0.032  Score=45.28  Aligned_cols=23  Identities=26%  Similarity=0.261  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+.+|+|..|.|||||+.+++--
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~   49 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFV   49 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Confidence            38899999999999999998763

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.84  E-value=0.036  Score=44.87  Aligned_cols=24  Identities=21%  Similarity=0.421  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|.+|+|||||...+...
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999999874

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.83  E-value=0.033  Score=48.96  Aligned_cols=22  Identities=18%  Similarity=0.536  Sum_probs=20.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .++|+|..|+|||||.+.++..
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999875

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.75  E-value=0.031  Score=45.47  Aligned_cols=21  Identities=29%  Similarity=0.396  Sum_probs=19.0

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .|+|+|.+|+|||||...+..
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999998876

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.73  E-value=0.057  Score=46.17  Aligned_cols=30  Identities=7%  Similarity=-0.066  Sum_probs=23.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc-cCcCc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS-SNFEG  198 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~-~~F~~  198 (311)
                      -.|.+.|.||+||||+|..+..... ..++.
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V   37 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRV   37 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCE
Confidence            3477889999999999999888744 34554

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=93.73  E-value=0.075  Score=45.14  Aligned_cols=29  Identities=21%  Similarity=0.208  Sum_probs=23.7

Q ss_pred             CeEEEEEec-cCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWG-IGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~G-mgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..++|+|++ -||+||||+|..++..+...
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~la~~   32 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFALSQE   32 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHHHHhC
Confidence            357888884 59999999999999886654

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=93.70  E-value=0.058  Score=44.48  Aligned_cols=26  Identities=23%  Similarity=0.261  Sum_probs=21.6

Q ss_pred             EEEEEe-ccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIW-GIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~-GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++|+|+ +-||+||||+|..++..+..
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~   28 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSR   28 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHH
Confidence            578888 67999999999998887554

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=93.70  E-value=0.064  Score=45.53  Aligned_cols=25  Identities=32%  Similarity=0.647  Sum_probs=21.3

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccC
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      |+|.|-||+||||+|..++..+...
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~   27 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASD   27 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTT
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHC
Confidence            6679999999999999998876543

>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=93.69  E-value=0.031  Score=50.13  Aligned_cols=24  Identities=29%  Similarity=0.423  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+..-
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~gl  103 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFRF  103 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTTS
T ss_pred             CCEEEEECCCCchHHHHHHHHHcC
Confidence            458999999999999999988653

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=93.64  E-value=0.04  Score=51.25  Aligned_cols=24  Identities=17%  Similarity=0.328  Sum_probs=21.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|.|.|+.|+||||||..++.+.
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            578999999999999999998874

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=93.63  E-value=0.037  Score=43.48  Aligned_cols=24  Identities=13%  Similarity=0.350  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            346889999999999999998764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.60  E-value=0.11  Score=49.10  Aligned_cols=55  Identities=18%  Similarity=0.089  Sum_probs=35.3

Q ss_pred             cchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          148 VGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       148 vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|...-...|..++. +-..-.++.|.|.+|+||||||..++.....+=..++|++
T Consensus       178 ~gi~TG~~~LD~~lg-Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          178 TGVPSGFTELDRMTY-GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             CSBCCSCHHHHHHHS-SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             CCcCCCcHHHHhhcC-CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            344444445555552 2223458899999999999999998887544312455554

>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=93.60  E-value=0.067  Score=50.18  Aligned_cols=29  Identities=21%  Similarity=0.142  Sum_probs=24.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ...+++|+|.+|+||||++..++..+...
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~  125 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK  125 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            35789999999999999999988865443

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.58  E-value=0.031  Score=48.94  Aligned_cols=24  Identities=33%  Similarity=0.356  Sum_probs=21.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+++|.|..|.|||||.+.++--.
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            489999999999999999988654

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.57  E-value=0.057  Score=43.73  Aligned_cols=26  Identities=12%  Similarity=0.282  Sum_probs=22.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .....|.|+|.+|+|||||...+...
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            34677899999999999999988764

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.54  E-value=0.084  Score=45.13  Aligned_cols=28  Identities=18%  Similarity=0.217  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -..|.|-|+.|+||||+++.+.+.+...
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~~   52 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQER   52 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            4589999999999999999999986543

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=93.54  E-value=0.059  Score=51.10  Aligned_cols=29  Identities=10%  Similarity=0.036  Sum_probs=24.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+|.++|+.|.||||+|+.+.+.....|
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~~~~   67 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLNFIG   67 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHhccC
Confidence            56889999999999999999998755444

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=93.53  E-value=0.043  Score=44.53  Aligned_cols=27  Identities=22%  Similarity=0.367  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .--|.|+|.+|+|||||.+.+.+....
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~~~~~   40 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYSKVPE   40 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHTSCG
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhhccc
Confidence            456889999999999999877765433

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=93.51  E-value=0.071  Score=44.77  Aligned_cols=30  Identities=13%  Similarity=0.368  Sum_probs=25.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      ..|.|-|.-|+||||+++.+.+.+...++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~~~~~v   32 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLVKDYDV   32 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCE
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHCCCCE
Confidence            468899999999999999999988665553

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.51  E-value=0.044  Score=50.16  Aligned_cols=26  Identities=8%  Similarity=0.151  Sum_probs=22.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|+|..|.|||||++.+...+.
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            56899999999999999999887643

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=93.44  E-value=0.043  Score=43.18  Aligned_cols=23  Identities=22%  Similarity=0.557  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --|.|+|.+|+|||||...+.+.
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998874

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.43  E-value=0.051  Score=43.14  Aligned_cols=24  Identities=25%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            456899999999999999988764

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=93.43  E-value=0.044  Score=49.24  Aligned_cols=26  Identities=27%  Similarity=0.326  Sum_probs=23.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.+++|.|+.|.|||||.+.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            47899999999999999999988653

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=93.38  E-value=0.026  Score=49.03  Aligned_cols=27  Identities=11%  Similarity=0.086  Sum_probs=23.4

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ....|.|.|..|+||||+|+.+.+.+.
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            367899999999999999998887753

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=93.37  E-value=0.047  Score=46.58  Aligned_cols=25  Identities=8%  Similarity=0.070  Sum_probs=22.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+|+|.|+.|+||||+|+.+.+++
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~l   38 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEEL   38 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHc
Confidence            5699999999999999999998864

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=93.35  E-value=0.04  Score=50.48  Aligned_cols=24  Identities=29%  Similarity=0.253  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|+|||||.+.++--
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl   53 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGF   53 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcC
Confidence            358999999999999999999863

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=93.34  E-value=0.058  Score=51.50  Aligned_cols=82  Identities=15%  Similarity=0.123  Sum_probs=46.2

Q ss_pred             EEEEEeccCcchhHHHH-HHHHHhhccCcCce-EEEecCccccCCCCChHHHHHHHHHHHhc--------CCCCC---CC
Q 042778          169 YALGIWGIGGIDRTTIA-RAIFNKISSNFEGS-CFLQNVREESQRPGGLGFLQQKLLSKLLQ--------DGIVI---PD  235 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA-~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l~~~ll~~l~~--------~~~~~---~~  235 (311)
                      ..++|.|-.|+|||+|| ..+.+...  -+.. +++-    +.++......+.+.+...-..        ..++.   .-
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~~~--~dv~~V~~~----iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~  237 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQQG--QNVICVYVA----IGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQY  237 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCT--TTCEEEEEE----ESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTT
T ss_pred             CEEEEecCCCCCccHHHHHHHHHhhc--CCcEEEEEE----cCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHH
Confidence            46799999999999996 47777654  3433 4443    333123344444444332110        11110   00


Q ss_pred             H---------HHHHHHhCCCeEEEEEecCCCh
Q 042778          236 I---------ALSFRQLSRRKVLIVLDDVTCF  258 (311)
Q Consensus       236 ~---------~~l~~~L~~kr~LlVLDdV~~~  258 (311)
                      .         +.+++  .++.+||++||+...
T Consensus       238 ~a~~~a~tiAEyfrd--~G~dVLli~Dsltr~  267 (507)
T 1fx0_A          238 LAPYTGAALAEYFMY--RERHTLIIYDDLSKQ  267 (507)
T ss_dssp             HHHHHHHHHHHHHHH--TTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHH--cCCcEEEEEecHHHH
Confidence            1         33443  589999999998654

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.33  E-value=0.044  Score=43.26  Aligned_cols=24  Identities=13%  Similarity=0.285  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus         6 ~~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            6 ELKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346889999999999999998875

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=93.33  E-value=0.058  Score=49.66  Aligned_cols=28  Identities=14%  Similarity=0.207  Sum_probs=23.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|+|..|.|||||.+.+...+...
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~~~~~~  163 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMIDYINQT  163 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCcC
Confidence            5689999999999999999998865443

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.32  E-value=0.043  Score=43.38  Aligned_cols=24  Identities=13%  Similarity=0.321  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456899999999999999988864

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=93.32  E-value=0.11  Score=44.62  Aligned_cols=36  Identities=11%  Similarity=0.195  Sum_probs=27.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~  203 (311)
                      ...|.|.|+.|+||||+++.+.+.+.. .+..+....
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~~~~~~~~~r   63 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTR   63 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCeeeeec
Confidence            468999999999999999999998644 455344443

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.31  E-value=0.044  Score=43.15  Aligned_cols=22  Identities=14%  Similarity=0.309  Sum_probs=19.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999988764

>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=93.31  E-value=0.038  Score=55.99  Aligned_cols=52  Identities=23%  Similarity=0.311  Sum_probs=38.8

Q ss_pred             CCCccchhhhHHHHHHhhccc-----------CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGAE-----------SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.++.|.+...++|.+.+...           ....+-+.++|++|.|||.||+++++.....
T Consensus       476 w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~  538 (806)
T 3cf2_A          476 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN  538 (806)
T ss_dssp             STTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCE
T ss_pred             HHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCc
Confidence            456778888888887765421           1124557899999999999999999986543

>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=93.30  E-value=0.043  Score=50.44  Aligned_cols=24  Identities=21%  Similarity=0.321  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL   77 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLL   77 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcC
Confidence            458999999999999999998763

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.28  E-value=0.043  Score=43.32  Aligned_cols=23  Identities=17%  Similarity=0.652  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.|.|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45789999999999999998864

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=93.28  E-value=0.047  Score=42.78  Aligned_cols=23  Identities=17%  Similarity=0.523  Sum_probs=20.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.|.|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35889999999999999988764

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.26  E-value=0.05  Score=45.30  Aligned_cols=25  Identities=12%  Similarity=0.037  Sum_probs=22.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4667899999999999999998875

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.25  E-value=0.12  Score=43.70  Aligned_cols=35  Identities=17%  Similarity=0.299  Sum_probs=26.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc-CcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS-NFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~-~F~~~~wv~  203 (311)
                      ..|.|-|..|.||||+++.+.+.+.. .+..+.+..
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~~v~~~r   39 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTR   39 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCCcceeee
Confidence            47899999999999999999998644 343334433

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.24  E-value=0.046  Score=44.29  Aligned_cols=24  Identities=8%  Similarity=0.095  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998774

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=93.23  E-value=0.037  Score=49.22  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            458999999999999999998775

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=93.21  E-value=0.068  Score=42.60  Aligned_cols=25  Identities=16%  Similarity=0.377  Sum_probs=22.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|..|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            4667899999999999999998875

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.14  E-value=0.055  Score=43.15  Aligned_cols=25  Identities=24%  Similarity=0.151  Sum_probs=21.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4667899999999999999998764

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.13  E-value=0.047  Score=49.97  Aligned_cols=24  Identities=33%  Similarity=0.378  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|+|||||.+.++--
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            358999999999999999998864

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=93.12  E-value=0.071  Score=52.01  Aligned_cols=26  Identities=19%  Similarity=0.245  Sum_probs=23.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.|.|+.|.||||+|+.+.+++.
T Consensus       396 ~~~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          396 GFTIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEeecCCCCCHHHHHHHHHHHhc
Confidence            57899999999999999999998864

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=93.11  E-value=0.054  Score=42.59  Aligned_cols=22  Identities=18%  Similarity=0.164  Sum_probs=19.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+...
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3789999999999999998764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.11  E-value=0.074  Score=43.76  Aligned_cols=24  Identities=17%  Similarity=-0.146  Sum_probs=20.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++.|+|..|.||||++..++.+.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~   27 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIY   27 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            478899999999999997766653

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.08  E-value=0.046  Score=43.99  Aligned_cols=23  Identities=13%  Similarity=0.208  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999998864

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.07  E-value=0.055  Score=43.14  Aligned_cols=26  Identities=15%  Similarity=0.365  Sum_probs=21.8

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +...-|.|+|.+|+|||||...+...
T Consensus         7 ~~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            7 DHLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHhcC
Confidence            34667899999999999999988654

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=93.07  E-value=0.1  Score=45.30  Aligned_cols=26  Identities=12%  Similarity=0.423  Sum_probs=22.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .....|+|+|.+|+|||||...+...
T Consensus        34 ~~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           34 MNSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             CCEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            34677899999999999999998874

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=93.06  E-value=0.046  Score=49.92  Aligned_cols=24  Identities=21%  Similarity=0.062  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaGl   49 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAGF   49 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCEEEEECCCCccHHHHHHHHHcC
Confidence            358999999999999999999864

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=93.05  E-value=0.13  Score=46.28  Aligned_cols=27  Identities=30%  Similarity=0.272  Sum_probs=21.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++...|-||+||||+|.+++.....
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~lA~   40 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALWMAR   40 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHHHHH
Confidence            466677799999999999998876544

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=93.04  E-value=0.051  Score=43.26  Aligned_cols=24  Identities=17%  Similarity=0.324  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            567899999999999999998875

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.04  E-value=0.046  Score=43.08  Aligned_cols=21  Identities=19%  Similarity=0.370  Sum_probs=18.5

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.|+|.+|+|||||...+.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            478999999999999998754

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.03  E-value=0.05  Score=44.24  Aligned_cols=25  Identities=8%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4677899999999999999998764

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.02  E-value=0.068  Score=42.63  Aligned_cols=25  Identities=20%  Similarity=0.415  Sum_probs=21.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3567899999999999999988764

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=93.02  E-value=0.05  Score=50.29  Aligned_cols=24  Identities=21%  Similarity=0.154  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|+|||||.+.+.--
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaGl   52 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAGL   52 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEEcCCCchHHHHHHHHHcC
Confidence            358999999999999999999764

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.02  E-value=0.055  Score=43.16  Aligned_cols=24  Identities=13%  Similarity=0.268  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            456889999999999999988764

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.02  E-value=0.064  Score=42.35  Aligned_cols=22  Identities=18%  Similarity=0.380  Sum_probs=19.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      --|.|+|.+|+|||||...+..
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4588999999999999998864

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=93.01  E-value=0.042  Score=50.30  Aligned_cols=24  Identities=33%  Similarity=0.383  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        31 Ge~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           31 GERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            458999999999999999998863

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=93.00  E-value=0.052  Score=43.66  Aligned_cols=24  Identities=29%  Similarity=0.630  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           18 TYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            567899999999999999998875

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=93.00  E-value=0.051  Score=49.85  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl   52 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAGI   52 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEEcCCCchHHHHHHHHHCC
Confidence            458999999999999999999863

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=92.97  E-value=0.084  Score=43.46  Aligned_cols=23  Identities=17%  Similarity=0.244  Sum_probs=19.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ...|+|+|.+|+|||||...+..
T Consensus        25 ~~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           25 TGKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            34688999999999999998865

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=92.97  E-value=0.1  Score=45.37  Aligned_cols=26  Identities=15%  Similarity=0.446  Sum_probs=22.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .....|.++|.+|+|||||...+...
T Consensus        37 ~~~~~I~vvG~~g~GKSSLin~l~~~   62 (270)
T 1h65_A           37 VNSLTILVMGKGGVGKSSTVNSIIGE   62 (270)
T ss_dssp             CCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            34678899999999999999998875

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=92.96  E-value=0.056  Score=42.55  Aligned_cols=24  Identities=8%  Similarity=0.288  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            6 QFKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998864

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=92.95  E-value=0.054  Score=43.18  Aligned_cols=24  Identities=13%  Similarity=0.463  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            456899999999999999998764

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=92.94  E-value=0.052  Score=49.83  Aligned_cols=24  Identities=17%  Similarity=0.189  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl   52 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAGI   52 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcC
Confidence            458999999999999999998864

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.93  E-value=0.077  Score=48.57  Aligned_cols=90  Identities=16%  Similarity=0.085  Sum_probs=49.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCC--CChHHH---HHHHHHHHhcCCCCCCCH-HHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRP--GGLGFL---QQKLLSKLLQDGIVIPDI-ALSFR  241 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~--~~~~~l---~~~ll~~l~~~~~~~~~~-~~l~~  241 (311)
                      -.+++|+|..|.|||||++.+...+.. -.+.+.+.+..+... .  .....+   +...+    + .....+. ..++.
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~~~~-~~g~I~ie~~~e~~~-~~~~~~v~~v~~q~~~~----~-~~~~~t~~~~i~~  247 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQEIPF-DQRLITIEDVPELFL-PDHPNHVHLFYPSEAKE----E-ENAPVTAATLLRS  247 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTTSCT-TSCEEEEESSSCCCC-TTCSSEEEEECC---------------CCHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCCC-CceEEEECCccccCc-cccCCEEEEeecCcccc----c-cccccCHHHHHHH
Confidence            347999999999999999999886544 245566664433211 0  000000   00000    0 0001122 56666


Q ss_pred             HhCCCeEEEEEecCCChHHHHHh
Q 042778          242 QLSRRKVLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       242 ~L~~kr~LlVLDdV~~~~~l~~l  264 (311)
                      .++...-.+++|.+...+.++.+
T Consensus       248 ~l~~~pd~~l~~e~r~~~~~~~l  270 (361)
T 2gza_A          248 CLRMKPTRILLAELRGGEAYDFI  270 (361)
T ss_dssp             HTTSCCSEEEESCCCSTHHHHHH
T ss_pred             HHhcCCCEEEEcCchHHHHHHHH
Confidence            66665556778888776655544

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=92.91  E-value=0.086  Score=48.38  Aligned_cols=38  Identities=16%  Similarity=0.122  Sum_probs=27.5

Q ss_pred             CCeEEEEEec-cCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          166 KDVYALGIWG-IGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       166 ~~~~vi~I~G-mgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...++|+|+| -||+||||+|..++..+...=..+..++
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~nLA~~La~~g~rVlliD  179 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAAACAIAHANMGKKVFYLN  179 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCceEEEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEE
Confidence            3478999985 8999999999998887554322334444

>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=92.90  E-value=0.17  Score=48.36  Aligned_cols=51  Identities=8%  Similarity=-0.029  Sum_probs=35.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEecCccccCCCCChHHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQNVREESQRPGGLGFLQQKLLSK  225 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~~~~~~s~~~~~~~~l~~~ll~~  225 (311)
                      -.++.|.|.+|+||||||..++....... ..++|+.    .   ......+...++..
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s----~---E~s~~~l~~r~~~~  293 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAM----L---EESVEETAEDLIGL  293 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEE----S---SSCHHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEe----c---cCCHHHHHHHHHHH
Confidence            45789999999999999999988765442 3456665    2   23445555555443

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=92.90  E-value=0.053  Score=49.96  Aligned_cols=24  Identities=25%  Similarity=0.169  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCcHHHHHHHHHHcC
Confidence            348999999999999999999864

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=92.89  E-value=0.11  Score=44.11  Aligned_cols=36  Identities=22%  Similarity=0.164  Sum_probs=25.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh-hccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK-ISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~-~~~~F~~~~wv~  203 (311)
                      -.++.|.|.+|+||||||..++.. ....-..++++.
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            458889999999999999887654 333233445554

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.88  E-value=0.11  Score=50.42  Aligned_cols=26  Identities=15%  Similarity=0.255  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+|.+.|+.|.||||+|+.+..++.
T Consensus       372 ~~~I~l~G~~GsGKSTia~~La~~L~  397 (546)
T 2gks_A          372 GFCVWLTGLPCAGKSTIAEILATMLQ  397 (546)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEccCCCCCCHHHHHHHHHHHhh
Confidence            57899999999999999999988754

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.88  E-value=0.055  Score=44.08  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=20.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhC
Confidence            456889999999999999888764

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=92.85  E-value=0.053  Score=43.40  Aligned_cols=24  Identities=13%  Similarity=0.296  Sum_probs=20.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            7 ELRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEEECCGGGCHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346889999999999999988774

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=92.84  E-value=0.057  Score=43.93  Aligned_cols=24  Identities=13%  Similarity=0.196  Sum_probs=20.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999877664

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=92.82  E-value=0.057  Score=43.31  Aligned_cols=24  Identities=13%  Similarity=0.350  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            457899999999999999998864

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=92.82  E-value=0.055  Score=49.85  Aligned_cols=24  Identities=29%  Similarity=0.202  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.++--
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            458999999999999999998763

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=92.81  E-value=0.057  Score=43.46  Aligned_cols=23  Identities=17%  Similarity=0.511  Sum_probs=20.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --|.|+|.+|+|||||...+.+.
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            45889999999999999998874

>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=92.79  E-value=0.062  Score=52.87  Aligned_cols=26  Identities=19%  Similarity=0.289  Sum_probs=23.6

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|.|.|+.|+||||+|+.+.+++
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L   76 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYL   76 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            36789999999999999999999886

>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=92.78  E-value=0.057  Score=50.23  Aligned_cols=49  Identities=10%  Similarity=0.209  Sum_probs=31.4

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh--hcc----CcCceEEEe
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK--ISS----NFEGSCFLQ  203 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~--~~~----~F~~~~wv~  203 (311)
                      ..|-.+|..+-..-.++.|+|.+|+|||||+..+.-.  ...    .-..++|+.
T Consensus       165 ~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid  219 (400)
T 3lda_A          165 KNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID  219 (400)
T ss_dssp             HHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE
T ss_pred             hhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEe
Confidence            3455555432223458999999999999999976543  211    123467776

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=92.78  E-value=0.1  Score=43.69  Aligned_cols=33  Identities=15%  Similarity=0.164  Sum_probs=24.2

Q ss_pred             EEEEe-ccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          170 ALGIW-GIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       170 vi~I~-GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +|+|+ +-||+||||+|..++..+...= .++-++
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la~~g-~VlliD   35 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLALQG-ETLLID   35 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHTTS-CEEEEE
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHHhcC-CEEEEE
Confidence            56665 7799999999999998765543 444444

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=92.72  E-value=0.058  Score=43.44  Aligned_cols=24  Identities=13%  Similarity=0.385  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            567899999999999999998764

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=92.71  E-value=0.078  Score=41.76  Aligned_cols=24  Identities=8%  Similarity=0.281  Sum_probs=20.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus         3 ~~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            3 IMKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            346899999999999999988764

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=92.68  E-value=0.063  Score=43.29  Aligned_cols=24  Identities=13%  Similarity=0.205  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            567899999999999999998864

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=92.67  E-value=0.065  Score=42.35  Aligned_cols=24  Identities=25%  Similarity=0.271  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.67  E-value=0.062  Score=43.03  Aligned_cols=24  Identities=13%  Similarity=0.112  Sum_probs=20.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999988764

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.66  E-value=0.061  Score=43.95  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           23 HGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             -CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            346899999999999999998874

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.66  E-value=0.08  Score=43.45  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=21.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3567899999999999999998774

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=92.64  E-value=0.15  Score=46.54  Aligned_cols=27  Identities=19%  Similarity=0.338  Sum_probs=23.1

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..+++.+.|-||+||||+|.+++....
T Consensus        17 ~~~i~~~~gkGGvGKTt~a~~lA~~la   43 (348)
T 3io3_A           17 SLKWIFVGGKGGVGKTTTSSSVAVQLA   43 (348)
T ss_dssp             TCSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHHHH
Confidence            467888999999999999998877655

>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=92.63  E-value=0.12  Score=47.70  Aligned_cols=28  Identities=18%  Similarity=0.312  Sum_probs=23.3

Q ss_pred             CCeEEEEEe-ccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIW-GIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~-GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|+|+ |-||+||||+|..++..+.
T Consensus       106 ~~~~vIav~s~KGGvGKTT~a~nLA~~La  134 (398)
T 3ez2_A          106 SEAYVIFISNLKGGVSKTVSTVSLAHAMR  134 (398)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEeCCCCccHHHHHHHHHHHHH
Confidence            347888888 7899999999999888765

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.63  E-value=0.065  Score=42.99  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            5 AIKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999988764

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=92.61  E-value=0.035  Score=54.44  Aligned_cols=49  Identities=14%  Similarity=0.030  Sum_probs=34.8

Q ss_pred             CCCccchhhhHHHHHHhhcccCC---------CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESK---------DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~---------~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.++|.+.....+...|..+..         .-.-|.++|.+|+|||+||+.+++..
T Consensus       294 ~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          294 APSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             SSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTC
T ss_pred             cchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhC
Confidence            56789999866666544443210         01158899999999999999998764

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=92.61  E-value=0.062  Score=42.97  Aligned_cols=24  Identities=13%  Similarity=0.163  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456889999999999999988764

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=92.60  E-value=0.075  Score=44.59  Aligned_cols=26  Identities=12%  Similarity=0.117  Sum_probs=22.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|+|+||.|+||+|+|..+-+.+
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~   35 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRL   35 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHc
Confidence            36799999999999999999886654

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.60  E-value=0.056  Score=43.74  Aligned_cols=24  Identities=17%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+...
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHcC
Confidence            557889999999999999998875

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.59  E-value=0.055  Score=43.65  Aligned_cols=22  Identities=14%  Similarity=0.229  Sum_probs=19.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|.|+|.+|+|||||...+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4789999999999999998774

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=92.59  E-value=0.066  Score=43.56  Aligned_cols=24  Identities=17%  Similarity=0.392  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|..|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            567899999999999999988874

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.56  E-value=0.064  Score=43.88  Aligned_cols=24  Identities=21%  Similarity=0.487  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999998774

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.53  E-value=0.063  Score=43.04  Aligned_cols=24  Identities=8%  Similarity=0.270  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            567899999999999999998853

>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=92.50  E-value=0.12  Score=48.22  Aligned_cols=29  Identities=17%  Similarity=0.117  Sum_probs=24.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .-.+++|+|..|.|||||.+.+...+...
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l~~~  194 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQELNSS  194 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCT
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhcCCC
Confidence            35689999999999999999998876543

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=92.47  E-value=0.066  Score=43.85  Aligned_cols=24  Identities=13%  Similarity=0.350  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        14 ~~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           14 LHKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            567899999999999999988764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.47  E-value=0.067  Score=43.43  Aligned_cols=24  Identities=13%  Similarity=0.289  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|+|+|..|+|||||...+...
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999998875

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=92.47  E-value=0.21  Score=45.33  Aligned_cols=29  Identities=21%  Similarity=0.238  Sum_probs=22.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ....++.+.|-||+||||+|.+++.....
T Consensus        24 ~~~~i~v~sgKGGvGKTTvA~~LA~~lA~   52 (349)
T 3ug7_A           24 DGTKYIMFGGKGGVGKTTMSAATGVYLAE   52 (349)
T ss_dssp             CSCEEEEEECSSSTTHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCccHHHHHHHHHHHHHH
Confidence            33566677799999999999988876433

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=92.45  E-value=0.066  Score=42.57  Aligned_cols=23  Identities=13%  Similarity=0.317  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.|.|+|..|+|||||...+...
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999998764

>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=92.43  E-value=0.093  Score=46.76  Aligned_cols=33  Identities=15%  Similarity=0.273  Sum_probs=25.2

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++++.+.+.     -.+++|.|..|+|||||.+.+. ..
T Consensus       156 i~~L~~~l~-----G~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          156 IDELVDYLE-----GFICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             HHHHHHHTT-----TCEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             HHHHHhhcc-----CcEEEEECCCCCCHHHHHHHHH-Hh
Confidence            444555543     2478999999999999999998 53

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.43  E-value=0.037  Score=45.77  Aligned_cols=24  Identities=8%  Similarity=0.127  Sum_probs=20.6

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHH
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ....|+|+|..|+|||||.+.+..
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g   48 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTN   48 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            356899999999999999987764

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=92.43  E-value=0.057  Score=48.13  Aligned_cols=21  Identities=24%  Similarity=0.513  Sum_probs=18.7

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|+|+|..|+|||||.+.++.
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            459999999999999999775

>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=92.42  E-value=0.065  Score=49.71  Aligned_cols=24  Identities=21%  Similarity=0.343  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|+|||||.+.+.--
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl   70 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRL   70 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            458999999999999999998863

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.41  E-value=0.071  Score=43.38  Aligned_cols=24  Identities=17%  Similarity=0.256  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            456889999999999999998875

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.39  E-value=0.085  Score=48.06  Aligned_cols=25  Identities=16%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +..+|+|+|.+|+|||||...+...
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~   97 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKM   97 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999999998864

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=92.39  E-value=0.053  Score=44.66  Aligned_cols=23  Identities=17%  Similarity=0.404  Sum_probs=20.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHH
Q 042778          167 DVYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      ....|.|+|.+|+|||||...+.
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHH
Confidence            36678999999999999999874

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.36  E-value=0.074  Score=42.45  Aligned_cols=24  Identities=13%  Similarity=0.263  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+...
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456899999999999999998764

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=92.29  E-value=0.069  Score=43.55  Aligned_cols=24  Identities=13%  Similarity=0.285  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|+|+|..|+|||||...+...
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            557899999999999999998764

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=92.28  E-value=0.06  Score=44.13  Aligned_cols=24  Identities=17%  Similarity=0.380  Sum_probs=20.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||.+.+.++
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc
Confidence            456889999999999999877664

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=92.27  E-value=0.18  Score=45.66  Aligned_cols=28  Identities=18%  Similarity=0.297  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..+++.+.|-||+||||+|.+++.....
T Consensus        15 ~~~i~~~sgkGGvGKTt~a~~lA~~la~   42 (334)
T 3iqw_A           15 SLRWIFVGGKGGVGKTTTSCSLAIQLAK   42 (334)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             CeEEEEEeCCCCccHHHHHHHHHHHHHh
Confidence            3677888899999999999998876544

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=92.26  E-value=0.073  Score=43.75  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhC
Confidence            567899999999999999998875

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=92.26  E-value=0.08  Score=44.36  Aligned_cols=26  Identities=12%  Similarity=0.133  Sum_probs=20.9

Q ss_pred             EEEEEecc-CcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGI-GGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~Gm-gGiGKTtLA~~v~~~~~~  194 (311)
                      ++|.|.|. ||+||||+|..++..+..
T Consensus         2 k~I~v~s~kgGvGKTt~a~nLa~~la~   28 (224)
T 1byi_A            2 KRYFVTGTDTEVGKTVASCALLQAAKA   28 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57888875 899999999998876443

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.25  E-value=0.074  Score=48.49  Aligned_cols=27  Identities=26%  Similarity=0.404  Sum_probs=23.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|.|..|.|||||.+.+......
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~I~g~~~~   97 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGMICNGASA   97 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            458999999999999999999998654

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=92.23  E-value=0.089  Score=43.48  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus        30 ~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           30 AIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            456789999999999999888764

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=92.20  E-value=0.081  Score=46.90  Aligned_cols=25  Identities=12%  Similarity=0.276  Sum_probs=22.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|+|+|..|+|||||..++...
T Consensus        23 ~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B           23 DLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            4788999999999999999998764

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.14  E-value=0.078  Score=43.16  Aligned_cols=24  Identities=17%  Similarity=0.533  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcC
Confidence            456899999999999999998763

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=92.14  E-value=0.079  Score=43.89  Aligned_cols=24  Identities=13%  Similarity=0.095  Sum_probs=20.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456889999999999999998764

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=92.12  E-value=0.096  Score=42.47  Aligned_cols=24  Identities=13%  Similarity=0.335  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+.+.
T Consensus        16 ~~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           16 LFKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            567899999999999999998874

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=92.10  E-value=0.35  Score=40.70  Aligned_cols=22  Identities=14%  Similarity=0.255  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|-+|+|||+|...+.+.
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4778999999999999987653

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=92.10  E-value=0.092  Score=44.66  Aligned_cols=25  Identities=12%  Similarity=0.303  Sum_probs=22.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|+|+|.+|+|||||...+...
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCC
Confidence            4678999999999999999998874

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=92.10  E-value=0.082  Score=42.93  Aligned_cols=24  Identities=21%  Similarity=0.202  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+.+.
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998864

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=92.09  E-value=0.082  Score=43.06  Aligned_cols=24  Identities=17%  Similarity=0.241  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999998875

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=92.09  E-value=0.08  Score=42.94  Aligned_cols=24  Identities=13%  Similarity=0.239  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+...
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            567899999999999999998774

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=92.08  E-value=0.076  Score=43.57  Aligned_cols=24  Identities=13%  Similarity=0.239  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            557899999999999999998774

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=92.07  E-value=0.08  Score=42.86  Aligned_cols=24  Identities=13%  Similarity=0.284  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           15 TLKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998775

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.06  E-value=0.08  Score=43.89  Aligned_cols=24  Identities=17%  Similarity=0.434  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+.+.
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            567899999999999999988764

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=92.05  E-value=0.093  Score=47.42  Aligned_cols=86  Identities=15%  Similarity=0.030  Sum_probs=50.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCCCe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSRRK  247 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~kr  247 (311)
                      .+++|+|..|.|||||++.+..-+... .+.+.+.+..+... . ....   . + .+...  .-... ..+.+.|..+.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~-~g~i~i~~~~e~~~-~-~~~~---~-i-~~~~g--gg~~~r~~la~aL~~~p  241 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKE-ERIISIEDTEEIVF-K-HHKN---Y-T-QLFFG--GNITSADCLKSCLRMRP  241 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTT-SCEEEEESSCCCCC-S-SCSS---E-E-EEECB--TTBCHHHHHHHHTTSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCC-CcEEEECCeecccc-c-cchh---E-E-EEEeC--CChhHHHHHHHHhhhCC
Confidence            479999999999999999998876442 55666664332211 0 0000   0 0 00000  01112 56677777777


Q ss_pred             EEEEEecCCChHHHHHh
Q 042778          248 VLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       248 ~LlVLDdV~~~~~l~~l  264 (311)
                      =+|+||++.+.+.++.+
T Consensus       242 ~ilildE~~~~e~~~~l  258 (330)
T 2pt7_A          242 DRIILGELRSSEAYDFY  258 (330)
T ss_dssp             SEEEECCCCSTHHHHHH
T ss_pred             CEEEEcCCChHHHHHHH
Confidence            78889998875554444

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=92.03  E-value=0.11  Score=43.23  Aligned_cols=24  Identities=8%  Similarity=0.095  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            567889999999999999998874

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=92.03  E-value=0.08  Score=43.43  Aligned_cols=25  Identities=8%  Similarity=0.275  Sum_probs=21.3

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhC
Confidence            3567899999999999999998764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=92.02  E-value=0.085  Score=42.90  Aligned_cols=24  Identities=17%  Similarity=0.318  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|..|+|||||...+.+.
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999988764

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=91.98  E-value=0.11  Score=42.66  Aligned_cols=23  Identities=17%  Similarity=0.349  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +-|.|.|..|+||||||.++..+
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            46889999999999999999885

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=91.95  E-value=0.075  Score=43.52  Aligned_cols=24  Identities=13%  Similarity=0.152  Sum_probs=20.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            556889999999999999988754

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=91.95  E-value=0.22  Score=54.27  Aligned_cols=54  Identities=13%  Similarity=0.192  Sum_probs=35.9

Q ss_pred             hhhhHHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          150 VESRVEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       150 r~~~~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ...-..+|..+|. .+-..-.++.|.|.+|+||||||..+.......=..++|+.
T Consensus       713 i~TG~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS  767 (1706)
T 3cmw_A          713 ISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  767 (1706)
T ss_dssp             ECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             cccCcHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEe
Confidence            3334445555554 22223458999999999999999999887554323466665

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=91.85  E-value=0.091  Score=42.58  Aligned_cols=24  Identities=8%  Similarity=0.261  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+...
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            567899999999999999998764

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.83  E-value=0.13  Score=41.21  Aligned_cols=24  Identities=25%  Similarity=0.288  Sum_probs=20.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHH
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ....|.|+|.+|+|||||...+..
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            466788999999999999988764

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=91.83  E-value=0.091  Score=46.75  Aligned_cols=24  Identities=13%  Similarity=0.272  Sum_probs=21.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|.+|+|||||...+...
T Consensus         8 ~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            8 CGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            568999999999999999998874

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=91.82  E-value=0.16  Score=43.21  Aligned_cols=28  Identities=11%  Similarity=-0.113  Sum_probs=23.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.++.|+|..|.||||++..+.++...+
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~   39 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYA   39 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            5688999999999999999888876544

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=91.81  E-value=0.16  Score=43.46  Aligned_cols=26  Identities=27%  Similarity=0.404  Sum_probs=20.9

Q ss_pred             EEEEEe-ccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIW-GIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~-GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++|+|+ +-||+||||+|..++..+..
T Consensus         3 ~vi~v~s~kgGvGKTt~a~~LA~~la~   29 (260)
T 3q9l_A            3 RIIVVTSGKGGVGKTTSSAAIATGLAQ   29 (260)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHh
Confidence            577776 56899999999998887554

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=91.78  E-value=0.072  Score=50.50  Aligned_cols=24  Identities=17%  Similarity=0.149  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+..-
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCc
Confidence            458999999999999999998774

>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=91.77  E-value=0.2  Score=47.15  Aligned_cols=27  Identities=26%  Similarity=0.324  Sum_probs=23.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +.+.|.|.+|.||||++..+...+...
T Consensus        46 ~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           46 HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            389999999999999999998875443

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.76  E-value=0.085  Score=51.02  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=21.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+++|+|..|.|||||++.++--.
T Consensus       313 e~~~i~G~NGsGKSTLlk~l~Gl~  336 (538)
T 1yqt_A          313 EVIGIVGPNGIGKTTFVKMLAGVE  336 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            489999999999999999998753

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=91.75  E-value=0.095  Score=42.96  Aligned_cols=23  Identities=22%  Similarity=0.418  Sum_probs=20.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .-.|.|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            45689999999999999998874

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=91.72  E-value=0.079  Score=43.60  Aligned_cols=24  Identities=8%  Similarity=0.365  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            567889999999999999988753

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.72  E-value=0.089  Score=42.78  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998875

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=91.70  E-value=0.096  Score=45.63  Aligned_cols=24  Identities=21%  Similarity=0.274  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999998764

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=91.70  E-value=0.11  Score=44.72  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=20.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+|||.|+.|+||||+|+.+..+
T Consensus         2 ~~i~ltG~~~sGK~tv~~~l~~~   24 (241)
T 1dek_A            2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999988664

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=91.63  E-value=0.1  Score=42.37  Aligned_cols=25  Identities=16%  Similarity=0.212  Sum_probs=21.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|..|+|||||...+...
T Consensus        16 ~~~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           16 TKLQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHSCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3678999999999999999988764

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.62  E-value=0.09  Score=42.53  Aligned_cols=26  Identities=19%  Similarity=0.133  Sum_probs=22.0

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .....|.|+|..|+|||||...+.+.
T Consensus        14 ~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           14 HQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhcC
Confidence            34567899999999999999998853

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=91.62  E-value=0.084  Score=42.51  Aligned_cols=24  Identities=21%  Similarity=0.123  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|..|+|||||...+...
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=91.60  E-value=0.18  Score=42.56  Aligned_cols=35  Identities=17%  Similarity=0.222  Sum_probs=24.7

Q ss_pred             EEEEEe-ccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIW-GIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~-GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|+|+ +-||+||||+|..++..+...=..+..++
T Consensus         3 ~~i~v~s~kgGvGKTt~a~~LA~~la~~g~~VlliD   38 (237)
T 1g3q_A            3 RIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVD   38 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEecCCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            577776 46899999999999887654422344444

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.59  E-value=0.096  Score=43.28  Aligned_cols=24  Identities=17%  Similarity=0.129  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           25 RKKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999988764

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=91.58  E-value=0.1  Score=43.93  Aligned_cols=25  Identities=4%  Similarity=0.115  Sum_probs=21.9

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....|.|+|.+|+|||||...+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4678899999999999999998764

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=91.54  E-value=0.078  Score=51.28  Aligned_cols=23  Identities=39%  Similarity=0.635  Sum_probs=21.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|+|..|+|||||++.++--
T Consensus       295 ei~~i~G~nGsGKSTLl~~l~Gl  317 (538)
T 3ozx_A          295 EIIGILGPNGIGKTTFARILVGE  317 (538)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=91.53  E-value=0.35  Score=53.54  Aligned_cols=57  Identities=12%  Similarity=0.175  Sum_probs=38.9

Q ss_pred             ccchhhhHHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          147 LVGVESRVEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       147 ~vGr~~~~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..+...-...|..+|. .+=..-.++-|+|.+|+||||||..+.......=..++|++
T Consensus       361 ~~~I~TG~~~LD~lLG~GGl~~G~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis  418 (2050)
T 3cmu_A          361 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (2050)
T ss_dssp             CCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             CceeeCCCHHHHHHhccCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3344444556666664 22223568999999999999999999887654434567776

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=91.52  E-value=0.11  Score=44.02  Aligned_cols=27  Identities=19%  Similarity=0.256  Sum_probs=24.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -..|.|-|+.|.||||+++.+.+.+..
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            457899999999999999999998765

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=91.48  E-value=0.12  Score=40.81  Aligned_cols=24  Identities=21%  Similarity=0.144  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..+..|+|..|.|||||..+++--
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~   46 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVG   46 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999999988753

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=91.48  E-value=0.1  Score=42.95  Aligned_cols=24  Identities=13%  Similarity=0.342  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            567899999999999999998764

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.48  E-value=0.089  Score=49.31  Aligned_cols=24  Identities=21%  Similarity=0.481  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +.-++|+|..|+|||||.+.++..
T Consensus        42 i~~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           42 CFNILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEEEEECSTTSSSHHHHHHHHTS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCc
Confidence            444999999999999999998764

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=91.45  E-value=0.1  Score=43.16  Aligned_cols=24  Identities=13%  Similarity=0.099  Sum_probs=20.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         9 ~~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A            9 FIKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999988764

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*

Probab=91.45  E-value=0.14  Score=44.07  Aligned_cols=28  Identities=21%  Similarity=0.310  Sum_probs=22.9

Q ss_pred             CeEEEEEe-ccCcchhHHHHHHHHHhhcc
Q 042778          167 DVYALGIW-GIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       167 ~~~vi~I~-GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++|+|+ +-||+||||+|..++..+..
T Consensus         5 ~~~vI~v~s~kGGvGKTt~a~~LA~~la~   33 (257)
T 1wcv_1            5 KVRRIALANQKGGVGKTTTAINLAAYLAR   33 (257)
T ss_dssp             CCCEEEECCSSCCHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCchHHHHHHHHHHHHHH
Confidence            35788887 67999999999998887554

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=91.45  E-value=0.087  Score=43.90  Aligned_cols=24  Identities=17%  Similarity=0.248  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|.|+|.+|+|||||...+.+.
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            457889999999999999988763

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=91.44  E-value=0.2  Score=43.20  Aligned_cols=28  Identities=25%  Similarity=0.227  Sum_probs=23.0

Q ss_pred             CCeEEEEEe-ccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIW-GIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~-GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|+|+ +-||+||||+|..++..+.
T Consensus        25 ~~~~vI~v~s~kGGvGKTT~a~~LA~~la   53 (267)
T 3k9g_A           25 KKPKIITIASIKGGVGKSTSAIILATLLS   53 (267)
T ss_dssp             -CCEEEEECCSSSSSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEEeCCCCchHHHHHHHHHHHHH
Confidence            346788886 6799999999999998876

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=91.44  E-value=0.13  Score=41.60  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=20.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHH
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ....|.|+|.+|+|||||...+..
T Consensus        21 ~~~~i~v~G~~~~GKssli~~l~~   44 (189)
T 2x77_A           21 RKIRVLMLGLDNAGKTSILYRLHL   44 (189)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHc
Confidence            456789999999999999998854

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.43  E-value=0.11  Score=42.90  Aligned_cols=24  Identities=8%  Similarity=0.281  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            567899999999999999988764

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=91.43  E-value=0.11  Score=43.75  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .-.|||.|.-|.||||+++.+..
T Consensus         9 ~~~iglTGgigsGKStv~~~l~~   31 (210)
T 4i1u_A            9 MYAIGLTGGIGSGKTTVADLFAA   31 (210)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHH
Confidence            55799999999999999998765

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=91.41  E-value=0.093  Score=42.91  Aligned_cols=23  Identities=17%  Similarity=0.148  Sum_probs=20.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ...|.|+|.+|+|||||...+..
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            45689999999999999998864

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=91.40  E-value=0.098  Score=50.60  Aligned_cols=24  Identities=21%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.-.
T Consensus        47 Ge~~~LvG~NGaGKSTLlk~l~Gl   70 (538)
T 1yqt_A           47 GMVVGIVGPNGTGKSTAVKILAGQ   70 (538)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998864

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=91.39  E-value=0.1  Score=42.84  Aligned_cols=24  Identities=21%  Similarity=0.141  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|.|+|.+|+|||||...+...
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           25 RKKLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456899999999999999988874

---

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	311
d1fyva_	161	c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (H	3e-18
d1fyxa_	149	c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (H	6e-16
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	8e-16

>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 = 78.2 bits (192), Expect = 3e-18
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 2/91 (2%)

Query: 14  PRNHKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQ-LNRGDEISQSLVDAIEAS 72
            RN ++  F S+ G D        L   L ++G++  + ++    G  I ++++  IE S
Sbjct: 8   QRNLQFHAFISYSGHD-SFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKS 66

Query: 73  AISLIIFSEAYASSRWCLDELVKILTRELEE 103
             S+ + S  +  S WC  EL         E
Sbjct: 67  YKSIFVLSPNFVQSEWCHYELYFAHHNLFHE 97

>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 = 71.3 bits (174), Expect = 6e-16
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 4/92 (4%)

Query: 15  RNHKYDVFQSFRGEDNRDNFTGHLYSAL--SQKGIETFIDDQ-LNRGDEISQSLVDAIEA 71
           RN  YD F S+   D        +   L       +  +  +    G  I  +++D+IE 
Sbjct: 2   RNICYDAFVSYSERD-AYWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEK 60

Query: 72  SAISLIIFSEAYASSRWCLDELVKILTRELEE 103
           S  ++ + SE +  S WC  EL     R  +E
Sbjct: 61  SHKTVFVLSENFVKSEWCKYELDFSHFRLFDE 92

>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 = 73.7 bits (180), Expect = 8e-16
 Identities = 28/185 (15%), Positives = 53/185 (28%), Gaps = 30/185 (16%)

Query: 147 LVGVESRVEEI-ESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK----ISSNFEGSCF 201
               E  V+ + + L      D + L + G  G  ++ IA    +K    I  N++   +
Sbjct: 22  CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVW 81

Query: 202 LQNVREESQRPGGLGFLQQKLLSKLLQDGIVIPD----------IALSFRQLSRRKVLIV 251
           L      + +     F    L+ K   D +  P             +    + R   L V
Sbjct: 82  L-KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFV 140

Query: 252 LDDV------TCFRQIKSLIGM--------LRNCCVKEKYEMKELGDDHALELFSRHAFK 297
            DDV         ++++    +               E  E+  L  D   +    +   
Sbjct: 141 FDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMP 200

Query: 298 QNNPH 302
                
Sbjct: 201 MPVGE 205

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	311
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.94
d1fyva_	161	Toll-like receptor 1, TLR1 {Human (Homo sapiens) [	99.71
d1fyxa_	149	Toll-like receptor 2, TLR2 {Human (Homo sapiens) [	99.59
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.74
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.69
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.58
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.5
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.43
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.32
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.3
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.29
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.28
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.18
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.15
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.13
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.09
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.07
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.97
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.93
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.91
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.87
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.85
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.84
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.7
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.57
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.52
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.52
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.5
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.44
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.4
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.32
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.32
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.3
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.29
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.29
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.25
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.2
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.19
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.17
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.15
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.06
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.04
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.01
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.98
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.96
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.95
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.94
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.89
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.88
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.87
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.76
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.74
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.7
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.68
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.62
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.61
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.6
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.49
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.48
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.46
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.42
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.38
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.37
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.37
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.36
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.33
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	96.32
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.31
d1okkd2	207	GTPase domain of the signal recognition particle r	96.26
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.26
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.2
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.19
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.18
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.15
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.12
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.12
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.1
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.09
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.06
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.06
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.06
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.05
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.03
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.97
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.96
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.91
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.89
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.87
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.86
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.82
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.73
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.66
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.59
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.58
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.54
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	95.52
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.49
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	95.48
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.41
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.28
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.21
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.19
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.16
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.09
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.04
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	95.03
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.0
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.97
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	94.91
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.85
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.8
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.79
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.77
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.75
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.71
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.71
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.66
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.64
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.64
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.62
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.6
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.59
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	94.53
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.52
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.51
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.5
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	94.48
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.44
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.42
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.42
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.42
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.41
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.37
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.27
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	94.09
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.06
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.93
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.93
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.91
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.88
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.86
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	93.83
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.83
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.81
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.73
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.72
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.72
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	93.67
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	93.61
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.61
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.54
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.52
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.42
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.38
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.34
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.34
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.32
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	93.32
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.25
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.21
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.1
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.09
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.04
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.01
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	92.99
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	92.96
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.92
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	92.89
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	92.88
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.88
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.86
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	92.81
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.75
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.74
d1nrjb_	209	Signal recognition particle receptor beta-subunit	92.7
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	92.7
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.66
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.64
d2fh5b1	207	Signal recognition particle receptor beta-subunit	92.59
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.59
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.58
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.58
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.58
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.36
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.33
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.3
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.24
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.24
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.16
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.13
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.13
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.12
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	92.04
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.02
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.96
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	91.92
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	91.9
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.87
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.83
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	91.83
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.78
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	91.77
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.75
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.73
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.65
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.64
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.61
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.61
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	91.61
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	91.59
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.44
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	91.23
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	91.23
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	91.11
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	91.07
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	90.95
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.9
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	90.84
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	90.54
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	90.53
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.4
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	90.27
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.15
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	90.01
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.92
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	89.71
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	88.76
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	88.71
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	88.53
d1tuea_	205	Replication protein E1 helicase domain {Human papi	88.43
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	88.24
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	87.84
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	87.67
d1wu7a1	97	Histidyl-tRNA synthetase (HisRS), C-terminal domai	87.5
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.4
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	86.33
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	85.91
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	85.21
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	84.99
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	84.65
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	84.52
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	84.42
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	83.28
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	82.83
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	82.82
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.57
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	80.36

>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=99.94  E-value=1e-26  Score=207.24  Aligned_cols=160  Identities=17%  Similarity=0.137  Sum_probs=119.3

Q ss_pred             CCCccchhhhHHHHHHhhcc-cCCCeEEEEEeccCcchhHHHHHHHHHh----hccCcCceEEEecCccccCCCCChHHH
Q 042778          144 KNQLVGVESRVEEIESLLGA-ESKDVYALGIWGIGGIDRTTIARAIFNK----ISSNFEGSCFLQNVREESQRPGGLGFL  218 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~GmgGiGKTtLA~~v~~~----~~~~F~~~~wv~~~~~~s~~~~~~~~l  218 (311)
                      ...++||+.++++|.++|.. .+.+.++|+|+|||||||||||+++|++    ...+|++++|++    ++. ..+...+
T Consensus        19 ~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~----vs~-~~~~~~l   93 (277)
T d2a5yb3          19 QMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK----DSG-TAPKSTF   93 (277)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE----CCC-CSTTHHH
T ss_pred             CCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEE----ecC-CCCHHHH
Confidence            56788999999999999865 3456899999999999999999999987    566799999999    666 6665655


Q ss_pred             HHHHHH---HHhcCCC-CC----CCH------HHHHHHhCCCeEEEEEecCCChHHHHHhhccCCC--------------
Q 042778          219 QQKLLS---KLLQDGI-VI----PDI------ALSFRQLSRRKVLIVLDDVTCFRQIKSLIGMLRN--------------  270 (311)
Q Consensus       219 ~~~ll~---~l~~~~~-~~----~~~------~~l~~~L~~kr~LlVLDdV~~~~~l~~l~~~~~~--------------  270 (311)
                      ...+..   .+..... ..    ...      ..+.+.|.++|+||||||||+.++++.+......              
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~~~srilvTTR~~~v~~~~  173 (277)
T d2a5yb3          94 DLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAA  173 (277)
T ss_dssp             HHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGC
T ss_pred             HHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcccCceEEEEeehHHHHHhc
Confidence            554433   3322221 11    111      4577889999999999999999999887532222              


Q ss_pred             cCCceEEEcCCCChHHHHHHHHHhhcCCCCCCCcHHHhh
Q 042778          271 CCVKEKYEMKELGDDHALELFSRHAFKQNNPHIGFEELS  309 (311)
Q Consensus       271 ~~~~~~y~v~~L~~~ea~~Lf~~~af~~~~~~~~~~~l~  309 (311)
                      .....+|+|++|+.+||++||+++||..+.++ ..++++
T Consensus       174 ~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~-~~~~~~  211 (277)
T d2a5yb3         174 SQTCEFIEVTSLEIDECYDFLEAYGMPMPVGE-KEEDVL  211 (277)
T ss_dssp             CSCEEEEECCCCCHHHHHHHHHHTSCCCC--C-HHHHHH
T ss_pred             CCCCceEECCCCCHHHHHHHHHHHhCCccCch-hhHHHH
Confidence            22336899999999999999999999876544 344443

>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=99.71  E-value=1.7e-18  Score=141.20  Aligned_cols=87  Identities=24%  Similarity=0.491  Sum_probs=78.5

Q ss_pred             CCCCCCCCCcccEEecCccccCCCChH-HHHHHHHHhCCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccc
Q 042778            9 SSPSSPRNHKYDVFQSFRGEDNRDNFT-GHLYSALSQKGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASS   86 (311)
Q Consensus         9 ~~s~~~~~~~~dvFis~~g~D~~~~f~-~~L~~~L~~~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S   86 (311)
                      +.+......+|||||||+++|.  .|+ ..|...|+++|+++|+|+ ++.+|+.+..+|.++|++|+.+|+|+||+|..|
T Consensus         3 pl~~~~~~~~yDvFisys~~D~--~~v~~~L~~~Le~~g~~v~~d~~d~~~G~~~~~~i~~~i~~s~~~i~vlS~~~~~s   80 (161)
T d1fyva_           3 PLEELQRNLQFHAFISYSGHDS--FWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQS   80 (161)
T ss_dssp             CSTTSSSCCCEEEEEECCGGGH--HHHHHTHHHHHHTTTCCEECTTTTCCTTSCHHHHHHHHHHHEEEEEEEESHHHHHH
T ss_pred             ChhHcCCCCeeEEEEecChhHH--HHHHHHHHHHHHhCCCcceEeccccccccccHHHHHHHHHhCCEEEEEecCccccC
Confidence            3444567789999999999995  477 579999999999999999 999999999999999999999999999999999


Q ss_pred             cchHHHHHHHH
Q 042778           87 RWCLDELVKIL   97 (311)
Q Consensus        87 ~wcl~El~~i~   97 (311)
                      .||..|+..++
T Consensus        81 ~w~~~E~~~a~   91 (161)
T d1fyva_          81 EWCHYELYFAH   91 (161)
T ss_dssp             TSHHHHHHTTS
T ss_pred             hHHHHHHHHHH
Confidence            99999986554

>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=99.59  E-value=1.1e-16  Score=128.73  Aligned_cols=81  Identities=26%  Similarity=0.449  Sum_probs=72.6

Q ss_pred             CCCcccEEecCccccCCCChH-HHHHHHHHh--CCCcEEeeC-CCCCCCcchHHHHHHHHhccceeeeeccCcccccchH
Q 042778           15 RNHKYDVFQSFRGEDNRDNFT-GHLYSALSQ--KGIETFIDD-QLNRGDEISQSLVDAIEASAISLIIFSEAYASSRWCL   90 (311)
Q Consensus        15 ~~~~~dvFis~~g~D~~~~f~-~~L~~~L~~--~gi~~f~d~-~~~~G~~~~~~i~~ai~~s~~~i~v~S~~y~~S~wcl   90 (311)
                      ....|||||||+++|.  .|+ .+|...|++  .|+++|+|+ ++.+|+.+..+|.++|++|++.|+|+||+|..|.||.
T Consensus         2 ~~~~YDvFiSys~~D~--~~V~~~l~~~LE~~~~g~~~~~~~rd~~~G~~~~~~i~~~i~~S~~~i~vlS~~~l~s~wc~   79 (149)
T d1fyxa_           2 RNICYDAFVSYSERDA--YWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWCK   79 (149)
T ss_dssp             CSCCEEEEEECCGGGH--HHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCCEEEEEEECchhhH--HHHHHHHHHHHHhcCCCceEEEecccccccchHHHHHHHHHHhCCEEEEEEcCccccccchH
Confidence            4578999999999995  576 568999976  499999998 9999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 042778           91 DELVKIL   97 (311)
Q Consensus        91 ~El~~i~   97 (311)
                      .|+..++
T Consensus        80 ~E~~~a~   86 (149)
T d1fyxa_          80 YELDFSH   86 (149)
T ss_dssp             HHSCCSC
T ss_pred             HHHHHHH
Confidence            9985543

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.74  E-value=5.4e-08  Score=83.17  Aligned_cols=47  Identities=13%  Similarity=0.304  Sum_probs=39.2

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++|+||+.++++|.+.      ..+.+.|+|++|+|||+|++.+.++....+
T Consensus        11 ~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~   57 (283)
T d2fnaa2          11 RKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGINELNLPY   57 (283)
T ss_dssp             GGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHHHHTCCE
T ss_pred             hhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHHHCCCCe
Confidence            67899999999988763      235788999999999999999998875543

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.69  E-value=1.8e-07  Score=79.65  Aligned_cols=147  Identities=15%  Similarity=0.131  Sum_probs=93.4

Q ss_pred             CCCccchhhhHHHHHHhhccc----CCCeEEEEEeccCcchhHHHHHHHHHhhccCcCce-EEEecCccccCCCCChHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAE----SKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGS-CFLQNVREESQRPGGLGFL  218 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~-~wv~~~~~~s~~~~~~~~l  218 (311)
                      +..++||+.++++|.++|...    ....+.+.|+|++|+||||+|+.+++.+....... +++.    ... ......+
T Consensus        15 p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~----~~~-~~~~~~~   89 (276)
T d1fnna2          15 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN----GFI-YRNFTAI   89 (276)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE----TTT-CCSHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEec----chh-hhhhhhh
Confidence            567999999999999988641    23367899999999999999999999987665543 3333    222 4556666


Q ss_pred             HHHHHHHHhcCCC-CCCCH----HHHHHHh--CCCeEEEEEecCCChHH-----HHHhhc------cCCC----------
Q 042778          219 QQKLLSKLLQDGI-VIPDI----ALSFRQL--SRRKVLIVLDDVTCFRQ-----IKSLIG------MLRN----------  270 (311)
Q Consensus       219 ~~~ll~~l~~~~~-~~~~~----~~l~~~L--~~kr~LlVLDdV~~~~~-----l~~l~~------~~~~----------  270 (311)
                      ...+......... .....    ..+.+.+  .....++++|++++...     +..+..      ....          
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  169 (276)
T d1fnna2          90 IGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDA  169 (276)
T ss_dssp             HHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH
T ss_pred             hhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchh
Confidence            6666666554433 22222    3333332  34667788888775321     111110      0000          


Q ss_pred             -----------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 -----------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 -----------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                 ......+.+.+++.++..+++.+++
T Consensus       170 ~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         170 VLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             HHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             hhhhcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence                       1122457899999999999988754

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.58  E-value=6.3e-07  Score=77.25  Aligned_cols=133  Identities=15%  Similarity=0.216  Sum_probs=83.3

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-----C-cCceEEEecCccccCC---CCCh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-----N-FEGSCFLQNVREESQR---PGGL  215 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-----~-F~~~~wv~~~~~~s~~---~~~~  215 (311)
                      +.++||+.+++++...|....  -.-+.++|.+|+|||+|+..+++++..     . ....+|..+....-..   ....
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~--k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~   95 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDF   95 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCH
T ss_pred             CcccChHHHHHHHHHHHhcCc--cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhH
Confidence            468999999999999997433  234569999999999999999987432     1 2345666544332220   1222


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh----------HHHHHhh-ccCCC--------------
Q 042778          216 GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF----------RQIKSLI-GMLRN--------------  270 (311)
Q Consensus       216 ~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~----------~~l~~l~-~~~~~--------------  270 (311)
                      ....+.++..                .-..++++|++|++...          ..+..++ |....              
T Consensus        96 e~r~~~i~~~----------------~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey  159 (268)
T d1r6bx2          96 EKRFKALLKQ----------------LEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEF  159 (268)
T ss_dssp             HHHHHHHHHH----------------HSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHH
T ss_pred             HHHHHHHHHH----------------hhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHH
Confidence            2222222222                22457799999998643          1233332 32222              


Q ss_pred             ----------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 ----------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 ----------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                                ...-.+..|++++.+++.+++...+
T Consensus       160 ~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         160 SNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             HCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence                      2334678999999999999997654

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.50  E-value=1e-06  Score=75.28  Aligned_cols=147  Identities=13%  Similarity=0.119  Sum_probs=89.3

Q ss_pred             CCCccchhhhHHHHHHhhcc----c--CCC-eEEEEEeccCcchhHHHHHHHHHhhccCc------CceEEEecCccccC
Q 042778          144 KNQLVGVESRVEEIESLLGA----E--SKD-VYALGIWGIGGIDRTTIARAIFNKISSNF------EGSCFLQNVREESQ  210 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~----~--~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~~F------~~~~wv~~~~~~s~  210 (311)
                      ++.++||+.++++|.+.|..    +  ... ..++.|+|++|+||||+++++++.+....      ....++.    ...
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~----~~~   90 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN----AFN   90 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE----GGG
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeec----ccc
Confidence            67899999999999887632    1  122 44567889999999999999999754321      1233444    333


Q ss_pred             CCCChHHHHHHHHHHHhcCCC-CCCCH----HHHHHHh--CCCeEEEEEecCCChH--------HHHHhh-------ccC
Q 042778          211 RPGGLGFLQQKLLSKLLQDGI-VIPDI----ALSFRQL--SRRKVLIVLDDVTCFR--------QIKSLI-------GML  268 (311)
Q Consensus       211 ~~~~~~~l~~~ll~~l~~~~~-~~~~~----~~l~~~L--~~kr~LlVLDdV~~~~--------~l~~l~-------~~~  268 (311)
                       ..........+...+..... .....    ..+.+.+  .....++++|.++...        ....+.       +..
T Consensus        91 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~  169 (287)
T d1w5sa2          91 -APNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRD  169 (287)
T ss_dssp             -CCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTT
T ss_pred             -ccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhh
Confidence             44555566666665554333 11222    3333333  3467788888876321        111111       111


Q ss_pred             CC--------------------------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          269 RN--------------------------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       269 ~~--------------------------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                      ..                          ........+++++.++..+++..++
T Consensus       170 ~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~  222 (287)
T d1w5sa2         170 GVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRA  222 (287)
T ss_dssp             SCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             cccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhH
Confidence            00                          2235678899999999999998765

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.43  E-value=5.3e-07  Score=73.88  Aligned_cols=61  Identities=11%  Similarity=0.224  Sum_probs=45.3

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc-----C-cCceEEEecCcc
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS-----N-FEGSCFLQNVRE  207 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~-----~-F~~~~wv~~~~~  207 (311)
                      +..+||+.+++++...|....  -.-+.++|.+|+|||+|+..++.++..     . -+..+|..+...
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~--k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~   88 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA   88 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccC--CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHH
Confidence            468999999999999997532  224679999999999999999997532     1 245566654433

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.32  E-value=1.8e-06  Score=72.01  Aligned_cols=138  Identities=12%  Similarity=0.177  Sum_probs=86.4

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      ..++||.+..+++|..++..+  .+..+-++|+.|+||||+|+.+++.+...+ ...++..+.   +. ..+...+...+
T Consensus        14 ~~d~ig~~~~~~~L~~~~~~~--~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~---~~-~~~~~~i~~~~   87 (224)
T d1sxjb2          14 LSDIVGNKETIDRLQQIAKDG--NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNA---SD-DRGIDVVRNQI   87 (224)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSC--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECT---TS-CCSHHHHHTHH
T ss_pred             HHHhcCCHHHHHHHHHHHHcC--CCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccc---cc-cCCceehhhHH
Confidence            467899999999999998743  344577999999999999999999865443 222333332   22 44444444333


Q ss_pred             HHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh-----ccCCC----------------cCCceEEEc
Q 042778          223 LSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI-----GMLRN----------------CCVKEKYEM  279 (311)
Q Consensus       223 l~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~-----~~~~~----------------~~~~~~y~v  279 (311)
                      ..........          ...+.-++|+|+++..  .....+.     +....                ......+++
T Consensus        88 ~~~~~~~~~~----------~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~  157 (224)
T d1sxjb2          88 KHFAQKKLHL----------PPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRY  157 (224)
T ss_dssp             HHHHHBCCCC----------CTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             HHHHHhhccC----------CCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhh
Confidence            3222221110          1235568889999753  2222221     11111                244568899


Q ss_pred             CCCChHHHHHHHHHhhcC
Q 042778          280 KELGDDHALELFSRHAFK  297 (311)
Q Consensus       280 ~~L~~~ea~~Lf~~~af~  297 (311)
                      ++++.++-...+.+.+-.
T Consensus       158 ~~~~~~~i~~~l~~i~~~  175 (224)
T d1sxjb2         158 SKLSDEDVLKRLLQIIKL  175 (224)
T ss_dssp             CCCCHHHHHHHHHHHHHH
T ss_pred             cccchhhhHHHHHHHHHh
Confidence            999999999998877654

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.30  E-value=1e-06  Score=73.89  Aligned_cols=148  Identities=14%  Similarity=0.151  Sum_probs=88.1

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc---CceEEEecCccccCCCCChHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF---EGSCFLQNVREESQRPGGLGFLQQ  220 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F---~~~~wv~~~~~~s~~~~~~~~l~~  220 (311)
                      -++++|.+..++.|..++...  ..+.+.++|++|+||||+|+.+++++....   ...+.+.    .+. ..+...+..
T Consensus        11 ~~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~----~~~-~~~~~~~~~   83 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSA--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN----ASD-ERGISIVRE   83 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCT--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC----SSS-CCCHHHHTT
T ss_pred             HHHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhee----ccc-cccchHHHH
Confidence            457899999999999998743  344578999999999999999999853321   1222222    222 334433332


Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh-----ccCCC----------------cCCceEE
Q 042778          221 KLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI-----GMLRN----------------CCVKEKY  277 (311)
Q Consensus       221 ~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~-----~~~~~----------------~~~~~~y  277 (311)
                      . +...............+......+.-+||+|+++..  .....+.     .....                ......+
T Consensus        84 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i  162 (237)
T d1sxjd2          84 K-VKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKF  162 (237)
T ss_dssp             H-HHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEE
T ss_pred             H-HHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhh
Confidence            2 222222211111113344444455557899999753  2232221     11111                2233678


Q ss_pred             EcCCCChHHHHHHHHHhhcCCC
Q 042778          278 EMKELGDDHALELFSRHAFKQN  299 (311)
Q Consensus       278 ~v~~L~~~ea~~Lf~~~af~~~  299 (311)
                      ++++++.++..+++.+.+.+..
T Consensus       163 ~f~~~~~~~~~~~L~~i~~~e~  184 (237)
T d1sxjd2         163 RFKALDASNAIDRLRFISEQEN  184 (237)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTT
T ss_pred             ccccccccccchhhhhhhhhhc
Confidence            9999999999999988776543

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.29  E-value=2.6e-06  Score=77.23  Aligned_cols=134  Identities=13%  Similarity=0.185  Sum_probs=76.4

Q ss_pred             CCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC------cCceEEEecCccccCC---CCCh
Q 042778          145 NQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN------FEGSCFLQNVREESQR---PGGL  215 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F~~~~wv~~~~~~s~~---~~~~  215 (311)
                      +.++||+.+++++...|.....  .-+.++|.+|+|||+|+..+++++...      .+..+|..+++.+-..   ....
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k--~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~   99 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTK--NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEF   99 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSC--CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CH
T ss_pred             CCCcCcHHHHHHHHHHHhcCCC--CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhH
Confidence            4689999999999998874321  123677999999999999888873221      3456776655443220   1122


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChHHH----------HHhh-----ccCCC----------
Q 042778          216 GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFRQI----------KSLI-----GMLRN----------  270 (311)
Q Consensus       216 ~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~~l----------~~l~-----~~~~~----------  270 (311)
                      ..-++.++..+..               ....++|++|++...-..          +-|.     |....          
T Consensus       100 e~r~~~i~~~~~~---------------~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~  164 (387)
T d1qvra2         100 EERLKAVIQEVVQ---------------SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYR  164 (387)
T ss_dssp             HHHHHHHHHHHHT---------------TCSSEEEEECCC-------------------HHHHHTTCCCEEEEECHHHHH
T ss_pred             HHHHHHHHHHhcc---------------CCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHH
Confidence            2222223222211               134799999999754211          1111     11111          


Q ss_pred             --------cCCceEEEcCCCChHHHHHHHHHhh
Q 042778          271 --------CCVKEKYEMKELGDDHALELFSRHA  295 (311)
Q Consensus       271 --------~~~~~~y~v~~L~~~ea~~Lf~~~a  295 (311)
                              ...-.+..|++.+.+++.+++...+
T Consensus       165 ~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         165 EIEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             HhcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence                    2344678899999999999988654

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.28  E-value=1.2e-06  Score=73.14  Aligned_cols=138  Identities=12%  Similarity=0.201  Sum_probs=83.6

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      ..++||.+..++.|..++..+  ....+-++|+.|+||||+|+.+++.+... +...+...+   .+. ..+.......+
T Consensus        13 ~~divg~~~~~~~L~~~i~~~--~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~---~~~-~~~~~~~~~~~   86 (227)
T d1sxjc2          13 LDEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN---ASD-DRGIDVVRNQI   86 (227)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC---TTS-CCSHHHHHTHH
T ss_pred             HHHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEec---ccc-cCCeeeeecch
Confidence            457999999999999998753  34446799999999999999999985432 322222222   222 33333332222


Q ss_pred             HHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh--HHHHHhh---c--cCCC----------------cCCceEEEc
Q 042778          223 LSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF--RQIKSLI---G--MLRN----------------CCVKEKYEM  279 (311)
Q Consensus       223 l~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~--~~l~~l~---~--~~~~----------------~~~~~~y~v  279 (311)
                      ........           ....++-++|+|+++..  .....|.   .  ....                ......+++
T Consensus        87 ~~~~~~~~-----------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          87 KDFASTRQ-----------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             HHHHHBCC-----------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             hhcccccc-----------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence            22111110           11234558889999753  3333332   1  1111                345578899


Q ss_pred             CCCChHHHHHHHHHhhcCC
Q 042778          280 KELGDDHALELFSRHAFKQ  298 (311)
Q Consensus       280 ~~L~~~ea~~Lf~~~af~~  298 (311)
                      ++++.++-.+++.+-+-..
T Consensus       156 ~~~~~~~i~~~l~~I~~~e  174 (227)
T d1sxjc2         156 QPLPQEAIERRIANVLVHE  174 (227)
T ss_dssp             CCCCHHHHHHHHHHHHHTT
T ss_pred             ccccccccccccccccccc
Confidence            9999999988888766543

>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=98.18  E-value=7.5e-07  Score=74.71  Aligned_cols=139  Identities=16%  Similarity=0.189  Sum_probs=82.9

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEecCccccCCCCChHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQNVREESQRPGGLGFLQQKL  222 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~~~~~~s~~~~~~~~l~~~l  222 (311)
                      ..+++|.+..+++|..++..+  ..+.+-|+|+.|+||||+|+.+++.+... +.......+.   +. ..+...+...+
T Consensus        23 ~~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~---s~-~~~~~~~~~~~   96 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNA---SD-ERGINVIREKV   96 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEET---TC-HHHHHTTHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEec---Cc-ccchhHHHHHH
Confidence            568999999999999999754  35567899999999999999999986442 2222222111   11 11111111111


Q ss_pred             HHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhhc-----cCCC----------------cCCceEEEc
Q 042778          223 LSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLIG-----MLRN----------------CCVKEKYEM  279 (311)
Q Consensus       223 l~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~~-----~~~~----------------~~~~~~y~v  279 (311)
                       .......          .....++.++++||++.  ......|..     ....                ......+.+
T Consensus        97 -~~~~~~~----------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~  165 (231)
T d1iqpa2          97 -KEFARTK----------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRF  165 (231)
T ss_dssp             -HHHHHSC----------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEEC
T ss_pred             -HHHHhhh----------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccc
Confidence             1111000          01124677889999864  233333321     1111                234467899


Q ss_pred             CCCChHHHHHHHHHhhcCCC
Q 042778          280 KELGDDHALELFSRHAFKQN  299 (311)
Q Consensus       280 ~~L~~~ea~~Lf~~~af~~~  299 (311)
                      .+.+.++....+.+.+....
T Consensus       166 ~~~~~~~~~~~l~~~~~~e~  185 (231)
T d1iqpa2         166 RPLRDEDIAKRLRYIAENEG  185 (231)
T ss_dssp             CCCCHHHHHHHHHHHHHTTT
T ss_pred             cccchhhHHHHHHHHHHHhC
Confidence            99999999998888776543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.15  E-value=4.2e-06  Score=70.60  Aligned_cols=48  Identities=25%  Similarity=0.281  Sum_probs=38.7

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++++|.+...+.|..++.... ....+.|+|++|+||||+|+++++.+
T Consensus        10 ~~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2          10 LNALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4578999988888888776432 34457799999999999999999874

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.13  E-value=8.1e-06  Score=69.78  Aligned_cols=146  Identities=16%  Similarity=0.246  Sum_probs=83.6

Q ss_pred             CCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          145 NQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      ++++|.+..+++|.+.+..           +-.-.+-+.++|++|+|||+||+++++....+|-   .+. ...+.....
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~---~i~-~~~l~~~~~   79 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFF---LIN-GPEIMSKLA   79 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEE---EEC-HHHHTTSCT
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEE---EEE-chhhccccc
Confidence            4678999988888775421           1122566899999999999999999998654422   111 111111011


Q ss_pred             Ch-HHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH-------------HHHHhh----ccCCC-----
Q 042778          214 GL-GFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR-------------QIKSLI----GMLRN-----  270 (311)
Q Consensus       214 ~~-~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~-------------~l~~l~----~~~~~-----  270 (311)
                      +. ....+.+                ....-..+.++|+|||++...             .+..+.    +....     
T Consensus        80 g~~~~~l~~~----------------f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlv  143 (258)
T d1e32a2          80 GESESNLRKA----------------FEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIV  143 (258)
T ss_dssp             THHHHHHHHH----------------HHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEE
T ss_pred             ccHHHHHHHH----------------HHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccE
Confidence            10 1111111                112224577899999987421             011111    10000     


Q ss_pred             -----------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          271 -----------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       271 -----------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                                       ...+..++++..+.++-.++|..+.=+.. .+..++.+|++
T Consensus       144 i~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~  201 (258)
T d1e32a2         144 MAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVAN  201 (258)
T ss_dssp             EEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHH
T ss_pred             EEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhh
Confidence                             23678999999999999999987642222 23346777654

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.09  E-value=3.2e-05  Score=65.94  Aligned_cols=52  Identities=21%  Similarity=0.247  Sum_probs=38.3

Q ss_pred             CCCccchhhhHHHHHHhhc---c-------cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLG---A-------ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~---~-------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+...++|.+.+.   .       +....+-+.++|++|+|||+||+++++.....
T Consensus        11 ~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~   72 (256)
T d1lv7a_          11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP   72 (256)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC
T ss_pred             HHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCC
Confidence            3578999988877765432   1       11225668899999999999999999887543

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.07  E-value=4e-05  Score=64.96  Aligned_cols=147  Identities=13%  Similarity=0.161  Sum_probs=82.4

Q ss_pred             CCCccchhhhHHHHHHhh---cc-------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCC
Q 042778          144 KNQLVGVESRVEEIESLL---GA-------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPG  213 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L---~~-------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~  213 (311)
                      -++++|.+...+.|.+.+   ..       +....+-|.++|++|+|||+||+++++.....|   +-+. ..+...+..
T Consensus         8 ~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~---~~i~-~~~l~~~~~   83 (247)
T d1ixza_           8 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPF---ITAS-GSDFVEMFV   83 (247)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCE---EEEE-HHHHHHSCT
T ss_pred             HHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCE---EEEE-hHHhhhccc
Confidence            357889998777666543   21       112255689999999999999999999865432   1222 111100001


Q ss_pred             C-hHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCChH----------------HHHHhh----c--cCCC
Q 042778          214 G-LGFLQQKLLSKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCFR----------------QIKSLI----G--MLRN  270 (311)
Q Consensus       214 ~-~~~l~~~ll~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~~----------------~l~~l~----~--~~~~  270 (311)
                      + .....++++                ...-...+++|+|||++..-                .+..++    +  ....
T Consensus        84 g~~~~~l~~~f----------------~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~  147 (247)
T d1ixza_          84 GVGAARVRDLF----------------ETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTA  147 (247)
T ss_dssp             THHHHHHHHHH----------------HHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCC
T ss_pred             cHHHHHHHHHH----------------HHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCC
Confidence            0 001111111                11223567888899875210                111111    1  0011


Q ss_pred             --------------------cCCceEEEcCCCChHHHHHHHHHhhcCCC-CCCCcHHHhhc
Q 042778          271 --------------------CCVKEKYEMKELGDDHALELFSRHAFKQN-NPHIGFEELSS  310 (311)
Q Consensus       271 --------------------~~~~~~y~v~~L~~~ea~~Lf~~~af~~~-~~~~~~~~l~~  310 (311)
                                          ...+..+++++.+.++..++|+.+.-+.. ....++..|++
T Consensus       148 vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~  208 (247)
T d1ixza_         148 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAK  208 (247)
T ss_dssp             EEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHH
T ss_pred             EEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHH
Confidence                                12467899999999999999998875433 34445666654

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.97  E-value=4.8e-06  Score=70.34  Aligned_cols=157  Identities=15%  Similarity=0.139  Sum_probs=85.8

Q ss_pred             CCCccchhhhHHHHHHhhcc---------------cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccc
Q 042778          144 KNQLVGVESRVEEIESLLGA---------------ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREE  208 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~---------------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~  208 (311)
                      ..+++|.+..+++|.++|..               +....+.+.++|++|+||||+|+++++.....   .+++. .   
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~---~~~~~-~---   85 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYD---ILEQN-A---   85 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCE---EEEEC-T---
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhh---hhccc-c---
Confidence            46789999999999998843               11235689999999999999999999986533   22333 1   


Q ss_pred             cCCCCChHHHHHHHHHHHhcCCCCCCCH--HHHHHHhCCCeEEEEEecCCChH-----HHHHhh---ccCCC--------
Q 042778          209 SQRPGGLGFLQQKLLSKLLQDGIVIPDI--ALSFRQLSRRKVLIVLDDVTCFR-----QIKSLI---GMLRN--------  270 (311)
Q Consensus       209 s~~~~~~~~l~~~ll~~l~~~~~~~~~~--~~l~~~L~~kr~LlVLDdV~~~~-----~l~~l~---~~~~~--------  270 (311)
                      +. ..+...+ ...+.............  .........+..++++|+++...     .+..+.   .....        
T Consensus        86 ~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~~  163 (253)
T d1sxja2          86 SD-VRSKTLL-NAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNE  163 (253)
T ss_dssp             TS-CCCHHHH-HHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEESC
T ss_pred             cc-chhhHHH-HHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhHHHhhhhccccccccccccc
Confidence            11 2222222 22222211111111111  11122234577889999986321     122221   00100        


Q ss_pred             ---------cCCceEEEcCCCChHHHHHHHHHhhcC--CCCCCCcHHHhh
Q 042778          271 ---------CCVKEKYEMKELGDDHALELFSRHAFK--QNNPHIGFEELS  309 (311)
Q Consensus       271 ---------~~~~~~y~v~~L~~~ea~~Lf~~~af~--~~~~~~~~~~l~  309 (311)
                               ......+++.+++.++-...+.+..=+  -.-.+..+.+|+
T Consensus       164 ~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~  213 (253)
T d1sxja2         164 RNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLI  213 (253)
T ss_dssp             TTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHH
T ss_pred             ccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence                     234568899999999888887764421  122334455554

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.93  E-value=5.2e-05  Score=63.62  Aligned_cols=50  Identities=22%  Similarity=0.237  Sum_probs=40.3

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -.+++|.+..++.|..++..+. -...+.|+|..|+||||+|+.+.+.+..
T Consensus        11 ~~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~   60 (239)
T d1njfa_          11 FADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNC   60 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHHHHC
T ss_pred             HHHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcC
Confidence            3578999999999999887432 2456789999999999999999887543

>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=97.91  E-value=1.2e-05  Score=68.88  Aligned_cols=52  Identities=23%  Similarity=0.309  Sum_probs=38.3

Q ss_pred             CCCccchhhhHHHHHHhhcc-----------cCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          144 KNQLVGVESRVEEIESLLGA-----------ESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      -.+++|.+..+++|.+.+..           +-...+-|.++|.+|.|||+||+++++....+
T Consensus         6 f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~   68 (265)
T d1r7ra3           6 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN   68 (265)
T ss_dssp             CSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCE
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCc
Confidence            45678888877777665421           11225678899999999999999999987554

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.87  E-value=3.6e-06  Score=70.73  Aligned_cols=53  Identities=23%  Similarity=0.396  Sum_probs=42.3

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -+++||.+..+++|..++...   ...++-+.++|++|+||||+|+.+++.....|
T Consensus         8 ~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~   63 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNL   63 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCE
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            357899999999988887542   23366788999999999999999999865443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.85  E-value=4.5e-06  Score=70.03  Aligned_cols=53  Identities=21%  Similarity=0.327  Sum_probs=42.4

Q ss_pred             CCCccchhhhHHHHHHhhccc---CCCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLGAE---SKDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -+++||.+..+++|..++...   ....+-+.++|++|+||||+|+.+++.+...|
T Consensus         8 ~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~   63 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNI   63 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCE
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCCc
Confidence            467899999999999888532   22355678999999999999999999866543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.84  E-value=4.3e-05  Score=63.20  Aligned_cols=133  Identities=16%  Similarity=0.130  Sum_probs=75.1

Q ss_pred             CccchhhhH--HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHH
Q 042778          146 QLVGVESRV--EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLL  223 (311)
Q Consensus       146 ~~vGr~~~~--~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll  223 (311)
                      .++|-..+.  .-+.++..........+-|||..|+|||.|++++++.........+++.    .       ..+...+.
T Consensus        12 F~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~----~-------~~~~~~~~   80 (213)
T d1l8qa2          12 FIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS----A-------DDFAQAMV   80 (213)
T ss_dssp             CCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE----H-------HHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEec----h-------HHHHHHHH
Confidence            345654332  3333444322222344789999999999999999999776666667766    1       22333333


Q ss_pred             HHHhcCCCCCCCHHHHHHHhCCCeEEEEEecCCCh---HHHHHh----hc----------------cC--CC--------
Q 042778          224 SKLLQDGIVIPDIALSFRQLSRRKVLIVLDDVTCF---RQIKSL----IG----------------ML--RN--------  270 (311)
Q Consensus       224 ~~l~~~~~~~~~~~~l~~~L~~kr~LlVLDdV~~~---~~l~~l----~~----------------~~--~~--------  270 (311)
                      ..+....     ...+.+.++ .--+|+||||+..   ..|+..    ..                +.  +.        
T Consensus        81 ~~~~~~~-----~~~~~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SR  154 (213)
T d1l8qa2          81 EHLKKGT-----INEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSR  154 (213)
T ss_dssp             HHHHHTC-----HHHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHH
T ss_pred             HHHHccc-----hhhHHHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHH
Confidence            3322211     122233332 2348899999732   233321    10                00  00        


Q ss_pred             cCCceEEEcCCCChHHHHHHHHHhhc
Q 042778          271 CCVKEKYEMKELGDDHALELFSRHAF  296 (311)
Q Consensus       271 ~~~~~~y~v~~L~~~ea~~Lf~~~af  296 (311)
                      .....+++++ +++++-.+++.++|=
T Consensus       155 L~~g~~~~i~-p~d~~~~~iL~~~a~  179 (213)
T d1l8qa2         155 FEGGILVEIE-LDNKTRFKIIKEKLK  179 (213)
T ss_dssp             HHTSEEEECC-CCHHHHHHHHHHHHH
T ss_pred             hhCceEEEEC-CCcHHHHHHHHHHHH
Confidence            3456788896 588888888888873

>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=97.70  E-value=1.6e-05  Score=67.39  Aligned_cols=53  Identities=13%  Similarity=0.070  Sum_probs=37.4

Q ss_pred             CCCccchhhhHHHHHHhhc-------ccC-CCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          144 KNQLVGVESRVEEIESLLG-------AES-KDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~-------~~~-~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .+.+||..+.++.+.+.+.       ... ...+-|.++|++|+|||+||+++++.....|
T Consensus         8 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~   68 (246)
T d1d2na_           8 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPF   68 (246)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSE
T ss_pred             ccCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccc
Confidence            3457887776665554332       111 2366788999999999999999999865543

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.57  E-value=1.8e-05  Score=62.59  Aligned_cols=26  Identities=8%  Similarity=0.151  Sum_probs=23.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++.|.|.|+.|+||||||+.+.++..
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            68899999999999999999998754

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.52  E-value=2.6e-05  Score=61.47  Aligned_cols=36  Identities=17%  Similarity=0.178  Sum_probs=28.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc-CceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF-EGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F-~~~~wv~  203 (311)
                      -.+|.|+|++|+||||+|+++..++...| +...++.
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~~L~~~~~~~~~~~~   42 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL   42 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCCchhhhh
Confidence            57889999999999999999999976543 4444443

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.52  E-value=6.4e-05  Score=60.17  Aligned_cols=51  Identities=18%  Similarity=0.281  Sum_probs=35.4

Q ss_pred             hhHHHHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEE
Q 042778          152 SRVEEIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFL  202 (311)
Q Consensus       152 ~~~~~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv  202 (311)
                      +.++.|.+.+. ....+.-+|||.|..|.||||||+.+.+...........+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~   56 (198)
T d1rz3a_           5 DRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (198)
T ss_dssp             HHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             HHHHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHHHhccccccceec
Confidence            34555554432 3445577999999999999999999998766554443333

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.50  E-value=1.7e-05  Score=61.50  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=22.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.|.|.|++|+||||+|+.+++++..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~~   28 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLNM   28 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            35788899999999999999998644

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=3.8e-05  Score=61.60  Aligned_cols=36  Identities=17%  Similarity=0.148  Sum_probs=29.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.+|-++|++|+||||||+.+..++...+....++.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~~~~~~~~~   54 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   54 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCccchh
Confidence            567889999999999999999998777666555543

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.40  E-value=0.0014  Score=53.35  Aligned_cols=43  Identities=16%  Similarity=0.138  Sum_probs=31.4

Q ss_pred             chhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          149 GVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       149 Gr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +.+...+++.+.+..+. -...+.++|..|+||||+|+.+++.+
T Consensus         6 w~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l   48 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYL   48 (207)
T ss_dssp             GGHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhc
Confidence            34455666766665321 14568899999999999999999864

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.32  E-value=3.7e-05  Score=60.26  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=21.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ..|.|.|++|+||||+|+.+.+++.
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4577999999999999999998753

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.32  E-value=5.3e-05  Score=59.16  Aligned_cols=25  Identities=16%  Similarity=0.278  Sum_probs=22.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|.|.|++|+||||+|+.+..++.
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~   27 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLD   27 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5799999999999999999988753

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.30  E-value=0.00011  Score=61.84  Aligned_cols=30  Identities=27%  Similarity=0.354  Sum_probs=25.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ..+.|.++|++|+||||||+++++.....|
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~~~~~   60 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEETQGNV   60 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTTTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhhcce
Confidence            367789999999999999999999876544

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.29  E-value=5.1e-05  Score=59.32  Aligned_cols=28  Identities=14%  Similarity=0.291  Sum_probs=24.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +++++|+|..|+|||||+.++.+....+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            4689999999999999999999875544

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.29  E-value=6.8e-05  Score=57.69  Aligned_cols=24  Identities=25%  Similarity=0.224  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++|.|+|++|+||||||+.+..+.
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            578899999999999999887653

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.25  E-value=6.8e-05  Score=59.03  Aligned_cols=26  Identities=19%  Similarity=0.376  Sum_probs=21.8

Q ss_pred             EEEeccCcchhHHHHHHHHHhhccCc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      |.+.||+|+||||+|+.+++++.-.|
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~f   29 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGL   29 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCe
Confidence            44569999999999999999976554

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=97.20  E-value=7.3e-05  Score=58.76  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=21.3

Q ss_pred             EEEeccCcchhHHHHHHHHHhhcc
Q 042778          171 LGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      |.|.||+|+||||+|+.+++++.-
T Consensus         3 I~liG~~GsGKsTi~k~La~~l~~   26 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDLDL   26 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            677899999999999999998744

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.19  E-value=8.4e-05  Score=58.21  Aligned_cols=27  Identities=11%  Similarity=0.155  Sum_probs=23.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .++|.|.|..|+||||+|+.+.+++..
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~   29 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPE   29 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            468999999999999999999998643

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.17  E-value=0.00011  Score=57.49  Aligned_cols=28  Identities=14%  Similarity=0.358  Sum_probs=24.8

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+.+++.|+|++|+||||+|+.+..++.
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3478999999999999999999998863

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.15  E-value=9.9e-05  Score=58.05  Aligned_cols=26  Identities=19%  Similarity=0.208  Sum_probs=22.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.|.|.|.+|+|||||++++...+..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            46899999999999999999987543

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.06  E-value=0.00021  Score=56.34  Aligned_cols=27  Identities=15%  Similarity=0.320  Sum_probs=24.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++|.|.|+.|+||||+++.+.+++...
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999886544

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.04  E-value=0.00014  Score=57.00  Aligned_cols=25  Identities=32%  Similarity=0.226  Sum_probs=22.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -++|.|.|++|+||||+|+.+.++.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998764

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=97.01  E-value=0.00014  Score=57.34  Aligned_cols=25  Identities=20%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .|.+.||+|+||||+|+.+++++.-
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg~   28 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALGY   28 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3568899999999999999998644

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.98  E-value=0.00018  Score=56.23  Aligned_cols=25  Identities=24%  Similarity=0.292  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...|.|.|++|+||||+|+.+++++
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            4568899999999999999999875

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.96  E-value=0.00022  Score=62.10  Aligned_cols=51  Identities=16%  Similarity=0.225  Sum_probs=37.2

Q ss_pred             CCccchhhhHHHHHHhhc-------c--c---CCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          145 NQLVGVESRVEEIESLLG-------A--E---SKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~-------~--~---~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..++|.+..++.|...+.       .  .   ....+-+.++|++|+|||.||+++++.....
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~   76 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAP   76 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCC
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccc
Confidence            467899988887765441       0  0   1135677899999999999999999976443

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.95  E-value=0.00025  Score=57.09  Aligned_cols=28  Identities=14%  Similarity=0.192  Sum_probs=25.2

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++..++|.|.|++|+||||+|+.+++++
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999998875

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.94  E-value=0.00022  Score=57.67  Aligned_cols=27  Identities=11%  Similarity=0.137  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.+|.++|.+|+||||||+++++....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            357899999999999999999987543

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.89  E-value=0.00043  Score=54.64  Aligned_cols=27  Identities=15%  Similarity=0.220  Sum_probs=24.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++|.|.|+.|+||||+|+.+...+...
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            688999999999999999999987554

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.88  E-value=0.00022  Score=55.92  Aligned_cols=27  Identities=11%  Similarity=0.070  Sum_probs=24.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ++++|+|..|+|||||+..+...++.+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            589999999999999999999986654

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.87  E-value=0.00033  Score=56.24  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=24.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+.+|.|.|++|+||||+|+.++++.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            347899999999999999999998875

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.0015  Score=53.23  Aligned_cols=27  Identities=11%  Similarity=0.249  Sum_probs=23.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..|+|-|+-|+||||+++.+.+.+..+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            578999999999999999999986554

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.74  E-value=0.0035  Score=51.25  Aligned_cols=40  Identities=10%  Similarity=0.186  Sum_probs=30.4

Q ss_pred             cCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          164 ESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       164 ~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .+....+|.++|+.|+||||.+..++.+...+=..+..+.
T Consensus         7 ~~~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit   46 (213)
T d1vmaa2           7 PPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA   46 (213)
T ss_dssp             CSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEe
Confidence            4456889999999999999998888887544434455554

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.70  E-value=0.00035  Score=55.41  Aligned_cols=26  Identities=12%  Similarity=0.134  Sum_probs=22.5

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ....+|.++|++|+||||+|+.+...
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            34779999999999999999988765

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.68  E-value=0.00042  Score=54.37  Aligned_cols=25  Identities=24%  Similarity=0.460  Sum_probs=21.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      -|+|.|..|+|||||++.+...+..
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            3899999999999999999987544

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.62  E-value=0.00052  Score=55.91  Aligned_cols=27  Identities=11%  Similarity=0.316  Sum_probs=23.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +-+|||.|..|.||||||+.+.+.+..
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            458999999999999999999887543

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.00044  Score=56.25  Aligned_cols=25  Identities=20%  Similarity=0.320  Sum_probs=23.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++|+|-|++|+||||+|+.+.+++
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4699999999999999999999987

>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=96.60  E-value=0.0025  Score=55.34  Aligned_cols=50  Identities=12%  Similarity=0.340  Sum_probs=37.4

Q ss_pred             CCccchhhhHHHHHHhhcc------cCCC-eEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          145 NQLVGVESRVEEIESLLGA------ESKD-VYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       145 ~~~vGr~~~~~~l~~~L~~------~~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ..++|.+..++.|...+..      .++. ..++.++|+.|+|||.||+.+++.+..
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~   79 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFD   79 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHS
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcC
Confidence            3578988888888765531      1222 457889999999999999999988643

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.49  E-value=0.0061  Score=49.53  Aligned_cols=37  Identities=16%  Similarity=0.082  Sum_probs=28.0

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +.+++.++|+.|+||||.+..++.....+-..+..+.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit   45 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA   45 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4688999999999999999988887554433445554

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=96.48  E-value=0.00083  Score=53.57  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++++| |.|++|+||||+|+.+++++
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHHh
Confidence            46677 68999999999999999875

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.46  E-value=0.0024  Score=54.34  Aligned_cols=87  Identities=15%  Similarity=0.205  Sum_probs=53.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh-ccCcCceEEEecCccccCCCCChHHHHHHHHHHHh-cCCC----------CC-CC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI-SSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLL-QDGI----------VI-PD  235 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~-~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~-~~~~----------~~-~~  235 (311)
                      ..++|.|-.|+|||+|+..+.+.. +.+=+.++++-    +.++.....++.+.+...-. ....          .. ..
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~----iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~  144 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG----VGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEP  144 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEE----ESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSC
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEEE----eccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCC
Confidence            358999999999999999998874 34445566665    44323345566666655311 1010          00 11


Q ss_pred             H----------HHHHHHhC---CCeEEEEEecCCChH
Q 042778          236 I----------ALSFRQLS---RRKVLIVLDDVTCFR  259 (311)
Q Consensus       236 ~----------~~l~~~L~---~kr~LlVLDdV~~~~  259 (311)
                      .          -.+.++++   ++++|+++||+....
T Consensus       145 ~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~A  181 (276)
T d2jdid3         145 PGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFT  181 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHHH
Confidence            1          23445553   689999999996543

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.42  E-value=0.0095  Score=48.47  Aligned_cols=29  Identities=17%  Similarity=0.384  Sum_probs=25.0

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+...+|.++|+.|+||||.+..++.+.+
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~   34 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFE   34 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34578999999999999999998888765

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.38  E-value=0.00096  Score=53.29  Aligned_cols=24  Identities=21%  Similarity=0.203  Sum_probs=22.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+|.|.|++|+||||+|+.+++++
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            588999999999999999999875

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.37  E-value=0.001  Score=54.30  Aligned_cols=29  Identities=10%  Similarity=0.212  Sum_probs=25.2

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ....+|-+.|++|.||||||+++.+++..
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~   50 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVR   50 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            45779999999999999999999988643

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=96.37  E-value=0.00072  Score=53.97  Aligned_cols=25  Identities=20%  Similarity=0.074  Sum_probs=21.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +..|.|.|++|+||||+|+.+.+++
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457799999999999999998876

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=96.36  E-value=0.0015  Score=55.03  Aligned_cols=27  Identities=22%  Similarity=0.495  Sum_probs=23.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      +.|+|+|=||+||||+|..+...+...
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~   28 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAM   28 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhC
Confidence            689999999999999999998876554

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.33  E-value=0.0065  Score=49.52  Aligned_cols=38  Identities=16%  Similarity=0.105  Sum_probs=24.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ....+|.++|+.|+||||.+..++.+.+..=..+..+.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit   47 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVG   47 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEE
Confidence            34789999999999999998888776543322345554

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=96.32  E-value=0.0016  Score=57.80  Aligned_cols=50  Identities=16%  Similarity=0.029  Sum_probs=36.4

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .+.|.+..+.+..+.+..+....+.+.++|++|+|||++|+++++.....
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~  181 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGK  181 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCE
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            35566665555444444444556789999999999999999999986544

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.31  E-value=0.00097  Score=52.50  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=20.2

Q ss_pred             EEEeccCcchhHHHHHHHHHhh
Q 042778          171 LGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      |.|.|++|+||||+|+.++++.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6799999999999999998875

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.26  E-value=0.01  Score=48.17  Aligned_cols=37  Identities=14%  Similarity=0.093  Sum_probs=27.7

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      +.++|.++|+.|+||||.+..++.....+=..+..+.
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit   41 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCA   41 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            4679999999999999999888877543323445554

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=96.26  E-value=0.007  Score=52.51  Aligned_cols=28  Identities=14%  Similarity=0.135  Sum_probs=23.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .++.++|.+|+|||.||++++..+..++
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~  151 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKD  151 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTS
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCC
Confidence            3566789999999999999999976543

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=96.20  E-value=0.0014  Score=52.59  Aligned_cols=25  Identities=20%  Similarity=0.325  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...|.|.|++|+||||+|+.+..++
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHH
Confidence            3345577999999999999999875

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.19  E-value=0.00099  Score=53.48  Aligned_cols=27  Identities=26%  Similarity=0.461  Sum_probs=22.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      .|.|.|+.|+|||||++.+.++....|
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            367999999999999999988765554

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.18  E-value=0.001  Score=53.18  Aligned_cols=30  Identities=20%  Similarity=0.363  Sum_probs=25.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEG  198 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~  198 (311)
                      +.|.|+|+.|+|||||++.+.++....|..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~~~   31 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSFGF   31 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcceeE
Confidence            347899999999999999999887666543

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=96.15  E-value=0.0014  Score=52.26  Aligned_cols=22  Identities=27%  Similarity=0.317  Sum_probs=19.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      .-+|||.|+.|+||||+|..+-
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            5689999999999999998763

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=96.12  E-value=0.0015  Score=51.61  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=20.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|++|+||||+|+.+++++
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46789999999999999999886

>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=96.12  E-value=0.0034  Score=54.32  Aligned_cols=31  Identities=23%  Similarity=0.232  Sum_probs=26.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      ...-+|||.|..|+||||+|+.+...++..+
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~  108 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLSRWP  108 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTST
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHhhhc
Confidence            3478999999999999999999988765443

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.10  E-value=0.0015  Score=51.63  Aligned_cols=23  Identities=22%  Similarity=0.245  Sum_probs=20.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|++|+||||+|+.++++.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36788999999999999999886

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.09  E-value=0.0027  Score=52.18  Aligned_cols=48  Identities=13%  Similarity=0.165  Sum_probs=37.0

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|.++|..+-..-.++.|+|.+|+|||+||..+......+...++|++
T Consensus        14 ~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          14 RLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            344555533234668999999999999999999998777777788887

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.06  E-value=0.0039  Score=52.47  Aligned_cols=40  Identities=20%  Similarity=0.348  Sum_probs=29.9

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ++..+.+.+.  .++.++|.+.|=||+||||+|..+...+..
T Consensus         7 ~~~~~~~~~~--~~~~~iii~sGKGGVGKTT~a~nLA~~lA~   46 (279)
T d1ihua2           7 SLSALVDDIA--RNEHGLIMLMGKGGVGKTTMAAAIAVRLAD   46 (279)
T ss_dssp             CHHHHHHHHH--TTSCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHhh--cCCCEEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3445555554  456899999999999999998887776433

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.06  E-value=0.014  Score=46.83  Aligned_cols=94  Identities=7%  Similarity=0.058  Sum_probs=55.3

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccCc---CceEEEecCccccCCCCChHHHHHHHHHHHhcC
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSNF---EGSCFLQNVREESQRPGGLGFLQQKLLSKLLQD  229 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F---~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~  229 (311)
                      .++.+..++..  +....+.++|.+|+||||+|..+.+.+...+   ....++..   ... .-++..+.. +...+...
T Consensus         2 ~~~~l~~~i~~--~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~---~~~-~I~Id~IR~-i~~~~~~~   74 (198)
T d2gnoa2           2 QLETLKRIIEK--SEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDP---EGE-NIGIDDIRT-IKDFLNYS   74 (198)
T ss_dssp             HHHHHHHHHHT--CSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECC---SSS-CBCHHHHHH-HHHHHTSC
T ss_pred             HHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeC---CcC-CCCHHHHHH-HHHHHhhC
Confidence            34555566653  3578999999999999999999988653322   23444441   111 334555443 43333322


Q ss_pred             CCCCCCHHHHHHHhCCCeEEEEEecCCC--hHHHHHhh
Q 042778          230 GIVIPDIALSFRQLSRRKVLIVLDDVTC--FRQIKSLI  265 (311)
Q Consensus       230 ~~~~~~~~~l~~~L~~kr~LlVLDdV~~--~~~l~~l~  265 (311)
                      .            ..+++=++|+|+++.  .+...+|+
T Consensus        75 ~------------~~~~~KviIId~ad~l~~~aqNaLL  100 (198)
T d2gnoa2          75 P------------ELYTRKYVIVHDCERMTQQAANAFL  100 (198)
T ss_dssp             C------------SSSSSEEEEETTGGGBCHHHHHHTH
T ss_pred             c------------ccCCCEEEEEeCccccchhhhhHHH
Confidence            1            123444888999984  45555554

>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=96.06  E-value=0.0031  Score=54.97  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=29.7

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..++.+.+.....+..+|||.|.+|.|||||.-++...
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            34455555545567899999999999999999988765

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.05  E-value=0.0015  Score=53.09  Aligned_cols=23  Identities=22%  Similarity=0.338  Sum_probs=21.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      +|+|-|++|+||||+|+.+..++
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999886

>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=96.03  E-value=0.0037  Score=54.26  Aligned_cols=50  Identities=14%  Similarity=0.256  Sum_probs=38.7

Q ss_pred             CCCccchhhhHHHHHHhhcc------cCCC-eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          144 KNQLVGVESRVEEIESLLGA------ESKD-VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~------~~~~-~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ...++|.+..++.|...+..      ..+. ..++.++|+.|+|||.||+.++.-+.
T Consensus        21 ~~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          21 KMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CCeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc
Confidence            45789999988888765531      1222 56888999999999999999998754

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=95.97  E-value=0.0018  Score=51.78  Aligned_cols=26  Identities=19%  Similarity=0.132  Sum_probs=23.2

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..++|.|.|++|+||||+|+.+.++.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            36789999999999999999998875

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.96  E-value=0.0055  Score=53.43  Aligned_cols=40  Identities=15%  Similarity=0.173  Sum_probs=30.2

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .++...|.....+..+|||.|.+|+|||||...+......
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~   80 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIR   80 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHh
Confidence            3444445445567999999999999999999988765433

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.91  E-value=0.021  Score=48.09  Aligned_cols=92  Identities=15%  Similarity=0.131  Sum_probs=54.9

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC---
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI---  231 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~---  231 (311)
                      .|...|. .+-..-+++-|+|..|+||||||..++......=..++|++    .-. ..+...     +.+++...+   
T Consensus        47 ~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyID----tE~-~~~~e~-----a~~~GvD~d~il  116 (269)
T d1mo6a1          47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFID----AEH-ALDPDY-----AKKLGVDTDSLL  116 (269)
T ss_dssp             HHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEE----SSC-CCCHHH-----HHHHTCCGGGCE
T ss_pred             HHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEE----CCc-cCCHHH-----HHHhCCCHHHeE
Confidence            3444553 33344679999999999999999877776444434578988    222 444443     333432222   


Q ss_pred             --CCCCH----HHHHHHhC-CCeEEEEEecCCC
Q 042778          232 --VIPDI----ALSFRQLS-RRKVLIVLDDVTC  257 (311)
Q Consensus       232 --~~~~~----~~l~~~L~-~kr~LlVLDdV~~  257 (311)
                        +..+.    +.+...++ ++.-|||+|-+-.
T Consensus       117 ~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~a  149 (269)
T d1mo6a1         117 VSQPDTGEQALEIADMLIRSGALDIVVIDSVAA  149 (269)
T ss_dssp             EECCSSHHHHHHHHHHHHHTTCEEEEEEECSTT
T ss_pred             EecCCCHHHHHHHHHHHHhcCCCCEEEEecccc
Confidence              22333    33333333 4577999999854

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.89  E-value=0.002  Score=51.09  Aligned_cols=31  Identities=23%  Similarity=0.368  Sum_probs=25.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCce
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGS  199 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~  199 (311)
                      +.|.|+|+.|+|||||++.+..+....|...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~~~~~~~   34 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHPDRFAYP   34 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCTTTEECC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCCcCeeec
Confidence            5788999999999999999998776666443

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.87  E-value=0.0021  Score=50.62  Aligned_cols=23  Identities=22%  Similarity=0.187  Sum_probs=20.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHhh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|.|.|++|+||||+|+.++++.
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36689999999999999999875

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.86  E-value=0.014  Score=49.30  Aligned_cols=91  Identities=15%  Similarity=0.069  Sum_probs=53.3

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCCCCChHHHHHHHHHHHhcCCC---
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQRPGGLGFLQQKLLSKLLQDGI---  231 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l~~~~~---  231 (311)
                      .|..+|. .+-..-+++-|+|.+|.||||||..+.......=..++|++    .-. ..+..     ++..++...+   
T Consensus        44 ~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiD----tE~-~~~~~-----~a~~~Gvd~d~i~  113 (268)
T d1xp8a1          44 SLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID----AEH-ALDPV-----YARALGVNTDELL  113 (268)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE----SSC-CCCHH-----HHHHTTCCGGGCE
T ss_pred             HHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEE----CCc-cCCHH-----HHHHhCCCchhEE
Confidence            3444553 22123569999999999999999887776433213468887    222 44443     4444443222   


Q ss_pred             --CCCCH----HHHHHHhCC-CeEEEEEecCC
Q 042778          232 --VIPDI----ALSFRQLSR-RKVLIVLDDVT  256 (311)
Q Consensus       232 --~~~~~----~~l~~~L~~-kr~LlVLDdV~  256 (311)
                        ...+.    +.+...++. ..-|||+|-+-
T Consensus       114 ~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         114 VSQPDNGEQALEIMELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             EECCSSHHHHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             EEcCCCHHHHHHHHHHHHhcCCCcEEEEeccc
Confidence              22233    444444444 45599999985

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.82  E-value=0.0022  Score=50.64  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=20.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+++ |.|++|+||||+|+.++++.
T Consensus         3 mrIv-l~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           3 IRMV-LIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             eEEE-EECCCCCCHHHHHHHHHHHh
Confidence            4444 77999999999999999875

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.73  E-value=0.0025  Score=50.37  Aligned_cols=25  Identities=16%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++|.|+|+.|+|||||++.+.++..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4788999999999999999987753

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=95.66  E-value=0.0027  Score=54.05  Aligned_cols=26  Identities=23%  Similarity=0.528  Sum_probs=21.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +.|+|+|=||+||||+|..+...+..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~   28 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAE   28 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            67889999999999999888776443

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.59  E-value=0.0064  Score=51.34  Aligned_cols=29  Identities=24%  Similarity=0.234  Sum_probs=24.2

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      +..++|.+.|=||+||||+|.+++.....
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~lA~   34 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIRLAE   34 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCcChHHHHHHHHHHHHHH
Confidence            44788999999999999999888876544

>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=95.58  E-value=0.011  Score=49.68  Aligned_cols=48  Identities=15%  Similarity=0.216  Sum_probs=33.4

Q ss_pred             HHHHhhc-ccCCCeEEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          156 EIESLLG-AESKDVYALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~-~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      .|..+|. .+-..-+++-|+|.+|+||||||..+.......=..++|++
T Consensus        41 ~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyid   89 (263)
T d1u94a1          41 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   89 (263)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEc
Confidence            3444553 22123469999999999999999988877544434568887

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.54  E-value=0.0028  Score=50.45  Aligned_cols=26  Identities=19%  Similarity=0.068  Sum_probs=22.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+|+|-|.-|+||||+++.+.+..
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHh
Confidence            36689999999999999999887654

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.52  E-value=0.0056  Score=49.79  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=27.7

Q ss_pred             EEEEEe-ccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIW-GIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~-GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|+|+ |-||+||||+|..++..++..=..++.++
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~~g~~VlliD   37 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQLGHDVTIVD   37 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEe
Confidence            788888 88999999999999887665544456664

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.49  E-value=0.0048  Score=52.71  Aligned_cols=29  Identities=14%  Similarity=0.136  Sum_probs=24.8

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhccC
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      ..-+|||.|..|+||||||..+...+...
T Consensus        26 ~P~iIGi~G~qGSGKSTl~~~l~~~L~~~   54 (286)
T d1odfa_          26 CPLFIFFSGPQGSGKSFTSIQIYNHLMEK   54 (286)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEeECCCCCCHHHHHHHHHHHHHHH
Confidence            36799999999999999999988876554

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.48  E-value=0.0044  Score=51.82  Aligned_cols=47  Identities=21%  Similarity=0.193  Sum_probs=36.1

Q ss_pred             CccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          146 QLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       146 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ++||....++++.+.+..-...-.-|.|.|..|+|||++|+.+++.-
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s   47 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLS   47 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            47888888888888776533323346889999999999999998753

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.41  E-value=0.0024  Score=54.71  Aligned_cols=27  Identities=11%  Similarity=0.151  Sum_probs=20.4

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +..+|||.|-.|.||||+|+++.+.+.
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~   29 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFR   29 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHh
Confidence            467999999999999999998877643

>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=95.28  E-value=0.0029  Score=54.10  Aligned_cols=47  Identities=11%  Similarity=-0.030  Sum_probs=31.9

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhc-cCcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKIS-SNFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~-~~F~~~~wv~  203 (311)
                      ++++.|..- ..-..++|.|-.|+|||||+..+.+... .+-++++++.
T Consensus        32 r~ID~l~Pi-grGQr~~I~g~~g~GKT~l~~~i~~~~~~~~~~~v~~~~   79 (289)
T d1xpua3          32 RVLDLASPI-GRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVL   79 (289)
T ss_dssp             HHHHHHSCC-BTTCEEEEEECSSSSHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             eeeeecccc-cCCCeeeEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEE
Confidence            455655432 1245789999999999999999988754 3344455544

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.21  E-value=0.0068  Score=49.49  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=21.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhcc
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      ||+|.|+.|.|||||...+.+....
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~   26 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLED   26 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Confidence            7899999999999999998765433

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.19  E-value=0.0061  Score=51.78  Aligned_cols=35  Identities=11%  Similarity=-0.010  Sum_probs=26.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ..++|.|-.|+|||+|+.........+-..++++.
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~~~~~~~v~V~~~  102 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILNQQGQNVICVYVA  102 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCTTTCEEEEEE
T ss_pred             ceEeeccCCCCChHHHHHHHHhhhcccCceeeeee
Confidence            35889999999999999876555555555666665

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.16  E-value=0.0086  Score=48.65  Aligned_cols=35  Identities=17%  Similarity=0.222  Sum_probs=27.3

Q ss_pred             EEEEEe-ccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIW-GIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~-GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      ++|+|+ +-||+||||+|..++..+...-..++.++
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD   38 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVD   38 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            689999 66999999999999887665534455555

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.09  E-value=0.022  Score=46.47  Aligned_cols=47  Identities=15%  Similarity=0.239  Sum_probs=31.7

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhccC------cCceEEEe
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISSN------FEGSCFLQ  203 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~~------F~~~~wv~  203 (311)
                      |-.+|..+=..-+++-|+|.+|+||||+|..+......+      ....+|+.
T Consensus        25 LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2          25 LDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             HHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             HHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            334454322335799999999999999999887764322      23456666

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.04  E-value=0.0088  Score=46.28  Aligned_cols=33  Identities=21%  Similarity=0.286  Sum_probs=23.6

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +.+.+.......+ |.|+|.+|+|||||...+..
T Consensus         3 ~~~~~~~~~k~~k-I~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_           3 VLQFLGLYKKTGK-LVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             HHHHHTCTTCCEE-EEEEEETTSSHHHHHHHHSC
T ss_pred             hHHhccccCCCCE-EEEECCCCCCHHHHHHHHhC
Confidence            4455554444444 66999999999999987744

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=95.03  E-value=0.0053  Score=49.65  Aligned_cols=19  Identities=26%  Similarity=0.338  Sum_probs=17.6

Q ss_pred             EEEEeccCcchhHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAI  188 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v  188 (311)
                      +|||+|+.|.||||.|+.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            8999999999999999865

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.00  E-value=0.0097  Score=47.52  Aligned_cols=26  Identities=15%  Similarity=0.348  Sum_probs=22.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccC
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSN  195 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~  195 (311)
                      .|+|-|+-|+||||+++.+.+++..+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            58899999999999999999887543

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.97  E-value=0.006  Score=50.71  Aligned_cols=23  Identities=26%  Similarity=0.224  Sum_probs=20.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|.|..|.|||||++.++--
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcC
Confidence            48999999999999999999763

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.91  E-value=0.0084  Score=49.14  Aligned_cols=26  Identities=15%  Similarity=0.174  Sum_probs=23.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      ++.|+|-|+-|+||||+++.+.+...
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            67899999999999999999998743

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.85  E-value=0.0046  Score=49.98  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|+|||||.+.++.-
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            348999999999999999999874

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.80  E-value=0.0058  Score=51.42  Aligned_cols=24  Identities=25%  Similarity=0.237  Sum_probs=21.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+.--
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcC
Confidence            458999999999999999998753

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.79  E-value=0.0058  Score=50.83  Aligned_cols=23  Identities=22%  Similarity=0.365  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.+++|.|..|.|||||++.++-
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHcC
Confidence            35899999999999999999865

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=94.77  E-value=0.0069  Score=52.56  Aligned_cols=45  Identities=18%  Similarity=0.172  Sum_probs=31.5

Q ss_pred             CCCccchhhhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          144 KNQLVGVESRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       144 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ..+++|.+..+..|.-.+...  +..-|.|.|.+|+||||||+.+..
T Consensus         6 f~~I~Gq~~~kral~laa~~~--~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           6 FSAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hhhccCcHHHHHHHHHHHhcc--CCCeEEEECCCCccHHHHHHHHHH
Confidence            356799987666544322211  123578999999999999999875

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.75  E-value=0.0062  Score=50.31  Aligned_cols=23  Identities=22%  Similarity=0.157  Sum_probs=20.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.+++|+|..|+|||||.+.+.-
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCcchhhHhccC
Confidence            34899999999999999998765

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.71  E-value=0.0078  Score=49.74  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.+++|.|..|.|||||.+.++-
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999998865

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.71  E-value=0.0077  Score=47.65  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=26.4

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .|-++|..+=..-.++-|.|.+|+||||||..+....
T Consensus        11 ~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          11 ELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             HHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3445554221224689999999999999999887763

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.66  E-value=0.0086  Score=45.26  Aligned_cols=21  Identities=19%  Similarity=0.181  Sum_probs=18.5

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|.+|+|||||...+...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999988654

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.64  E-value=0.0078  Score=48.48  Aligned_cols=20  Identities=40%  Similarity=0.524  Sum_probs=18.1

Q ss_pred             EEEEEeccCcchhHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAI  188 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v  188 (311)
                      -+|||.|..|+||||+|+.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            48999999999999999865

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.64  E-value=0.0074  Score=50.59  Aligned_cols=23  Identities=26%  Similarity=0.306  Sum_probs=20.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -..++|+|..|.|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999865

>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=94.62  E-value=0.013  Score=51.68  Aligned_cols=25  Identities=16%  Similarity=0.254  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ...+..+|+.|+|||.||+.++...
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcceeeeCCCCccHHHHHHHHHhhc
Confidence            4568888999999999999998754

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.60  E-value=0.008  Score=50.00  Aligned_cols=23  Identities=26%  Similarity=0.403  Sum_probs=20.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..++|+|..|.|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            47999999999999999998663

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.59  E-value=0.0086  Score=49.69  Aligned_cols=24  Identities=29%  Similarity=0.202  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl   55 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGL   55 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC
Confidence            358999999999999999998763

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.0054  Score=50.16  Aligned_cols=25  Identities=12%  Similarity=0.094  Sum_probs=22.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .+.|+|-|+-|+||||+|+.+.+.+
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999999988865

>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=94.52  E-value=0.0086  Score=50.98  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|+|..|.|||||++.+.--
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            458999999999999999999764

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.51  E-value=0.0093  Score=48.24  Aligned_cols=25  Identities=8%  Similarity=0.165  Sum_probs=21.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .++.|+|+.|+|||||.+.+..+..
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4788999999999999999988754

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.50  E-value=0.0086  Score=50.11  Aligned_cols=23  Identities=22%  Similarity=0.251  Sum_probs=20.6

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.+++|+|..|.|||||++.+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            45899999999999999998865

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.48  E-value=0.061  Score=42.83  Aligned_cols=35  Identities=17%  Similarity=0.267  Sum_probs=27.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccC-cCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSN-FEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~-F~~~~wv~  203 (311)
                      +.|+|-|+-|+||||+++.+.+.+... +....+..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~~~~~   38 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTR   38 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEec
Confidence            468899999999999999999886543 45555543

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.44  E-value=0.0099  Score=49.43  Aligned_cols=23  Identities=17%  Similarity=0.127  Sum_probs=20.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -..++|+|..|.|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999865

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.42  E-value=0.0093  Score=49.15  Aligned_cols=24  Identities=21%  Similarity=0.062  Sum_probs=21.3

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.+.--
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl   49 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGF   49 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            458999999999999999999763

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.42  E-value=0.01  Score=49.29  Aligned_cols=23  Identities=13%  Similarity=0.065  Sum_probs=20.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -+++|.|+.|.|||||.+.++.-
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl   47 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCChHHHHHHHHHcC
Confidence            37889999999999999999874

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.42  E-value=0.015  Score=45.04  Aligned_cols=27  Identities=11%  Similarity=0.277  Sum_probs=20.9

Q ss_pred             CCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          165 SKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       165 ~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ++.---|.|+|.+|+|||||...+...
T Consensus        13 ~~~~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          13 PDQEVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             CSSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHhcC
Confidence            333445779999999999999887553

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.41  E-value=0.02  Score=46.73  Aligned_cols=48  Identities=15%  Similarity=0.178  Sum_probs=32.7

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc------CcCceEEEe
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS------NFEGSCFLQ  203 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~------~F~~~~wv~  203 (311)
                      .|-++|..+=..-+++.|+|.+|.|||++|..+......      ....+.|+.
T Consensus        25 ~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~   78 (258)
T d1v5wa_          25 EFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID   78 (258)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             HHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEec
Confidence            344555433344679999999999999999988765322      234456665

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.37  E-value=0.01  Score=45.13  Aligned_cols=22  Identities=27%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3779999999999999988775

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=94.27  E-value=0.011  Score=46.78  Aligned_cols=25  Identities=8%  Similarity=0.312  Sum_probs=22.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHH
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ++++.|+|+|.+|+|||||...+.+
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcC
Confidence            3467899999999999999999985

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=94.09  E-value=0.01  Score=49.24  Aligned_cols=23  Identities=35%  Similarity=0.430  Sum_probs=20.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -.+++|.|..|.|||||.+.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            35899999999999999999876

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.06  E-value=0.019  Score=48.82  Aligned_cols=23  Identities=22%  Similarity=0.029  Sum_probs=19.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..++|.|-.|+|||+|+..+...
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHh
Confidence            46789999999999999877654

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.93  E-value=0.015  Score=44.61  Aligned_cols=22  Identities=9%  Similarity=0.161  Sum_probs=19.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|.+|+|||||...+.+.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999988764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.93  E-value=0.016  Score=44.82  Aligned_cols=24  Identities=13%  Similarity=0.272  Sum_probs=21.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +..|+|+|.+|+|||||..++.++
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            678999999999999999999864

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.91  E-value=0.018  Score=52.13  Aligned_cols=55  Identities=20%  Similarity=0.241  Sum_probs=35.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc---CceEEEecCccccCCCCChHHHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF---EGSCFLQNVREESQRPGGLGFLQQKLLSKL  226 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F---~~~~wv~~~~~~s~~~~~~~~l~~~ll~~l  226 (311)
                      .+-|.++|+.|+|||.||+.++..+.--|   +++-|.. ++  .. ..+..++...|+...
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fTe-aG--Yv-G~DVesii~~L~~~a  106 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE-VG--YV-GKEVDSIIRDLTDSA  106 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC-------C-CCCTHHHHHHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceeee-cc--ee-ecchhHHHHHHHHHH
Confidence            34588999999999999999998764444   2222221 00  11 467777777776543

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=93.88  E-value=0.014  Score=48.38  Aligned_cols=24  Identities=29%  Similarity=0.314  Sum_probs=21.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.++||+|+.|.|||||.+.+..-
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998764

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.86  E-value=0.012  Score=49.19  Aligned_cols=23  Identities=22%  Similarity=0.163  Sum_probs=20.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++|.|+.|.|||||++.+.--
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCC
Confidence            48999999999999999998764

>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=93.83  E-value=0.09  Score=43.96  Aligned_cols=24  Identities=21%  Similarity=0.292  Sum_probs=21.5

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-.|+|+||+.+||+||...+..+
T Consensus       112 ~~~v~vvG~PNvGKSsliN~L~~~  135 (273)
T d1puja_         112 AIRALIIGIPNVGKSTLINRLAKK  135 (273)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             ceEEEEEecCccchhhhhhhhhcc
Confidence            556899999999999999999885

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.83  E-value=0.013  Score=48.69  Aligned_cols=24  Identities=25%  Similarity=0.225  Sum_probs=21.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|+.|.|||||.+.+.--
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            348999999999999999998663

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.81  E-value=0.018  Score=47.09  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=20.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ++|||.|.-|+||||+|+.+.++
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999988765

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.73  E-value=0.02  Score=46.42  Aligned_cols=29  Identities=21%  Similarity=0.273  Sum_probs=24.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNF  196 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F  196 (311)
                      -+.|+|-|+-|+||||+++.+.+.+..+.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~~~   31 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQPNC   31 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTTSE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHhCC
Confidence            35789999999999999999999876543

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.72  E-value=0.016  Score=44.80  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=19.2

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .|+|+|..|+|||||...+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999875

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.72  E-value=0.018  Score=44.73  Aligned_cols=24  Identities=13%  Similarity=0.206  Sum_probs=21.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ...|+|+|.+|+|||||...+..+
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999999999864

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.67  E-value=0.017  Score=44.25  Aligned_cols=21  Identities=10%  Similarity=0.328  Sum_probs=18.3

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.++|.+|+|||||...+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999887753

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.61  E-value=0.014  Score=47.23  Aligned_cols=36  Identities=11%  Similarity=0.233  Sum_probs=25.8

Q ss_pred             HHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          156 EIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       156 ~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|-.+|..+=..-+++-|+|.+|+||||||..+...
T Consensus        22 ~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          22 NLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             HHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             HHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            344555432223568999999999999999887654

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.61  E-value=0.017  Score=44.73  Aligned_cols=22  Identities=18%  Similarity=0.243  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3678999999999999987654

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=93.54  E-value=0.018  Score=46.57  Aligned_cols=37  Identities=22%  Similarity=0.267  Sum_probs=26.9

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|-++|..+-..-.++.|.|.+|+||||+|..++..
T Consensus        21 ~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          21 SELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             HHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            3444555422223578999999999999999998765

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=93.52  E-value=0.017  Score=44.21  Aligned_cols=22  Identities=23%  Similarity=0.339  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3679999999999999987653

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=93.42  E-value=0.031  Score=44.39  Aligned_cols=27  Identities=11%  Similarity=0.139  Sum_probs=22.7

Q ss_pred             EEEEEeccC-cchhHHHHHHHHHhhccC
Q 042778          169 YALGIWGIG-GIDRTTIARAIFNKISSN  195 (311)
Q Consensus       169 ~vi~I~Gmg-GiGKTtLA~~v~~~~~~~  195 (311)
                      +.+-|.|-| |+||||++..++.-++..
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~   29 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA   29 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC
Confidence            467899998 999999999998876444

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.38  E-value=0.016  Score=45.09  Aligned_cols=20  Identities=15%  Similarity=0.373  Sum_probs=18.5

Q ss_pred             EEEeccCcchhHHHHHHHHH
Q 042778          171 LGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~  190 (311)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999865

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.34  E-value=0.021  Score=44.02  Aligned_cols=22  Identities=14%  Similarity=0.160  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|.+|+|||||...+.+.
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999987653

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.34  E-value=0.02  Score=43.91  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=19.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|-+|+|||+|...+.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4788999999999999887763

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.32  E-value=0.021  Score=44.13  Aligned_cols=22  Identities=18%  Similarity=0.370  Sum_probs=19.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=93.32  E-value=0.017  Score=47.60  Aligned_cols=24  Identities=17%  Similarity=0.177  Sum_probs=21.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -.+++|.|..|.|||||.+.+..-
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            348999999999999999988763

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.25  E-value=0.02  Score=44.05  Aligned_cols=21  Identities=14%  Similarity=0.601  Sum_probs=18.2

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|.+|+|||||...+.+.
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999887763

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.21  E-value=0.021  Score=43.61  Aligned_cols=21  Identities=14%  Similarity=0.273  Sum_probs=18.5

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|.+|+|||||...+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987763

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.10  E-value=0.022  Score=43.88  Aligned_cols=22  Identities=18%  Similarity=0.327  Sum_probs=18.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3778999999999999987653

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.09  E-value=0.033  Score=43.28  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=18.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      --|.++|.+|+|||||...+..
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3455999999999999988754

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.04  E-value=0.025  Score=43.47  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=19.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4689999999999999987763

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.01  E-value=0.028  Score=45.79  Aligned_cols=25  Identities=28%  Similarity=0.364  Sum_probs=22.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+++..|.|.-|.|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            4789999999999999999988875

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=92.99  E-value=0.02  Score=46.05  Aligned_cols=47  Identities=13%  Similarity=0.081  Sum_probs=29.1

Q ss_pred             HHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh-hccCcCceEEEe
Q 042778          157 IESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK-ISSNFEGSCFLQ  203 (311)
Q Consensus       157 l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~-~~~~F~~~~wv~  203 (311)
                      |-++|..+=..-.++-|+|.+|+|||+||..+... ....-..++|+.
T Consensus        15 LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          15 FDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             HHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            44555432223568889999999999999876543 222222345554

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.96  E-value=0.026  Score=43.46  Aligned_cols=22  Identities=9%  Similarity=0.259  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987753

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.92  E-value=0.014  Score=48.87  Aligned_cols=23  Identities=17%  Similarity=0.224  Sum_probs=20.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -..++|+|..|.|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            35899999999999999998754

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.89  E-value=0.026  Score=43.55  Aligned_cols=21  Identities=24%  Similarity=0.401  Sum_probs=18.6

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.|+|.+|+|||||...+.+
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            478999999999999998765

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.88  E-value=0.026  Score=43.31  Aligned_cols=21  Identities=14%  Similarity=0.362  Sum_probs=18.4

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|-+|+|||||...+.+.
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999988763

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.88  E-value=0.021  Score=44.27  Aligned_cols=22  Identities=14%  Similarity=0.229  Sum_probs=19.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|+|+|.+|+|||||..++.++
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999864

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=92.86  E-value=0.051  Score=45.15  Aligned_cols=39  Identities=18%  Similarity=0.379  Sum_probs=28.5

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .+.++...|.....+.-.|.|+|..|+|||||...++.+
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            444555555544444556789999999999999999875

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.81  E-value=0.027  Score=43.10  Aligned_cols=22  Identities=9%  Similarity=0.262  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|.+|+|||||...+.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999988764

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.75  E-value=0.027  Score=43.50  Aligned_cols=21  Identities=10%  Similarity=0.279  Sum_probs=18.5

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.++|.+|+|||||+..+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999998765

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=92.74  E-value=0.053  Score=41.53  Aligned_cols=34  Identities=21%  Similarity=0.163  Sum_probs=23.8

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..+..++.   +.-..|.|+|.+|+|||||...+...
T Consensus         5 ~~~~~~~~---~k~~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           5 TRIWRLFN---HQEHKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHHT---TSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHhC---CCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            34454444   22345679999999999999987653

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.70  E-value=0.028  Score=44.47  Aligned_cols=23  Identities=13%  Similarity=0.102  Sum_probs=20.3

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +.|.|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999988764

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.70  E-value=0.025  Score=44.19  Aligned_cols=22  Identities=23%  Similarity=0.243  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|-+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4778999999999999887753

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.66  E-value=0.031  Score=41.88  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=19.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+-+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999987764

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.029  Score=42.94  Aligned_cols=22  Identities=14%  Similarity=0.428  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|-+|+|||||...+.+.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4778999999999999988764

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.59  E-value=0.031  Score=44.48  Aligned_cols=23  Identities=13%  Similarity=0.121  Sum_probs=20.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +.|.|+|.+|+|||||...+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999988764

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.59  E-value=0.029  Score=43.21  Aligned_cols=22  Identities=18%  Similarity=0.418  Sum_probs=18.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4788999999999999987664

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=92.58  E-value=0.12  Score=42.79  Aligned_cols=24  Identities=13%  Similarity=0.094  Sum_probs=20.8

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      .++.|.|.+|+||||+|..+...+
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~   59 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQW   59 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhh
Confidence            467899999999999999887764

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.58  E-value=0.03  Score=43.29  Aligned_cols=24  Identities=17%  Similarity=0.356  Sum_probs=19.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .--|.|+|.+|+|||+|...+.+.
T Consensus         6 ~~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           6 THKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCcCHHHHHHHHHhC
Confidence            345779999999999999887763

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.58  E-value=0.03  Score=43.05  Aligned_cols=21  Identities=24%  Similarity=0.610  Sum_probs=18.5

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.++|.+|+|||+|...+.+.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578899999999999988764

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.36  E-value=0.031  Score=43.54  Aligned_cols=21  Identities=24%  Similarity=0.333  Sum_probs=17.6

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.++|-+|+|||+|...+-.
T Consensus         4 KivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            367899999999999987644

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.33  E-value=0.04  Score=42.59  Aligned_cols=22  Identities=23%  Similarity=0.158  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678899999999999887764

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.30  E-value=0.031  Score=43.86  Aligned_cols=19  Identities=16%  Similarity=0.379  Sum_probs=17.1

Q ss_pred             EEEEeccCcchhHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAI  188 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v  188 (311)
                      -|.|.|.+|+|||||...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4678999999999999987

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.24  E-value=0.037  Score=42.40  Aligned_cols=21  Identities=19%  Similarity=0.493  Sum_probs=18.4

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|-+|+|||+|...+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678999999999999987654

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.24  E-value=0.025  Score=44.13  Aligned_cols=21  Identities=14%  Similarity=0.434  Sum_probs=18.9

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|+|+|.+|+|||||..++.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999998865

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.16  E-value=0.036  Score=43.74  Aligned_cols=22  Identities=14%  Similarity=0.268  Sum_probs=19.2

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            4789999999999999988764

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.13  E-value=0.038  Score=42.69  Aligned_cols=22  Identities=9%  Similarity=0.267  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|..|+|||||+..+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987663

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.13  E-value=0.037  Score=42.46  Aligned_cols=22  Identities=14%  Similarity=0.309  Sum_probs=18.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|..|+|||+|...+.+.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999987664

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.12  E-value=0.038  Score=42.30  Aligned_cols=24  Identities=8%  Similarity=0.270  Sum_probs=19.8

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..-|.|+|-.|+|||||...+.+.
T Consensus         4 ~~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           4 SRKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCcCHHHHHHHHHhC
Confidence            345788999999999999987653

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.04  E-value=0.04  Score=42.95  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=19.0

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999988763

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.02  E-value=0.041  Score=42.28  Aligned_cols=22  Identities=14%  Similarity=0.208  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|+|-+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999987653

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=91.96  E-value=0.042  Score=41.93  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=18.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|.|.+|+|||||...+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3568899999999999987654

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.92  E-value=0.042  Score=46.34  Aligned_cols=25  Identities=24%  Similarity=0.238  Sum_probs=22.0

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHH
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +++|-|+|+|-+|.|||||+.++..
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHH
Confidence            3588999999999999999998754

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.90  E-value=0.041  Score=42.05  Aligned_cols=21  Identities=19%  Similarity=0.545  Sum_probs=18.6

Q ss_pred             EEEeccCcchhHHHHHHHHHh
Q 042778          171 LGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~~  191 (311)
                      |.|+|-+|+|||||...+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            778899999999999988764

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.87  E-value=0.051  Score=42.28  Aligned_cols=23  Identities=13%  Similarity=0.163  Sum_probs=19.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --|.|+|-+|+|||+|...+.+.
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35789999999999999887764

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.83  E-value=0.038  Score=42.91  Aligned_cols=23  Identities=30%  Similarity=0.460  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --|+|+|-.|+|||||..++.+.
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            34799999999999999998864

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=91.83  E-value=0.038  Score=41.78  Aligned_cols=22  Identities=14%  Similarity=0.220  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|+|+|.+|+|||||..++..+
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999998753

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.78  E-value=0.042  Score=42.39  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=18.3

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.++|.+|+|||||...+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477999999999999988764

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=91.77  E-value=0.073  Score=46.08  Aligned_cols=30  Identities=20%  Similarity=0.282  Sum_probs=25.0

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhccCcC
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISSNFE  197 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~~F~  197 (311)
                      +..|.|=|+=|+||||+++.+.+....+..
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l~~~~~   35 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAASGGSP   35 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGGGCSSC
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHhccCCC
Confidence            456778899999999999999998766543

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.75  E-value=0.024  Score=42.98  Aligned_cols=22  Identities=18%  Similarity=0.374  Sum_probs=19.7

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|+++|.+|+|||||..++..+
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999998764

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.73  E-value=0.042  Score=42.97  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=19.5

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --|.|+|-+|+|||+|...+.+.
T Consensus        10 ~Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          10 LKCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhhC
Confidence            34889999999999999887664

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.65  E-value=0.047  Score=42.25  Aligned_cols=20  Identities=15%  Similarity=0.338  Sum_probs=18.2

Q ss_pred             EEEeccCcchhHHHHHHHHH
Q 042778          171 LGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~v~~  190 (311)
                      |.|+|.+|+|||||...+.+
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998765

>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=91.64  E-value=0.09  Score=40.37  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=22.1

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHh
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      --+|.+.|-=|.||||+++.+.+.
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEecCCCccHHHHHHHHHhh
Confidence            568999999999999999999986

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=91.61  E-value=0.044  Score=43.05  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=20.0

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .-|.|.|.+|+||||||..+..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45788999999999999998775

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=91.61  E-value=0.031  Score=43.10  Aligned_cols=25  Identities=8%  Similarity=0.129  Sum_probs=21.1

Q ss_pred             CCeEEEEEeccCcchhHHHHHHHHH
Q 042778          166 KDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       166 ~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +....|+|+|.+++|||||..++..
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhC
Confidence            3467899999999999999987744

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=91.61  E-value=0.058  Score=42.31  Aligned_cols=23  Identities=17%  Similarity=0.312  Sum_probs=20.2

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +-|.|.|.+|+||||||..+..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45788999999999999988875

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=91.59  E-value=0.045  Score=45.37  Aligned_cols=25  Identities=16%  Similarity=0.242  Sum_probs=20.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhc
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      .+..|+|.+|+||||||..++-.+.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3677999999999999988877643

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.44  E-value=0.049  Score=42.39  Aligned_cols=22  Identities=9%  Similarity=0.137  Sum_probs=18.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|..|+|||+|...+.+.
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999987764

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=91.23  E-value=0.053  Score=41.61  Aligned_cols=23  Identities=13%  Similarity=0.358  Sum_probs=19.4

Q ss_pred             eEEEEEeccCcchhHHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +--|.|+|-+|+|||||...+.+
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHHh
Confidence            34578999999999999998765

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.23  E-value=0.053  Score=41.66  Aligned_cols=22  Identities=27%  Similarity=0.569  Sum_probs=18.8

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|-.|+|||||...+.+.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3667899999999999988764

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.11  E-value=0.055  Score=41.64  Aligned_cols=21  Identities=14%  Similarity=0.408  Sum_probs=18.2

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.|+|-+|+|||||...+.+
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            378999999999999987655

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=91.07  E-value=0.058  Score=42.01  Aligned_cols=23  Identities=22%  Similarity=0.323  Sum_probs=20.4

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +-|.|.|..|+||||||..+..+
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45789999999999999988876

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.95  E-value=0.063  Score=41.71  Aligned_cols=22  Identities=14%  Similarity=0.351  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|-+|+|||||...+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4788999999999999987764

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.90  E-value=0.059  Score=41.98  Aligned_cols=22  Identities=18%  Similarity=0.232  Sum_probs=18.4

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.|.|.+|+|||+|...+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999987554

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.84  E-value=0.029  Score=43.28  Aligned_cols=21  Identities=29%  Similarity=0.433  Sum_probs=17.2

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.|+|.+|+|||||...+.+
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377889999999999987654

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=90.54  E-value=0.046  Score=42.08  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=19.5

Q ss_pred             CeEEEEEeccCcchhHHHHHHHHHh
Q 042778          167 DVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       167 ~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .++ |.|+|.+|+|||||...+.+.
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            355 568899999999999987653

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.53  E-value=0.067  Score=41.92  Aligned_cols=22  Identities=14%  Similarity=0.181  Sum_probs=18.3

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      -|.++|-.|+|||+|...+.+.
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678899999999999877654

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.40  E-value=0.063  Score=43.37  Aligned_cols=22  Identities=23%  Similarity=0.283  Sum_probs=18.7

Q ss_pred             EEEEEeccCcchhHHHHHHHHH
Q 042778          169 YALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      .-|.|.|.+|+|||||.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999988754

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=90.27  E-value=0.089  Score=44.04  Aligned_cols=22  Identities=23%  Similarity=0.499  Sum_probs=19.9

Q ss_pred             eEEEEEeccCcchhHHHHHHHH
Q 042778          168 VYALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~  189 (311)
                      +|-|+|.|-.|.|||||+.++.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            5789999999999999999874

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=90.15  E-value=0.043  Score=47.36  Aligned_cols=84  Identities=14%  Similarity=0.025  Sum_probs=51.5

Q ss_pred             EEEEeccCcchhHHHHHHHHHhhccCcCceEEEecCccccCC-CCChHHHHHHHHHHHhcCCCCCCCH-HHHHHHhCCCe
Q 042778          170 ALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQNVREESQR-PGGLGFLQQKLLSKLLQDGIVIPDI-ALSFRQLSRRK  247 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~~~~~~s~~-~~~~~~l~~~ll~~l~~~~~~~~~~-~~l~~~L~~kr  247 (311)
                      -|.|.|..|.||||+.+++...+...- ..+-+.+..+..-. ..+..        ++.  ...--+. ..++..|+...
T Consensus       168 nili~G~tgSGKTT~l~al~~~i~~~~-rivtiEd~~El~l~~~~~~~--------~~~--~~~~~~~~~ll~~~lR~~p  236 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFIPKEE-RIISIEDTEEIVFKHHKNYT--------QLF--FGGNITSADCLKSCLRMRP  236 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSCTTC-CEEEEESSCCCCCSSCSSEE--------EEE--CBTTBCHHHHHHHHTTSCC
T ss_pred             CEEEEeeccccchHHHHHHhhhccccc-ceeeccchhhhhcccccccc--------eec--cccchhHHHHHHHHhccCC
Confidence            378999999999999999998765432 23444444332110 00000        000  0001122 67778888877


Q ss_pred             EEEEEecCCChHHHHHh
Q 042778          248 VLIVLDDVTCFRQIKSL  264 (311)
Q Consensus       248 ~LlVLDdV~~~~~l~~l  264 (311)
                      =.||+..|.+.+.++.+
T Consensus       237 d~iivgEiR~~ea~~~l  253 (323)
T d1g6oa_         237 DRIILGELRSSEAYDFY  253 (323)
T ss_dssp             SEEEESCCCSTHHHHHH
T ss_pred             CcccCCccCchhHHHHH
Confidence            78999999988876655

>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=90.01  E-value=0.11  Score=42.33  Aligned_cols=32  Identities=22%  Similarity=0.404  Sum_probs=24.2

Q ss_pred             HHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          154 VEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       154 ~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +++|.++|.   +  +...++|..|+|||||..++..
T Consensus        86 ~~~L~~~l~---~--kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          86 IEELKEYLK---G--KISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             HHHHHHHHS---S--SEEEEECSTTSSHHHHHHHHST
T ss_pred             HhhHHHHhc---C--CeEEEECCCCCCHHHHHHhhcc
Confidence            455666664   2  3567899999999999998864

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.71  E-value=0.05  Score=41.93  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=8.7

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|.|+|-+|+|||||...+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477899999999999986654

>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=88.76  E-value=0.21  Score=41.62  Aligned_cols=38  Identities=16%  Similarity=0.156  Sum_probs=29.1

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      ..+..+|......-..+-++|.|+.|||+++..+.+-+
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34555665444557788999999999999999988743

>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=88.71  E-value=0.11  Score=45.41  Aligned_cols=36  Identities=17%  Similarity=0.030  Sum_probs=24.7

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhcc---CcCceEEEe
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKISS---NFEGSCFLQ  203 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~~---~F~~~~wv~  203 (311)
                      -++..|.|.+|.||||++..+...+..   .-...+.+.
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~  201 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLA  201 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEE
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEe
Confidence            358899999999999998766554322   223356666

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=88.53  E-value=0.18  Score=43.47  Aligned_cols=35  Identities=17%  Similarity=0.194  Sum_probs=26.6

Q ss_pred             EEEEEeccCcchhHHHHHHHHHhhccCcCceEEEe
Q 042778          169 YALGIWGIGGIDRTTIARAIFNKISSNFEGSCFLQ  203 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~~~~~F~~~~wv~  203 (311)
                      -.|.|=|.=|+||||+++.+.+....+-..+.++.
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~~   40 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLHHFAITPNRILLIG   40 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEe
Confidence            35788899999999999999988665544444443

>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=88.43  E-value=0.2  Score=39.95  Aligned_cols=39  Identities=13%  Similarity=0.165  Sum_probs=29.9

Q ss_pred             hHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhh
Q 042778          153 RVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKI  192 (311)
Q Consensus       153 ~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~  192 (311)
                      -+..+..+|. +..+-..+.|+|+++.|||++|.++.+-+
T Consensus        39 Fl~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          39 FLGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHHh
Confidence            4555666664 33456789999999999999999887754

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=88.24  E-value=0.057  Score=41.74  Aligned_cols=22  Identities=18%  Similarity=0.214  Sum_probs=18.9

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      +..|+|..|.|||||..++.--
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~   47 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTA   47 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            5568899999999999998754

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=87.84  E-value=0.47  Score=41.75  Aligned_cols=44  Identities=16%  Similarity=0.231  Sum_probs=31.6

Q ss_pred             cchh-hhHHHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHHhhcc
Q 042778          148 VGVE-SRVEEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFNKISS  194 (311)
Q Consensus       148 vGr~-~~~~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~~~~  194 (311)
                      .|.. ..++.+..++.   ..-.+|.|.|+.|.||||...++.+.+..
T Consensus       140 LG~~~~~~~~l~~l~~---~~~GliLvtGpTGSGKSTTl~~~l~~~~~  184 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIK---RPHGIILVTGPTGSGKSTTLYAGLQELNS  184 (401)
T ss_dssp             SCCCHHHHHHHHHHHT---SSSEEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             hcccHHHHHHHHHHHh---hhhceEEEEcCCCCCccHHHHHHhhhhcC
Confidence            3444 34445555554   23679999999999999999999887543

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.67  E-value=0.21  Score=43.11  Aligned_cols=35  Identities=11%  Similarity=0.308  Sum_probs=27.2

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      +.|.+++. ..+.+|-|+|+|-.|.|||||+-.+..
T Consensus         5 ~~~~~lm~-~~~~IRNI~iiGhvd~GKTTL~d~Ll~   39 (341)
T d1n0ua2           5 DQMRSLMD-KVTNVRNMSVIAHVDHGKSTLTDSLVQ   39 (341)
T ss_dssp             HHHHHHHH-CGGGEEEEEEECCGGGTHHHHHHHHHH
T ss_pred             HHHHHHhc-CcccCcEEEEEeCCCCcHHHHHHHHHH
Confidence            44555554 345699999999999999999988753

>d1wu7a1 c.51.1.1 (A:330-426) Histidyl-tRNA synthetase (HisRS), C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a/b)
fold: Anticodon-binding domain-like
superfamily: Class II aaRS ABD-related
family: Anticodon-binding domain of Class II aaRS
domain: Histidyl-tRNA synthetase (HisRS), C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=87.50  E-value=0.44  Score=32.86  Aligned_cols=61  Identities=21%  Similarity=0.234  Sum_probs=46.5

Q ss_pred             CcccEEecCccccCCCChHHHHHHHHHhCCCcEEeeCCCCCCCcchHHHHHHHHhccceeeeecc
Q 042778           17 HKYDVFQSFRGEDNRDNFTGHLYSALSQKGIETFIDDQLNRGDEISQSLVDAIEASAISLIIFSE   81 (311)
Q Consensus        17 ~~~dvFis~~g~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~~~~~i~~ai~~s~~~i~v~S~   81 (311)
                      ...+|||..-|++.. .++-.|+..|+++||+|.+|.   .+..+...+..|-..---.++|+.+
T Consensus         2 ~~~~V~i~~~g~~~~-~~~~~l~~~Lr~~gi~v~~d~---~~~~l~kq~~~A~~~~~~~~iiiG~   62 (97)
T d1wu7a1           2 EKKSVYICRVGKINS-SIMNEYSRKLRERGMNVTVEI---MERGLSAQLKYASAIGADFAVIFGE   62 (97)
T ss_dssp             SSCEEEEEEESSCCH-HHHHHHHHHHHTTTCEEEECC---SCCCHHHHHHHHHHTTCSEEEEEEH
T ss_pred             CCceEEEEEeCHHHH-HHHHHHHHHHHHCCCEEEEEC---CCCcHHHHHHHHHhcCCCeEEecCC
Confidence            357899998888765 589999999999999999976   2446777777776655556666664

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.33  E-value=0.2  Score=40.43  Aligned_cols=23  Identities=17%  Similarity=0.137  Sum_probs=19.9

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ++|+|.|-.+.|||||..++...
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhh
Confidence            46999999999999999987653

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=85.91  E-value=0.16  Score=43.65  Aligned_cols=26  Identities=23%  Similarity=0.204  Sum_probs=20.2

Q ss_pred             eEEEEEeccCcchhHHHHHHHHHhhc
Q 042778          168 VYALGIWGIGGIDRTTIARAIFNKIS  193 (311)
Q Consensus       168 ~~vi~I~GmgGiGKTtLA~~v~~~~~  193 (311)
                      +..|.|=|.=|+||||+++.+.+...
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC---
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHHhC
Confidence            45688999999999999999876543

>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=85.21  E-value=0.26  Score=43.46  Aligned_cols=36  Identities=14%  Similarity=0.229  Sum_probs=24.9

Q ss_pred             HHHHHhhcccCCCeEEEEEeccCcchhHHHHHHHHH
Q 042778          155 EEIESLLGAESKDVYALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       155 ~~l~~~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ..+.+.|..-++..--|+|+|.+|+|||||..++..
T Consensus        43 ~~i~~~l~~~~~~~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          43 SAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             HHHHHHHHHHHHCCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHhcccCCcEEEEECCCCCCHHHHHHHHhC
Confidence            334444432223345689999999999999999874

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.99  E-value=0.33  Score=40.58  Aligned_cols=32  Identities=16%  Similarity=0.270  Sum_probs=26.0

Q ss_pred             hhcccCCCeEEEEEeccCcchhHHHHHHHHHh
Q 042778          160 LLGAESKDVYALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       160 ~L~~~~~~~~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|..-...+.+|+|+|.-+.|||||.-.++..
T Consensus        24 ~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          24 ILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            44433445999999999999999999998874

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=84.65  E-value=0.22  Score=41.50  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.6

Q ss_pred             EEEEeccCcchhHHHHHHHHHh
Q 042778          170 ALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      .|||+|++.+|||||=.++-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999998888764

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=84.42  E-value=0.23  Score=38.21  Aligned_cols=21  Identities=29%  Similarity=0.504  Sum_probs=19.1

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      -|+|+|-.+.|||||..++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            589999999999999998864

>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=83.28  E-value=0.17  Score=41.21  Aligned_cols=21  Identities=19%  Similarity=0.297  Sum_probs=17.4

Q ss_pred             EEEEeccCcchhHHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIFN  190 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~~  190 (311)
                      ...+.|..|+|||||..++..
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~  119 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISP  119 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC
T ss_pred             eEEEECCCCccHHHHHHhhcc
Confidence            345889999999999988754

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

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: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=82.83  E-value=0.28  Score=41.21  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=20.1

Q ss_pred             EEEEEeccCcchhHHHHHHHHHh
Q 042778          169 YALGIWGIGGIDRTTIARAIFNK  191 (311)
Q Consensus       169 ~vi~I~GmgGiGKTtLA~~v~~~  191 (311)
                      ..|||+|.+.+|||||-.++-+.
T Consensus        11 ~kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          11 LKTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHCC
Confidence            35999999999999999988763

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=82.82  E-value=0.35  Score=38.29  Aligned_cols=20  Identities=25%  Similarity=0.307  Sum_probs=18.0

Q ss_pred             EEEEeccCcchhHHHHHHHH
Q 042778          170 ALGIWGIGGIDRTTIARAIF  189 (311)
Q Consensus       170 vi~I~GmgGiGKTtLA~~v~  189 (311)
                      -|+|.|-.+.|||||+.++.
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHH
Confidence            48999999999999998874

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=80.57  E-value=0.35  Score=40.49  Aligned_cols=17  Identities=24%  Similarity=0.196  Sum_probs=13.8

Q ss_pred             EEEeccCcchhHHHHHH
Q 042778          171 LGIWGIGGIDRTTIARA  187 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~~  187 (311)
                      +.|.|.+|.||||.+.+
T Consensus        27 ~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          27 LLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             EEEEECTTSCHHHHHHH
T ss_pred             EEEEecCCccHHHHHHH
Confidence            56789999999987643

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=80.36  E-value=0.34  Score=40.14  Aligned_cols=16  Identities=13%  Similarity=0.106  Sum_probs=13.4

Q ss_pred             EEEeccCcchhHHHHH
Q 042778          171 LGIWGIGGIDRTTIAR  186 (311)
Q Consensus       171 i~I~GmgGiGKTtLA~  186 (311)
                      +.|.|.+|.||||.+.
T Consensus        17 ~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             EEECCCTTSCHHHHHH
T ss_pred             EEEEeeCCccHHHHHH
Confidence            5688999999998654