Citrus Sinensis ID: 009306

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------54
Protein Sequence
MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE
Secondary Structure (PSIPRED)
cccccccccccccccccEEEEEcccccccccccHHHHHHHHHccccEEEEcccccccccccHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHHHHHccccEEEEEEccccccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHccccEEccccccHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHHcccccEEEEccccHHHHHHccHHHHHHHHHHHHHccccccccccccHHHHHHHHcccEEEEEEcccccHHHHHHHHccccccccccEEEEEcccHHHHHHccccEEEEcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHccccHHHHHHccccccccHHHHHHHHHHHHcccccHHHHHHHHcccccccccccHHHHEccccccccHHHHHHHHHHccccccccHHHHHccccEEEEcccEEEccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHcccccccEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccEEEcccccccccccHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHHHHHHcccEEEEEEEEccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHHHHHHHHHHHHHHcccHHHHHHHccccccccHHHHHHHHHHHHHccccccccHHccHHHHHHHHcccEEEEEEcccccHHHHHHHHccccccccccEEEEEEccHHHHHHccccEEEEEccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHEEEEcccccHHHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHcEEEEEcccccEEHHHHHHHHcHHHHHccccccccccEEEccHHHHHHHHHccccccEEEEEEEEc
Coil and Loop (DISEMBL)
massshpyasltnpeikyDVFLsfggedtreSFTSHLYSALSRETVETFidddlrrgdEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPvfyrvdpshvrkqtgnfgdsFLKLEERFPDKMQSWRNALTEaadlsgfdslvvspesALIEEIVNAILKRLddtfhsenedlvgvrlpmKEIESLLrtgstnvyklgiwgiggigktTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLlndgnvknflntDLNFQSRRLTRKKVLIvfddvdhprQIKILVGRldlfasgsriiittrDRQVLANCGVDEVYQMEELVHDDALRLfsrhafggdhpheshtELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKskwetappkgiQDALKISydglddkeqNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVrqestndpgkrsrlwhHKEVYKILSenrvsnndfsFLLFE
Flexible Loop (DISEMBL)
massshpyasltnpeiKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYrvdpshvrkqtgnfgdsfLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTfhsenedlvgvrlpMKEIESLLrtgstnvyklGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTllndgnvknflntdlnfqsrrltrkkvlivfddvdhprqikilvgrldlfasgsriiittrdrqvlaNCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWEnakskwetappkgiqDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQestndpgkrsrlwHHKEVYkilsenrvsnnDFSFLLFE
Low Complexity Region (SEG)
MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDaieassisiiifsesyassRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLgiwgiggigkttiagaiFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE
Disordered region (IsUnstruct)
**************EIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIV************RLWHHKEVYKILSENRVSNNDFSFLL**
Disordered Region (DISOPRED)
*****************YDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE
Disordered Region (DISEMBL)
*********SLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVR**********SRLWHHKEVYKILSENRVSNNDFSFLLFE
Disordered Region (DISPRO)
*************PEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	538	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.933	0.438	0.425	1e-109
O82500	1095	Putative disease resistan	no	no	0.947	0.465	0.395	7e-97
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.925	0.382	0.384	3e-86
Q9FL92	1372	Probable WRKY transcripti	no	no	0.866	0.339	0.356	5e-70
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.888	0.252	0.340	2e-67
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.892	0.297	0.332	1e-60
Q9FH83	1288	Probable WRKY transcripti	no	no	0.842	0.351	0.333	1e-55
Q9C5Q9	411	Protein PHLOEM PROTEIN 2-	no	no	0.310	0.406	0.368	2e-24
Q9FHE9	354	Protein PHLOEM PROTEIN 2-	no	no	0.280	0.426	0.364	5e-23
Q9SYC9	571	Vesicle-associated protei	no	no	0.286	0.269	0.362	2e-20

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

 Score =  396 bits (1018), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 221/519 (42%), Positives = 325/519 (62%), Gaps = 17/519 (3%)

Query: 18  YDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEISQSLLDAIEASSISII 76
           YDVFLSF GEDTR++FTSHLY  L+ + ++TF DD  L  G  I   L  AIE S  +I+
Sbjct: 12  YDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKAIEESQFAIV 71

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           +FSE+YA+SRWCL+EL+KI+ECK  + Q V+P+FY VDPSHVR Q  +F  +F + E ++
Sbjct: 72  VFSENYATSRWCLNELVKIMECKTRFKQTVIPIFYDVDPSHVRNQKESFAKAFEEHETKY 131

Query: 137 PDK---MQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGV 193
            D    +Q WR AL EAA+L G        ++  I +IV+ I  +L     S  +++VG+
Sbjct: 132 KDDVEGIQRWRIALNEAANLKGSCDNRDKTDADCIRQIVDQISSKLCKISLSYLQNIVGI 191

Query: 194 RLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI------SRHFSGSYFARN 247
              +++IESLL  G   V  +GIWG+GG+GKTTIA AIF+ +      S  F G+ F ++
Sbjct: 192 DTHLEKIESLLEIGINGVRIMGIWGMGGVGKTTIARAIFDTLLGRMDSSYQFDGACFLKD 251

Query: 248 VREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-RQ 306
           ++E +    +  L+  LLS LL +    N      +  + RL  KKVLIV DD+D+    
Sbjct: 252 IKENKRG--MHSLQNALLSELLREKANYNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHY 309

Query: 307 IKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHP 366
           ++ L G LD F +GSRIIITTRD+ ++     D +Y++  L   ++++LF +HAFG + P
Sbjct: 310 LEYLAGDLDWFGNGSRIIITTRDKHLIEK--NDIIYEVTALPDHESIQLFKQHAFGKEVP 367

Query: 367 HESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISY 426
           +E+  +L+ + + YA+G+PLAL+V G  L+  R   W++A    +     GI D LKISY
Sbjct: 368 NENFEKLSLEVVNYAKGLPLALKVWGSLLHNLRLTEWKSAIEHMKNNSYSGIIDKLKISY 427

Query: 427 DGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEM 486
           DGL+ K+Q +FLDIACF   E++D   + L+ C   A   + +L+DK L+ IS  N+++M
Sbjct: 428 DGLEPKQQEMFLDIACFLRGEEKDYILQILESCHIGAEYGLRILIDKSLVFISEYNQVQM 487

Query: 487 HYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           H L++ MG+ IV  +   DPG+RSRLW  KEV +++S N
Sbjct: 488 HDLIQDMGKYIVNFQK--DPGERSRLWLAKEVEEVMSNN 524

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

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

 Score =  354 bits (909), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 209/529 (39%), Positives = 308/529 (58%), Gaps = 19/529 (3%)

Query: 9   ASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAI 68
           AS ++   +YDVF SF GED R +F SHL      + + TF DD ++R   I   L  AI
Sbjct: 2   ASSSSNSWRYDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDHIKRSHTIGHELRAAI 61

Query: 69  EASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDS 128
             S IS+++FSE+YASS WCLDEL++I++CK+E    V+PVFY+VDPS +RKQTG FG S
Sbjct: 62  RESKISVVLFSENYASSSWCLDELIEIMKCKEEQGLKVMPVFYKVDPSDIRKQTGKFGMS 121

Query: 129 FL-----KLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTF 183
           FL     K EER      +WR ALT+AA++ G        E+  I  I   +L++L+ T 
Sbjct: 122 FLETCCGKTEER----QHNWRRALTDAANILGDHPQNWDNEAYKITTISKDVLEKLNATP 177

Query: 184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSY 243
             +  DLVG+   + ++ESLL   S  V  +GIWG  G+GKTTIA A++N+   +F+ S 
Sbjct: 178 SRDFNDLVGMEAHIAKMESLLCLESQGVRIVGIWGPAGVGKTTIARALYNQYHENFNLSI 237

Query: 244 FARNVREAEETCRLGD------LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIV 297
           F  NVRE+     L D      L+Q+ LS LL+    K+     L     RL  +KVLI+
Sbjct: 238 FMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQ---KDLRVRHLGAIEERLKSQKVLII 294

Query: 298 FDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFS 357
            DDVD+  Q+K L      F + SRI++TT+++Q+L +  ++ +YQ+      +AL +F 
Sbjct: 295 LDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQLLVSHDINHMYQVAYPSKQEALTIFC 354

Query: 358 RHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKG 417
           +HAF    P +    LA +    A  +PLAL VLG ++ GK +E WE +    ++     
Sbjct: 355 QHAFKQSSPSDDLKHLAIEFTTLAGHLPLALRVLGSFMRGKGKEEWEFSLPTLKSRLDGE 414

Query: 418 IQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKF-LDDCEFFATSAIEVLVDKHLI 476
           ++  LK+ YDGL D E+++FL IAC F  +  +   +  + + + + +  ++VL DK LI
Sbjct: 415 VEKVLKVGYDGLHDHEKDLFLHIACIFSGQHENYLKQMIIANNDTYVSFGLQVLADKSLI 474

Query: 477 TISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
                 +IEMH LLR +G+E+VR++S  +PGKR  L + KE   +LS N
Sbjct: 475 QKFENGRIEMHSLLRQLGKEVVRKQSIYEPGKRQFLMNAKETCGVLSNN 523

Arabidopsis thaliana (taxid: 3702)

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

 Score =  319 bits (818), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 197/512 (38%), Positives = 291/512 (56%), Gaps = 14/512 (2%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISII 76
           +YDVF SF GED R+SF SHL   L  + + TFIDD++ R   I   LL AI+ S I+I+
Sbjct: 11  RYDVFPSFRGEDVRDSFLSHLLKELRGKAI-TFIDDEIERSRSIGPELLSAIKESRIAIV 69

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLK-LEER 135
           IFS++YASS WCL+EL++I +C     Q+V+P+F+ VD S V+KQTG FG  F +  + +
Sbjct: 70  IFSKNYASSTWCLNELVEIHKCYTNLNQMVIPIFFHVDASEVKKQTGEFGKVFEETCKAK 129

Query: 136 FPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRL 195
             D+ QSW+ AL   A ++G+D      E+A+IEE+   +L++   T   +  DLVG+  
Sbjct: 130 SEDEKQSWKQALAAVAVMAGYDLRKWPSEAAMIEELAEDVLRK-TMTPSDDFGDLVGIEN 188

Query: 196 PMKEIESLLRTGSTNV-YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET 254
            ++ I+S+L   S      +GIWG  GIGK+TI  A+++K+S  F    F      +   
Sbjct: 189 HIEAIKSVLCLESKEARIMVGIWGQSGIGKSTIGRALYSKLSIQFHHRAFITYKSTSGSD 248

Query: 255 CRLGDLR--QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVG 312
                LR  ++LLS +L   ++K           +RL ++KVLI+ DDVD    +K LVG
Sbjct: 249 VSGMKLRWEKELLSEILGQKDIKI---EHFGVVEQRLKQQKVLILLDDVDSLEFLKTLVG 305

Query: 313 RLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTE 372
           + + F SGSRII+ T+DRQ+L    +D +Y++E      AL +  R AFG D P +   E
Sbjct: 306 KAEWFGSGSRIIVITQDRQLLKAHEIDLIYEVEFPSEHLALTMLCRSAFGKDSPPDDFKE 365

Query: 373 LACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDK 432
           LA +  K A  +PL L VLG  L G+ +E W     +        I   L++SYD L  K
Sbjct: 366 LAFEVAKLAGNLPLGLSVLGSSLKGRTKEWWMEMMPRLRNGLNGDIMKTLRVSYDRLHQK 425

Query: 433 EQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRA 492
           +Q++FL IAC F   +       L D   F      +L +K LI I+    IEMH LL  
Sbjct: 426 DQDMFLYIACLFNGFEVSYVKDLLKDNVGFT-----MLTEKSLIRITPDGYIEMHNLLEK 480

Query: 493 MGREIVRQESTNDPGKRSRLWHHKEVYKILSE 524
           +GREI R +S  +PGKR  L + ++++++++E
Sbjct: 481 LGREIDRAKSKGNPGKRRFLTNFEDIHEVVTE 512

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 =  265 bits (678), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 185/519 (35%), Positives = 276/519 (53%), Gaps = 53/519 (10%)

Query: 27  EDTRESFTSHLYSALSRETV-ETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASS 85
           E+ R SF SHL  AL R+ V + FID D    D +S      +E + +S++I   +   S
Sbjct: 14  EEVRYSFVSHLSKALQRKGVNDVFIDSD----DSLSNESQSMVERARVSVMILPGNRTVS 69

Query: 86  RWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRN 145
              LD+L+K+L+C+K   Q+VVPV Y V  S                          W +
Sbjct: 70  ---LDKLVKVLDCQKNKDQVVVPVLYGVRSSETE-----------------------WLS 103

Query: 146 ALTEAADLSGFDSLVVS----PESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIE 201
           AL    D  GF S+  S     +S L++E V  + ++L   F+ E    +G+   + EIE
Sbjct: 104 AL----DSKGFSSVHHSRKECSDSQLVKETVRDVYEKL---FYMER---IGIYSKLLEIE 153

Query: 202 SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREA-EETCRLGDL 260
            ++     ++  +GIWG+ GIGKTT+A A+F+++S  F    F  +  +A +E      L
Sbjct: 154 KMINKQPLDIRCVGIWGMPGIGKTTLAKAVFDQMSGEFDAHCFIEDYTKAIQEKGVYCLL 213

Query: 261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASG 320
            +Q L    N G       T L+    RL  K+VL+V DDV  P  ++  +G  D F   
Sbjct: 214 EEQFLKE--NAGASGTV--TKLSLLRDRLNNKRVLVVLDDVRSPLVVESFLGGFDWFGPK 269

Query: 321 SRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKY 380
           S IIIT++D+ V   C V+++Y+++ L   +AL+LFS  A   D   ++  E++ K IKY
Sbjct: 270 SLIIITSKDKSVFRLCRVNQIYEVQGLNEKEALQLFSLCASIDDMAEQNLHEVSMKVIKY 329

Query: 381 ARGVPLALEVLGRYLYGKRREV-WENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLD 439
           A G PLAL + GR L GK+R    E A  K +  PP    DA+K SYD L+D+E+NIFLD
Sbjct: 330 ANGHPLALNLYGRELMGKKRPPEMEIAFLKLKECPPAIFVDAIKSSYDTLNDREKNIFLD 389

Query: 440 IACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVR 499
           IACFF  E+ D   + L+ C FF    I+VLV+K L+TIS  N++ MH L++ +GR+I+ 
Sbjct: 390 IACFFQGENVDYVMQLLEGCGFFPHVGIDVLVEKSLVTISE-NRVRMHNLIQDVGRQIIN 448

Query: 500 QESTNDPGKRSRLWHHKEVYKILSENRVSNNDFSFLLFE 538
           +E T    +RSRLW    +  +L +   + N+     FE
Sbjct: 449 RE-TRQTKRRSRLWEPCSIKYLLEDKEQNENEEQKTTFE 486

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 =  256 bits (655), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 174/511 (34%), Positives = 269/511 (52%), Gaps = 33/511 (6%)

Query: 6    HPYASLTNPEIKYDVFLSFGGED-TRESFTSHLYSALSRETVETFIDDDLRRGDEISQSL 64
            +PY   ++ +  YDV + +G  D + E F SHL ++L R  +  +      + +E+    
Sbjct: 657  NPYPRFSSSK-DYDVVIRYGRADISNEDFISHLRASLCRRGISVY-----EKFNEV---- 706

Query: 65   LDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGN 124
             DA+    + II+ + +Y  S      LL ILE +    ++V P+FYR+ P      + N
Sbjct: 707  -DALPKCRVLIIVLTSTYVPS-----NLLNILEHQHTEDRVVYPIFYRLSPYDFVCNSKN 760

Query: 125  FGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFH 184
            +   +L+      D+ + W+ AL E   + G+ +L    ES LI+EIV   LK L     
Sbjct: 761  YERFYLQ------DEPKKWQAALKEITQMPGY-TLTDKSESELIDEIVRDALKVL---CS 810

Query: 185  SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF 244
            ++  +++G+ + ++EI SLL   S +V  +GIWG  GIGKTTIA  IF KIS  +     
Sbjct: 811  ADKVNMIGMDMQVEEILSLLCIESLDVRSIGIWGTVGIGKTTIAEEIFRKISVQYETCVV 870

Query: 245  ARNVREAEETCRLGDLRQQLLSTLLN-DGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDH 303
             +++ +  E      +R+  LS +L  + +V    +   +F   RL RK++L++ DDV+ 
Sbjct: 871  LKDLHKEVEVKGHDAVRENFLSEVLEVEPHVIRISDIKTSFLRSRLQRKRILVILDDVND 930

Query: 304  PRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGG 363
             R +   +G L+ F  GSRII+T+R+R+V   C +D VY+++ L    +L L  R     
Sbjct: 931  YRDVDTFLGTLNYFGPGSRIIMTSRNRRVFVLCKIDHVYEVKPLDIPKSLLLLDRGTCQI 990

Query: 364  DHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALK 423
                E +  L+ + +K++ G P  L+    +L    RE W     + +T  P  I    +
Sbjct: 991  VLSPEVYKTLSLELVKFSNGNPQVLQ----FLSSIDRE-WNKLSQEVKTTSPIYIPGIFE 1045

Query: 424  ISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNK 483
             S  GLDD E+ IFLDIACFF   D+D     LD C F A      LVDK L+TIS  N 
Sbjct: 1046 KSCCGLDDNERGIFLDIACFFNRIDKDNVAMLLDGCGFSAHVGFRGLVDKSLLTISQHNL 1105

Query: 484  IEMHYLLRAMGREIVRQESTNDPGKRSRLWH 514
            ++M   ++A GREIVRQES + PG RSRLW+
Sbjct: 1106 VDMLSFIQATGREIVRQESADRPGDRSRLWN 1136

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 =  234 bits (597), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 176/529 (33%), Positives = 266/529 (50%), Gaps = 49/529 (9%)

Query: 7   PYASLTNPEIKYDVFLSFG---GEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEIS- 61
           P A+   P IK D   S      E    S  SHL +AL RE +  F+D   L+     S 
Sbjct: 3   PPAARVTPSIKADCSHSVNIICEETVLHSLVSHLSAALRREGISVFVDACGLQETKFFSI 62

Query: 62  ---QSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHV 118
              Q L D   A  + ++I  E      W   + LK+++  +    +VVPVFY VD    
Sbjct: 63  KQNQPLTDG--ARVLVVVISDEVEFYDPW-FPKFLKVIQGWQNNGHVVVPVFYGVD---- 115

Query: 119 RKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVS----PESALIEEIVNA 174
              T  +G                W N+  EA  L+   S ++S     +S L+EEIV  
Sbjct: 116 -SLTRVYG----------------WANSWLEAEKLTSHQSKILSNNVLTDSELVEEIVRD 158

Query: 175 ILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK 234
           +  +L   + +E    VG+   + EIE LL     ++  +GIWG+ GIGKTT+A A+FN 
Sbjct: 159 VYGKL---YPAER---VGIYARLLEIEKLLYKQHRDIRSIGIWGMPGIGKTTLAKAVFNH 212

Query: 235 ISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDG-NVKNFLNTDLNFQSRRLTRKK 293
           +S  +  S F  N  EA     L  L ++ +  +L D  ++++           +L  K+
Sbjct: 213 MSTDYDASCFIENFDEAFHKEGLHRLLKERIGKILKDEFDIESSYIMRPTLHRDKLYDKR 272

Query: 294 VLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDAL 353
           +L+V DDV      +  + RLD F SGS IIIT+ D+QV A C ++++Y ++ L   +AL
Sbjct: 273 ILVVLDDVRDSLAAESFLKRLDWFGSGSLIIITSVDKQVFAFCQINQIYTVQGLNVHEAL 332

Query: 354 RLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETA 413
           +LFS+  FG + P ++  +L+ K I Y  G PLAL + GR L GK+ E+ E A  + +  
Sbjct: 333 QLFSQSVFGINEPEQNDRKLSMKVIDYVNGNPLALSIYGRELMGKKSEM-ETAFFELKHC 391

Query: 414 PPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDK 473
           PP  IQD LK +Y  L D E+NI LDIA FF  E  +   + L++  +F   AI+VLVDK
Sbjct: 392 PPLKIQDVLKNAYSALSDNEKNIVLDIAFFFKGETVNYVMQLLEESHYFPRLAIDVLVDK 451

Query: 474 HLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKIL 522
            ++TIS  N ++M+ L++   +EI   E        +R+W    +  +L
Sbjct: 452 CVLTISE-NTVQMNNLIQDTCQEIFNGEIET----CTRMWEPSRIRYLL 495

Arabidopsis thaliana (taxid: 3702)

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

 Score =  218 bits (554), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 170/510 (33%), Positives = 255/510 (50%), Gaps = 57/510 (11%)

Query: 27  EDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSR 86
           E+ R SF SHL  AL R+ +   + D         +S    IE + +S+++   +   S 
Sbjct: 17  EEVRYSFVSHLSEALRRKGINNVVVDVDIDDLLFKESQ-AKIEKAGVSVMVLPGNCDPSE 75

Query: 87  WCLDELLKILECKKEYA-QIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKMQSWRN 145
             LD+  K+LEC++    Q VV V Y              GDS L+           W +
Sbjct: 76  VWLDKFAKVLECQRNNKDQAVVSVLY--------------GDSLLR---------DQWLS 112

Query: 146 ALTEAADLSGFDSLVVS----PESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIE 201
            L    D  G   +  S     +S L+EEIV  +    +  F+      +G+   + EIE
Sbjct: 113 EL----DFRGLSRIHQSRKECSDSILVEEIVRDVY---ETHFYVGR---IGIYSKLLEIE 162

Query: 202 SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA----RNVREAEETCRL 257
           +++      +  +GIWG+ GIGKTT+A A+F+++S  F  S F     +++ E    C L
Sbjct: 163 NMVNKQPIGIRCVGIWGMPGIGKTTLAKAVFDQMSSAFDASCFIEDYDKSIHEKGLYCLL 222

Query: 258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLF 317
               +QLL    ND  +       L+    RL  K+VL+V DDV +    +  +   D  
Sbjct: 223 ---EEQLLPG--NDATI-----MKLSSLRDRLNSKRVLVVLDDVRNALVGESFLEGFDWL 272

Query: 318 ASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHA-FGGDHPHESHTELACK 376
             GS IIIT+RD+QV   CG++++Y+++ L   +A +LF   A    D   ++  EL+ +
Sbjct: 273 GPGSLIIITSRDKQVFCLCGINQIYEVQGLNEKEARQLFLLSASIKEDMGEQNLQELSVR 332

Query: 377 TIKYARGVPLALEVLGRYLYGKRR-EVWENAKSKWETAPPKGIQDALKISYDGLDDKEQN 435
            I YA G PLA+ V GR L GK++    E A  K +  PP  I DA K +YD L D E+N
Sbjct: 333 VINYANGNPLAISVYGRELKGKKKLSEMETAFLKLKRRPPFKIVDAFKSTYDTLSDNEKN 392

Query: 436 IFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGR 495
           IFLDIACFF  E+ +   + L+ C FF    I+VLVDK L+TIS  N++ +H L + +GR
Sbjct: 393 IFLDIACFFQGENVNYVIQLLEGCGFFPHVEIDVLVDKCLVTISE-NRVWLHKLTQDIGR 451

Query: 496 EIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           EI+  E+     +R RLW    +  +L  N
Sbjct: 452 EIINGETVQIE-RRRRLWEPWSIKYLLEYN 480

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 =  114 bits (285), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 100/179 (55%), Gaps = 12/179 (6%)

Query: 20  VFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFS 79
           VF++F G+D R+ F S L  AL +E +  FID+   RG  +  SL D I  S I+++IFS
Sbjct: 24  VFINFRGKDLRKGFMSFLKPALKKEKINVFIDEQEERGKYLI-SLFDTIGESKIALVIFS 82

Query: 80  ESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF--- 136
           E Y  S WC+DEL+KI E   +   I++P+FYR+D   V+  TG FGD+F  L +++   
Sbjct: 83  EGYCESHWCMDELVKIKEYMDQNRLIIIPIFYRLDLDVVKDLTGKFGDNFWDLVDKYQPE 142

Query: 137 PDKMQSWRNALTEAADLSGFDSLVVSPESAL-----IEEIVNAILKRLDDTFHSENEDL 190
           P K+  W  AL    +L    SL++   S +     ++ IV A+ K   + F   N ++
Sbjct: 143 PKKLHKWTEALFSVCELF---SLILPKHSDISDRDFVKSIVKAVKKVQKNFFQRRNGEI 198

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (273), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 90/159 (56%), Gaps = 8/159 (5%)

Query: 1   MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEI 60
           MA+SS    + T P+    VF++F G+D R  F S L  A+    +  FID D   G ++
Sbjct: 1   MAASSSVRPTPTGPQ----VFINFRGKDLRNGFLSFLEPAMREANINVFIDKDEVVGTDL 56

Query: 61  SQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRK 120
             +L   I+ S ++++IFS+ Y SS WCLDEL +I +C  +     +P+FY++ PS V +
Sbjct: 57  V-NLFVRIQESRVAVVIFSKDYTSSEWCLDELAEIKDCINQGGLNAIPIFYKLAPSSVLE 115

Query: 121 QTGNFGDSFLKLEERF---PDKMQSWRNALTEAADLSGF 156
             G FGD+F  L+E++   P++ Q W+ AL     L G 
Sbjct: 116 LKGGFGDTFRVLKEKYKNDPERTQKWQEALESIPKLKGL 154

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (250), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 90/160 (56%), Gaps = 6/160 (3%)

Query: 2   ASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEIS 61
           A+SS     +T P+  Y VF++F G++ R SF   L  A+  E +  F D+   RG  ++
Sbjct: 344 AASSTDDHGITLPQ--YQVFINFRGDELRNSFVGFLVKAMRLEKINVFTDEVELRGTNLN 401

Query: 62  QSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQ 121
             L   IE S +++ IFSE Y  S WCLDEL+K+ E  ++   +VVPVFYR++ +  ++ 
Sbjct: 402 Y-LFRRIEESRVAVAIFSERYTESCWCLDELVKMKEQMEQGKLVVVPVFYRLNATACKRF 460

Query: 122 TGNFGDSFLKLEERF---PDKMQSWRNALTEAADLSGFDS 158
            G FGD+   LE  +   P+++Q W+ AL+      G  S
Sbjct: 461 MGAFGDNLRNLEWEYRSEPERIQKWKEALSSVFSNIGLTS 500

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	538
255561496	876	TMV resistance protein N, putative [Rici	0.949	0.583	0.509	1e-139
255555357	1094	leucine-rich repeat-containing protein,	0.940	0.462	0.513	1e-135
255564976	944	TMV resistance protein N, putative [Rici	0.944	0.538	0.504	1e-133
359486075	1291	PREDICTED: TMV resistance protein N-like	0.938	0.391	0.497	1e-131
224127917	1470	tir-nbs-lrr resistance protein [Populus	0.942	0.344	0.493	1e-131
359486071	1261	PREDICTED: TMV resistance protein N-like	0.944	0.402	0.488	1e-131
359486073	1296	PREDICTED: TMV resistance protein N-like	0.946	0.392	0.483	1e-130
356550897	970	PREDICTED: TMV resistance protein N-like	0.936	0.519	0.478	1e-129
359496034	1132	PREDICTED: TMV resistance protein N-like	0.938	0.446	0.496	1e-128
359495270	1154	PREDICTED: TMV resistance protein N-like	0.947	0.441	0.485	1e-128

>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 =  500 bits (1287), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 268/526 (50%), Positives = 361/526 (68%), Gaps = 15/526 (2%)

Query: 9   ASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAI 68
           A L   E KYDVFLSF GEDTR++FTSHLYSAL+++ + TF+D +++RG+EIS S+  AI
Sbjct: 2   APLATSEKKYDVFLSFRGEDTRDNFTSHLYSALNKKKIFTFMDKEIKRGEEISPSIAKAI 61

Query: 69  EASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDS 128
           + S +S+IIFSE YA S+WCLDEL KILECKK   QIV+PVFYRVDP HVR Q G+F  +
Sbjct: 62  KGSKLSVIIFSEKYAFSKWCLDELTKILECKKMNGQIVIPVFYRVDPVHVRNQRGSFACA 121

Query: 129 FLKLEERFPDKM---QSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHS 185
           F K EE   ++M   +SWR+AL EA  +SG++SLV  PES LIEEIV  I K+L+ T  S
Sbjct: 122 FAKHEETLKERMEKVESWRSALNEAGSISGWNSLVARPESKLIEEIVKDISKKLNQTSPS 181

Query: 186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA 245
            +  LVG+   +++IES+L    ++V  +G+WG+GGIGKTT+AGAIF++IS  +  SYF 
Sbjct: 182 HSIGLVGIDSRLEQIESMLCLDMSDVRIIGVWGMGGIGKTTLAGAIFDQISAQYESSYFL 241

Query: 246 RNVREAEETCRLGDLRQQLLSTLLNDGNV----KNFLNTDLNFQSRRLTRKKVLIVFDDV 301
            NVRE  + C L +LR++L S +L + N+     N  NT   F   RL+RKK+L+V DDV
Sbjct: 242 GNVREQLKRCLLAELREKLFSKILEEKNLDTRTPNLGNT---FLKDRLSRKKILVVLDDV 298

Query: 302 DHPRQIK-ILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHA 360
           D   Q++ +L G+ DLF  GSRII+T+RD+QVL N  VDE+Y++E L   +AL+LFS +A
Sbjct: 299 DSTMQLQELLPGQHDLFGPGSRIIVTSRDKQVLKNV-VDEIYKVEGLNQHEALQLFSLNA 357

Query: 361 FGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQD 420
           F  + P     E++ +   YA+G PLAL VLG  L+ K +E WE+A  K    P   IQ 
Sbjct: 358 FKKNSPTNDRVEISTRVADYAKGNPLALRVLGCALFDKSKEDWESALEKLRNVPNGEIQK 417

Query: 421 ALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISV 480
            L+ SYDGLD +E+NIFLDIACFF  EDR+ ATK LD C       I  L+DK L+++  
Sbjct: 418 VLRFSYDGLDREERNIFLDIACFFRGEDRNYATKILDGCYSSVGFIISTLIDKSLVSV-Y 476

Query: 481 LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENR 526
            +K+EMH LL+  G  IVR+E   +  KRSRLW+ K+VY +L++ +
Sbjct: 477 RSKLEMHDLLQETGWSIVREEPELE--KRSRLWNPKDVYYVLTKKK 520

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 =  488 bits (1257), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 266/518 (51%), Positives = 356/518 (68%), Gaps = 12/518 (2%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISII 76
           KYDVFLSF GEDTR +FTSHL++AL+ + + TFIDDDL RG+EIS SLL AIE S IS++
Sbjct: 22  KYDVFLSFRGEDTRYNFTSHLHAALNGKKIPTFIDDDLERGNEISPSLLKAIEESKISVV 81

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           I S+ Y SS+WCL+EL+KILEC K   Q+V+PVFYRVDPSHVR QTG+F D F + EE  
Sbjct: 82  IISQDYPSSKWCLEELVKILECMKNRGQMVIPVFYRVDPSHVRNQTGSFEDVFARHEESL 141

Query: 137 P---DKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDD-TFHSENEDLVG 192
               +K+QSWR AL E A+LSG+ S    PE+  ++EI+  I+K+L+  + +  +  LVG
Sbjct: 142 SVSKEKVQSWRAALKEVANLSGWHSTSTRPEAEAVKEIIEVIVKKLNQMSPNCYSRGLVG 201

Query: 193 VRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAE 252
           +   ++EIESLL   S+NV  +GIWG+GG+GKTT+A AI+++I+  F   YF  N RE  
Sbjct: 202 MESRIQEIESLLCLRSSNVRIVGIWGMGGLGKTTLARAIYDRIAPQFEICYFLSNAREQL 261

Query: 253 ETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIK--IL 310
           + C L +L+ QL STLL +   ++ LN   +F   RL RKKVLIV DD D   Q++  +L
Sbjct: 262 QRCTLSELQNQLFSTLLEE---QSTLNLQRSFIKDRLCRKKVLIVIDDADDSTQLQELLL 318

Query: 311 VGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESH 370
               D F SGSRIIIT+RD+QVL N   D++Y M++L   +AL+LFS  AF  D+P   H
Sbjct: 319 ESEPDYFGSGSRIIITSRDKQVLRNIARDKIYAMQKLKKHEALQLFSLKAFKQDNPTCRH 378

Query: 371 TEL-ACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGL 429
             L A + +KYA+G PLAL VLG  L+GKR + W++A  + E  P K I D L+ISYDGL
Sbjct: 379 CRLQAERVVKYAKGNPLALTVLGSALFGKREKDWKSALERLERNPNKKIDDVLRISYDGL 438

Query: 430 DDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISV-LNKIEMHY 488
           D +E++IFLDIACFF  +DRD  TK LD     A S I  L+D+ +I +S   +K+++H 
Sbjct: 439 DSEERSIFLDIACFFRGQDRDFVTKTLDGYYGSAHSVISTLIDRSVIMLSSDSSKLDLHD 498

Query: 489 LLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENR 526
           LL+ MGR+IV +ES N P  RSRLW  ++V  +L+ENR
Sbjct: 499 LLQEMGRKIVFEESKN-PENRSRLWTPEDVCYVLNENR 535

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 261/517 (50%), Positives = 355/517 (68%), Gaps = 9/517 (1%)

Query: 13  NPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASS 72
           +P++KYDVF+SF GEDTR++FTSHLY+AL ++ ++ F+DD L RG+EIS +L+  IE S 
Sbjct: 11  DPQLKYDVFVSFRGEDTRDNFTSHLYAALHQKQIKAFVDDKLSRGEEISAALVKVIEESM 70

Query: 73  ISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKL 132
           +S+IIFSE+YA S WCLDEL+KILECKK   QIV+PVFY VDPS V +Q G FG +F++ 
Sbjct: 71  VSVIIFSENYAFSPWCLDELVKILECKKTVGQIVLPVFYHVDPSDVAEQKGGFGAAFIEH 130

Query: 133 EERFP---DKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHS-ENE 188
           E+ F    DK+Q WR ALTEAA++SG+ S V+  ES LI+EI   ILK+L+    S +++
Sbjct: 131 EKCFKERIDKLQKWRAALTEAANISGWSSSVIRSESKLIQEIAEDILKKLNHMSSSTDSK 190

Query: 189 DLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNV 248
            LVG+   + +IE LL     +V  LG+WG+GG GKTT A  +FN+IS  F    F  NV
Sbjct: 191 GLVGINSRIDKIELLLCVELADVRFLGLWGMGGAGKTTTAEVVFNRISTQFDSCCFLANV 250

Query: 249 REAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIK 308
            E  E   L  L++QL S LL   NV N+   +  F   RL  +KVLIV DDV++ RQ++
Sbjct: 251 NEESERYGLLKLQRQLFSKLLGQDNV-NY--AEGIFDKSRLKHRKVLIVLDDVNNLRQLE 307

Query: 309 ILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHE 368
            L G  + F  GSRII+T+RD+ VL N   D +Y++E+L H +AL+LFS +AF  + P  
Sbjct: 308 NLAGEHNWFGPGSRIILTSRDKDVLKN-KTDAIYKIEDLDHHEALQLFSLNAFRQECPKA 366

Query: 369 SHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDG 428
            + +L+ + I YA+G PL L+VLG +LY +  + WE+A  K E +  K IQ+ LK+SYDG
Sbjct: 367 DYMKLSKRVINYAKGNPLGLKVLGSFLYQRNIKEWESALHKLERSTNKEIQNVLKVSYDG 426

Query: 429 LDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHY 488
           LDD+E++IFLD+ACFF  EDRD  T+ L+ C F A  AI VLV K L+TIS  N + +H 
Sbjct: 427 LDDEEKDIFLDVACFFNGEDRDFVTRILNGCGFSADIAISVLVSKSLLTISN-NTLAIHN 485

Query: 489 LLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           LL+ MG  IVRQEST +PG+RSRL   ++V  +LS+N
Sbjct: 486 LLQQMGWGIVRQESTKEPGRRSRLCTSEDVVHVLSKN 522

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486075|ref|XP_002273047.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  476 bits (1225), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 255/513 (49%), Positives = 336/513 (65%), Gaps = 8/513 (1%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISII 76
           KY+VFLSF GEDTR+SFT HL+ AL R  + TFIDD LRRG++IS +LL AIE S  SII
Sbjct: 20  KYEVFLSFRGEDTRKSFTDHLHEALHRCGINTFIDDQLRRGEQISSALLQAIEESRFSII 79

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           IFSE YASS WCLDEL KILEC K     V PVFY VDPSHVRKQTG++G +F K E+ +
Sbjct: 80  IFSEHYASSSWCLDELTKILECVKVGGHTVFPVFYNVDPSHVRKQTGSYGVAFTKHEKVY 139

Query: 137 PDKMQ---SWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGV 193
            D M+    WR ALT A+ LSG+DS     ES +I+EIV+ I   L+D      E LVG+
Sbjct: 140 RDNMEKVLKWREALTVASGLSGWDS-RDRHESKVIKEIVSKIWNELNDASSCNMEALVGM 198

Query: 194 RLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE 253
              ++ + SLL  GS +V  +GIWG+ GIGKTTIA A++ KI   F G  F  NVRE  +
Sbjct: 199 DSHIQNMVSLLCIGSDDVRMVGIWGMAGIGKTTIAEAVYQKICTQFEGCCFLSNVREKSQ 258

Query: 254 TCRLGDLRQQLLSTLLNDGNVKN-FLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVG 312
                 ++ +LLS +  +GN+     N  +N   + L   +VLIV DDVD P+Q+++L G
Sbjct: 259 KNDPAVIQMELLSQVFWEGNLNTRIFNRGINAIKKTLHSMRVLIVLDDVDRPQQLEVLAG 318

Query: 313 RLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTE 372
             + F  GSRIIITTR++ +L      E+Y+++EL  D+A RLF +HAF    P     +
Sbjct: 319 NHNWFGPGSRIIITTREKHLLDE--KVEIYEVKELNKDEARRLFYQHAFKYKPPAGDFVQ 376

Query: 373 LACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDK 432
           L  + + Y +G+PLAL++LGR+LY + ++ WE+   K    P K IQD L+IS+DGLDD 
Sbjct: 377 LCDRALNYTKGIPLALKILGRFLYNRSKKEWESELEKLRRIPNKEIQDVLRISFDGLDDN 436

Query: 433 EQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRA 492
           +++IF DIACFF  +D+D   K L  C+FF    I  L+DK L+TIS  NK+ MH L++ 
Sbjct: 437 QKDIFFDIACFFKGQDKDYVIKLLKSCDFFPEIGIRNLIDKSLVTISY-NKLCMHDLIQE 495

Query: 493 MGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           MG EIVRQES  DPGKRSRLW + +V  +L+ N
Sbjct: 496 MGWEIVRQESMKDPGKRSRLWVNDDVIDMLTTN 528

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  476 bits (1224), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 253/513 (49%), Positives = 350/513 (68%), Gaps = 6/513 (1%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISII 76
           KYDVFLSF G+DTR++F SHL  AL R+ ++TFIDD L RG+EI+ +LL  IE S IS+I
Sbjct: 12  KYDVFLSFRGKDTRDNFVSHLRDALCRKQIKTFIDDKLERGEEITGALLRTIEESRISVI 71

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           IFS +YASS WC+DEL+KILECKK Y QIV+PVFY VDPS V +QTG+FG++F +LE  F
Sbjct: 72  IFSRNYASSPWCVDELVKILECKKAYGQIVLPVFYHVDPSDVDQQTGSFGNAFAELERNF 131

Query: 137 P---DKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGV 193
               DK+  WR  LT AA++SG+DS V  PES+L+E+IV+ ILK+L+    S+ + LVG+
Sbjct: 132 KQKMDKVPRWRADLTSAANISGWDSQVTRPESSLVEQIVHHILKKLNYASSSDLKGLVGM 191

Query: 194 RLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE 253
              M++IE+ L T       +GIWG+GG GKTTIAG IFNKI+R + G YF  NVRE+E+
Sbjct: 192 DSRMEQIEASLCTKLPEFCFVGIWGMGGTGKTTIAGEIFNKIAREYEGHYFLANVRESEK 251

Query: 254 TCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVG 312
              L  +R +L S +  + N+          F   R+ RKK+LIVFDDV+   QI++L+G
Sbjct: 252 NGGLFRIRDELFSKITEEENLHIRTPRIGHPFIKDRICRKKILIVFDDVNDVDQIEMLLG 311

Query: 313 RLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTE 372
             + F  GSRII+T+RD+QVL     D+++++E L H +AL LFS HAF  + P  ++ E
Sbjct: 312 GCESFGPGSRIILTSRDKQVLKK-YADKIFEVEGLNHREALHLFSLHAFKDNQPPYNYME 370

Query: 373 LACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDK 432
           L+ + I YA+G PLAL+VLG  L+G+  + WE+A +K E    + +   L+ISY+ LD +
Sbjct: 371 LSVRAINYAKGNPLALKVLGSSLFGRTTKEWESALNKVEKLTRQKVHSVLRISYEALDSE 430

Query: 433 EQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRA 492
           E++IFLDIACFF     D   + LD C F       VL+D+ LI IS  +K+EMH LL+ 
Sbjct: 431 EKSIFLDIACFFRGHRVDFVKRILDGCGFKTDIGFSVLIDRCLIKISD-DKVEMHDLLQE 489

Query: 493 MGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           M  ++VR+ES ++ G +SRLW  K+VY++L+ N
Sbjct: 490 MAHDVVRKESLDELGGQSRLWSPKDVYQVLTNN 522

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486071|ref|XP_002272667.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  473 bits (1218), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 256/524 (48%), Positives = 342/524 (65%), Gaps = 16/524 (3%)

Query: 6   HPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLL 65
           HP+        KY+VFLSF GEDTR+SFT HL+ AL R  +  FIDD LRRG++IS +LL
Sbjct: 17  HPW--------KYEVFLSFRGEDTRKSFTDHLHKALRRCGIHAFIDDRLRRGEQISSALL 68

Query: 66  DAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNF 125
            AIE S  SIIIFSE YASS WCLDEL KIL+C KE      PVFY VDPSHVRKQ G++
Sbjct: 69  RAIEESRFSIIIFSEHYASSSWCLDELTKILQCVKEGRHTAFPVFYNVDPSHVRKQEGSY 128

Query: 126 GDSFLKLEERFPDKMQS---WRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDT 182
           G +F K E+ + D M+    WR ALT A++LSG+DS     ES +I+EIV+ I K+L+D 
Sbjct: 129 GVAFTKHEQVYRDNMEKVVEWRKALTVASNLSGWDS-RDKHESEVIKEIVSKIWKKLNDA 187

Query: 183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGS 242
                E LVG+   ++ + SLLR GS +V  +GIWG+ GIGKTTIA A++ KI   F G 
Sbjct: 188 SSCNMEALVGMASHIQNMVSLLRIGSDDVRMVGIWGMAGIGKTTIAEAVYQKIRTRFEGC 247

Query: 243 YFARNVREAEETCRLGDLRQQLLSTLLNDGNVKN-FLNTDLNFQSRRLTRKKVLIVFDDV 301
            F  NVRE  +      ++ +LLS +  +GN+    L+  +N   + L   +VLIV DDV
Sbjct: 248 CFLSNVREKSQKNDPAVIQMELLSQIFEEGNLNTGVLSGGINVIEKTLHSMRVLIVLDDV 307

Query: 302 DHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAF 361
           D P+Q+++L G  + F+ GSRIIITTR++ +L      E+Y  +EL  D+A +LF +HAF
Sbjct: 308 DCPQQLEVLAGNHNWFSPGSRIIITTREKHLLDE--KVEIYVAKELNKDEARKLFYQHAF 365

Query: 362 GGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDA 421
               P     +L  + + Y +G+PLAL++LGR+LY + ++ WE+   K    P K IQD 
Sbjct: 366 KYKPPVGDFVQLCDRALNYTKGIPLALKILGRFLYNRSKKEWESELEKLRRIPNKEIQDV 425

Query: 422 LKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVL 481
           L+IS+DGLDD +++IFLDIACFF  +D+D   K L  C+FF    I  L+DK L+TIS  
Sbjct: 426 LRISFDGLDDNQKDIFLDIACFFKGQDKDYVIKLLKSCDFFPEIEIRNLIDKSLVTISY- 484

Query: 482 NKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           NK+ MH L++ MG EIVRQES  DPGKRSRLW + +V  +L+ N
Sbjct: 485 NKLCMHDLIQEMGWEIVRQESIKDPGKRSRLWVNDDVIDMLTTN 528

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486073|ref|XP_002272820.2| PREDICTED: TMV resistance protein N-like, partial [Vitis vinifera]

 Score =  473 bits (1217), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 254/525 (48%), Positives = 338/525 (64%), Gaps = 16/525 (3%)

Query: 5   SHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSL 64
           +HP+        KY+VFLSF GEDTR++FT HL+ AL R  +  FIDD LRRG++IS +L
Sbjct: 21  THPW--------KYEVFLSFRGEDTRKNFTDHLHEALRRNGIHAFIDDQLRRGEQISSAL 72

Query: 65  LDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGN 124
           L AIE S  SIIIFSE YASS WCLDEL KILEC K       PVFY VDPSHVRKQTG+
Sbjct: 73  LRAIEESRFSIIIFSEHYASSSWCLDELTKILECVKVGGHTAFPVFYNVDPSHVRKQTGS 132

Query: 125 FGDSFLKLEERFPDKMQ---SWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDD 181
           +G +F K E+ + D M+    WR ALT  + LSG+DS     ES  I+EIV+ I K L+D
Sbjct: 133 YGVAFTKHEQVYRDNMEKVSKWREALTAVSGLSGWDS-RNEHESEFIKEIVSKIWKELND 191

Query: 182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG 241
                 E LVG+   ++++ SLLR GS +V  +GIWG+ GIGKTTIA A++ KI   F G
Sbjct: 192 ASSCNMEALVGMDSHIQKMFSLLRIGSDDVRMVGIWGMAGIGKTTIAEAVYQKIRTQFEG 251

Query: 242 SYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRLTRKKVLIVFDD 300
             F  NVRE  +      ++ +LLS +   GN+    L+  +N   + L   +VLIV DD
Sbjct: 252 CCFLSNVREKSQNNDPAVIQMKLLSQIFEKGNLNTGLLSGGINVIEKTLHSMRVLIVLDD 311

Query: 301 VDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHA 360
           VD P+Q+++L G  + F  GSRIIITTR++ +L      E+Y ++EL  D+A +LF +HA
Sbjct: 312 VDCPQQLEVLAGNHNWFGPGSRIIITTREKHLLDE--KVEIYIVKELNKDEARKLFYQHA 369

Query: 361 FGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQD 420
           F    P     +L  + + Y +G+PLAL++LGR+LY + ++ WE+   K    P   IQD
Sbjct: 370 FKYKPPAGDFVQLCDRALNYTKGIPLALKILGRFLYNRSKKEWESELEKLRRIPNNEIQD 429

Query: 421 ALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISV 480
            L+IS+DGLDD +++IFLDIACFF  +D+D   K L  C+FF    I  L+DK L+TIS 
Sbjct: 430 VLRISFDGLDDNQKDIFLDIACFFKGQDKDYVIKLLKSCDFFPEIGIRNLIDKSLVTISY 489

Query: 481 LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
            NK+ MH L++ MG EIVRQES  DPGKRSRLW + +V  +L+ N
Sbjct: 490 -NKLCMHDLIQKMGWEIVRQESIKDPGKRSRLWVNDDVIDMLTTN 533

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 246/514 (47%), Positives = 341/514 (66%), Gaps = 10/514 (1%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISII 76
           KYDVFLSF GEDTR++FTSHLY AL ++ +ET+ID  L +GDEIS +L+ AIE S +S++
Sbjct: 19  KYDVFLSFRGEDTRKNFTSHLYEALKQKKIETYIDYRLEKGDEISAALIKAIEDSHVSVV 78

Query: 77  IFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           IFSE+YASS+WCL EL KI+ECKKE  QIV+PVFY +DPSHVRKQTG++  SF K     
Sbjct: 79  IFSENYASSKWCLGELGKIMECKKERGQIVIPVFYNIDPSHVRKQTGSYEQSFAK--HTG 136

Query: 137 PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRLP 196
             +   W+ ALTEAA+L+ +DS +   ES  +++IV  +L++L   + +  ++LVGV   
Sbjct: 137 EPRCSKWKAALTEAANLAAWDSQIYRTESEFLKDIVKDVLRKLAPRYPNHRKELVGVEEN 196

Query: 197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR 256
            ++IESLL+ GS+ V  LGIWG+GGIGKTT+A A+++K+S  F G  F  NVRE  +   
Sbjct: 197 YEKIESLLKIGSSKVRILGIWGMGGIGKTTLASALYDKLSPEFEGCCFLANVREESDKHG 256

Query: 257 LGDLRQQLLSTLLNDGNV----KNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVG 312
              LR +L S LL + N+     +FL +  +F   RL RKKV IV DDVD   Q++ L+ 
Sbjct: 257 FKALRNKLFSELLENENLCFDASSFLVS--HFVLSRLGRKKVFIVLDDVDTSEQLENLIE 314

Query: 313 RLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTE 372
             D    GSR+I+TTR++Q+ +   VD++Y+++EL    +L+LF    F    P   + +
Sbjct: 315 DFDFLGLGSRVIVTTRNKQIFSQ--VDKIYKVKELSIHHSLKLFCLSVFREKQPKHGYED 372

Query: 373 LACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDK 432
           L+   I Y +G+PLAL+VLG  L  + ++ WE    K +  P   I + LK+SYDGLD  
Sbjct: 373 LSRSAISYCKGIPLALKVLGASLRSRSKQAWECELRKLQKFPNMEIHNVLKLSYDGLDYS 432

Query: 433 EQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRA 492
           ++ IFLDIACF   + RD  T  L+  +F A S IEVL+DK LITIS   +IEMH L++ 
Sbjct: 433 QKEIFLDIACFLRGKQRDHVTSILEAFDFPAASGIEVLLDKALITISGGIQIEMHDLIQE 492

Query: 493 MGREIVRQESTNDPGKRSRLWHHKEVYKILSENR 526
           MG +IV QE   DPG+RSRLW H+EV+ +L  N+
Sbjct: 493 MGWKIVHQEHIKDPGRRSRLWKHEEVHDVLKYNK 526

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496034|ref|XP_002277500.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  466 bits (1199), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 255/514 (49%), Positives = 344/514 (66%), Gaps = 9/514 (1%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFID-DDLRRGDEISQSLLDAIEASSISI 75
           KYDVFLSF GEDTR +FT+HLY AL  + +  FID D LR G+ IS +LL AIE S  SI
Sbjct: 9   KYDVFLSFRGEDTRNNFTAHLYDALHCKGINAFIDADKLRIGEIISPALLSAIEGSRFSI 68

Query: 76  IIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEER 135
           ++ SE+YASSRWCL+EL+KILECKK   Q+V+P+FY+VDPS VRKQ G++G +F K EE 
Sbjct: 69  VVLSENYASSRWCLEELVKILECKKTKGQVVLPIFYQVDPSDVRKQKGSYGKAFAKHEEN 128

Query: 136 FPDKMQS---WRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENED-LV 191
             + M+    WR AL+E  ++SG DS     ES LI+EIV+ +L  L  T  S+ ED LV
Sbjct: 129 MKENMEKVHIWREALSEVGNISGRDSRN-KDESVLIKEIVSMLLNELLSTPSSDAEDQLV 187

Query: 192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREA 251
           G+   ++E+E LL T ST+V  +GIWG+GGIGKTT+A AI+N++S  F G  +  +  E 
Sbjct: 188 GIGSQIREMELLLCTESTDVRMVGIWGMGGIGKTTLAQAIYNQVSSQFEGCSYLEDAGED 247

Query: 252 EETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV 311
                L  L+++LLS +L   N+K  LN  ++ ++R L  ++V IV D+V     ++ LV
Sbjct: 248 LRKRGLIGLQEKLLSQILGHENIK--LNGPISLKAR-LCSREVFIVLDNVYDQDILECLV 304

Query: 312 GRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHT 371
           G  D F  GSRIIITTRD+++L + GV  VY++++LVH +A+    R+A       +   
Sbjct: 305 GSHDWFGQGSRIIITTRDKRLLMSHGVRVVYEVKKLVHTEAIEFLGRYASKQQIVIDEFM 364

Query: 372 ELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDD 431
           EL+   I YA+G+PL L+VLG +L+   +  W +   K +  P   IQ+ L+ISYDGLDD
Sbjct: 365 ELSNSIITYAQGLPLVLKVLGSFLFSMSKHEWRSELDKLKDTPHGRIQEVLRISYDGLDD 424

Query: 432 KEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLR 491
           KE+NIFLDIACFF  ED+D   K LD C FFA   I  L+DK LITIS  +KI MH LL+
Sbjct: 425 KEKNIFLDIACFFKGEDKDHVIKILDGCGFFAVCGIRGLIDKSLITISNNDKIVMHDLLQ 484

Query: 492 AMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
            MGR+I+RQ S  +PGKRSRLW +K+ Y +LS+N
Sbjct: 485 EMGRKIIRQTSPKEPGKRSRLWIYKDAYHVLSKN 518

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495270|ref|XP_002276075.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  466 bits (1198), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 251/517 (48%), Positives = 341/517 (65%), Gaps = 7/517 (1%)

Query: 15  EIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEISQSLLDAIEASSI 73
           + +YDVFLSF GEDTR +FT+HLY AL ++ + TFIDDD L RG  IS +L+ AIE S  
Sbjct: 12  QTRYDVFLSFRGEDTRNNFTAHLYHALCQKGINTFIDDDKLERGQVISPALVAAIENSMF 71

Query: 74  SIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLE 133
           SI++ S++YA SRWCL EL+KI+EC K   Q VVP+FY VDPS VR+Q G FG++  K E
Sbjct: 72  SIVVLSKNYAFSRWCLQELVKIVECMKSRRQRVVPIFYNVDPSDVRRQRGIFGEALAKHE 131

Query: 134 ERFPD--KMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLV 191
           E   +  ++QSW++ALT+ A+LSG+DS   + E  LI+EIV  IL +L  T  S+ E+LV
Sbjct: 132 ENSENMERVQSWKDALTQVANLSGWDSRNKN-EPLLIKEIVTDILNKLLSTSISDTENLV 190

Query: 192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREA 251
           G+   M+EIE  L  GS +   +GIWG+GGIGKTT+A AI+ KI+  F    F  NV E 
Sbjct: 191 GIDARMQEIEMRLCLGSDDFLMVGIWGMGGIGKTTLARAIYRKITCQFEACCFFENVGED 250

Query: 252 EETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV 311
                L  L+Q+ L+ LL + N+     T +     RL  KKVLIV D+V+ P  +K LV
Sbjct: 251 LAKEGLIGLQQKFLAQLLEEPNLNMKALTSI---KGRLHSKKVLIVLDNVNDPIILKCLV 307

Query: 312 GRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHT 371
           G  D F  GSRIIITTRD+++L + GV   Y+ +   +D+A    + ++     P +   
Sbjct: 308 GNYDWFGRGSRIIITTRDKRLLISHGVLNYYEAQRFNYDEASEFLTPYSLKHKIPCDDFM 367

Query: 372 ELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDD 431
           E++ + I YA+G+PLALEVLG +L+   +E W N   K ++ P   IQ+ LK+SYDGLDD
Sbjct: 368 EVSKEVIGYAQGLPLALEVLGSFLFSMTKEEWRNQLDKLKSTPNMKIQEVLKVSYDGLDD 427

Query: 432 KEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLR 491
           KE+NI LDIACFF  ED+D   + LD C FF+ S I  L+DK L+TIS  N+I MH L++
Sbjct: 428 KEKNILLDIACFFKGEDKDYVMEILDGCGFFSLSGIRALIDKSLVTISWSNEIMMHDLIQ 487

Query: 492 AMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVS 528
            MGREIVRQ+S  +PGKRSRLW H+++  +L +N  +
Sbjct: 488 EMGREIVRQQSLEEPGKRSRLWFHEDINGVLKKNTAT 524

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	538
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.946	0.444	0.377	1.8e-85
TAIR|locus:2175991	1294	AT5G17680 [Arabidopsis thalian	0.960	0.399	0.357	4.7e-79
TAIR|locus:2167457	1191	AT5G36930 [Arabidopsis thalian	0.944	0.426	0.370	6.6e-78
TAIR|locus:2146243	900	AT5G18360 [Arabidopsis thalian	0.946	0.565	0.354	3.1e-76
TAIR|locus:2205824	1384	AT1G27170 [Arabidopsis thalian	0.942	0.366	0.346	5.5e-76
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.955	0.469	0.344	9.8e-74
TAIR|locus:2118106	1219	AT4G12010 [Arabidopsis thalian	0.886	0.391	0.368	1.1e-71
TAIR|locus:2032602	1163	AT1G72860 [Arabidopsis thalian	0.959	0.443	0.352	2.2e-71
TAIR|locus:2175075	1068	AT5G41750 [Arabidopsis thalian	0.934	0.470	0.343	1.7e-70
TAIR|locus:2151491	1123	AT5G46450 [Arabidopsis thalian	0.962	0.461	0.334	2.7e-70

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

 Score = 855 (306.0 bits), Expect = 1.8e-85, P = 1.8e-85
 Identities = 200/530 (37%), Positives = 299/530 (56%)

Query:     9 ASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEISQSLLDX 67
             +S ++    YDVFLSF GEDTR++FTSHLY  L+ + ++TF DD  L  G  I   L   
Sbjct:     3 SSSSSSRWSYDVFLSFRGEDTRKTFTSHLYEVLNDKGIKTFQDDKRLEYGATIPGELCKA 62

Query:    68 XXXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGD 127
                               RWCL+EL+KI+ECK  + Q V+P+FY VDPSHVR Q  +F  
Sbjct:    63 IEESQFAIVVFSENYATSRWCLNELVKIMECKTRFKQTVIPIFYDVDPSHVRNQKESFAK 122

Query:   128 SFLKLEERFPDKM---QSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFH 184
             +F + E ++ D +   Q WR AL EAA+L G        ++  I +IV+ I  +L     
Sbjct:   123 AFEEHETKYKDDVEGIQRWRIALNEAANLKGSCDNRDKTDADCIRQIVDQISSKLCKISL 182

Query:   185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKI------SRH 238
             S  +++VG+   +++IESLL  G   V  +                 F+ +      S  
Sbjct:   183 SYLQNIVGIDTHLEKIESLLEIGINGVRIMGIWGMGGVGKTTIARAIFDTLLGRMDSSYQ 242

Query:   239 FSGSYFARNVREAEETCRLGDLRQQLLSTLLND-GNVKNFLNTDLNFQ-SRRLTRKKVLI 296
             F G+ F ++++E +    +  L+  LLS LL +  N  N    D   Q + RL  KKVLI
Sbjct:   243 FDGACFLKDIKENKRG--MHSLQNALLSELLREKANYNN--EEDGKHQMASRLRSKKVLI 298

Query:   297 VFDDVDHP-RQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRL 355
             V DD+D+    ++ L G LD F +GSRIIITTRD+ ++     D +Y++  L   ++++L
Sbjct:   299 VLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRDKHLIEKN--DIIYEVTALPDHESIQL 356

Query:   356 FSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPP 415
             F +HAFG + P+E+  +L+ + + YA+G+PLAL+V G  L+  R   W++A    +    
Sbjct:   357 FKQHAFGKEVPNENFEKLSLEVVNYAKGLPLALKVWGSLLHNLRLTEWKSAIEHMKNNSY 416

Query:   416 KGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHL 475
              GI D LKISYDGL+ K+Q +FLDIACF   E++D   + L+ C   A   + +L+DK L
Sbjct:   417 SGIIDKLKISYDGLEPKQQEMFLDIACFLRGEEKDYILQILESCHIGAEYGLRILIDKSL 476

Query:   476 ITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
             + IS  N+++MH L++ MG+ IV  +   DPG+RSRLW  KEV +++S N
Sbjct:   477 VFISEYNQVQMHDLIQDMGKYIVNFQK--DPGERSRLWLAKEVEEVMSNN 524

GO:0005515 "protein binding" evidence=IPI

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

 Score = 802 (287.4 bits), Expect = 4.7e-79, P = 4.7e-79
 Identities = 189/529 (35%), Positives = 289/529 (54%)

Query:     1 MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDE 59
             MAS     +S ++   K DVF+SF GED R++F SHL+    R  ++ F DD DL+RG  
Sbjct:     1 MASLPSSSSSSSSTVWKTDVFVSFRGEDVRKTFVSHLFCEFDRMGIKAFRDDLDLQRGKS 60

Query:    60 ISQSLLDXXXXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVR 119
             IS  L+D                    WCLDELLKI+EC K+    +VP+FY VDPS VR
Sbjct:    61 ISPELIDAIKGSRFAIVVVSRNYAASSWCLDELLKIMECNKD---TIVPIFYEVDPSDVR 117

Query:   120 KQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRL 179
             +Q G+FG+      ++  +K+  W+ AL + A +SG DS     +S LI++IV  I  +L
Sbjct:   118 RQRGSFGEDVESHSDK--EKVGKWKEALKKLAAISGEDSRNWD-DSKLIKKIVKDISDKL 174

Query:   180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHF 239
               T   +++ L+G+   M  ++S++     +V  L                 +N++S  F
Sbjct:   175 VSTSWDDSKGLIGMSSHMDFLQSMISIVDKDVRMLGIWGMGGVGKTTIAKYLYNQLSGQF 234

Query:   240 SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDL-NFQSRRLTRKKVLIVF 298
                 F  NV+E      +  L+ + L  +  + + + + +    N    R   K V IV 
Sbjct:   235 QVHCFMENVKEVCNRYGVRRLQVEFLCRMFQERDKEAWSSVSCCNIIKERFRHKMVFIVL 294

Query:   299 DDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSR 358
             DDVD   Q+  LV     F  GSRII+TTRDR +L + G++ VY+++ L   +AL+LF  
Sbjct:   295 DDVDRSEQLNELVKETGWFGPGSRIIVTTRDRHLLLSHGINLVYKVKCLPKKEALQLFCN 354

Query:   359 HAFGGDH--PHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPK 416
             +AF  +   PH    EL+ + + YA G+PLAL VLG +LY + +  WE+  ++ +T P  
Sbjct:   355 YAFREEIILPH-GFEELSVQAVNYASGLPLALRVLGSFLYRRSQIEWESTLARLKTYPHS 413

Query:   417 GIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLI 476
              I + L++SYDGLD++E+ IFL I+CF+  +  D   K LD C + A   I +L +K LI
Sbjct:   414 DIMEVLRVSYDGLDEQEKAIFLYISCFYNMKQVDYVRKLLDLCGYAAEIGITILTEKSLI 473

Query:   477 TISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
               S    +++H LL  MGRE+VRQ++ N+P +R  LW  +++  +LSEN
Sbjct:   474 VESN-GCVKIHDLLEQMGRELVRQQAVNNPAQRLLLWDPEDICHLLSEN 521

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

 Score = 789 (282.8 bits), Expect = 6.6e-78, P = 6.6e-78
 Identities = 191/516 (37%), Positives = 277/516 (53%)

Query:    18 YDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDXXXXXXXXXX 76
             YDVF+SF G D R++F SHLY +L R  + TF+DD +L+RG+ IS  LL+          
Sbjct:    17 YDVFVSFRGADVRKNFLSHLYDSLRRCGISTFMDDVELQRGEYISPELLNAIETSKILIV 76

Query:    77 XXXXXXXXXRWCLDELLKILECKKEY-AQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEER 135
                       WCLDEL+ I++  K   + +V P+F  VDPS +R Q G++  SF K +  
Sbjct:    77 VLTKDYASSAWCLDELVHIMKSHKNNPSHMVFPIFLYVDPSDIRWQQGSYAKSFSKHKNS 136

Query:   136 FP-DKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVR 194
              P +K++ WR ALT+ A++SG+D +    E+  I +I   ILKRL   +       VG+R
Sbjct:   137 HPLNKLKDWREALTKVANISGWD-IKNRNEAECIADITREILKRLPCQYLHVPSYAVGLR 195

Query:   195 LPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARNVRE-AEE 253
               ++ I SLL  GS  V  +                 FN+ S  F GS F  N RE +++
Sbjct:   196 SRLQHISSLLSIGSDGVRVIVIYGMGGIGKTTLAKVAFNEFSHLFEGSSFLENFREYSKK 255

Query:   254 TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGR 313
                   L+ QLLS +L   +++ F   D +    R   K+VL+V DDVD   Q+      
Sbjct:   256 PEGRTHLQHQLLSDILRRNDIE-FKGLD-HAVKERFRSKRVLLVVDDVDDVHQLNSAAID 313

Query:   314 LDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTEL 373
              D F  GSRIIITTR+  +L     +  Y  +EL  D++L LFS HAF    P +   + 
Sbjct:   314 RDCFGHGSRIIITTRNMHLLKQLRAEGSYSPKELDGDESLELFSWHAFRTSEPPKEFLQH 373

Query:   374 ACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKE 433
             + + + Y  G+PLA+EVLG +L  +    WE+     +  P   IQ  L+IS++ L  ++
Sbjct:   374 SEEVVTYCAGLPLAVEVLGAFLIERSIREWESTLKLLKRIPNDNIQAKLQISFNALTIEQ 433

Query:   434 QNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAM 493
             +++FLDIACFFI  D       LD C  +    + +L+++ LITIS  N I MH LLR M
Sbjct:   434 KDVFLDIACFFIGVDSYYVACILDGCNLYPDIVLSLLMERCLITISG-NNIMMHDLLRDM 492

Query:   494 GREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSN 529
             GR+IVR+ S    G+RSRLW H +V  +L +   +N
Sbjct:   493 GRQIVREISPKKCGERSRLWSHNDVVGVLKKKSGTN 528

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 768 (275.4 bits), Expect = 3.1e-76, P = 3.1e-76
 Identities = 186/525 (35%), Positives = 286/525 (54%)

Query:    10 SLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDXXX 69
             SL +   ++ VF SF G+D R +F SHL     R+ + TFID+D++R   IS  L+    
Sbjct:     8 SLQSCNWRHHVFPSFSGKDVRRTFLSHLLKEFRRKGIRTFIDNDIKRSQMISSELVRAIR 67

Query:    70 XXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSF 129
                              WCL+EL++I    K+ +Q+++PVFY VDPS VRK+TG FG +F
Sbjct:    68 ESRIAVVVLSRTYASSSWCLNELVEI----KKVSQMIMPVFYEVDPSDVRKRTGEFGKAF 123

Query:   130 LKLEERFPDK--MQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSEN 187
              +  ER PD+   Q WR AL   A+++G  S     E+ LI++I  +I   L+ T   ++
Sbjct:   124 EEACERQPDEEVKQKWREALVYIANIAGESSQNWDNEADLIDKIAMSISYELNSTLSRDS 183

Query:   188 EDLVGVRLPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARN 247
              +LVG+   M+E++SLL   ST V  +                 FN++S +F  + F  N
Sbjct:   184 YNLVGIDNHMRELDSLLCLESTEVKMVGIWGPAGIGKTTIARALFNRLSENFQHTIFMEN 243

Query:   248 VREAEETCRLGD------LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDV 301
             V+ +  T  L        L++Q LS +++  ++K     DL     RL   KVL+V DDV
Sbjct:   244 VKGSSRTSELDAYGFQLRLQEQFLSEVIDHKHMKIH---DLGLVKERLQDLKVLVVLDDV 300

Query:   302 DHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAF 361
             D   Q+  LV +   F SGSRII+TT ++Q+L   G+  +Y++      D+L++F ++AF
Sbjct:   301 DKLEQLDALVKQSQWFGSGSRIIVTTENKQLLRAHGITCIYELGFPSRSDSLQIFCQYAF 360

Query:   362 GGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDA 421
             G     +   ELA +  K A  +PLAL+VLG  L G  ++  ++A  +  T+  + I++ 
Sbjct:   361 GESSAPDGCIELATEITKLAGYLPLALKVLGSSLRGMSKDEQKSALPRLRTSLNEDIRNV 420

Query:   422 LKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVL 481
             L++ YDG+ DK++ IFL IAC F  E+ D   + L       T  ++VL  + LI IS  
Sbjct:   421 LRVGYDGIHDKDKVIFLHIACLFNGENVDYVKQILASSGLDVTFGLQVLTSRSLIHISRC 480

Query:   482 NK-IEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
             N+ I MH LL  +GREIV ++S  +PGKR  L    E+Y +L++N
Sbjct:   481 NRTITMHNLLEQLGREIVCEQSIAEPGKRQFLMDASEIYDVLADN 525

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2205824 AT1G27170 [Arabidopsis thaliana (taxid:3702)]

 Score = 775 (277.9 bits), Expect = 5.5e-76, P = 5.5e-76
 Identities = 179/517 (34%), Positives = 275/517 (53%)

Query:    16 IKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEISQSLLDXXXXXXXX 74
             +KYDVFLSF G DTR++F  HLY AL ++ V  F D++ + RGDEIS SL          
Sbjct:    12 LKYDVFLSFRGADTRDNFGDHLYKAL-KDKVRVFRDNEGMERGDEISSSLKAGMEDSAAS 70

Query:    75 XXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEE 134
                        RWCLDEL  + + K    + ++P+FY VDPSHVRKQ+ +    F + + 
Sbjct:    71 VIVISRNYSGSRWCLDELAMLCKMKSSLDRRILPIFYHVDPSHVRKQSDHIKKDFEEHQV 130

Query:   135 RFPD---KMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLV 191
             RF +   K+Q WR ALT   +L+G+     S +  +IE +V  +L  L +T     E +V
Sbjct:   131 RFSEEKEKVQEWREALTLVGNLAGYVCDKDSKDDDMIELVVKRVLAELSNTPEKVGEFIV 190

Query:   192 GVRLPMKEIESLLRT-GSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARNVRE 250
             G+  P+K++  L+ T  S+ V  L                 +NKI  +F    F  ++RE
Sbjct:   191 GLESPLKDLTGLIDTESSSGVQVLGLYGMGGIGKTTLAKAFYNKIVGNFEQRAFISDIRE 250

Query:   251 AEETCR-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKI 309
                    L  L++ L+  L         ++  L      +  KK+++V DDVDH  Q+  
Sbjct:   251 RSSAENGLVTLQKTLIKELFRLVPEIEDVSIGLEKIKANVHEKKIIVVLDDVDHIDQVHA 310

Query:   310 LVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHES 369
             LVG    +  G+ I+ITTRD ++L+   V++ Y+++ L    AL+LFS H+   + P ++
Sbjct:   311 LVGETRWYGQGTLIVITTRDSEILSKLSVNQQYEVKCLTEPQALKLFSYHSLRKEEPTKN 370

Query:   370 HTELACKTIKYARGVPLALEVLGRYLYGKRREV-WENAKSKWETAPPKGIQDALKISYDG 428
                L+ K ++ +  +PLA+EV G  LY K+ E  W+    K +   P  +QD L++S+  
Sbjct:   371 LLALSKKIVQISGLLPLAVEVFGSLLYDKKEEKDWQTQLDKLKKTQPGNLQDVLELSFKS 430

Query:   429 LDDKEQNIFLDIACFFIDED--RDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEM 486
             LDD+E+ +FLDIAC F+  +  +D     L  C   A +A+ VL  K L+ I   + + M
Sbjct:   431 LDDEEKKVFLDIACLFLKMEIKKDEVVIVLKGCGLNAEAALSVLRQKSLVKILANDTLWM 490

Query:   487 HYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILS 523
             H  +R MGR++V +ES  DPG RSRLW   E+  +L+
Sbjct:   491 HDQIRDMGRQMVLKESREDPGLRSRLWDRGEIMTVLN 527

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:2136108 AT4G11170 [Arabidopsis thaliana (taxid:3702)]

 Score = 748 (268.4 bits), Expect = 9.8e-74, P = 9.8e-74
 Identities = 181/525 (34%), Positives = 278/525 (52%)

Query:     9 ASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDXX 68
             AS ++   +YDVF SF GED R +F SHL      + + TF DD ++R   I   L    
Sbjct:     2 ASSSSNSWRYDVFPSFRGEDVRNNFLSHLLKEFESKGIVTFRDDHIKRSHTIGHELRAAI 61

Query:    69 XXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDS 128
                               WCLDEL++I++CK+E    V+PVFY+VDPS +RKQTG FG S
Sbjct:    62 RESKISVVLFSENYASSSWCLDELIEIMKCKEEQGLKVMPVFYKVDPSDIRKQTGKFGMS 121

Query:   129 FLKLE-ERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSEN 187
             FL+    +  ++  +WR ALT+AA++ G        E+  I  I   +L++L+ T   + 
Sbjct:   122 FLETCCGKTEERQHNWRRALTDAANILGDHPQNWDNEAYKITTISKDVLEKLNATPSRDF 181

Query:   188 EDLVGVRLPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARN 247
              DLVG+   + ++ESLL   S  V  +                 +N+   +F+ S F  N
Sbjct:   182 NDLVGMEAHIAKMESLLCLESQGVRIVGIWGPAGVGKTTIARALYNQYHENFNLSIFMEN 241

Query:   248 VREAEETCRLGD------LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDV 301
             VRE+     L D      L+Q+ LS LL+    K+     L     RL  +KVLI+ DDV
Sbjct:   242 VRESYGEAGLDDYGLKLHLQQRFLSKLLDQ---KDLRVRHLGAIEERLKSQKVLIILDDV 298

Query:   302 DHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAF 361
             D+  Q+K L      F + SRI++TT+++Q+L +  ++ +YQ+      +AL +F +HAF
Sbjct:   299 DNIEQLKALAKENQWFGNKSRIVVTTQNKQLLVSHDINHMYQVAYPSKQEALTIFCQHAF 358

Query:   362 GGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDA 421
                 P +    LA +    A  +PLAL VLG ++ GK +E WE +    ++     ++  
Sbjct:   359 KQSSPSDDLKHLAIEFTTLAGHLPLALRVLGSFMRGKGKEEWEFSLPTLKSRLDGEVEKV 418

Query:   422 LKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFL-DDCEFFATSAIEVLVDKHLITISV 480
             LK+ YDGL D E+++FL IAC F  +  +   + +  + + + +  ++VL DK LI    
Sbjct:   419 LKVGYDGLHDHEKDLFLHIACIFSGQHENYLKQMIIANNDTYVSFGLQVLADKSLIQKFE 478

Query:   481 LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
               +IEMH LLR +G+E+VR++S  +PGKR  L + KE   +LS N
Sbjct:   479 NGRIEMHSLLRQLGKEVVRKQSIYEPGKRQFLMNAKETCGVLSNN 523

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:2118106 AT4G12010 [Arabidopsis thaliana (taxid:3702)]

 Score = 733 (263.1 bits), Expect = 1.1e-71, P = 1.1e-71
 Identities = 180/489 (36%), Positives = 265/489 (54%)

Query:    17 KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDXXXXXXXXXX 76
             ++DVFLSF G DTR +FT HL  AL    +++FIDD LRRGD ++ +L D          
Sbjct:    10 EFDVFLSFRGFDTRNNFTGHLQKALRLRGIDSFIDDRLRRGDNLT-ALFDRIEKSKIAII 68

Query:    77 XXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
                       WCL EL+KILEC+    Q+VVP+FY+VD S V KQ  +F   F   E  F
Sbjct:    69 VFSTNYANSAWCLRELVKILECRNSNQQLVVPIFYKVDKSDVEKQRNSFAVPFKLPELTF 128

Query:   137 P----DKMQSWRNALTEAADLSGFDSLVVSP-ESALIEEIVNAILKRLDDTFHSENEDLV 191
             P    +++ SW+ AL  A+++ G+    +S  E+ L++EI     K+L+D   S NE LV
Sbjct:   129 PGVTPEEISSWKAALASASNILGYVVKEISTSEAKLVDEIAVDTFKKLNDLAPSGNEGLV 188

Query:   192 GVRLPMKEIESLLRTGSTN-VYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARNVRE 250
             G+   +K +E LL     + V+ +                 + ++   F GS F  N+RE
Sbjct:   189 GIESRLKNLEKLLSWEDLDTVHIIGIVGMVGIGKTTLADCLYGRMRGQFDGSCFLTNIRE 248

Query:   251 AEETCRLGDLRQQLLSTLLNDGNVKNFL--NTDLNFQSRRLTRKKVLIVFDDVDHPRQIK 308
                   L  L Q+L ST+LND +++     N    F+ RRL  K++LIV DDV+  +QI+
Sbjct:   249 NSGRSGLESLLQKLFSTVLNDRDLEIGAPGNAHERFE-RRLKSKRLLIVLDDVNDEKQIR 307

Query:   309 ILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHE 368
              L+G    +  GSRIIITTRD +++        Y + +L   +AL+LFS +AF    P +
Sbjct:   308 YLMGHCKWYQGGSRIIITTRDSKLIETIK-GRKYVLPKLNDREALKLFSLNAFSNSFPLK 366

Query:   369 SHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDG 428
                 L    + YA+G PLAL+VLG  L  +    WE    + ++     I + L+ SY+ 
Sbjct:   367 EFEGLTNMVLDYAKGHPLALKVLGSDLCERDDLYWEAKLDRLKSRSHGDIYEVLETSYEE 426

Query:   429 LDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHY 488
             L  +++N+FLDIACFF  E+ D  T  L+      +  ++ LVDK LIT+S  N+IEMH 
Sbjct:   427 LTTEQKNVFLDIACFFRSENVDYVTSLLNSHGVDVSGVVKDLVDKCLITLSD-NRIEMHD 485

Query:   489 LLRAMGREI 497
             +L+ M +EI
Sbjct:   486 MLQTMAKEI 494

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

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

 Score = 729 (261.7 bits), Expect = 2.2e-71, P = 2.2e-71
 Identities = 187/530 (35%), Positives = 277/530 (52%)

Query:     9 ASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEISQSLLDX 67
             +S ++P  KYDVFLSF GEDTR++  SHL+  L  + V TF DD  L  GD IS+ +   
Sbjct:     3 SSSSSPIWKYDVFLSFRGEDTRKNIVSHLHKQLVDKGVVTFKDDKKLELGDSISEEISRA 62

Query:    68 XXXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGD 127
                                WCLDEL  +++   +    VVP+FY VDPSHVR QTG+F  
Sbjct:    63 IQNSTYALVILSENYASSSWCLDELRMVMDLHLKNKIKVVPIFYGVDPSHVRHQTGSF-- 120

Query:   128 SFLKLEE-RFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSE 186
             +F K ++ + P+K+ +WR ALT+ A L+G D      E+++IEEIV  I K+L      +
Sbjct:   121 TFDKYQDSKMPNKVTTWREALTQIASLAGKDFETCEDEASMIEEIVKDISKKLLIMQPVD 180

Query:   187 NEDLVGVRLPMKEIESLLRTGSTN-VYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFA 245
               D+VG+   M+ +  LL   S N V  +                 F++ S+ F    F 
Sbjct:   181 FSDIVGMNAHMERLSPLLSMDSENEVRMIGIWGMGGIGKTTIAKCLFDQFSQGFPARCFL 240

Query:   246 RNVREAEETCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQS--RRLTRKKVLIVFDDVD 302
              NV +      +  L ++ LST L     K       L  Q    R   +KV +V D+VD
Sbjct:   241 ENVSKIYRKGGVSSLAEKFLSTTLGLSKKKMKGSGVKLGPQEIKARFGCRKVFVVLDNVD 300

Query:   303 HPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFG 362
               RQ+         F  GSRIIITTRD+ +L   GV  VY+++ + +D AL+LF++ AF 
Sbjct:   301 DMRQMHAFAQESSWFGPGSRIIITTRDKGLLNTYGVRTVYEVKCMDNDAALQLFNQLAFK 360

Query:   363 GD-HPHESHTELACKTIKYARGVPLALEVLGRYLYGKRR---EVWENAKSKWETAPPKGI 418
             G   P E + +L+ +    A+G+P+A+E  G  L+ +R    + W++A  ++  AP + +
Sbjct:   361 GALPPSELYEKLSIRASWLAQGLPVAIEAYG--LFFRRMTSLKEWDDALCRFIEAPDESV 418

Query:   419 QDALKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITI 478
              + LKISYDGL++ ++N+FL +AC F  E    AT  LDD        +++L +K LI I
Sbjct:   419 MEILKISYDGLEETDKNVFLHVACLFNGEPLRRATTLLDDGVLQGCLGLKILAEKSLIEI 478

Query:   479 SVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVS 528
             +    I+MH L+    R IV QES      R  LW+  E+Y++L  N  S
Sbjct:   479 TASGYIKMHNLVDQTARAIVNQESMQRRHGRGVLWNPYEIYELLKRNTTS 528

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:2175075 AT5G41750 [Arabidopsis thaliana (taxid:3702)]

 Score = 718 (257.8 bits), Expect = 1.7e-70, P = 1.7e-70
 Identities = 177/516 (34%), Positives = 270/516 (52%)

Query:    17 KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDXXXXXXXXXX 76
             +Y VF SF G D R+ F SHL+S  + + + TF D  + RG  I   L+           
Sbjct:    12 RYQVFSSFHGPDVRKGFLSHLHSVFASKGITTFNDQKIDRGQTIGPELIQGIREARVSIV 71

Query:    77 XXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
                       WCLDEL++IL+CK+   QIV+ VFY VDPS V+KQ+G FG++F K  +  
Sbjct:    72 VLSKKYASSSWCLDELVEILKCKEALGQIVMTVFYEVDPSDVKKQSGVFGEAFEKTCQGK 131

Query:   137 PDKMQ-SWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLDDTFHSENEDLVGVRL 195
              ++++  WRNAL   A ++G  SL    E+ +I++IV  +  +L+ T   + E +VG+  
Sbjct:   132 NEEVKIRWRNALAHVATIAGEHSLNWDNEAKMIQKIVTDVSDKLNLTPSRDFEGMVGMEA 191

Query:   196 PMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHFSGSYFARNVRE----- 250
              +K + SLL   S  V  +                 FNKIS  F    F  N++      
Sbjct:   192 HLKRLNSLLCLESDEVKMIGIWGPAGIGKTTIARTLFNKISSIFPFKCFMENLKGSIKGG 251

Query:   251 AEETCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKI 309
             AE   +L  L++QLLS +L   N+K + L T   +    L  +KVLI+ DDVD   Q+++
Sbjct:   252 AEHYSKLS-LQKQLLSEILKQENMKIHHLGTIKQW----LHDQKVLIILDDVDDLEQLEV 306

Query:   310 LVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHES 369
             L      F SGSRII+TT D+ +L    + ++Y ++    ++AL +    AF      + 
Sbjct:   307 LAEDPSWFGSGSRIIVTTEDKNILKAHRIQDIYHVDFPSEEEALEILCLSAFKQSSIPDG 366

Query:   370 HTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGL 429
               ELA K  +    +PL L V+G  L  K +  WE   S+ E++  K I + L+I YD L
Sbjct:   367 FEELANKVAELCGNLPLGLCVVGASLRRKSKNEWERLLSRIESSLDKNIDNILRIGYDRL 426

Query:   430 DDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMH-Y 488
               ++Q++FL IACFF +E  D  T  L D +    +   +L D+ L+ IS    + MH Y
Sbjct:   427 STEDQSLFLHIACFFNNEKVDYLTALLADRKLDVVNGFNILADRSLVRISTDGHVVMHHY 486

Query:   489 LLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSE 524
             LL+ +GR IV ++  N+PGKR  L   +E+  +L++
Sbjct:   487 LLQKLGRRIVHEQWPNEPGKRQFLIEAEEIRDVLTK 522

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

 Score = 718 (257.8 bits), Expect = 2.7e-70, P = 2.7e-70
 Identities = 178/532 (33%), Positives = 281/532 (52%)

Query:     1 MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEI 60
             MASSS   +S  N    YDVF SF GED R++F SH    L R+++ TF D+++ R   I
Sbjct:     1 MASSS---SSSRN--WSYDVFPSFSGEDVRKTFLSHFLRELERKSIITFKDNEMERSQSI 55

Query:    61 SQSLLDXXXXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRK 120
             +  L++                    WCL+ELL+I+ C K   Q V+PVFY +DPSH+RK
Sbjct:    56 APELVEAIKDSRIAVIVFSKNYASSSWCLNELLEIMRCNKYLGQQVIPVFYYLDPSHLRK 115

Query:   121 QTGNFGDSFLKLEERFPDKMQS-WRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRL 179
             Q+G FG++F K  +   +++++ W+ ALT+ +++ G+ S   + E+ +IEEI + IL +L
Sbjct:   116 QSGEFGEAFKKTCQNQTEEVKNQWKQALTDVSNILGYHSKNCNSEATMIEEISSHILGKL 175

Query:   180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLXXXXXXXXXXXXXXXXXFNKISRHF 239
               T  ++ E+ VG++  ++++  LL   S  V  +                 F+ +S  F
Sbjct:   176 SLTPSNDFEEFVGIKDHIEKVRLLLHLESDEVRMVGIWGTSGIGKTTIARALFSNLSSQF 235

Query:   240 SGS-YFARN-VREAEETCRLGDLRQQLLSTLLNDGNVKNFL---NTDLNFQSRRLTRKKV 294
               S Y  R  + ++ E     +     +   L +  +   L   N  +     RL  +KV
Sbjct:   236 QSSVYIDRAFISKSMEGYGRANPDDYNMKLRLRENFLFEILGKKNMKIGAMEERLKHQKV 295

Query:   295 LIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALR 354
             LI+ DD+D    +  LVGR   F SGSRII+ T+++  L   G+D VY+      + AL 
Sbjct:   296 LIIIDDLDDQDVLDALVGRTQWFGSGSRIIVVTKNKHFLRAHGIDHVYEACLPSEELALE 355

Query:   355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAP 414
             +F R+AF  + P +   EL+ +    A  +PL L+VLG YL G+  E W +   + +   
Sbjct:   356 MFCRYAFRKNSPPDGFMELSSEVALRAGNLPLGLKVLGSYLRGRDIEDWMDMMPRLQNDL 415

Query:   415 PKGIQDALKISYDGLDDK-EQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDK 473
                I+  L++SYDGL++K ++ IF  IAC F  E  +     L + +      ++ LVDK
Sbjct:   416 DGKIEKTLRVSYDGLNNKKDEAIFRHIACLFNGEKVNDIKLLLAESDLDVNIGLKNLVDK 475

Query:   474 HLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
              LI +   + IEMH LL+ MG+EIVR +S N+PG+R  L   K +Y +L +N
Sbjct:   476 SLIFVRE-DTIEMHRLLQDMGKEIVRAQS-NEPGEREFLVDSKHIYDVLEDN 525

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

---

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.01250003 tir-nbs-lrr resistance protein (1470 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	538
PLN03210	1153	PLN03210, PLN03210, Resistant to P	1e-116
pfam01582	135	pfam01582, TIR, TIR domain	5e-39
smart00255	140	smart00255, TIR, Toll - interleukin 1 - resistance	3e-35
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	8e-35
PLN03194	187	PLN03194, PLN03194, putative disease resistance pr	5e-15
pfam13676	102	pfam13676, TIR_2, TIR domain	3e-11

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

 Score =  369 bits (948), Expect = e-116
 Identities = 205/538 (38%), Positives = 308/538 (57%), Gaps = 23/538 (4%)

Query: 1   MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEI 60
           MASSS      ++    YDVF SF GED R +F SH    L R+ +  F D+++ R   +
Sbjct: 1   MASSSS-----SSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSL 55

Query: 61  SQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRK 120
              L  AI  S I++++FS++YASS WCL+ELL+I+ CK+E  Q+V+PVFY +DPSHVRK
Sbjct: 56  DPELKQAIRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRK 115

Query: 121 QTGNFGDSFLKL-EERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRL 179
           QTG+FG++F K  + +  D+   W+ ALT+ A++ G+ S     E+ +IEEI N +L +L
Sbjct: 116 QTGDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQNWPNEAKMIEEIANDVLGKL 175

Query: 180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF 239
           + T  ++ ED VG+   + ++ SLL   S  V  +GIWG  GIGKTTIA A+F+++SR F
Sbjct: 176 NLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQF 235

Query: 240 SGSYFARNV-----REAEETCRLGD------LRQQLLSTLLNDGNVKNFLNTDLNFQSRR 288
             S F          E   +    D      L++  LS +L+  ++K +    L     R
Sbjct: 236 QSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIY---HLGAMEER 292

Query: 289 LTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELV 348
           L  +KVLI  DD+D    +  L G+   F SGSRII+ T+D+  L   G+D +Y++    
Sbjct: 293 LKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPS 352

Query: 349 HDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKS 408
           ++ AL +F R AF  + P +   ELA +    A  +PL L VLG YL G+ +E W +   
Sbjct: 353 NELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLP 412

Query: 409 KWETAPPKGIQDALKISYDGLDD-KEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAI 467
           +        I+  L++SYDGL++ K++ IF  IAC F  E  +     L + +      +
Sbjct: 413 RLRNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVNDIKLLLANSDLDVNIGL 472

Query: 468 EVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSEN 525
           + LVDK LI +   + +EMH LL+ MG+EIVR +S N+PG+R  L   K++  +L +N
Sbjct: 473 KNLVDKSLIHVR-EDIVEMHSLLQEMGKEIVRAQS-NEPGEREFLVDAKDICDVLEDN 528

syringae 6; Provisional. Length = 1153

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

 Score =  138 bits (350), Expect = 5e-39
 Identities = 61/135 (45%), Positives = 89/135 (65%), Gaps = 6/135 (4%)

Query: 20  VFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIF 78
           VF+SF G+D R++F SHL   L  + ++  IDD D   G+ I ++L +AIE S  +I+IF
Sbjct: 1   VFVSFSGKDDRDTFVSHLLKELEEKGIKLCIDDRDELPGESILENLFEAIEKSRRAIVIF 60

Query: 79  SESYASSRWCLDELLKILECKKE--YAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF 136
           S +YASS WCLDEL++I++C  E    ++++P+FY+VDPS VR Q+G FG +FLK  +  
Sbjct: 61  SSNYASSEWCLDELVEIVKCALEGGGKKVILPIFYKVDPSDVRPQSGKFGKAFLKTLKWS 120

Query: 137 PDKMQS---WRNALT 148
            DK      W+ AL 
Sbjct: 121 GDKEDKIRFWKKALY 135

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

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

 Score =  128 bits (324), Expect = 3e-35
 Identities = 59/141 (41%), Positives = 80/141 (56%), Gaps = 5/141 (3%)

Query: 17  KYDVFLSFGG-EDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISI 75
           +YDVF+S+ G ED R  F SHL   L    +  FIDD    G ++ + + +AIE S I+I
Sbjct: 1   EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDL-EEIDEAIEKSRIAI 59

Query: 76  IIFSESYASSRWCLDELLKILECKKEYAQI-VVPVFYRVDPSHVRKQTGNFGDSFLKLEE 134
           ++ S +YA S WCLDEL+  LE   E   + V+P+FY V PS VRKQ G F   F K   
Sbjct: 60  VVLSPNYAESEWCLDELVAALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVFKKNYL 119

Query: 135 RFPD--KMQSWRNALTEAADL 153
           ++P+  K Q W+ AL      
Sbjct: 120 KWPEDEKEQFWKKALYAVPSK 140

Length = 140

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

 Score =  132 bits (333), Expect = 8e-35
 Identities = 78/263 (29%), Positives = 119/263 (45%), Gaps = 25/263 (9%)

Query: 200 IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK--ISRHFSGSYFARNVREAEETCRL 257
           IE LL   S N+  +GI G+GG+GKTT+A  I+N   +  HF    +    +   E    
Sbjct: 9   IEKLLE-MSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTE---- 63

Query: 258 GDLRQQLLSTLLNDGNVKNFLNT-----DLNFQSRRLTRKKVLIVFDDV-DHPRQIKILV 311
             L++ +L  L  D +     N       +      L RK+ L+V DDV +     KI V
Sbjct: 64  FRLQKDILQELGLDDSDWVEKNESELAVKIK---EALLRKRFLLVLDDVWEKNDWDKIGV 120

Query: 312 GRLDLFASGSRIIITTRDRQVLANCGV-DEVYQMEELVHDDALRLFSRHAF-GGDHPHES 369
              D   +GSR+I+TTR   V    G   + +++E L  +++  LFS   F     P   
Sbjct: 121 PFPD-GENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPE 179

Query: 370 HTELACKTIKYARGVPLALEVLGRYLYGKRR-EVWENAKSKWETAPPK-----GIQDALK 423
             E+A + ++  +G+PLAL+VLG  L  K   + WE+   +             +   L 
Sbjct: 180 LEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNEVLSILS 239

Query: 424 ISYDGLDDKEQNIFLDIACFFID 446
           +SYD L    +  FL +A F  D
Sbjct: 240 LSYDNLPMHLKRCFLYLALFPED 262

Length = 285

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

 Score = 73.3 bits (180), Expect = 5e-15
 Identities = 47/156 (30%), Positives = 76/156 (48%), Gaps = 16/156 (10%)

Query: 7   PYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLL 65
            Y S ++     DVF++  G DT+ +  + LY  LSR  +  F+D+ +++ GD++   + 
Sbjct: 16  HYPSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKIN 75

Query: 66  DAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNF 125
            AI    + + +FS  Y  S +CL EL  I+E KK     V+P+F  V PS +R      
Sbjct: 76  SAIRNCKVGVAVFSPRYCESYFCLHELALIMESKKR----VIPIFCDVKPSQLRVVDNG- 130

Query: 126 GDSFLKLEERFPDKMQSWRNALTEAADLSG--FDSL 159
                       ++++ +  AL EA    G  FDSL
Sbjct: 131 --------TCPDEEIRRFNWALEEAKYTVGLTFDSL 158

Length = 187

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

 Score = 59.9 bits (146), Expect = 3e-11
 Identities = 23/97 (23%), Positives = 47/97 (48%), Gaps = 8/97 (8%)

Query: 20  VFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFS 79
           VF+S+   D    +   L  AL    +  ++D D+  G++    + +A+ ++ + +++ S
Sbjct: 1   VFISYASAD--REWAEWLADALEAAGIRVWLDWDIPPGEDWRDEIEEALRSADVVLVLLS 58

Query: 80  ESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPS 116
            +Y +S WC  E    LE  K     ++PV  R++  
Sbjct: 59  PAYLASPWCRAEWGAALERGK----RLIPV--RLEDC 89

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	538
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03194	187	putative disease resistance protein; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
smart00255	140	TIR Toll - interleukin 1 - resistance.	99.84
PF01582	141	TIR: TIR domain; InterPro: IPR000157 In Drosophila	99.83
PRK04841	903	transcriptional regulator MalT; Provisional	99.76
PF13676	102	TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_	99.66
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.61
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.57
COG3899	849	Predicted ATPase [General function prediction only	99.54
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.47
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.47
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.46
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.43
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.23
PF05729	166	NACHT: NACHT domain	99.19
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.08
PRK06893	229	DNA replication initiation factor; Validated	99.06
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.06
COG3903	414	Predicted ATPase [General function prediction only	99.04
KOG3678	832	consensus SARM protein (with sterile alpha and arm	99.0
PF14516	331	AAA_35: AAA-like domain	98.99
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.96
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.94
PRK13342	413	recombination factor protein RarA; Reviewed	98.94
PRK04195	482	replication factor C large subunit; Provisional	98.94
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.93
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.92
PLN03025	319	replication factor C subunit; Provisional	98.92
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.88
PTZ00202	550	tuzin; Provisional	98.88
PRK12402	337	replication factor C small subunit 2; Reviewed	98.88
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.87
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.85
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.84
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.84
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.83
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.83
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.82
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.81
PRK08727	233	hypothetical protein; Validated	98.79
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.76
PRK09087	226	hypothetical protein; Validated	98.73
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.73
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.71
PRK05642	234	DNA replication initiation factor; Validated	98.71
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.71
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.7
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.7
PRK08084	235	DNA replication initiation factor; Provisional	98.7
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.69
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.68
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.68
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.67
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.67
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.67
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.67
PF13173	128	AAA_14: AAA domain	98.64
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.63
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.63
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.62
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.59
PRK13341	725	recombination factor protein RarA/unknown domain f	98.59
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.58
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.57
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.57
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.56
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.55
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.55
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.54
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.53
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.53
PRK06620	214	hypothetical protein; Validated	98.53
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.5
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.49
PHA02544	316	44 clamp loader, small subunit; Provisional	98.49
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.49
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.49
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.48
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.47
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.47
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.47
KOG2028	554	consensus ATPase related to the helicase subunit o	98.46
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.45
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.44
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.42
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.41
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.4
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.39
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.38
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.36
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.36
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.35
PRK12422	445	chromosomal replication initiation protein; Provis	98.35
PF08937	130	DUF1863: MTH538 TIR-like domain (DUF1863); InterPr	98.35
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.33
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.31
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.29
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.28
CHL00095	821	clpC Clp protease ATP binding subunit	98.28
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.25
PRK10865	857	protein disaggregation chaperone; Provisional	98.24
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.23
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.23
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.22
PRK07399	314	DNA polymerase III subunit delta'; Validated	98.22
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.22
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.21
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.2
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.19
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.19
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.14
CHL00176	638	ftsH cell division protein; Validated	98.13
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.11
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.11
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.1
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.1
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.07
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.07
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.05
CHL00181	287	cbbX CbbX; Provisional	98.03
PF00004	132	AAA: ATPase family associated with various cellula	98.01
CHL00195	489	ycf46 Ycf46; Provisional	98.0
PRK08116	268	hypothetical protein; Validated	97.95
cd01128	249	rho_factor Transcription termination factor rho is	97.94
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.92
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.91
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.91
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.9
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.9
PF08357	150	SEFIR: SEFIR domain; InterPro: IPR013568 This doma	97.88
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.88
smart00382	148	AAA ATPases associated with a variety of cellular	97.84
PRK07952	244	DNA replication protein DnaC; Validated	97.83
PRK08181	269	transposase; Validated	97.82
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.82
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.82
PRK09376	416	rho transcription termination factor Rho; Provisio	97.81
PRK12377	248	putative replication protein; Provisional	97.78
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.78
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.76
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.75
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.73
PRK04132	846	replication factor C small subunit; Provisional	97.71
TIGR00767	415	rho transcription termination factor Rho. Members	97.7
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.68
PRK09183	259	transposase/IS protein; Provisional	97.67
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.66
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.65
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.64
PRK06526	254	transposase; Provisional	97.63
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.62
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.62
PRK06921	266	hypothetical protein; Provisional	97.62
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.59
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.59
PRK10536	262	hypothetical protein; Provisional	97.58
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.57
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.56
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.55
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.55
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.54
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.53
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.53
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.51
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.5
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.49
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.49
PRK10865	857	protein disaggregation chaperone; Provisional	97.49
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.48
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.48
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.46
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.46
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.45
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.43
PRK08939	306	primosomal protein DnaI; Reviewed	97.41
PRK06835	329	DNA replication protein DnaC; Validated	97.4
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.39
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.38
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.38
PRK06067	234	flagellar accessory protein FlaH; Validated	97.37
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.37
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.37
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.36
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.35
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.34
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.32
PRK04296	190	thymidine kinase; Provisional	97.3
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.29
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.28
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	97.28
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	97.25
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.25
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.24
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.23
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.22
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.21
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.2
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.2
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.2
PRK05541	176	adenylylsulfate kinase; Provisional	97.19
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	97.19
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.14
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.14
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.13
CHL00095	821	clpC Clp protease ATP binding subunit	97.12
PRK12608	380	transcription termination factor Rho; Provisional	97.12
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.1
PRK14974	336	cell division protein FtsY; Provisional	97.1
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.09
PHA00729	226	NTP-binding motif containing protein	97.08
PRK11608	326	pspF phage shock protein operon transcriptional ac	97.08
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.07
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.07
PRK09354	349	recA recombinase A; Provisional	97.06
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.06
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	97.05
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.04
PRK08118	167	topology modulation protein; Reviewed	97.04
PRK04328	249	hypothetical protein; Provisional	97.04
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.03
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	97.02
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.01
PTZ00494	664	tuzin-like protein; Provisional	97.0
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	96.98
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.96
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.96
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.96
PRK11823	446	DNA repair protein RadA; Provisional	96.95
PRK06696	223	uridine kinase; Validated	96.95
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.94
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.94
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.93
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.93
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.92
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.91
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	96.9
KOG3928	461	consensus Mitochondrial ribosome small subunit com	96.87
PRK07667	193	uridine kinase; Provisional	96.87
PRK07261	171	topology modulation protein; Provisional	96.86
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.85
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.84
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.84
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.84
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.83
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.82
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.81
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.81
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.81
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.79
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.79
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.78
PRK06762	166	hypothetical protein; Provisional	96.78
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.73
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.7
CHL00206	2281	ycf2 Ycf2; Provisional	96.7
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.68
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	96.67
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.67
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.66
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.64
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.63
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.61
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.61
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.57
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.56
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.55
PRK05973	237	replicative DNA helicase; Provisional	96.52
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.52
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.51
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.5
PRK15455	644	PrkA family serine protein kinase; Provisional	96.5
PRK00889	175	adenylylsulfate kinase; Provisional	96.5
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.5
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.5
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.5
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.49
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.48
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.47
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	96.47
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.47
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.47
KOG0736	953	consensus Peroxisome assembly factor 2 containing	96.47
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.47
cd03246	173	ABCC_Protease_Secretion This family represents the	96.46
COG0488	530	Uup ATPase components of ABC transporters with dup	96.46
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.46
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	96.45
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.44
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.44
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.42
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.41
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.41
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.4
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.39
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.38
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.37
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.37
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.37
COG3910	233	Predicted ATPase [General function prediction only	96.37
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.37
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.36
PRK13531	498	regulatory ATPase RavA; Provisional	96.34
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.34
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.34
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.34
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.32
PF10137	125	TIR-like: Predicted nucleotide-binding protein con	96.32
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.32
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	96.3
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.29
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.28
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.28
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.27
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.27
PF07726	131	AAA_3: ATPase family associated with various cellu	96.27
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.27
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.26
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.25
PRK08233	182	hypothetical protein; Provisional	96.25
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.25
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.24
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.23
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.22
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	96.21
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.16
PRK05480	209	uridine/cytidine kinase; Provisional	96.16
PRK09302	509	circadian clock protein KaiC; Reviewed	96.14
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	96.13
PTZ00301	210	uridine kinase; Provisional	96.13
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.12
PRK04040	188	adenylate kinase; Provisional	96.11
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.1
PRK03839	180	putative kinase; Provisional	96.1
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.1
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.1
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.1
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.09
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	96.09
PTZ00035	337	Rad51 protein; Provisional	96.07
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.07
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.06
PRK00131	175	aroK shikimate kinase; Reviewed	96.06
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.05
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	96.05
KOG0927	614	consensus Predicted transporter (ABC superfamily)	96.04
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	96.02
PRK10416	318	signal recognition particle-docking protein FtsY;	96.02
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	96.01
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.0
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.0
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.99
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.98
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.98
COG4133	209	CcmA ABC-type transport system involved in cytochr	95.98
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.97
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.94
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.93
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.93
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	95.93
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	95.92
PRK14528	186	adenylate kinase; Provisional	95.92
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	95.92
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.91
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	95.91
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	95.9
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	95.9
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.9
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.89
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.88
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	95.88
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	95.88
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.88
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.88
PRK00625	173	shikimate kinase; Provisional	95.87
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	95.86
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	95.86
PRK06547	172	hypothetical protein; Provisional	95.85
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.85
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	95.84
PRK03846	198	adenylylsulfate kinase; Provisional	95.82
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.81
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.81
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	95.81
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.78
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.78
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	95.78
PRK05917	290	DNA polymerase III subunit delta'; Validated	95.78
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.77
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	95.77
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.77
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	95.77
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.76
PRK09302	509	circadian clock protein KaiC; Reviewed	95.74
PTZ00088	229	adenylate kinase 1; Provisional	95.74
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.73
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.7
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.69
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	95.69
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.66
PRK10436	462	hypothetical protein; Provisional	95.66
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	95.65
PRK13947	171	shikimate kinase; Provisional	95.64
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	95.64
PF13245	76	AAA_19: Part of AAA domain	95.63
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.63
COG0488	530	Uup ATPase components of ABC transporters with dup	95.62
PRK06217	183	hypothetical protein; Validated	95.6
PRK13765	637	ATP-dependent protease Lon; Provisional	95.6
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	95.59
TIGR00959	428	ffh signal recognition particle protein. This mode	95.57
PRK15115	444	response regulator GlrR; Provisional	95.56
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	95.55
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.55
PRK10867	433	signal recognition particle protein; Provisional	95.55
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.54
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.54
PRK13764	602	ATPase; Provisional	95.54
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.53
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	95.53
PRK00409	782	recombination and DNA strand exchange inhibitor pr	95.53
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	95.53
PRK00279	215	adk adenylate kinase; Reviewed	95.52
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	95.5
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	95.49
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.48
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.48
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	95.47
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.46
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.46
PRK14738	206	gmk guanylate kinase; Provisional	95.46
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.46
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.46
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	95.46
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	95.45
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	95.45
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.44
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	95.43
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	95.43
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	95.43
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	95.41
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	95.41
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.41
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.38
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.37
PRK15453	290	phosphoribulokinase; Provisional	95.37
PRK08506	472	replicative DNA helicase; Provisional	95.35
COG0714	329	MoxR-like ATPases [General function prediction onl	95.34
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	95.33
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.33
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	95.32
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	95.32
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	95.3
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	95.3
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	95.29
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	95.29
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.29
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	95.29
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	95.28
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	95.28
PRK09435	332	membrane ATPase/protein kinase; Provisional	95.28
PRK05439	311	pantothenate kinase; Provisional	95.28
KOG0062	582	consensus ATPase component of ABC transporters wit	95.27
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.27
PHA02244	383	ATPase-like protein	95.27
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	95.26
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	95.24
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.21
PRK13949	169	shikimate kinase; Provisional	95.21
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.18
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.17
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.16
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	95.13
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	95.13
COG4619	223	ABC-type uncharacterized transport system, ATPase	95.12
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	95.12
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.1
PRK14530	215	adenylate kinase; Provisional	95.1
PRK13948	182	shikimate kinase; Provisional	95.09
PLN02674	244	adenylate kinase	95.09
PRK12339	197	2-phosphoglycerate kinase; Provisional	95.08
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	95.07
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	95.06
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.06
PRK13946	184	shikimate kinase; Provisional	95.06
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.03
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	95.03
PRK00300	205	gmk guanylate kinase; Provisional	95.01
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.01
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.01
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.0
PRK14737	186	gmk guanylate kinase; Provisional	94.98
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	94.98
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	94.97
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.97
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	94.97
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	94.96
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	94.93

>PLN03210 Resistant to P

Probab=100.00  E-value=5.2e-88  Score=771.69  Aligned_cols=516  Identities=38%  Similarity=0.663  Sum_probs=465.5

Q ss_pred             CCCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeCCCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHH
Q 009306           13 NPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDEL   92 (538)
Q Consensus        13 ~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El   92 (538)
                      ++.++|||||||+|+|+|++|++||+.+|.++||.+|.|+++++|+.|.+++.+||++|++.|+|||++|++|.||++||
T Consensus         8 ~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el   87 (1153)
T PLN03210          8 SRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNEL   87 (1153)
T ss_pred             CCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCeEEEEEEeecCCcccccCCchHHHHHHHHhhC-hhhHHHHHHHhhhhccccCcccCCCChhhHHHHHH
Q 009306           93 LKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF-PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEI  171 (538)
Q Consensus        93 ~~~~~~~~~~~~~v~pv~~~v~~~~v~~~~~~~~~~~~~~~~~~-~~~~~~w~~al~~~~~~~g~~~~~~~~e~~~i~~i  171 (538)
                      ++|++|++..++.|+||||+|+|++||+|+|.|+++|.++.++. .+++++|++||++++++.|+++.....|+++|++|
T Consensus        88 ~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~~~~E~~~i~~I  167 (1153)
T PLN03210         88 LEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQNWPNEAKMIEEI  167 (1153)
T ss_pred             HHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcccchhHHHHHHHHHHHHhCcCceecCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999987664 45699999999999999999997666699999999


Q ss_pred             HHhhhccccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeeh--h
Q 009306          172 VNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNV--R  249 (538)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~--~  249 (538)
                      ++++.+++...++...+++|||+.++++|..+|..+.+++++++|+||||+||||||+.+|+++..+|++.+|+...  .
T Consensus       168 v~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~v~  247 (1153)
T PLN03210        168 ANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFIS  247 (1153)
T ss_pred             HHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeeccccc
Confidence            99999999988888889999999999999999987777899999999999999999999999999999998887531  1


Q ss_pred             hh---hh------cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCC
Q 009306          250 EA---EE------TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASG  320 (538)
Q Consensus       250 ~~---~~------~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~  320 (538)
                      ..   ..      ......+.++++..+........   .....+++++.++|+||||||||+..+++.+.....++++|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~---~~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~G  324 (1153)
T PLN03210        248 KSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKI---YHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSG  324 (1153)
T ss_pred             cchhhcccccccccchhHHHHHHHHHHHhCCCCccc---CCHHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCC
Confidence            10   00      01123455666666554433221   11256778899999999999999999999999888888999


Q ss_pred             CEEEEeccchhhhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCH
Q 009306          321 SRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRR  400 (538)
Q Consensus       321 ~~iiiTtR~~~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~  400 (538)
                      ++||||||+..++...+...+|+++.|+.++|++||++++|+...+++...+++.+++++|+|+||||+++|++|++++.
T Consensus       325 srIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~  404 (1153)
T PLN03210        325 SRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDK  404 (1153)
T ss_pred             cEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCH
Confidence            99999999999988777788999999999999999999999887777778999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCCcHHHHHHHhHhCCCH-HhHHHhhccccccCCCCHHHHHHHHHhCCCChHHHHHHHhhCCceeEe
Q 009306          401 EVWENAKSKWETAPPKGIQDALKISYDGLDD-KEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITIS  479 (538)
Q Consensus       401 ~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~-~~k~~l~~la~f~~~~~~~~l~~l~~~~~~~~~~~l~~L~~~~Li~~~  479 (538)
                      .+|+..++.+....+..+..+|+.||+.|++ .+|.+|+++|||+.+.+.+.+..++..++.....+++.|++++||+..
T Consensus       405 ~~W~~~l~~L~~~~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~~v~~~l~~~~~~~~~~l~~L~~ksLi~~~  484 (1153)
T PLN03210        405 EDWMDMLPRLRNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVNDIKLLLANSDLDVNIGLKNLVDKSLIHVR  484 (1153)
T ss_pred             HHHHHHHHHHHhCccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHHHHHHHHHhcCCCchhChHHHHhcCCEEEc
Confidence            9999999999988888999999999999976 599999999999999999999999988888888899999999999987


Q ss_pred             cCCcEEecHHHHHHHHHHHhhcCCCCCCCcccccCcchHHHHHccCCCcchhhh
Q 009306          480 VLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNNDFS  533 (538)
Q Consensus       480 ~~~~~~~H~lv~~~~~~~~~~~~~~~~~~r~rl~~~~~i~~~l~~~~~~~~~~~  533 (538)
                       .+++.||+++|+||++++++++ .+|++|+|+|++.+|+++|++++||++++.
T Consensus       485 -~~~~~MHdLl~~~~r~i~~~~~-~~~~~r~~l~~~~di~~vl~~~~g~~~v~~  536 (1153)
T PLN03210        485 -EDIVEMHSLLQEMGKEIVRAQS-NEPGEREFLVDAKDICDVLEDNTGTKKVLG  536 (1153)
T ss_pred             -CCeEEhhhHHHHHHHHHHHhhc-CCCCcceeEeCHHHHHHHHHhCcccceeeE
Confidence             6889999999999999999987 689999999999999999999999988764

syringae 6; Provisional

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=1.5e-39  Score=354.84  Aligned_cols=303  Identities=27%  Similarity=0.358  Sum_probs=265.3

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh---hccceeeEEEEeehhhhhhcCChHHHHHHHHHH
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK---ISRHFSGSYFARNVREAEETCRLGDLRQQLLST  267 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~---~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~  267 (538)
                      ||.+..++++...|..++.  .+++|+||||+||||||+++++.   ...+|+.++|+.    +++......++.+++..
T Consensus       161 VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~----VSk~f~~~~iq~~Il~~  234 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVV----VSKEFTTRKIQQTILER  234 (889)
T ss_pred             ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEE----EcccccHHhHHHHHHHH
Confidence            9999999999999986544  88999999999999999999995   457899999999    66778899999999998


Q ss_pred             HhcCCCCC--CchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhh-cCCCeeEEc
Q 009306          268 LLNDGNVK--NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLAN-CGVDEVYQM  344 (538)
Q Consensus       268 l~~~~~~~--~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~-~~~~~~~~l  344 (538)
                      ++......  ...++....+.+.|.++|++|||||||+..+|+.+...++....|++|++|||+..+... ++....+++
T Consensus       235 l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v  314 (889)
T KOG4658|consen  235 LGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEV  314 (889)
T ss_pred             hccCCcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccc
Confidence            87754433  334678888999999999999999999999999999888877789999999999999888 677789999


Q ss_pred             CCCCHHHHHHHHHhhhcCCC-CCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCC-CHHHHHHHHHHhhcC-------CC
Q 009306          345 EELVHDDALRLFSRHAFGGD-HPHESHTELACKTIKYARGVPLALEVLGRYLYGK-RREVWENAKSKWETA-------PP  415 (538)
Q Consensus       345 ~~L~~~ea~~Lf~~~~~~~~-~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~-~~~~~~~~l~~l~~~-------~~  415 (538)
                      +.|+.+|||.||++.++... ...+..++++++++++|+|+|||++++|+.|+.+ +..+|+.+.+.+...       ..
T Consensus       315 ~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~  394 (889)
T KOG4658|consen  315 ECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGME  394 (889)
T ss_pred             cccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchh
Confidence            99999999999999997763 3334479999999999999999999999999885 466899999987654       13


Q ss_pred             CcHHHHHHHhHhCCCHHhHHHhhccccccCC--CCHHHHHHHHHhCCCC------------hHHHHHHHhhCCceeEecC
Q 009306          416 KGIQDALKISYDGLDDKEQNIFLDIACFFID--EDRDTATKFLDDCEFF------------ATSAIEVLVDKHLITISVL  481 (538)
Q Consensus       416 ~~v~~~l~~s~~~L~~~~k~~l~~la~f~~~--~~~~~l~~l~~~~~~~------------~~~~l~~L~~~~Li~~~~~  481 (538)
                      +.+..+|..||+.|+++.|.||+|||.||++  ++.+.+..+|.++|+.            +..++..|++++|+.....
T Consensus       395 ~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~  474 (889)
T KOG4658|consen  395 ESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERD  474 (889)
T ss_pred             hhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhccc
Confidence            5788999999999998899999999999998  5789999999998843            4568999999999997642


Q ss_pred             ----CcEEecHHHHHHHHHHHh
Q 009306          482 ----NKIEMHYLLRAMGREIVR  499 (538)
Q Consensus       482 ----~~~~~H~lv~~~~~~~~~  499 (538)
                          ..+.|||++|+||..+++
T Consensus       475 ~~~~~~~kmHDvvRe~al~ias  496 (889)
T KOG4658|consen  475 EGRKETVKMHDVVREMALWIAS  496 (889)
T ss_pred             ccceeEEEeeHHHHHHHHHHhc
Confidence                469999999999999998

>PLN03194 putative disease resistance protein; Provisional

Probab=100.00  E-value=2.1e-39  Score=281.78  Aligned_cols=160  Identities=29%  Similarity=0.500  Sum_probs=143.8

Q ss_pred             CCCCCCCCCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccc
Q 009306            7 PYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASS   85 (538)
Q Consensus         7 ~~~~~~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s   85 (538)
                      .+++|++..++|||||||+|+|+|++|++||+.+|+++||+||+|+ ++++|+.|.+.|.+||++|++.|+||||+|++|
T Consensus        16 ~~~~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S   95 (187)
T PLN03194         16 HYPSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCES   95 (187)
T ss_pred             ccccCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccc
Confidence            5667777889999999999999999999999999999999999999 999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHHHhhcCCeEEEEEEeecCCccccc-CCchHHHHHHHHhhChhhHHHHHHHhhhhccccCcccCC-CCh
Q 009306           86 RWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQ-TGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLV-VSP  163 (538)
Q Consensus        86 ~~c~~El~~~~~~~~~~~~~v~pv~~~v~~~~v~~~-~~~~~~~~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~-~~~  163 (538)
                      .||++||.+|+++.    .+|+||||+|+|++||+| .|.          ...+++++|+.||++++++.|+++.. ...
T Consensus        96 ~WCLdEL~~I~e~~----~~ViPIFY~VdPsdVr~q~~~~----------~~~e~v~~Wr~AL~~va~l~G~~~~~~~~~  161 (187)
T PLN03194         96 YFCLHELALIMESK----KRVIPIFCDVKPSQLRVVDNGT----------CPDEEIRRFNWALEEAKYTVGLTFDSLKGN  161 (187)
T ss_pred             hhHHHHHHHHHHcC----CEEEEEEecCCHHHhhccccCC----------CCHHHHHHHHHHHHHHhccccccCCCCCCC
Confidence            99999999999864    479999999999999997 443          13467999999999999999987643 233


Q ss_pred             hhHHHHHHHHhhhcccc
Q 009306          164 ESALIEEIVNAILKRLD  180 (538)
Q Consensus       164 e~~~i~~i~~~~~~~~~  180 (538)
                      |++++++|+..+.+.+.
T Consensus       162 e~e~i~~iv~~v~k~l~  178 (187)
T PLN03194        162 WSEVVTMASDAVIKNLI  178 (187)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999887754

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

Probab=100.00  E-value=5.1e-37  Score=302.45  Aligned_cols=266  Identities=29%  Similarity=0.433  Sum_probs=210.8

Q ss_pred             ccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh--hccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhc
Q 009306          193 VRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK--ISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN  270 (538)
Q Consensus       193 R~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~--~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~  270 (538)
                      ||.++++|.+.|....++.++|+|+||||+||||||.+++++  ...+|+.++|+..    ........++..++..+..
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~----~~~~~~~~~~~~i~~~l~~   76 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSL----SKNPSLEQLLEQILRQLGE   76 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEE----ES-SCCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccccccccccccccccc----ccccccccccccccccccc
Confidence            788999999999876678999999999999999999999998  8889999999883    3344557888888888877


Q ss_pred             CCC---CCCchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCC-CeeEEcCC
Q 009306          271 DGN---VKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGV-DEVYQMEE  346 (538)
Q Consensus       271 ~~~---~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~-~~~~~l~~  346 (538)
                      ...   ...+.......+.+.+.++++|||||||++...++.+...+.....+++||||||+..+...... ...++|++
T Consensus        77 ~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~  156 (287)
T PF00931_consen   77 PDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEP  156 (287)
T ss_dssp             C-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS
T ss_pred             cccccccccccccccccchhhhccccceeeeeeecccccccccccccccccccccccccccccccccccccccccccccc
Confidence            632   23667778899999999999999999999999888887766666679999999999988766543 57899999


Q ss_pred             CCHHHHHHHHHhhhcCCC-CCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC-CCHHHHHHHHHHhhcCC------CCcH
Q 009306          347 LVHDDALRLFSRHAFGGD-HPHESHTELACKTIKYARGVPLALEVLGRYLYG-KRREVWENAKSKWETAP------PKGI  418 (538)
Q Consensus       347 L~~~ea~~Lf~~~~~~~~-~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~-~~~~~~~~~l~~l~~~~------~~~v  418 (538)
                      |+.+|+++||.+.++... .......+.+.+|++.|+|+||||+++|++|+. .+..+|+..++.+....      ...+
T Consensus       157 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~  236 (287)
T PF00931_consen  157 LSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSV  236 (287)
T ss_dssp             --HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            999999999999986554 233455678899999999999999999999954 25678888888765543      3668


Q ss_pred             HHHHHHhHhCCCHHhHHHhhccccccCC--CCHHHHHHHHHhCCCC
Q 009306          419 QDALKISYDGLDDKEQNIFLDIACFFID--EDRDTATKFLDDCEFF  462 (538)
Q Consensus       419 ~~~l~~s~~~L~~~~k~~l~~la~f~~~--~~~~~l~~l~~~~~~~  462 (538)
                      ..++..||+.|+++.|.||++||+||.+  ++.+.+..+|.++++.
T Consensus       237 ~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i  282 (287)
T PF00931_consen  237 FSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFI  282 (287)
T ss_dssp             HHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHT
T ss_pred             cccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCC
Confidence            9999999999999999999999999987  5699999999887654

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.

>smart00255 TIR Toll - interleukin 1 - resistance

Probab=99.84  E-value=1.8e-20  Score=163.65  Aligned_cols=134  Identities=42%  Similarity=0.679  Sum_probs=113.1

Q ss_pred             cccEEEcCcc-cccccchHHHHHHHHhhCCCeeEeeCCCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHHHHH
Q 009306           17 KYDVFLSFGG-EDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKI   95 (538)
Q Consensus        17 ~~dvFiSy~~-~D~~~~~~~~l~~~l~~~g~~~~~d~~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~   95 (538)
                      +|||||||++ .+....|+.+|...|...|+.+|.|+....|. ...+|.++|++|+++|+|+||+|+.|.||..|+..+
T Consensus         1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~-~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a   79 (140)
T smart00255        1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGG-DLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA   79 (140)
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccc-hHHHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence            5999999999 44457899999999999999999987443333 334999999999999999999999999999999999


Q ss_pred             HHHHhh-cCCeEEEEEEeecCCcccccCCchHHHHHHHHhhChhhH--HHHHHHhhhhc
Q 009306           96 LECKKE-YAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFPDKM--QSWRNALTEAA  151 (538)
Q Consensus        96 ~~~~~~-~~~~v~pv~~~v~~~~v~~~~~~~~~~~~~~~~~~~~~~--~~w~~al~~~~  151 (538)
                      +++... ...+||||+++..|..+..+.+.+...+..+..++++..  ..|++++..+.
T Consensus        80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~~fW~~~~~~l~  138 (140)
T smart00255       80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKERFWKKALYAVP  138 (140)
T ss_pred             HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhHHHHHHHHHHhc
Confidence            988754 567999999998888899999999999888756666655  48988877654

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

Probab=99.83  E-value=1.6e-21  Score=170.09  Aligned_cols=129  Identities=37%  Similarity=0.605  Sum_probs=109.3

Q ss_pred             EEEcCcccccccchHHHHHHHHhhC--CCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHHHHHH
Q 009306           20 VFLSFGGEDTRESFTSHLYSALSRE--TVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKIL   96 (538)
Q Consensus        20 vFiSy~~~D~~~~~~~~l~~~l~~~--g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~~   96 (538)
                      |||||++.|.+.+|+.+|...|++.  |+++|+++ |+.+|..+.++|.++|++|+++|+|+|++|+.|.||+.|+..|+
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            7999999444679999999999999  99999998 99999999999999999999999999999999999999999999


Q ss_pred             HHHhhcC--CeEEEEEEeecCCccc-ccCCchHHHHHHHHhhCh-----hhHHHHHHHhh
Q 009306           97 ECKKEYA--QIVVPVFYRVDPSHVR-KQTGNFGDSFLKLEERFP-----DKMQSWRNALT  148 (538)
Q Consensus        97 ~~~~~~~--~~v~pv~~~v~~~~v~-~~~~~~~~~~~~~~~~~~-----~~~~~w~~al~  148 (538)
                      ++....+  ..|+|||+++.+++++ .+.+.+...+........     .....|++++.
T Consensus        81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~  140 (141)
T PF01582_consen   81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY  140 (141)
T ss_dssp             HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred             hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence            9986654  7899999999999999 688888777766443332     23677887754

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 ....

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.76  E-value=1.4e-16  Score=181.78  Aligned_cols=315  Identities=13%  Similarity=0.091  Sum_probs=199.7

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      +|..+..+|-|..-++.|..     ....+++.|+|++|.||||++..+.....    .+.|+..-.   .......+..
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~-----~~~~~~~~v~apaG~GKTtl~~~~~~~~~----~~~w~~l~~---~d~~~~~f~~   76 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSG-----ANNYRLVLVTSPAGYGKTTLISQWAAGKN----NLGWYSLDE---SDNQPERFAS   76 (903)
T ss_pred             CCCCccccCcchHHHHHHhc-----ccCCCeEEEECCCCCCHHHHHHHHHHhCC----CeEEEecCc---ccCCHHHHHH
Confidence            45566788988876665543     23578899999999999999999886432    577886321   2234444555


Q ss_pred             HHHHHHhcCCCCC-------------CchhhcHHHHHHHhc--CCCeEEEEecCCCh---HHHHHHhcCcCCCCCCCEEE
Q 009306          263 QLLSTLLNDGNVK-------------NFLNTDLNFQSRRLT--RKKVLIVFDDVDHP---RQIKILVGRLDLFASGSRII  324 (538)
Q Consensus       263 ~l~~~l~~~~~~~-------------~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~---~~~~~l~~~l~~~~~~~~ii  324 (538)
                      .++..+.......             .........+...+.  +.+++|||||++..   ...+.+...+....++.++|
T Consensus        77 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv  156 (903)
T PRK04841         77 YLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLV  156 (903)
T ss_pred             HHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEE
Confidence            5555553211110             111122222333332  68999999999542   22223322233335678899


Q ss_pred             Eeccchhhhh--hc-CCCeeEEcC----CCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC
Q 009306          325 ITTRDRQVLA--NC-GVDEVYQME----ELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYG  397 (538)
Q Consensus       325 iTtR~~~~~~--~~-~~~~~~~l~----~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~  397 (538)
                      ||||...-+.  .+ ......++.    +|+.+|+.+||....  +   .....+.+.++++.|+|+|+++..++..+..
T Consensus       157 ~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~--~---~~~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~  231 (903)
T PRK04841        157 VLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRL--S---SPIEAAESSRLCDDVEGWATALQLIALSARQ  231 (903)
T ss_pred             EEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhcc--C---CCCCHHHHHHHHHHhCChHHHHHHHHHHHhh
Confidence            9999842211  11 112345565    999999999998765  1   1234567889999999999999999987754


Q ss_pred             CCHHHHHHHHHHhhcCCCCcHHHHHHHh-HhCCCHHhHHHhhccccccCCCCHHHHHHHHHhCCCChHHHHHHHhhCCce
Q 009306          398 KRREVWENAKSKWETAPPKGIQDALKIS-YDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLI  476 (538)
Q Consensus       398 ~~~~~~~~~l~~l~~~~~~~v~~~l~~s-~~~L~~~~k~~l~~la~f~~~~~~~~l~~l~~~~~~~~~~~l~~L~~~~Li  476 (538)
                      .+.. .......+....+..+...+... ++.|+++.+.++..+|+++ .++.+.+..+.+.  ......++.|.+.+|+
T Consensus       232 ~~~~-~~~~~~~~~~~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~-~~~~~l~~~l~~~--~~~~~~L~~l~~~~l~  307 (903)
T PRK04841        232 NNSS-LHDSARRLAGINASHLSDYLVEEVLDNVDLETRHFLLRCSVLR-SMNDALIVRVTGE--ENGQMRLEELERQGLF  307 (903)
T ss_pred             CCCc-hhhhhHhhcCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccc-cCCHHHHHHHcCC--CcHHHHHHHHHHCCCe
Confidence            3210 11111222222344577765544 8999999999999999985 7787777777642  3457789999999996


Q ss_pred             eE-ec--CCcEEecHHHHHHHHHHHhhcCCCCCCCcccccCcchHHHHHc
Q 009306          477 TI-SV--LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILS  523 (538)
Q Consensus       477 ~~-~~--~~~~~~H~lv~~~~~~~~~~~~~~~~~~r~rl~~~~~i~~~l~  523 (538)
                      .. .+  ...|++|++++++.+..+..+   .+..+.++  |......+.
T Consensus       308 ~~~~~~~~~~yr~H~L~r~~l~~~l~~~---~~~~~~~l--h~raa~~~~  352 (903)
T PRK04841        308 IQRMDDSGEWFRYHPLFASFLRHRCQWE---LAQELPEL--HRAAAEAWL  352 (903)
T ss_pred             eEeecCCCCEEehhHHHHHHHHHHHHhc---CchHHHHH--HHHHHHHHH
Confidence            63 22  236999999999999998554   24445555  444444333

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

Probab=99.66  E-value=3.4e-17  Score=134.44  Aligned_cols=87  Identities=30%  Similarity=0.549  Sum_probs=75.8

Q ss_pred             EEEcCcccccccchHHHHHHHHhhCCCeeEeeCCCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHHHHHHHHH
Q 009306           20 VFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECK   99 (538)
Q Consensus        20 vFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~~~~~   99 (538)
                      |||||+++|  +.++.+|...|+..|+++|+|.++.+|+.+.+.|.++|++|+.+|+++|++|+.|+||..|+..+.+  
T Consensus         1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~--   76 (102)
T PF13676_consen    1 VFISYSSED--REFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK--   76 (102)
T ss_dssp             EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC--
T ss_pred             eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH--
Confidence            899999999  7799999999999999999999999999999999999999999999999999999999999998832  


Q ss_pred             hhcCCeEEEEEEe
Q 009306          100 KEYAQIVVPVFYR  112 (538)
Q Consensus       100 ~~~~~~v~pv~~~  112 (538)
                        .+.+|+||.++
T Consensus        77 --~~~~iipv~~~   87 (102)
T PF13676_consen   77 --RGKPIIPVRLD   87 (102)
T ss_dssp             --TSESEEEEECS
T ss_pred             --CCCEEEEEEEC
Confidence              44579999954

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.61  E-value=3.2e-14  Score=149.25  Aligned_cols=296  Identities=14%  Similarity=0.142  Sum_probs=198.2

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      +|..+.+.|-|..-++.|...     .+.+++.|..|+|.|||||+.+++. ....-..+.|+.....   ...+..+..
T Consensus        14 ~P~~~~~~v~R~rL~~~L~~~-----~~~RL~li~APAGfGKttl~aq~~~-~~~~~~~v~Wlslde~---dndp~rF~~   84 (894)
T COG2909          14 RPVRPDNYVVRPRLLDRLRRA-----NDYRLILISAPAGFGKTTLLAQWRE-LAADGAAVAWLSLDES---DNDPARFLS   84 (894)
T ss_pred             CCCCcccccccHHHHHHHhcC-----CCceEEEEeCCCCCcHHHHHHHHHH-hcCcccceeEeecCCc---cCCHHHHHH
Confidence            445567788887655554442     3688999999999999999999998 4445567888874332   455666667


Q ss_pred             HHHHHHhcCCCCC-------------CchhhcHHHHHHHhc--CCCeEEEEecCC---Ch---HHHHHHhcCcCCCCCCC
Q 009306          263 QLLSTLLNDGNVK-------------NFLNTDLNFQSRRLT--RKKVLIVFDDVD---HP---RQIKILVGRLDLFASGS  321 (538)
Q Consensus       263 ~l~~~l~~~~~~~-------------~~~~~~~~~l~~~l~--~k~~LlVlDdv~---~~---~~~~~l~~~l~~~~~~~  321 (538)
                      .++..+....+..             .++......+..-+.  .+|+.+||||..   ++   +.++.++...   +++.
T Consensus        85 yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~---P~~l  161 (894)
T COG2909          85 YLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHA---PENL  161 (894)
T ss_pred             HHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhC---CCCe
Confidence            7766665332211             222223333333332  478999999984   22   3456665554   5789


Q ss_pred             EEEEeccchhhhhhc--C-CCeeEEc----CCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHH
Q 009306          322 RIIITTRDRQVLANC--G-VDEVYQM----EELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRY  394 (538)
Q Consensus       322 ~iiiTtR~~~~~~~~--~-~~~~~~l----~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~  394 (538)
                      .+|+|||...-+...  . .+...++    -.|+.+|+.++|..+.     ..+.+...++.+.+.++|++-||.+.+=.
T Consensus       162 ~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~-----~l~Ld~~~~~~L~~~teGW~~al~L~aLa  236 (894)
T COG2909         162 TLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRG-----SLPLDAADLKALYDRTEGWAAALQLIALA  236 (894)
T ss_pred             EEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcC-----CCCCChHHHHHHHhhcccHHHHHHHHHHH
Confidence            999999987332111  1 1223333    3489999999998775     12344667889999999999999999988


Q ss_pred             hcCC-CHHHHHHHHHHhhcCCCCcHHHH-HHHhHhCCCHHhHHHhhccccccCCCCHHHHHHHHHhCCCChHHHHHHHhh
Q 009306          395 LYGK-RREVWENAKSKWETAPPKGIQDA-LKISYDGLDDKEQNIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVD  472 (538)
Q Consensus       395 L~~~-~~~~~~~~l~~l~~~~~~~v~~~-l~~s~~~L~~~~k~~l~~la~f~~~~~~~~l~~l~~~~~~~~~~~l~~L~~  472 (538)
                      ++++ +.+.   ....+... ...+.+. .+..++.||++.+.+++.+|++ ..++.+....+.+.  ......|+.|.+
T Consensus       237 ~~~~~~~~q---~~~~LsG~-~~~l~dYL~eeVld~Lp~~l~~FLl~~svl-~~f~~eL~~~Ltg~--~ng~amLe~L~~  309 (894)
T COG2909         237 LRNNTSAEQ---SLRGLSGA-ASHLSDYLVEEVLDRLPPELRDFLLQTSVL-SRFNDELCNALTGE--ENGQAMLEELER  309 (894)
T ss_pred             ccCCCcHHH---Hhhhccch-HHHHHHHHHHHHHhcCCHHHHHHHHHHHhH-HHhhHHHHHHHhcC--CcHHHHHHHHHh
Confidence            8743 3322   22222222 2334443 4556899999999999999998 44555555555533  235567999999


Q ss_pred             CCceeE--e-cCCcEEecHHHHHHHHHHHhhcC
Q 009306          473 KHLITI--S-VLNKIEMHYLLRAMGREIVRQES  502 (538)
Q Consensus       473 ~~Li~~--~-~~~~~~~H~lv~~~~~~~~~~~~  502 (538)
                      ++|+-+  + +++.|++|+++.+|.+...+.+.
T Consensus       310 ~gLFl~~Ldd~~~WfryH~LFaeFL~~r~~~~~  342 (894)
T COG2909         310 RGLFLQRLDDEGQWFRYHHLFAEFLRQRLQREL  342 (894)
T ss_pred             CCCceeeecCCCceeehhHHHHHHHHhhhcccc
Confidence            998773  2 36679999999999999987753

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.57  E-value=7.7e-13  Score=136.30  Aligned_cols=284  Identities=14%  Similarity=0.096  Sum_probs=171.0

Q ss_pred             CCCCCceeccchhHHHHHhhhcC--CCCceEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTG--STNVYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..|+.|+||+.++++|...+...  +.....+.|+|++|+|||++++.+++.+....  -..+++.+    ........+
T Consensus        27 ~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~----~~~~~~~~~  102 (394)
T PRK00411         27 YVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINC----QIDRTRYAI  102 (394)
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEEC----CcCCCHHHH
Confidence            46688999999999999988542  23445688999999999999999999876543  22344442    222345677


Q ss_pred             HHHHHHHHhcCCCC--CCchhhcHHHHHHHhc--CCCeEEEEecCCChH------HHHHHhcCcCCCC-CCCEEEEeccc
Q 009306          261 RQQLLSTLLNDGNV--KNFLNTDLNFQSRRLT--RKKVLIVFDDVDHPR------QIKILVGRLDLFA-SGSRIIITTRD  329 (538)
Q Consensus       261 ~~~l~~~l~~~~~~--~~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~~------~~~~l~~~l~~~~-~~~~iiiTtR~  329 (538)
                      +..++.++......  ..+..+....+.+.+.  +++.+||||+++...      .+..+........ .+..+|.++..
T Consensus       103 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~  182 (394)
T PRK00411        103 FSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSD  182 (394)
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECC
Confidence            77787777652221  1344555566666654  456899999997643      3444433222111 12335655554


Q ss_pred             hhhhhhc-------CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh----cCCcHHHHHHHHHh---
Q 009306          330 RQVLANC-------GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA----RGVPLALEVLGRYL---  395 (538)
Q Consensus       330 ~~~~~~~-------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~----~G~PLal~~~~~~L---  395 (538)
                      ..+...+       -....+.+++++.++..+++..++.....+.....+.++.+++.+    |..+.++.++-...   
T Consensus       183 ~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a  262 (394)
T PRK00411        183 LTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIA  262 (394)
T ss_pred             cchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence            4322211       113467899999999999999886322112223344555555555    44667776664432   


Q ss_pred             --cCC---CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhcccccc----CCCCHHHHHH----HHHhCCC-
Q 009306          396 --YGK---RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFF----IDEDRDTATK----FLDDCEF-  461 (538)
Q Consensus       396 --~~~---~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~----~~~~~~~l~~----l~~~~~~-  461 (538)
                        ++.   +.+....+.+..       -...+...+..|+..+|.+|..++...    ..++...+..    ++..-+. 
T Consensus       263 ~~~~~~~I~~~~v~~a~~~~-------~~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~  335 (394)
T PRK00411        263 EREGSRKVTEEDVRKAYEKS-------EIVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYE  335 (394)
T ss_pred             HHcCCCCcCHHHHHHHHHHH-------HHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCC
Confidence              111   234444444433       123355678999999999998877543    2344444432    2222222 


Q ss_pred             -----ChHHHHHHHhhCCceeEe
Q 009306          462 -----FATSAIEVLVDKHLITIS  479 (538)
Q Consensus       462 -----~~~~~l~~L~~~~Li~~~  479 (538)
                           ....+++.|.+.|||...
T Consensus       336 ~~~~~~~~~~l~~L~~~glI~~~  358 (394)
T PRK00411        336 PRTHTRFYEYINKLDMLGIINTR  358 (394)
T ss_pred             cCcHHHHHHHHHHHHhcCCeEEE
Confidence                 234589999999999954

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.54  E-value=1.4e-13  Score=152.06  Aligned_cols=326  Identities=16%  Similarity=0.222  Sum_probs=197.2

Q ss_pred             CceeccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEee----hhhhhhcCChHHHHHH
Q 009306          189 DLVGVRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARN----VREAEETCRLGDLRQQ  263 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~----~~~~~~~~~~~~l~~~  263 (538)
                      .++||+.+++.|...+.. ..+...++.+.|.+|||||+|++++...+.+...  .++..    .....+-..+...++.
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~--~~i~~~f~q~~~~ipl~~lvq~~r~   78 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRG--YFIKGKFDQFERNIPLSPLVQAFRD   78 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccce--eeeHhhcccccCCCchHHHHHHHHH
Confidence            378999999999998875 3345679999999999999999999998766521  12110    0001111111112222


Q ss_pred             H-------------------HHHHhcCCCCC----------------------Cchhhc-----HHHHHHHh-cCCCeEE
Q 009306          264 L-------------------LSTLLNDGNVK----------------------NFLNTD-----LNFQSRRL-TRKKVLI  296 (538)
Q Consensus       264 l-------------------~~~l~~~~~~~----------------------~~~~~~-----~~~l~~~l-~~k~~Ll  296 (538)
                      +                   +..++......                      ...+..     ...+.... +.+|.++
T Consensus        79 l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi  158 (849)
T COG3899          79 LMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVI  158 (849)
T ss_pred             HHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEE
Confidence            2                   22221110000                      000000     11111222 4569999


Q ss_pred             EEecC-CCh-HH---HHHHhcCcC--CC-CCCCEEEEeccch--hhhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCC
Q 009306          297 VFDDV-DHP-RQ---IKILVGRLD--LF-ASGSRIIITTRDR--QVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHP  366 (538)
Q Consensus       297 VlDdv-~~~-~~---~~~l~~~l~--~~-~~~~~iiiTtR~~--~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  366 (538)
                      |+||+ |-+ ..   ++.++....  .+ ....-.+.|.+..  .+.........+.|.||+..+...+........   
T Consensus       159 ~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~---  235 (849)
T COG3899         159 VLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCT---  235 (849)
T ss_pred             EEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCc---
Confidence            99999 432 22   333333321  00 0011122222222  222222344789999999999999999887332   


Q ss_pred             CCchHHHHHHHHHHhcCCcHHHHHHHHHhcCC-------CHHHHHHHHHHhhcCC-CCcHHHHHHHhHhCCCHHhHHHhh
Q 009306          367 HESHTELACKTIKYARGVPLALEVLGRYLYGK-------RREVWENAKSKWETAP-PKGIQDALKISYDGLDDKEQNIFL  438 (538)
Q Consensus       367 ~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~-------~~~~~~~~l~~l~~~~-~~~v~~~l~~s~~~L~~~~k~~l~  438 (538)
                      .....+....+++++.|+|++++.+-..+...       +...|+.-...+.... .+.+...+...++.||...++++.
T Consensus       236 ~~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l~~rl~kL~~~t~~Vl~  315 (849)
T COG3899         236 KLLPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLK  315 (849)
T ss_pred             ccccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHHHHHHhcCCHHHHHHHH
Confidence            23346778899999999999999999988653       2334544433332221 133555788999999999999999


Q ss_pred             ccccccCCCCHHHHHHHHHhCCCChHHHHHHHhhCCceeEec--------CC---cEEecHHHHHHHHHHHhhcCCCCCC
Q 009306          439 DIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISV--------LN---KIEMHYLLRAMGREIVRQESTNDPG  507 (538)
Q Consensus       439 ~la~f~~~~~~~~l~~l~~~~~~~~~~~l~~L~~~~Li~~~~--------~~---~~~~H~lv~~~~~~~~~~~~~~~~~  507 (538)
                      ..||+++.++.+.+..++..........+......++|....        ..   +-..|+++|+.+...+-+.      
T Consensus       316 ~AA~iG~~F~l~~La~l~~~~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~F~H~~vqqaaY~~i~~~------  389 (849)
T COG3899         316 AAACIGNRFDLDTLAALAEDSPALEAAALLDALQEGLILPLSETYRFGSNVDIATYKFLHDRVQQAAYNLIPES------  389 (849)
T ss_pred             HHHHhCccCCHHHHHHHHhhchHHHHHHHHHHhHhhceeccccccccccccchhhHHhhHHHHHHHHhccCchh------
Confidence            999999999999999998754333333444444555554321        11   1256888888877665433      


Q ss_pred             CcccccCcchHHHHHccCCC
Q 009306          508 KRSRLWHHKEVYKILSENRV  527 (538)
Q Consensus       508 ~r~rl~~~~~i~~~l~~~~~  527 (538)
                        +|...|..|...|+.+..
T Consensus       390 --~rq~~H~~i~~lL~~~~~  407 (849)
T COG3899         390 --QRQYLHLRIGQLLEQNIP  407 (849)
T ss_pred             --hHHHHHHHHHHHHHHhCC
Confidence              344559999999988876

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.47  E-value=8.4e-13  Score=131.09  Aligned_cols=258  Identities=18%  Similarity=0.191  Sum_probs=154.0

Q ss_pred             CCceeccchhHHHHHhhhcC---CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTG---STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~---~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      ..|+|++..++.|..++...   ....+.+.|+|++|+|||+||+.+++.+...+.   ... .   ........+. ..
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~---~~~-~---~~~~~~~~l~-~~   75 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLK---ITS-G---PALEKPGDLA-AI   75 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEE---Eec-c---chhcCchhHH-HH
Confidence            57999999999999888641   223456889999999999999999998764432   111 0   0001111111 11


Q ss_pred             HHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcC-------------------CCCCCCEE
Q 009306          265 LSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLD-------------------LFASGSRI  323 (538)
Q Consensus       265 ~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~-------------------~~~~~~~i  323 (538)
                      +..+                      ....+|+|||++..  ...+.+...+.                   ...+.+-|
T Consensus        76 l~~~----------------------~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li  133 (305)
T TIGR00635        76 LTNL----------------------EEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLV  133 (305)
T ss_pred             HHhc----------------------ccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEE
Confidence            1111                      23346677776432  12222221110                   01223344


Q ss_pred             EEeccchhhhhhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHH
Q 009306          324 IITTRDRQVLANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRRE  401 (538)
Q Consensus       324 iiTtR~~~~~~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~  401 (538)
                      ..||+...+...+  .....+.+++++.++..+++.+.+..  .......+.+..+++.|+|.|..+..++..+.     
T Consensus       134 ~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~--~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~-----  206 (305)
T TIGR00635       134 GATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGL--LNVEIEPEAALEIARRSRGTPRIANRLLRRVR-----  206 (305)
T ss_pred             EecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHH--hCCCcCHHHHHHHHHHhCCCcchHHHHHHHHH-----
Confidence            5556654332221  12346789999999999999988732  22345577889999999999977765555431     


Q ss_pred             HHHHHH-HHhhcCCCCc---HHHHHHHhHhCCCHHhHHHhh-ccccccC-CCCHHHHHHHHHhCCCChHHHHH-HHhhCC
Q 009306          402 VWENAK-SKWETAPPKG---IQDALKISYDGLDDKEQNIFL-DIACFFI-DEDRDTATKFLDDCEFFATSAIE-VLVDKH  474 (538)
Q Consensus       402 ~~~~~l-~~l~~~~~~~---v~~~l~~s~~~L~~~~k~~l~-~la~f~~-~~~~~~l~~l~~~~~~~~~~~l~-~L~~~~  474 (538)
                        .... ..-.....+.   ....+...+..++..++..|. .+..+.. +++.+.+...++.+....+..++ .|++++
T Consensus       207 --~~a~~~~~~~it~~~v~~~l~~l~~~~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~  284 (305)
T TIGR00635       207 --DFAQVRGQKIINRDIALKALEMLMIDELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIG  284 (305)
T ss_pred             --HHHHHcCCCCcCHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcC
Confidence              1000 0000011111   111244456788888888777 4455543 47889999999888888888899 699999


Q ss_pred             ceeEecCCcE
Q 009306          475 LITISVLNKI  484 (538)
Q Consensus       475 Li~~~~~~~~  484 (538)
                      ||.....|++
T Consensus       285 li~~~~~g~~  294 (305)
T TIGR00635       285 FLQRTPRGRI  294 (305)
T ss_pred             CcccCCchhh
Confidence            9986655543

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.47  E-value=2.4e-11  Score=123.95  Aligned_cols=285  Identities=14%  Similarity=0.100  Sum_probs=162.2

Q ss_pred             CCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhcccee------eEEEEeehhhhhhcCC
Q 009306          185 SENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS------GSYFARNVREAEETCR  256 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~------~~~~~~~~~~~~~~~~  256 (538)
                      ..|+.++||+.++++|...|..  .+.....+.|+|++|+|||++++.+++.+.....      ..+|+.+.    ....
T Consensus        12 ~~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~----~~~~   87 (365)
T TIGR02928        12 YVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ----ILDT   87 (365)
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC----CCCC
Confidence            4567899999999999998874  2233456899999999999999999987643221      23444422    2234


Q ss_pred             hHHHHHHHHHHHhc--CCCC--CCchhhcHHHHHHHh--cCCCeEEEEecCCChH-----HHHHHhcC--cCCC-CCCCE
Q 009306          257 LGDLRQQLLSTLLN--DGNV--KNFLNTDLNFQSRRL--TRKKVLIVFDDVDHPR-----QIKILVGR--LDLF-ASGSR  322 (538)
Q Consensus       257 ~~~l~~~l~~~l~~--~~~~--~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~-----~~~~l~~~--l~~~-~~~~~  322 (538)
                      ...++..++.++..  ....  ..+..+....+.+.+  .+++++||||+++...     .+..+...  .... +....
T Consensus        88 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~  167 (365)
T TIGR02928        88 LYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVG  167 (365)
T ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEE
Confidence            55677777777642  1111  123334444455554  3567899999997651     12333322  1111 12334


Q ss_pred             EEEeccchhhhhhcC-------CCeeEEcCCCCHHHHHHHHHhhhcC---CCCCCCchHHHHHHHHHHhcCCcHHH-HHH
Q 009306          323 IIITTRDRQVLANCG-------VDEVYQMEELVHDDALRLFSRHAFG---GDHPHESHTELACKTIKYARGVPLAL-EVL  391 (538)
Q Consensus       323 iiiTtR~~~~~~~~~-------~~~~~~l~~L~~~ea~~Lf~~~~~~---~~~~~~~~~~~~~~i~~~~~G~PLal-~~~  391 (538)
                      +|.++........+.       ....+.+++++.+|..+++..++..   .....+...+.+..++..+.|.|..+ ..+
T Consensus       168 lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l  247 (365)
T TIGR02928       168 VIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLL  247 (365)
T ss_pred             EEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHH
Confidence            555554432221111       1246889999999999999988631   11122222234556677777888443 332


Q ss_pred             HHHh----c-C---CCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhcccccc----CCCCHHHHHH----H
Q 009306          392 GRYL----Y-G---KRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFF----IDEDRDTATK----F  455 (538)
Q Consensus       392 ~~~L----~-~---~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~----~~~~~~~l~~----l  455 (538)
                      -...    . +   -+.+..+.+.+.+       -.......+..|+.+++.+|..++...    ..+....+..    +
T Consensus       248 ~~a~~~a~~~~~~~it~~~v~~a~~~~-------~~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~  320 (365)
T TIGR02928       248 RVAGEIAEREGAERVTEDHVEKAQEKI-------EKDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEV  320 (365)
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHH
Confidence            2221    1 1   1233333333333       123455678899999998887766322    1233333322    2


Q ss_pred             HHhCCC------ChHHHHHHHhhCCceeEec
Q 009306          456 LDDCEF------FATSAIEVLVDKHLITISV  480 (538)
Q Consensus       456 ~~~~~~------~~~~~l~~L~~~~Li~~~~  480 (538)
                      ....+.      ....+++.|...|||....
T Consensus       321 ~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~  351 (365)
T TIGR02928       321 CEDIGVDPLTQRRISDLLNELDMLGLVEAEE  351 (365)
T ss_pred             HHhcCCCCCcHHHHHHHHHHHHhcCCeEEEE
Confidence            221121      1345799999999999653

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

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.46  E-value=5e-13  Score=133.68  Aligned_cols=262  Identities=17%  Similarity=0.160  Sum_probs=158.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |....+|+|++..++.+..++..   .....+.+.|+|++|+|||+||+.+++.+...+.   +.. ..   ..... ..
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~---~~~-~~---~~~~~-~~   92 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR---ITS-GP---ALEKP-GD   92 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeE---EEe-cc---cccCh-HH
Confidence            34557899999999999887763   2234567899999999999999999998765432   111 00   00000 11


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH--HHHHHhcCcC-------------------CCCC
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR--QIKILVGRLD-------------------LFAS  319 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--~~~~l~~~l~-------------------~~~~  319 (538)
                      +..++..                     + ....+|+||+++...  ..+.+...+.                   ...+
T Consensus        93 l~~~l~~---------------------l-~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~  150 (328)
T PRK00080         93 LAAILTN---------------------L-EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPP  150 (328)
T ss_pred             HHHHHHh---------------------c-ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCC
Confidence            1111111                     1 234577777775321  1111111100                   0012


Q ss_pred             CCEEEEeccchhhhhhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC
Q 009306          320 GSRIIITTRDRQVLANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYG  397 (538)
Q Consensus       320 ~~~iiiTtR~~~~~~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~  397 (538)
                      .+-|..|++...+...+  .....+++++++.++..+++.+.+..  .......+.+..|++.|+|.|-.+..+...+  
T Consensus       151 ~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~--~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~--  226 (328)
T PRK00080        151 FTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARI--LGVEIDEEGALEIARRSRGTPRIANRLLRRV--  226 (328)
T ss_pred             ceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHH--cCCCcCHHHHHHHHHHcCCCchHHHHHHHHH--
Confidence            33345555544332221  12346899999999999999988732  3334567789999999999997665555543  


Q ss_pred             CCHHHHHHHHHHhhcCCCC---cHHHHHHHhHhCCCHHhHHHhh-ccccccC-CCCHHHHHHHHHhCCCChHHHHH-HHh
Q 009306          398 KRREVWENAKSKWETAPPK---GIQDALKISYDGLDDKEQNIFL-DIACFFI-DEDRDTATKFLDDCEFFATSAIE-VLV  471 (538)
Q Consensus       398 ~~~~~~~~~l~~l~~~~~~---~v~~~l~~s~~~L~~~~k~~l~-~la~f~~-~~~~~~l~~l~~~~~~~~~~~l~-~L~  471 (538)
                         ..|.... .-......   .....+...+..|++..+..|. .+..|.. ++..+.+...++.+....+..++ .|+
T Consensus       227 ---~~~a~~~-~~~~I~~~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li  302 (328)
T PRK00080        227 ---RDFAQVK-GDGVITKEIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLI  302 (328)
T ss_pred             ---HHHHHHc-CCCCCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHH
Confidence               1111110 00011111   1223344566788888888886 5555544 57899999999888888888888 999


Q ss_pred             hCCceeEecCCc
Q 009306          472 DKHLITISVLNK  483 (538)
Q Consensus       472 ~~~Li~~~~~~~  483 (538)
                      +.+||.....|+
T Consensus       303 ~~~li~~~~~gr  314 (328)
T PRK00080        303 QQGFIQRTPRGR  314 (328)
T ss_pred             HcCCcccCCchH
Confidence            999998665554

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

Probab=99.43  E-value=8.9e-13  Score=125.43  Aligned_cols=198  Identities=19%  Similarity=0.202  Sum_probs=103.8

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH------HHH
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL------RQQ  263 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l------~~~  263 (538)
                      |+||+.+++.|.+++..+  ..+.+.|+|+.|+|||+|++.+.+........++|+........ .....+      ...
T Consensus         1 F~gR~~el~~l~~~l~~~--~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~-~~~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESG--PSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNE-SSLRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHH-HHHHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhh--cCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhh-hHHHHHHHHHHHHHH
Confidence            799999999999999753  35679999999999999999999988554444555443222111 011111      111


Q ss_pred             ----HHHHHhcCCC------CCCchhhcHHHHHHHhc--CCCeEEEEecCCChH--------HHHHHhcCcCC--CCCCC
Q 009306          264 ----LLSTLLNDGN------VKNFLNTDLNFQSRRLT--RKKVLIVFDDVDHPR--------QIKILVGRLDL--FASGS  321 (538)
Q Consensus       264 ----l~~~l~~~~~------~~~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~~--------~~~~l~~~l~~--~~~~~  321 (538)
                          +...+.....      ...........+.+.+.  +++++||+||++...        .+..+...+..  ...+.
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  157 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV  157 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc
Confidence                1111111100      01122223333333332  345999999996443        12222222111  13344


Q ss_pred             EEEEeccchhhhhh--------cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          322 RIIITTRDRQVLAN--------CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       322 ~iiiTtR~~~~~~~--------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      .+|+++....+...        .+....+.|++|+.+++.+++....-..... ....+..+++++.+||+|..|..+
T Consensus       158 ~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~~~~-~~~~~~~~~i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  158 SIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKELIKL-PFSDEDIEEIYSLTGGNPRYLQEL  234 (234)
T ss_dssp             EEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHHHH
T ss_pred             eEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHhhcc-cCCHHHHHHHHHHhCCCHHHHhcC
Confidence            55555555544433        2333459999999999999999875222111 235677899999999999998753

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

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

Probab=99.23  E-value=1.1e-09  Score=106.83  Aligned_cols=178  Identities=13%  Similarity=0.094  Sum_probs=107.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchh----hcHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLN----TDLNFQS  286 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~----~~~~~l~  286 (538)
                      ...+.|+|++|+|||||++.++..+...-...+++..     .......++..++..++.... .....    .+...+.
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~-----~~~~~~~~l~~i~~~lG~~~~-~~~~~~~~~~l~~~l~  116 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVN-----TRVDAEDLLRMVAADFGLETE-GRDKAALLRELEDFLI  116 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeC-----CCCCHHHHHHHHHHHcCCCCC-CCCHHHHHHHHHHHHH
Confidence            4578999999999999999999886532112223221     123445667777766654322 11111    1222222


Q ss_pred             HH-hcCCCeEEEEecCCChH--HHHHHh---cCcCCCCCCCEEEEeccchhhhhhc----------CCCeeEEcCCCCHH
Q 009306          287 RR-LTRKKVLIVFDDVDHPR--QIKILV---GRLDLFASGSRIIITTRDRQVLANC----------GVDEVYQMEELVHD  350 (538)
Q Consensus       287 ~~-l~~k~~LlVlDdv~~~~--~~~~l~---~~l~~~~~~~~iiiTtR~~~~~~~~----------~~~~~~~l~~L~~~  350 (538)
                      .. ..+++.+||+||++...  .++.+.   ...........|++|.... ....+          .....+.+++|+.+
T Consensus       117 ~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~  195 (269)
T TIGR03015       117 EQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDRE  195 (269)
T ss_pred             HHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHH
Confidence            22 25678999999997642  334332   2111112223455555432 11111          12346789999999


Q ss_pred             HHHHHHHhhhcCCC--CCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          351 DALRLFSRHAFGGD--HPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       351 ea~~Lf~~~~~~~~--~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      |..+++........  .......+..+.|++.++|+|..|+.++..+
T Consensus       196 e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       196 ETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            99999987763221  1223557889999999999999999999876

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.

>PF05729 NACHT: NACHT domain

Probab=99.19  E-value=2.2e-10  Score=102.68  Aligned_cols=142  Identities=19%  Similarity=0.287  Sum_probs=85.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQ  285 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l  285 (538)
                      |++.|+|.+|+||||+++.++..+....      ...+|.. .+..........+...+........   .....   .+
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~l~~~~~~~~---~~~~~---~~   73 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS-LRDISDSNNSRSLADLLFDQLPESI---APIEE---LL   73 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEe-ehhhhhccccchHHHHHHHhhccch---hhhHH---HH
Confidence            5789999999999999999998766543      2333333 3333332222233333333332211   11111   11


Q ss_pred             HHH-hcCCCeEEEEecCCChHH---------HHHHh-cCcCC-CCCCCEEEEeccchhh---hhhcCCCeeEEcCCCCHH
Q 009306          286 SRR-LTRKKVLIVFDDVDHPRQ---------IKILV-GRLDL-FASGSRIIITTRDRQV---LANCGVDEVYQMEELVHD  350 (538)
Q Consensus       286 ~~~-l~~k~~LlVlDdv~~~~~---------~~~l~-~~l~~-~~~~~~iiiTtR~~~~---~~~~~~~~~~~l~~L~~~  350 (538)
                      ... ...++++||||++|+...         +..++ ..+.. ..++++++||+|....   .........+++.+|+.+
T Consensus        74 ~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~  153 (166)
T PF05729_consen   74 QELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEE  153 (166)
T ss_pred             HHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHH
Confidence            112 246889999999975422         11122 11211 2568999999998755   333444468999999999


Q ss_pred             HHHHHHHhhh
Q 009306          351 DALRLFSRHA  360 (538)
Q Consensus       351 ea~~Lf~~~~  360 (538)
                      +..+++.+..
T Consensus       154 ~~~~~~~~~f  163 (166)
T PF05729_consen  154 DIKQYLRKYF  163 (166)
T ss_pred             HHHHHHHHHh
Confidence            9999998764

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.08  E-value=3.6e-09  Score=112.65  Aligned_cols=283  Identities=13%  Similarity=0.111  Sum_probs=150.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccc-----ee--eEEEEeehhhhhh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----FS--GSYFARNVREAEE  253 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f~--~~~~~~~~~~~~~  253 (538)
                      ...|+.++||+.|+++|...|..   +.....++.|+|++|.|||+.++.+..++...     .+  ..+++.+.    .
T Consensus       751 DYVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm----~  826 (1164)
T PTZ00112        751 DVVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM----N  826 (1164)
T ss_pred             ccCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC----c
Confidence            35678899999999999998865   23334567899999999999999998876432     11  23444421    1


Q ss_pred             cCChHHHHHHHHHHHhcCCCCC-CchhhcHHHHHHHhc---CCCeEEEEecCCChH--HHHHHhcCcCCC-CCCCEEEE-
Q 009306          254 TCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRLT---RKKVLIVFDDVDHPR--QIKILVGRLDLF-ASGSRIII-  325 (538)
Q Consensus       254 ~~~~~~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l~---~k~~LlVlDdv~~~~--~~~~l~~~l~~~-~~~~~iii-  325 (538)
                      ......+...+..++....... ......+..+...+.   ....+||||+++...  .-+.|...+.+. ..+++|++ 
T Consensus       827 Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLI  906 (1164)
T PTZ00112        827 VVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLI  906 (1164)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEE
Confidence            2344555666666664433221 222334444444431   234589999997542  112222111111 23455443 


Q ss_pred             -eccchhh----hhhcC---CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHH---HhcC-CcHHHHHHHH
Q 009306          326 -TTRDRQV----LANCG---VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIK---YARG-VPLALEVLGR  393 (538)
Q Consensus       326 -TtR~~~~----~~~~~---~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~---~~~G-~PLal~~~~~  393 (538)
                       ++.+..+    .+.+.   ....+..+|++.++..+++..++-..  ......+....+++   ...| .=.||.++-.
T Consensus       907 GISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A--~gVLdDdAIELIArkVAq~SGDARKALDILRr  984 (1164)
T PTZ00112        907 AISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENC--KEIIDHTAIQLCARKVANVSGDIRKALQICRK  984 (1164)
T ss_pred             EecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhC--CCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHH
Confidence             3332111    11111   12246679999999999999998322  11122333333332   3334 4456655554


Q ss_pred             HhcCC-----CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccccC-----CCCHHHH----HHHHH--
Q 009306          394 YLYGK-----RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFI-----DEDRDTA----TKFLD--  457 (538)
Q Consensus       394 ~L~~~-----~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~-----~~~~~~l----~~l~~--  457 (538)
                      ....+     ..+....+...+       -...+...+..||.++|.+|..+.....     .++...+    ..++.  
T Consensus       985 AgEikegskVT~eHVrkAleei-------E~srI~e~IktLPlHqKLVLlALIlLlk~tg~~~i~TGEVYerYk~Lce~~ 1057 (1164)
T PTZ00112        985 AFENKRGQKIVPRDITEATNQL-------FDSPLTNAINYLPWPFKMFLTCLIVELRMLNDFIIPYKKVLNRYKVLVETS 1057 (1164)
T ss_pred             HHhhcCCCccCHHHHHHHHHHH-------HhhhHHHHHHcCCHHHHHHHHHHHHHHhhcCCCceeHHHHHHHHHHHHHhh
Confidence            44221     111222222211       1122445667899998888875543321     1332222    22222  


Q ss_pred             -----hCCCC--hHHHHHHHhhCCceeEe
Q 009306          458 -----DCEFF--ATSAIEVLVDKHLITIS  479 (538)
Q Consensus       458 -----~~~~~--~~~~l~~L~~~~Li~~~  479 (538)
                           .+...  ....|.+|...|+|.+.
T Consensus      1058 Gk~iGv~plTqRV~d~L~eL~~LGIIl~e 1086 (1164)
T PTZ00112       1058 GKYIGMCSNNELFKIMLDKLVKMGILLIR 1086 (1164)
T ss_pred             hhhcCCCCcHHHHHHHHHHHHhcCeEEec
Confidence                 11111  34578899999999986

>PRK06893 DNA replication initiation factor; Validated

Probab=99.06  E-value=4.3e-09  Score=99.52  Aligned_cols=155  Identities=16%  Similarity=0.201  Sum_probs=96.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.+.|+|++|+|||+|+.++++....+...+.|+...    ..   ......                     +.+.+
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~----~~---~~~~~~---------------------~~~~~   89 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLS----KS---QYFSPA---------------------VLENL   89 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHH----Hh---hhhhHH---------------------HHhhc
Confidence            345789999999999999999999876655566666521    00   000001                     11111


Q ss_pred             cCCCeEEEEecCCCh---HHHH-HHhcCcCCC-CCCCEEE-Eeccc---------hhhhhhcCCCeeEEcCCCCHHHHHH
Q 009306          290 TRKKVLIVFDDVDHP---RQIK-ILVGRLDLF-ASGSRII-ITTRD---------RQVLANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~---~~~~-~l~~~l~~~-~~~~~ii-iTtR~---------~~~~~~~~~~~~~~l~~L~~~ea~~  354 (538)
                       .+.-+|+|||++..   ..++ .+...+... ..+..+| +|+..         +.+...+.....+++++++.++.++
T Consensus        90 -~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~  168 (229)
T PRK06893         90 -EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKII  168 (229)
T ss_pred             -ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHH
Confidence             13359999999753   2222 222222111 2355554 44443         2344444455688999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ++.+.++..  .....++...-+++.+.|..-.+..+-..|
T Consensus       169 iL~~~a~~~--~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        169 VLQRNAYQR--GIELSDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            999888533  234557888899999988876665555444

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

Probab=99.06  E-value=1.8e-08  Score=101.02  Aligned_cols=282  Identities=14%  Similarity=0.143  Sum_probs=169.9

Q ss_pred             CCCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccceee--EEEEeehhhhhhcCChHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG--SYFARNVREAEETCRLGD  259 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~--~~~~~~~~~~~~~~~~~~  259 (538)
                      ...|+.+.+|+.+++++...|..  .+....-+.|+|++|.|||+.++.+++++......  .+++.+    ........
T Consensus        13 ~~iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc----~~~~t~~~   88 (366)
T COG1474          13 DYIPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINC----LELRTPYQ   88 (366)
T ss_pred             CCCcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEee----eeCCCHHH
Confidence            34556799999999999988765  22223348999999999999999999988766433  466653    23456677


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHhc--CCCeEEEEecCCChH-----HHHHHhcCcCCCCCCCEE--EEeccch
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT--RKKVLIVFDDVDHPR-----QIKILVGRLDLFASGSRI--IITTRDR  330 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~~-----~~~~l~~~l~~~~~~~~i--iiTtR~~  330 (538)
                      ++..++..++..........+....+.+.+.  ++.++||||+++...     .+-.+.......  .++|  |..+-+.
T Consensus        89 i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~--~~~v~vi~i~n~~  166 (366)
T COG1474          89 VLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGEN--KVKVSIIAVSNDD  166 (366)
T ss_pred             HHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhcccc--ceeEEEEEEeccH
Confidence            7778888776444434556666677777664  477899999997542     222333222211  3443  3333333


Q ss_pred             hhh--------hhcCCCeeEEcCCCCHHHHHHHHHhhh---cCCCCCCCchHHHHHHHHHHhcCCc-HHHHHHHHHh--c
Q 009306          331 QVL--------ANCGVDEVYQMEELVHDDALRLFSRHA---FGGDHPHESHTELACKTIKYARGVP-LALEVLGRYL--Y  396 (538)
Q Consensus       331 ~~~--------~~~~~~~~~~l~~L~~~ea~~Lf~~~~---~~~~~~~~~~~~~~~~i~~~~~G~P-Lal~~~~~~L--~  396 (538)
                      ...        ..++. ..+..+|.+.+|..+++..++   |......+.--+++..++...+|-. .||..+-...  .
T Consensus       167 ~~~~~ld~rv~s~l~~-~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiA  245 (366)
T COG1474         167 KFLDYLDPRVKSSLGP-SEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIA  245 (366)
T ss_pred             HHHHHhhhhhhhccCc-ceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHH
Confidence            222        22222 347899999999999999987   3334444455556666666666533 3444333322  1


Q ss_pred             C--C----CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccccCCCCHHHH----HHHHHhCCC---Ch
Q 009306          397 G--K----RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFIDEDRDTA----TKFLDDCEF---FA  463 (538)
Q Consensus       397 ~--~----~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~~~~~~~l----~~l~~~~~~---~~  463 (538)
                      .  .    ..+.-..+..       .--...+...+..|+.+++.++..++....++....+    ..+......   ..
T Consensus       246 e~~~~~~v~~~~v~~a~~-------~~~~~~~~~~~~~L~~~~ki~L~~i~~~~~~~~~~~~y~~y~~~~~~~~~~~~~~  318 (366)
T COG1474         246 EREGSRKVSEDHVREAQE-------EIERDVLEEVLKTLPLHQKIVLLAIVELTVEISTGELYDVYESLCERLRTSQRRF  318 (366)
T ss_pred             HhhCCCCcCHHHHHHHHH-------HhhHHHHHHHHHcCCHhHHHHHHHHHHhcCCCChHHHHHHHHHHHhhhCchHHHH
Confidence            1  0    1111111100       0112234556889999999888877766444444333    333333333   33


Q ss_pred             HHHHHHHhhCCceeEe
Q 009306          464 TSAIEVLVDKHLITIS  479 (538)
Q Consensus       464 ~~~l~~L~~~~Li~~~  479 (538)
                      ...+..|...|+|...
T Consensus       319 ~~ii~~L~~lgiv~~~  334 (366)
T COG1474         319 SDIISELEGLGIVSAS  334 (366)
T ss_pred             HHHHHHHHhcCeEEee
Confidence            4578899999999854

>COG3903 Predicted ATPase [General function prediction only]

Probab=99.04  E-value=3.7e-10  Score=110.57  Aligned_cols=283  Identities=17%  Similarity=0.174  Sum_probs=189.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.+.++|+|||||||++-+... .+..|...++..+.....++..+...+..   .++...   ..-+.....+....
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~~~~~~v~~vdl~pitD~~~v~~~~ag---~~gl~~---~~g~~~~~~~~~~~   85 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AASEYADGVAFVDLAPITDPALVFPTLAG---ALGLHV---QPGDSAVDTLVRRI   85 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-HhhhcccceeeeeccccCchhHhHHHHHh---hccccc---ccchHHHHHHHHHH
Confidence            467899999999999999999999 88889888887777665554443333222   222211   11122333455666


Q ss_pred             cCCCeEEEEecCCChH-HHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEcCCCCHH-HHHHHHHhhhcCCC---
Q 009306          290 TRKKVLIVFDDVDHPR-QIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHD-DALRLFSRHAFGGD---  364 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~-~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l~~L~~~-ea~~Lf~~~~~~~~---  364 (538)
                      .+++.++|+||-.+.. +...+...+....+...++.|+|....   ......+.+++|+.. ++.++|...+....   
T Consensus        86 ~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l---~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f  162 (414)
T COG3903          86 GDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAIL---VAGEVHRRVPSLSLFDEAIELFVCRAVLVALSF  162 (414)
T ss_pred             hhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhc---ccccccccCCccccCCchhHHHHHHHHHhccce
Confidence            7889999999986543 333333333333456678888887643   233567788888876 78899887762221   


Q ss_pred             CCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHH----hhcCC------CCcHHHHHHHhHhCCCHHhH
Q 009306          365 HPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSK----WETAP------PKGIQDALKISYDGLDDKEQ  434 (538)
Q Consensus       365 ~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~----l~~~~------~~~v~~~l~~s~~~L~~~~k  434 (538)
                      -...........|.++..|.|++|+.+++..+.-.....-.-++.    +....      .......+.-|+.-|+..++
T Consensus       163 ~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe~  242 (414)
T COG3903         163 WLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWER  242 (414)
T ss_pred             eecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHHH
Confidence            112334566789999999999999999999877655433333322    22221      13455678888999999999


Q ss_pred             HHhhccccccCCCCHHHHHHHHHhCC-----CChHHHHHHHhhCCceeEec---CCcEEecHHHHHHHHHHHhhcC
Q 009306          435 NIFLDIACFFIDEDRDTATKFLDDCE-----FFATSAIEVLVDKHLITISV---LNKIEMHYLLRAMGREIVRQES  502 (538)
Q Consensus       435 ~~l~~la~f~~~~~~~~l~~l~~~~~-----~~~~~~l~~L~~~~Li~~~~---~~~~~~H~lv~~~~~~~~~~~~  502 (538)
                      ..+..++.|...+..+..........     +..-..+..|++++++...+   .-+|+.-.-++.|+.+.+.+..
T Consensus       243 ~~~~rLa~~~g~f~~~l~~~~a~g~~~~~~~y~~~~a~~ll~~kslv~a~~~~~~a~~Rl~eT~r~YalaeL~r~~  318 (414)
T COG3903         243 ALFGRLAVFVGGFDLGLALAVAAGADVDVPRYLVLLALTLLVDKSLVVALDLLGRARYRLLETGRRYALAELHRSG  318 (414)
T ss_pred             HHhcchhhhhhhhcccHHHHHhcCCccccchHHHHHHHHHHhhccchhhhhhhhHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999998888774333332222     22334677899999988553   3357888888888888877653

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

Probab=99.00  E-value=2.2e-09  Score=105.11  Aligned_cols=97  Identities=26%  Similarity=0.415  Sum_probs=81.9

Q ss_pred             CCCCCCCCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCccc--
Q 009306            8 YASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYAS--   84 (538)
Q Consensus         8 ~~~~~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~--   84 (538)
                      .+.-....++.||||||+.. +....++-|...|.-+|++||+|- .+..|. |-+.+.+.|..++.+|.|+|||.++  
T Consensus       603 ~v~~a~~skq~DVFISYRRs-tGnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~  680 (832)
T KOG3678|consen  603 DVEVAMLSKQIDVFISYRRS-TGNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRL  680 (832)
T ss_pred             ccccccccCCcceEEEeecc-ccHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHH
Confidence            33445567899999999765 345789999999999999999997 888887 5689999999999999999998764  


Q ss_pred             ------chhhHHHHHHHHHHHhhcCCeEEEEE
Q 009306           85 ------SRWCLDELLKILECKKEYAQIVVPVF  110 (538)
Q Consensus        85 ------s~~c~~El~~~~~~~~~~~~~v~pv~  110 (538)
                            -.|...|+..+++++++    |||||
T Consensus       681 lnD~nCeDWVHKEl~~Afe~~KN----IiPI~  708 (832)
T KOG3678|consen  681 LNDDNCEDWVHKELKCAFEHQKN----IIPIF  708 (832)
T ss_pred             hccccHHHHHHHHHHHHHHhcCC----eeeee
Confidence                  35888999999998865    99999

>PF14516 AAA_35: AAA-like domain

Probab=98.99  E-value=1.9e-07  Score=93.32  Aligned_cols=282  Identities=12%  Similarity=0.103  Sum_probs=153.7

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhh--hcCChHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAE--ETCRLGDLR  261 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~--~~~~~~~l~  261 (538)
                      +...+..|+|...-+++.+.+..   ....+.|.|+..+|||+|...+.+...+.--.+++++ +....  .......++
T Consensus         7 ~~~~~~Yi~R~~~e~~~~~~i~~---~G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id-~~~~~~~~~~~~~~f~   82 (331)
T PF14516_consen    7 PLDSPFYIERPPAEQECYQEIVQ---PGSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYID-LQQLGSAIFSDLEQFL   82 (331)
T ss_pred             CCCCCcccCchHHHHHHHHHHhc---CCCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEE-eecCCCcccCCHHHHH
Confidence            45667888999666666666653   2447999999999999999999988765533444554 32222  123455555


Q ss_pred             HHHHHHHhcCCCCCC-----------chhhcHHHHHHHh---cCCCeEEEEecCCChH----HHHHHhcCcC-------C
Q 009306          262 QQLLSTLLNDGNVKN-----------FLNTDLNFQSRRL---TRKKVLIVFDDVDHPR----QIKILVGRLD-------L  316 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~-----------~~~~~~~~l~~~l---~~k~~LlVlDdv~~~~----~~~~l~~~l~-------~  316 (538)
                      +.++..+........           ........+.+.+   .+++++|+||++|..-    ....++..+.       .
T Consensus        83 ~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~  162 (331)
T PF14516_consen   83 RWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKN  162 (331)
T ss_pred             HHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhccc
Confidence            555555443322211           1112223333322   2689999999997431    1122222211       0


Q ss_pred             CCC--CCEEEEeccch-hhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          317 FAS--GSRIIITTRDR-QVLA-----NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       317 ~~~--~~~iiiTtR~~-~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...  ..++++....+ ....     ..+....++|++++.+|...|+..+..      .......+.+...+||||..+
T Consensus       163 ~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~------~~~~~~~~~l~~~tgGhP~Lv  236 (331)
T PF14516_consen  163 NPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGL------EFSQEQLEQLMDWTGGHPYLV  236 (331)
T ss_pred             CcccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhc------cCCHHHHHHHHHHHCCCHHHH
Confidence            011  11222222111 1111     113345789999999999999987751      122344899999999999999


Q ss_pred             HHHHHHhcCCCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCC--CHHhHHHhhccccccCCCCHHHHHHHHHhC--CCChH
Q 009306          389 EVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGL--DDKEQNIFLDIACFFIDEDRDTATKFLDDC--EFFAT  464 (538)
Q Consensus       389 ~~~~~~L~~~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L--~~~~k~~l~~la~f~~~~~~~~l~~l~~~~--~~~~~  464 (538)
                      +.++..+..... ..+..+..-.... ..-..-|+.-+..|  .+..+.++..               ++...  .....
T Consensus       237 ~~~~~~l~~~~~-~~~~l~~~a~~~~-~~~~~hL~~l~~~L~~~~~L~~~~~~---------------il~~~~~~~~~~  299 (331)
T PF14516_consen  237 QKACYLLVEEQI-TLEQLLEEAITDN-GIYNDHLDRLLDRLQQNPELLEAYQQ---------------ILFSGEPVDLDS  299 (331)
T ss_pred             HHHHHHHHHccC-cHHHHHHHHHHhc-ccHHHHHHHHHHHHccCHHHHHHHHH---------------HHhCCCCcccCh
Confidence            999999965321 1222222211111 11112233333334  2233333332               22221  11123


Q ss_pred             HHHHHHhhCCceeEecCCcEEe-cHHHHHH
Q 009306          465 SAIEVLVDKHLITISVLNKIEM-HYLLRAM  493 (538)
Q Consensus       465 ~~l~~L~~~~Li~~~~~~~~~~-H~lv~~~  493 (538)
                      .....|...|||... +|.+.. .++-+.+
T Consensus       300 ~~~~~L~~~GLV~~~-~~~~~~~n~iY~~y  328 (331)
T PF14516_consen  300 DDIYKLESLGLVKRD-GNQLEVRNPIYRQY  328 (331)
T ss_pred             HHHHHHHHCCeEEEe-CCEEEEEcHHHHHH
Confidence            457789999999998 666554 4454444

>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=98.96  E-value=7e-09  Score=94.54  Aligned_cols=180  Identities=21%  Similarity=0.279  Sum_probs=101.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |..-++|||.+..+..+.-++..   ..+....+.+|||+|+||||||..++++....|.   +.+.    +.-....++
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~---~~sg----~~i~k~~dl   92 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNFK---ITSG----PAIEKAGDL   92 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--EE---EEEC----CC--SCHHH
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCeE---eccc----hhhhhHHHH
Confidence            34558999999999888766653   2344667999999999999999999999877663   2220    000111111


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCC--hHHHHHHhcCcCCC--------CCC----------
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDH--PRQIKILVGRLDLF--------ASG----------  320 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~--------~~~----------  320 (538)
                      .. ++                     ..+ .++.+|.+|+++.  ..+-+.+.+.+..+        +++          
T Consensus        93 ~~-il---------------------~~l-~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~  149 (233)
T PF05496_consen   93 AA-IL---------------------TNL-KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPP  149 (233)
T ss_dssp             HH-HH---------------------HT---TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE---
T ss_pred             HH-HH---------------------Hhc-CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCC
Confidence            11 11                     112 2455888899964  34445554433211        111          


Q ss_pred             -CEEEEeccchhhhhhcCC--CeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          321 -SRIIITTRDRQVLANCGV--DEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       321 -~~iiiTtR~~~~~~~~~~--~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                       .-|=.|||...+...+..  .-+.+++..+.+|..+++.+.+  ....-+..++.+.+|+..+.|.|--..-+-+.+
T Consensus       150 FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a--~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll~rv  225 (233)
T PF05496_consen  150 FTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSA--RILNIEIDEDAAEEIARRSRGTPRIANRLLRRV  225 (233)
T ss_dssp             -EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCC--HCTT-EE-HHHHHHHHHCTTTSHHHHHHHHHHH
T ss_pred             ceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHH--HHhCCCcCHHHHHHHHHhcCCChHHHHHHHHHH
Confidence             224456776544333322  2345899999999999998876  233445678899999999999996555444444

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.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.94  E-value=3.9e-08  Score=104.44  Aligned_cols=201  Identities=12%  Similarity=0.089  Sum_probs=115.5

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      |...+++||.+..++.|..++..+. -...+.++|+.|+||||+|+.+++.+...-.. -... ++   .......+...
T Consensus        12 PqtFdEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~-~~~P-CG---~C~sCr~I~~G   85 (830)
T PRK07003         12 PKDFASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGV-TSQP-CG---VCRACREIDEG   85 (830)
T ss_pred             CCcHHHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCC-CCCC-Cc---ccHHHHHHhcC
Confidence            3445789999999999999987542 24567899999999999999999876421000 0000 00   00000000000


Q ss_pred             HHHHHhcCC-CCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchhh-hhh
Q 009306          264 LLSTLLNDG-NVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQV-LAN  335 (538)
Q Consensus       264 l~~~l~~~~-~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~-~~~  335 (538)
                      -...+.... .....+++....+...    ..++.-++|||+++..  .....|+..+.....+.++|++|.+... ...
T Consensus        86 ~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~T  165 (830)
T PRK07003         86 RFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVT  165 (830)
T ss_pred             CCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccch
Confidence            000000000 0001111111111111    1234458899999755  3467777766655667888887776533 222


Q ss_pred             c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc-HHHHHHH
Q 009306          336 C-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP-LALEVLG  392 (538)
Q Consensus       336 ~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-Lal~~~~  392 (538)
                      + .....+.+.+++.++..+.+.+.+..  .......+....|++.++|.. -+|.++-
T Consensus       166 IrSRCq~f~Fk~Ls~eeIv~~L~~Il~~--EgI~id~eAL~lIA~~A~GsmRdALsLLd  222 (830)
T PRK07003        166 VLSRCLQFNLKQMPAGHIVSHLERILGE--ERIAFEPQALRLLARAAQGSMRDALSLTD  222 (830)
T ss_pred             hhhheEEEecCCcCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            2 23468999999999999999887622  223345777889999998866 4555433

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.94  E-value=9.6e-08  Score=98.58  Aligned_cols=179  Identities=20%  Similarity=0.308  Sum_probs=109.1

Q ss_pred             CCCCCceeccchhHH---HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKE---IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~---l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      ...+.+||++..+..   |..++..+  ....+.|+|++|+||||||+.+++.....|..   +...     ..+... .
T Consensus         9 ~~l~d~vGq~~~v~~~~~L~~~i~~~--~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~---l~a~-----~~~~~~-i   77 (413)
T PRK13342          9 KTLDEVVGQEHLLGPGKPLRRMIEAG--RLSSMILWGPPGTGKTTLARIIAGATDAPFEA---LSAV-----TSGVKD-L   77 (413)
T ss_pred             CCHHHhcCcHHHhCcchHHHHHHHcC--CCceEEEECCCCCCHHHHHHHHHHHhCCCEEE---Eecc-----cccHHH-H
Confidence            344679999988766   77777643  45568899999999999999999876554321   1100     011111 1


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEE--eccchh--hhh
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIII--TTRDRQ--VLA  334 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iii--TtR~~~--~~~  334 (538)
                      +.++..                 .... ..+++.+|+||+++..  .+.+.++..+.   .+..++|  ||.+..  +..
T Consensus        78 r~ii~~-----------------~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~  137 (413)
T PRK13342         78 REVIEE-----------------ARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLIGATTENPSFEVNP  137 (413)
T ss_pred             HHHHHH-----------------HHHhhhcCCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccH
Confidence            111111                 1111 1357789999999754  45556655543   2444444  233331  111


Q ss_pred             h-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCC-CchHHHHHHHHHHhcCCcHHHHHHHHH
Q 009306          335 N-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPH-ESHTELACKTIKYARGVPLALEVLGRY  394 (538)
Q Consensus       335 ~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~-~~~~~~~~~i~~~~~G~PLal~~~~~~  394 (538)
                      . ......+.+.+++.++..+++.+.+....... ....+....+++.++|.+..+..+...
T Consensus       138 aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~  199 (413)
T PRK13342        138 ALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLEL  199 (413)
T ss_pred             HHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            1 12236789999999999999988653211111 345677889999999999766554443

>PRK04195 replication factor C large subunit; Provisional

Probab=98.94  E-value=3.9e-08  Score=103.49  Aligned_cols=222  Identities=15%  Similarity=0.162  Sum_probs=127.2

Q ss_pred             cccCCCCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          180 DDTFHSENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       180 ~~~~~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      ....|.....++|.+..++.|..++..  .+...+.+.|+|++|+||||+|+.+++.+.  ++. +.+. .   +... .
T Consensus         6 eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~--~~~-ieln-a---sd~r-~   77 (482)
T PRK04195          6 EKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG--WEV-IELN-A---SDQR-T   77 (482)
T ss_pred             hhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC--CCE-EEEc-c---cccc-c
Confidence            334455667899999999999998864  222267899999999999999999999863  221 1111 1   1111 1


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH------HHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR------QIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~------~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ......+.........              ....++-+||||+++...      .+..+...+.  ..+..+|+|+.+..
T Consensus        78 ~~~i~~~i~~~~~~~s--------------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~  141 (482)
T PRK04195         78 ADVIERVAGEAATSGS--------------LFGARRKLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPY  141 (482)
T ss_pred             HHHHHHHHHHhhccCc--------------ccCCCCeEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCcc
Confidence            1222233222211100              011356799999997542      2455544433  23455666664431


Q ss_pred             h-hh-h-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC-CCHHHHHHHH
Q 009306          332 V-LA-N-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYG-KRREVWENAK  407 (538)
Q Consensus       332 ~-~~-~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~-~~~~~~~~~l  407 (538)
                      - .. . ......+++++++.++....+...+...  ......+....|++.++|....+......+.. +..-.-..+-
T Consensus       142 ~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~e--gi~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~~~~~it~~~v~  219 (482)
T PRK04195        142 DPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKE--GIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDVK  219 (482)
T ss_pred             ccchhhHhccceEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCcHHHHH
Confidence            1 11 1 1234678999999999999988876332  22345778899999999987655443333332 2111111111


Q ss_pred             HHhhcCCCCcHHHHHHHhHh
Q 009306          408 SKWETAPPKGIQDALKISYD  427 (538)
Q Consensus       408 ~~l~~~~~~~v~~~l~~s~~  427 (538)
                      .........++..++...+.
T Consensus       220 ~~~~~d~~~~if~~l~~i~~  239 (482)
T PRK04195        220 TLGRRDREESIFDALDAVFK  239 (482)
T ss_pred             HhhcCCCCCCHHHHHHHHHC
Confidence            11223344566666665554

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

Probab=98.93  E-value=1.1e-08  Score=99.75  Aligned_cols=169  Identities=21%  Similarity=0.332  Sum_probs=104.5

Q ss_pred             CCCceeccchh---HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          187 NEDLVGVRLPM---KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       187 ~~~~vGR~~~l---~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      -+.+||.+.-+   .-|..++..  +....+.+|||+|+||||||+.++......|...--+        ..++.++.. 
T Consensus        23 lde~vGQ~HLlg~~~~lrr~v~~--~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv--------~~gvkdlr~-   91 (436)
T COG2256          23 LDEVVGQEHLLGEGKPLRRAVEA--GHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAV--------TSGVKDLRE-   91 (436)
T ss_pred             HHHhcChHhhhCCCchHHHHHhc--CCCceeEEECCCCCCHHHHHHHHHHhhCCceEEeccc--------cccHHHHHH-
Confidence            35566665443   234444443  4567799999999999999999999877765422111        122222211 


Q ss_pred             HHHHHhcCCCCCCchhhcHHHH-HHHhcCCCeEEEEecCC--ChHHHHHHhcCcCCCCCCCEEEE--eccchhh---hhh
Q 009306          264 LLSTLLNDGNVKNFLNTDLNFQ-SRRLTRKKVLIVFDDVD--HPRQIKILVGRLDLFASGSRIII--TTRDRQV---LAN  335 (538)
Q Consensus       264 l~~~l~~~~~~~~~~~~~~~~l-~~~l~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~~~iii--TtR~~~~---~~~  335 (538)
                                       ..+.- .....+++.+|+||+|.  +..+-+.|++.+.   .|.-|+|  ||-++..   ...
T Consensus        92 -----------------i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~lLp~vE---~G~iilIGATTENPsF~ln~AL  151 (436)
T COG2256          92 -----------------IIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVE---NGTIILIGATTENPSFELNPAL  151 (436)
T ss_pred             -----------------HHHHHHHHHhcCCceEEEEehhhhcChhhhhhhhhhhc---CCeEEEEeccCCCCCeeecHHH
Confidence                             11111 12234789999999995  5677888887763   4655555  3444422   111


Q ss_pred             cCCCeeEEcCCCCHHHHHHHHHhhhcCCCC-----CCCchHHHHHHHHHHhcCCcH
Q 009306          336 CGVDEVYQMEELVHDDALRLFSRHAFGGDH-----PHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       336 ~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~-----~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      .....++++++|+.++..+++.+-+.....     .....++....++..++|-..
T Consensus       152 lSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R  207 (436)
T COG2256         152 LSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDAR  207 (436)
T ss_pred             hhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHH
Confidence            223578999999999999999883311111     112446677788888888754

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.92  E-value=2.3e-08  Score=94.64  Aligned_cols=175  Identities=17%  Similarity=0.186  Sum_probs=104.3

Q ss_pred             CCcee--ccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHH
Q 009306          188 EDLVG--VRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLL  265 (538)
Q Consensus       188 ~~~vG--R~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~  265 (538)
                      ++|++  .+..++.+.+++..  ...+.+.|+|++|+|||+||+.+++.........+++. .......  .    ..++
T Consensus        15 ~~~~~~~~~~~~~~l~~~~~~--~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~-~~~~~~~--~----~~~~   85 (226)
T TIGR03420        15 DNFYAGGNAELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP-LAELAQA--D----PEVL   85 (226)
T ss_pred             cCcCcCCcHHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEe-HHHHHHh--H----HHHH
Confidence            45653  33466677776542  34567999999999999999999987654433445554 2111100  0    0111


Q ss_pred             HHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----HHHHHhcCcCC-CCCCCEEEEeccchh---------
Q 009306          266 STLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----QIKILVGRLDL-FASGSRIIITTRDRQ---------  331 (538)
Q Consensus       266 ~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----~~~~l~~~l~~-~~~~~~iiiTtR~~~---------  331 (538)
                                           ..+. +.-+|||||++...    ..+.+...+.. ...+..+|+|++...         
T Consensus        86 ---------------------~~~~-~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~  143 (226)
T TIGR03420        86 ---------------------EGLE-QADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPD  143 (226)
T ss_pred             ---------------------hhcc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHH
Confidence                                 1111 23489999996432    12333222211 123457888887432         


Q ss_pred             hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          332 VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       332 ~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      +...+.....+++++++.++...++...+-.  .......+....+.+.++|+|..+..+...+
T Consensus       144 L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~--~~~~~~~~~l~~L~~~~~gn~r~L~~~l~~~  205 (226)
T TIGR03420       144 LRTRLAWGLVFQLPPLSDEEKIAALQSRAAR--RGLQLPDEVADYLLRHGSRDMGSLMALLDAL  205 (226)
T ss_pred             HHHHHhcCeeEecCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            1122222457899999999999999876521  1233456778888999999998877665544

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.

>PLN03025 replication factor C subunit; Provisional

Probab=98.92  E-value=4.3e-08  Score=97.70  Aligned_cols=186  Identities=14%  Similarity=0.184  Sum_probs=109.6

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHH
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..|..-..++|.+..++.|..++..+  ..+.+.++|++|+||||+|..+++.+.. .|...+.-.+   .+...+.. .
T Consensus         7 yrP~~l~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln---~sd~~~~~-~   80 (319)
T PLN03025          7 YRPTKLDDIVGNEDAVSRLQVIARDG--NMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELN---ASDDRGID-V   80 (319)
T ss_pred             cCCCCHHHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeec---ccccccHH-H
Confidence            34555678899999898888887643  3345789999999999999999988632 2322221111   11111111 2


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc-
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANC-  336 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~-  336 (538)
                      .+.....+......             ...++.-+++||+++..  .....+...+...+..+++++++... .+...+ 
T Consensus        81 vr~~i~~~~~~~~~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~  147 (319)
T PLN03025         81 VRNKIKMFAQKKVT-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQ  147 (319)
T ss_pred             HHHHHHHHHhcccc-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHH
Confidence            22222211111000             00134569999999754  33444444444335567777766443 222211 


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      .....+++++++.++..+.+...+-.  .......+....+++.++|..-.+
T Consensus       148 SRc~~i~f~~l~~~~l~~~L~~i~~~--egi~i~~~~l~~i~~~~~gDlR~a  197 (319)
T PLN03025        148 SRCAIVRFSRLSDQEILGRLMKVVEA--EKVPYVPEGLEAIIFTADGDMRQA  197 (319)
T ss_pred             HhhhcccCCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHH
Confidence            12357899999999999999887722  222344677889999999886433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.88  E-value=6.3e-08  Score=96.84  Aligned_cols=185  Identities=14%  Similarity=0.143  Sum_probs=109.2

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      .|..-.+++|++..++.+..++..+  ..+.+.|+|++|+||||+++.+++.+........++. .. .+...... ...
T Consensus        12 rP~~~~~~~g~~~~~~~l~~~i~~~--~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~-~~-~~~~~~~~-~~~   86 (319)
T PRK00440         12 RPRTLDEIVGQEEIVERLKSYVKEK--NMPHLLFAGPPGTGKTTAALALARELYGEDWRENFLE-LN-ASDERGID-VIR   86 (319)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEE-ec-cccccchH-HHH
Confidence            3444567999999999999988753  3345799999999999999999987643321111111 00 01111111 111


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-CC
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-GV  338 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-~~  338 (538)
                      ..+..+.....              .....+-+|+||+++..  .....+...+....+.+.+|+++.... +.... ..
T Consensus        87 ~~i~~~~~~~~--------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr  152 (319)
T PRK00440         87 NKIKEFARTAP--------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSR  152 (319)
T ss_pred             HHHHHHHhcCC--------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHH
Confidence            11111111100              00123458999999754  334445444444455677777764321 11111 12


Q ss_pred             CeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          339 DEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       339 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...+++++++.++....+...+...  ......+.+..+++.++|.+.-+
T Consensus       153 ~~~~~~~~l~~~ei~~~l~~~~~~~--~~~i~~~al~~l~~~~~gd~r~~  200 (319)
T PRK00440        153 CAVFRFSPLKKEAVAERLRYIAENE--GIEITDDALEAIYYVSEGDMRKA  200 (319)
T ss_pred             hheeeeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            3468999999999999998877322  22345778889999999998654

>PTZ00202 tuzin; Provisional

Probab=98.88  E-value=1.7e-07  Score=93.18  Aligned_cols=182  Identities=12%  Similarity=0.074  Sum_probs=108.7

Q ss_pred             HHHHHhhhccccc------cCCCCCCCceeccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccceee
Q 009306          169 EEIVNAILKRLDD------TFHSENEDLVGVRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG  241 (538)
Q Consensus       169 ~~i~~~~~~~~~~------~~~~~~~~~vGR~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~  241 (538)
                      .-.++.+.+..++      ..|.....|+||+.++..|...|.. +....+++.|+|++|+|||||++.+.....    .
T Consensus       237 ~~Av~tL~~~~~~~~~~~~~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~  312 (550)
T PTZ00202        237 KVAVSTLTQPLNPRPSTLQSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----M  312 (550)
T ss_pred             HHHHHHhhcccCCCcccccCCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----c
Confidence            3344555555444      3567889999999999999999975 333456899999999999999999997654    2


Q ss_pred             EEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCC--CchhhcHHHHHHHh-c-CCCeEEEEe--cCCChHHHHHHhcCcC
Q 009306          242 SYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK--NFLNTDLNFQSRRL-T-RKKVLIVFD--DVDHPRQIKILVGRLD  315 (538)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~--~~~~~~~~~l~~~l-~-~k~~LlVlD--dv~~~~~~~~l~~~l~  315 (538)
                      ..++.+.      .+..++++.++.+++......  .-.+.+.+.+.+.- . +++.+|||-  +-.+..-+-.-.-.+.
T Consensus       313 ~qL~vNp------rg~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~v~la  386 (550)
T PTZ00202        313 PAVFVDV------RGTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEVVALA  386 (550)
T ss_pred             eEEEECC------CCHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHHHHHH
Confidence            2444432      256889999999988632211  12233333333322 2 455555544  3333322111111122


Q ss_pred             CCCCCCEEEEeccchhhh---hhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          316 LFASGSRIIITTRDRQVL---ANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       316 ~~~~~~~iiiTtR~~~~~---~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      +-..-|+|++----+.+-   ..+..-..|-+++++.++|.++.....
T Consensus       387 ~drr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        387 CDRRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             ccchhheeeeeehHhhcchhcccCccceeEecCCCCHHHHHHHHhhcc
Confidence            223467777644322211   011123578899999999999776554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.88  E-value=7e-08  Score=97.30  Aligned_cols=202  Identities=14%  Similarity=0.093  Sum_probs=111.6

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce-ee-EEEEeehhhhhhcCChHHH
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-SG-SYFARNVREAEETCRLGDL  260 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~-~~~~~~~~~~~~~~~~~~l  260 (538)
                      .|.....++|++..++.|..++..+  ..+.+.|+|++|+||||+|+.+++.+.... .. .+++. ..+.... ....+
T Consensus        10 ~P~~~~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~-~~~~~~~-~~~~~   85 (337)
T PRK12402         10 RPALLEDILGQDEVVERLSRAVDSP--NLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFN-VADFFDQ-GKKYL   85 (337)
T ss_pred             CCCcHHHhcCCHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEec-hhhhhhc-chhhh
Confidence            3444577999999999999988753  334588999999999999999998765432 21 23332 1111000 00000


Q ss_pred             HH--HHHHHHhcCCCCC-CchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          261 RQ--QLLSTLLNDGNVK-NFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       261 ~~--~l~~~l~~~~~~~-~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ..  .+...+....... ...+.....+....     ...+-+|||||++..  .....+...+......+++|+|+...
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~  165 (337)
T PRK12402         86 VEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQP  165 (337)
T ss_pred             hcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCCh
Confidence            00  0000000000000 00111111111111     133458999999754  22333443333334567788777543


Q ss_pred             -hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          331 -QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       331 -~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                       .+...+ .....+++.+++.++...++...+...  ......+....+++.++|++-.+..
T Consensus       166 ~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~--~~~~~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        166 SKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAE--GVDYDDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             hhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHH
Confidence             222222 223578899999999999998876322  2235577888999999998765543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.87  E-value=4.1e-08  Score=102.72  Aligned_cols=194  Identities=13%  Similarity=0.068  Sum_probs=113.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc--ceeeEEEEeehhh-hhh--cCChH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR--HFSGSYFARNVRE-AEE--TCRLG  258 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~--~f~~~~~~~~~~~-~~~--~~~~~  258 (538)
                      |..-+.++|.+..++.|..++..+. -...+.++|++|+||||+|+.+++.+..  .....|+.+..-. ...  ...+.
T Consensus        10 P~~~~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~   88 (504)
T PRK14963         10 PITFDEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVL   88 (504)
T ss_pred             CCCHHHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceE
Confidence            3344678999999999988887542 3456799999999999999999987642  1222333321000 000  00000


Q ss_pred             HHHHHHHHHHhcCCCCC-CchhhcHHHHHH-HhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhh
Q 009306          259 DLRQQLLSTLLNDGNVK-NFLNTDLNFQSR-RLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVL  333 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~-~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~  333 (538)
                      .+        ....... ..+.+....+.. -..+++-++|||+++..  ..+..++..+....++..+|+++... .+.
T Consensus        89 el--------~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~  160 (504)
T PRK14963         89 EI--------DAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMP  160 (504)
T ss_pred             Ee--------cccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCC
Confidence            00        0000000 111111111111 01245568999999754  45666766665444555666555433 332


Q ss_pred             hhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          334 ANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       334 ~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ..+ .....+++.+++.++..+.+.+.+...  ......+.+..+++.++|.+.-+
T Consensus       161 ~~I~SRc~~~~f~~ls~~el~~~L~~i~~~e--gi~i~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        161 PTILSRTQHFRFRRLTEEEIAGKLRRLLEAE--GREAEPEALQLVARLADGAMRDA  214 (504)
T ss_pred             hHHhcceEEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            222 234689999999999999998877322  22345678899999999998544

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

Probab=98.85  E-value=5.9e-08  Score=90.35  Aligned_cols=261  Identities=18%  Similarity=0.224  Sum_probs=155.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |..-..|||.+...++|.-.+..   .....--+.++||+|.||||||.-+++++...+....       ...-....++
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~ts-------Gp~leK~gDl   94 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITS-------GPALEKPGDL   94 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecc-------cccccChhhH
Confidence            34457899999988888777654   2233556999999999999999999998765532110       0000011111


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH--HHHHHhcCcCCC--------CCCCE--------
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR--QIKILVGRLDLF--------ASGSR--------  322 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--~~~~l~~~l~~~--------~~~~~--------  322 (538)
                      . .++..                     | ...-++.+|+++...  .-+.+.+.+..+        +++++        
T Consensus        95 a-aiLt~---------------------L-e~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLpp  151 (332)
T COG2255          95 A-AILTN---------------------L-EEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPP  151 (332)
T ss_pred             H-HHHhc---------------------C-CcCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCC
Confidence            1 11111                     1 233466788885431  112222222111        23332        


Q ss_pred             ---EEEeccchhhhhhcC--CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC
Q 009306          323 ---IIITTRDRQVLANCG--VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYG  397 (538)
Q Consensus       323 ---iiiTtR~~~~~~~~~--~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~  397 (538)
                         |=-|||.-.+...+.  ..-+.+++-.+.+|..+++.+.+  ..-..+..++.+.+|++++.|-|.--.-+.+..+ 
T Consensus       152 FTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a--~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVR-  228 (332)
T COG2255         152 FTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSA--KILGIEIDEEAALEIARRSRGTPRIANRLLRRVR-  228 (332)
T ss_pred             eeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHH--HHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHH-
Confidence               446777654432221  22467899999999999999887  3333455678899999999999953333322221 


Q ss_pred             CCHHHHHHHHHHhhcCC--CC----cHHHHHHHhHhCCCHHhHHHhhcccccc--CCCCHHHHHHHHHhCCCChHHHHH-
Q 009306          398 KRREVWENAKSKWETAP--PK----GIQDALKISYDGLDDKEQNIFLDIACFF--IDEDRDTATKFLDDCEFFATSAIE-  468 (538)
Q Consensus       398 ~~~~~~~~~l~~l~~~~--~~----~v~~~l~~s~~~L~~~~k~~l~~la~f~--~~~~~~~l~~l~~~~~~~~~~~l~-  468 (538)
                          ++..    .....  ..    .....|..-=.+|+...+++|..+.-.+  +++..+.+...+..+....++.++ 
T Consensus       229 ----Dfa~----V~~~~~I~~~ia~~aL~~L~Vd~~GLd~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~TiEdv~EP  300 (332)
T COG2255         229 ----DFAQ----VKGDGDIDRDIADKALKMLDVDELGLDEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRDTIEDVIEP  300 (332)
T ss_pred             ----HHHH----HhcCCcccHHHHHHHHHHhCcccccccHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchhHHHHHHhH
Confidence                1111    11111  11    1222333333467788888887776555  557888888888766666666665 


Q ss_pred             HHhhCCceeEecCCcEE
Q 009306          469 VLVDKHLITISVLNKIE  485 (538)
Q Consensus       469 ~L~~~~Li~~~~~~~~~  485 (538)
                      .|++.|+|+....|++-
T Consensus       301 yLiq~gfi~RTpRGR~a  317 (332)
T COG2255         301 YLIQQGFIQRTPRGRIA  317 (332)
T ss_pred             HHHHhchhhhCCCccee
Confidence            69999999998878754

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.84  E-value=1.8e-07  Score=94.73  Aligned_cols=192  Identities=13%  Similarity=0.104  Sum_probs=111.3

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      .....++|.+..++.+...+..+ .-.+.+.++|++|+||||+|+.+++.+.....   ..|-.+        .....+.
T Consensus        13 ~~~~~iiGq~~~~~~l~~~~~~~-~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c--------~~c~~~~   83 (363)
T PRK14961         13 QYFRDIIGQKHIVTAISNGLSLG-RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKC--------IICKEIE   83 (363)
T ss_pred             CchhhccChHHHHHHHHHHHHcC-CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC--------HHHHHHh
Confidence            34478999999999999888753 23456799999999999999999987642110   000000        0000000


Q ss_pred             HHHHHHHhcCCCC-CCchhhcHHHHHHHh-----cCCCeEEEEecCCChH--HHHHHhcCcCCCCCCCEEEEeccch-hh
Q 009306          262 QQLLSTLLNDGNV-KNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHPR--QIKILVGRLDLFASGSRIIITTRDR-QV  332 (538)
Q Consensus       262 ~~l~~~l~~~~~~-~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~~~iiiTtR~~-~~  332 (538)
                      ......+...... ....++. ..+.+.+     .+++-++|||+++...  ....++..+....+..++|++|.+. .+
T Consensus        84 ~~~~~d~~~~~~~~~~~v~~i-r~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l  162 (363)
T PRK14961         84 KGLCLDLIEIDAASRTKVEEM-REILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKI  162 (363)
T ss_pred             cCCCCceEEecccccCCHHHH-HHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhh
Confidence            0000000000000 0011111 1111111     2344599999997653  4566766666555667777766544 33


Q ss_pred             hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          333 LANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       333 ~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...+ .....+++.+++.++..+.+...+...  .....++.+..+++.++|.|..+
T Consensus       163 ~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~--g~~i~~~al~~ia~~s~G~~R~a  217 (363)
T PRK14961        163 PKTILSRCLQFKLKIISEEKIFNFLKYILIKE--SIDTDEYALKLIAYHAHGSMRDA  217 (363)
T ss_pred             hHHHHhhceEEeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            3222 224688999999999999988866222  23345677888999999988543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.84  E-value=4.9e-07  Score=90.92  Aligned_cols=196  Identities=13%  Similarity=0.107  Sum_probs=112.3

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce--eeE-EEE--eehhhhhhcCChH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGS-YFA--RNVREAEETCRLG  258 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~-~~~--~~~~~~~~~~~~~  258 (538)
                      |....+++|.+...+.|.+.+..+. -...+.++|+.|+||+|+|..++..+-..-  ... +-.  .... .....   
T Consensus        15 P~~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~-~~~~c---   89 (365)
T PRK07471         15 PRETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLA-IDPDH---   89 (365)
T ss_pred             CCchhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCcccccccccc-CCCCC---
Confidence            4455789999999999998887542 345688999999999999999998753211  000 000  0000 00000   


Q ss_pred             HHHHHHHHHH-------h---cCCC----CCCchhhcHHHHHHHh-----cCCCeEEEEecCCC--hHHHHHHhcCcCCC
Q 009306          259 DLRQQLLSTL-------L---NDGN----VKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDH--PRQIKILVGRLDLF  317 (538)
Q Consensus       259 ~l~~~l~~~l-------~---~~~~----~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~l~~~  317 (538)
                      ...+.+....       .   ....    ....+++. ..+.+.+     .+.+-++|||+++.  ......++..+...
T Consensus        90 ~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~Vdqi-R~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEep  168 (365)
T PRK07471         90 PVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEV-RELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP  168 (365)
T ss_pred             hHHHHHHccCCCCeEEEecccccccccccccccHHHH-HHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcC
Confidence            0001110000       0   0000    00112221 1222222     24667999999964  45566777666654


Q ss_pred             CCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          318 ASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       318 ~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      .++..+|++|.+. .++..+ .....+.+.+++.++..+++....  .    ....+....++..++|+|+....+
T Consensus       169 p~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~--~----~~~~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        169 PARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAG--P----DLPDDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             CCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhc--c----cCCHHHHHHHHHHcCCCHHHHHHH
Confidence            5566677766655 333332 234689999999999999998764  1    111223367899999999755444

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.83  E-value=2.4e-07  Score=100.46  Aligned_cols=196  Identities=14%  Similarity=0.075  Sum_probs=115.3

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEee-hhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFARN-VREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~~-~~~~~~~~~~~~l  260 (538)
                      .....+||.+..++.|..++..+. -...+.++|+.|+||||+|+.+++.+.....   ..|..+. +........ ..+
T Consensus        13 ~tFddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~-~Dv   90 (944)
T PRK14949         13 ATFEQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRF-VDL   90 (944)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCC-ceE
Confidence            345789999999999998887532 2455689999999999999999987643210   0111110 000000000 000


Q ss_pred             HHHHHHHHhcCCCCC-CchhhcHHHHHH-HhcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hhhhh
Q 009306          261 RQQLLSTLLNDGNVK-NFLNTDLNFQSR-RLTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QVLAN  335 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~-~~~~~~~~~l~~-~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~  335 (538)
                           ..+....... ..+.++...+.. -..++.-++|||+++.  ......|+..+.....+.++|++|.+. .+...
T Consensus        91 -----iEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~T  165 (944)
T PRK14949         91 -----IEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (944)
T ss_pred             -----EEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHH
Confidence                 0000000000 111111111111 1235667999999974  456777777776656677776666543 33322


Q ss_pred             c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          336 C-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       336 ~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      + .....|++.+|+.++..+.+...+-.  .......+.+..|++.++|.|.-+.
T Consensus       166 IlSRCq~f~fkpLs~eEI~~~L~~il~~--EgI~~edeAL~lIA~~S~Gd~R~AL  218 (944)
T PRK14949        166 VLSRCLQFNLKSLTQDEIGTQLNHILTQ--EQLPFEAEALTLLAKAANGSMRDAL  218 (944)
T ss_pred             HHHhheEEeCCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            2 23468999999999999999886622  1233456778899999999985443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.83  E-value=4.7e-07  Score=95.12  Aligned_cols=194  Identities=11%  Similarity=0.081  Sum_probs=113.4

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---e-----EEEEe-ehhhhhhc
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---G-----SYFAR-NVREAEET  254 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~-----~~~~~-~~~~~~~~  254 (538)
                      |....++||.+..++.|...+..+. -...+.++|+.|+||||+|+.+++.+-..-.   .     -|-.+ .+......
T Consensus        12 PqtFddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG   90 (700)
T PRK12323         12 PRDFTTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAG   90 (700)
T ss_pred             CCcHHHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcC
Confidence            3445789999999999999987542 2456789999999999999999987643100   0     00000 00000000


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEecc
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTR  328 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR  328 (538)
                      ... +++     .+...  ....+++..+.+...    ..++.-++|||+++..  .....|+..+.....++.+|++|.
T Consensus        91 ~hp-Dvi-----EIdAa--s~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTt  162 (700)
T PRK12323         91 RFV-DYI-----EMDAA--SNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATT  162 (700)
T ss_pred             CCC-cce-----Eeccc--ccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeC
Confidence            000 000     00000  001122222222111    1345569999999754  567778877766566777666555


Q ss_pred             ch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          329 DR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       329 ~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      +. .+...+ .....+.+..++.++..+.+.+.+..  .......+....|++.++|.|.-.
T Consensus       163 ep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~--Egi~~d~eAL~~IA~~A~Gs~RdA  222 (700)
T PRK12323        163 DPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGE--EGIAHEVNALRLLAQAAQGSMRDA  222 (700)
T ss_pred             ChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHH
Confidence            43 333222 12357899999999999998876622  122334566788999999998543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.82  E-value=6.5e-08  Score=91.63  Aligned_cols=174  Identities=17%  Similarity=0.195  Sum_probs=100.6

Q ss_pred             CCCCce-eccch-hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          186 ENEDLV-GVRLP-MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       186 ~~~~~v-GR~~~-l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      ..++|+ |...+ +..+.++.. +....+.+.|+|++|+|||+||+.+++.....-....++.....          ...
T Consensus        16 ~~d~f~~~~~~~~~~~l~~~~~-~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~----------~~~   84 (227)
T PRK08903         16 TFDNFVAGENAELVARLRELAA-GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASP----------LLA   84 (227)
T ss_pred             hhcccccCCcHHHHHHHHHHHh-ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHh----------HHH
Confidence            345555 44333 334444433 22345679999999999999999999876443334455542110          000


Q ss_pred             HHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCC-CCCC-EEEEeccchhh-------
Q 009306          264 LLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLF-ASGS-RIIITTRDRQV-------  332 (538)
Q Consensus       264 l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~-~~~~-~iiiTtR~~~~-------  332 (538)
                      +                      .. ....-+|||||++..  ...+.+...+... ..+. .+|+|++....       
T Consensus        85 ~----------------------~~-~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~  141 (227)
T PRK08903         85 F----------------------DF-DPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLRED  141 (227)
T ss_pred             H----------------------hh-cccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHH
Confidence            0                      00 123347899999643  2223332222111 1233 36666654321       


Q ss_pred             -hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          333 -LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       333 -~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                       ...+.....+++++++.++-..++...+-  .......++....+++.+.|++..+..+...+
T Consensus       142 L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~--~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        142 LRTRLGWGLVYELKPLSDADKIAALKAAAA--ERGLQLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HHHHHhcCeEEEecCCCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence             11222246889999999988887776541  12234557788889999999998887777665

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.81  E-value=2.2e-07  Score=97.75  Aligned_cols=192  Identities=14%  Similarity=0.116  Sum_probs=114.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhh--cCCh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEE--TCRL  257 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~--~~~~  257 (538)
                      |.....+||.+...+.|..++..+. -...+.++|++|+||||+|+.+++.+-....   ..|-.+ .+.....  ..++
T Consensus        11 PktFddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDv   89 (702)
T PRK14960         11 PRNFNELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDL   89 (702)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCce
Confidence            3445789999999999999987542 2467899999999999999999987542110   000000 0000000  0000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHH----HhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSR----RLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~----~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ..+        ...  ....+++..+.+..    -..++.-++|||+++..  .....++..+.....+..+|++|.+..
T Consensus        90 iEI--------DAA--s~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~  159 (702)
T PRK14960         90 IEI--------DAA--SRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQ  159 (702)
T ss_pred             EEe--------ccc--ccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChH
Confidence            000        000  00111111111111    11245568999999754  456667766665556777887776542


Q ss_pred             h-h-hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          332 V-L-ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       332 ~-~-~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      . . +.......+++.+++.++..+.+...+..  .......+....|++.++|.+..+
T Consensus       160 kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~k--EgI~id~eAL~~IA~~S~GdLRdA  216 (702)
T PRK14960        160 KLPITVISRCLQFTLRPLAVDEITKHLGAILEK--EQIAADQDAIWQIAESAQGSLRDA  216 (702)
T ss_pred             hhhHHHHHhhheeeccCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHH
Confidence            2 1 11223468899999999999999887622  223455777889999999988444

>PRK08727 hypothetical protein; Validated

Probab=98.79  E-value=1.7e-07  Score=88.88  Aligned_cols=169  Identities=14%  Similarity=0.083  Sum_probs=99.9

Q ss_pred             CCCceeccc-hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHH
Q 009306          187 NEDLVGVRL-PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLL  265 (538)
Q Consensus       187 ~~~~vGR~~-~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~  265 (538)
                      .++|++... .+..+..... + .....+.|+|++|+|||+|+.++++....+...+.|+. ..+         ....+.
T Consensus        18 f~~f~~~~~n~~~~~~~~~~-~-~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~-~~~---------~~~~~~   85 (233)
T PRK08727         18 FDSYIAAPDGLLAQLQALAA-G-QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP-LQA---------AAGRLR   85 (233)
T ss_pred             hhhccCCcHHHHHHHHHHHh-c-cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe-HHH---------hhhhHH
Confidence            355665544 3333333332 1 23356999999999999999999988766554556654 111         111110


Q ss_pred             HHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccch---------h
Q 009306          266 STLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRDR---------Q  331 (538)
Q Consensus       266 ~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~~---------~  331 (538)
                      .                  ..+.+ .+.-+|||||++..    .....+...+.. ...+..+|+|++..         .
T Consensus        86 ~------------------~~~~l-~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~d  146 (233)
T PRK08727         86 D------------------ALEAL-EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPD  146 (233)
T ss_pred             H------------------HHHHH-hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHH
Confidence            0                  01111 23358999999632    222233322211 13466799998753         2


Q ss_pred             hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          332 VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       332 ~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      +...+.....+++++++.++..+++.+++...  .-...++....+++.++|-.-.+
T Consensus       147 L~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~--~l~l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        147 LRSRLAQCIRIGLPVLDDVARAAVLRERAQRR--GLALDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHHHHhcCceEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHhCCCCHHHH
Confidence            22222335688999999999999999876332  23455777888888888766544

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

Probab=98.76  E-value=6.4e-08  Score=83.06  Aligned_cols=114  Identities=20%  Similarity=0.272  Sum_probs=75.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc-----eeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH-----FSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNF  284 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~  284 (538)
                      +.+.+.|+|++|+|||++++.++......     -..++|+.    .........+...++..+................
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~   78 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVN----CPSSRTPRDFAQEILEALGLPLKSRQTSDELRSL   78 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEE----HHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEE----eCCCCCHHHHHHHHHHHhCccccccCCHHHHHHH
Confidence            34679999999999999999999976543     24455665    3334478888999999888765554556666677


Q ss_pred             HHHHhcCCC-eEEEEecCCCh---HHHHHHhcCcCCCCCCCEEEEeccc
Q 009306          285 QSRRLTRKK-VLIVFDDVDHP---RQIKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       285 l~~~l~~k~-~LlVlDdv~~~---~~~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                      +.+.+...+ .+|||||++..   ..++.+.....  ..+..+|+..+.
T Consensus        79 ~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   79 LIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            777776555 59999999765   33444433333  566777777655

>PRK09087 hypothetical protein; Validated

Probab=98.73  E-value=5.1e-07  Score=84.88  Aligned_cols=143  Identities=12%  Similarity=0.113  Sum_probs=90.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      .+.+.|+|++|+|||+|++.++....     ..|+..          ..+...+...                     +.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~~-----~~~i~~----------~~~~~~~~~~---------------------~~   87 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKSD-----ALLIHP----------NEIGSDAANA---------------------AA   87 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhcC-----CEEecH----------HHcchHHHHh---------------------hh
Confidence            46699999999999999999887642     224431          0111111111                     11


Q ss_pred             CCCeEEEEecCCCh----HHHHHHhcCcCCCCCCCEEEEeccch---------hhhhhcCCCeeEEcCCCCHHHHHHHHH
Q 009306          291 RKKVLIVFDDVDHP----RQIKILVGRLDLFASGSRIIITTRDR---------QVLANCGVDEVYQMEELVHDDALRLFS  357 (538)
Q Consensus       291 ~k~~LlVlDdv~~~----~~~~~l~~~l~~~~~~~~iiiTtR~~---------~~~~~~~~~~~~~l~~L~~~ea~~Lf~  357 (538)
                      +  -+|+|||++..    +.+-.+...+.  ..|..+|+|++..         .+...+....++++++++.++-.+++.
T Consensus        88 ~--~~l~iDDi~~~~~~~~~lf~l~n~~~--~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~  163 (226)
T PRK09087         88 E--GPVLIEDIDAGGFDETGLFHLINSVR--QAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIF  163 (226)
T ss_pred             c--CeEEEECCCCCCCCHHHHHHHHHHHH--hCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHH
Confidence            1  27888999532    22222232222  3467789888642         233344455789999999999999999


Q ss_pred             hhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          358 RHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       358 ~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      +.+-.  ......++...-|++.+.|..-.+..+...|
T Consensus       164 ~~~~~--~~~~l~~ev~~~La~~~~r~~~~l~~~l~~L  199 (226)
T PRK09087        164 KLFAD--RQLYVDPHVVYYLVSRMERSLFAAQTIVDRL  199 (226)
T ss_pred             HHHHH--cCCCCCHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            88722  2344567888899999988877766544433

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

Probab=98.73  E-value=3.4e-07  Score=85.75  Aligned_cols=186  Identities=17%  Similarity=0.233  Sum_probs=103.2

Q ss_pred             CCc-eeccchh--HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHHH
Q 009306          188 EDL-VGVRLPM--KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       188 ~~~-vGR~~~l--~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      ++| +|-..+.  ..+.......+.....+.|+|+.|.|||.|.+++++++...++  .++|+.          ...+..
T Consensus         8 dnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~----------~~~f~~   77 (219)
T PF00308_consen    8 DNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS----------AEEFIR   77 (219)
T ss_dssp             CCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE----------HHHHHH
T ss_pred             ccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec----------HHHHHH
Confidence            344 4654432  2333333333333556899999999999999999998765443  344444          223333


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh---HH-HHHHhcCcCC-CCCCCEEEEeccch-------
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP---RQ-IKILVGRLDL-FASGSRIIITTRDR-------  330 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~-~~~l~~~l~~-~~~~~~iiiTtR~~-------  330 (538)
                      .+...+..         .....+++.++ .-=+|+|||++..   .. .+.+...+.. ...|.++|+|++..       
T Consensus        78 ~~~~~~~~---------~~~~~~~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~  147 (219)
T PF00308_consen   78 EFADALRD---------GEIEEFKDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGL  147 (219)
T ss_dssp             HHHHHHHT---------TSHHHHHHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS
T ss_pred             HHHHHHHc---------ccchhhhhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcccccc
Confidence            33333322         11223344444 3448899999643   11 2222222211 13577899998543       


Q ss_pred             --hhhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          331 --QVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       331 --~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                        .+.+.+...-++++++++.++-.+++.+++.  .......++.+.-+++.+.+..-.|..+-..|
T Consensus       148 ~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~--~~~~~l~~~v~~~l~~~~~~~~r~L~~~l~~l  212 (219)
T PF00308_consen  148 LPDLRSRLSWGLVVELQPPDDEDRRRILQKKAK--ERGIELPEEVIEYLARRFRRDVRELEGALNRL  212 (219)
T ss_dssp             -HHHHHHHHCSEEEEE----HHHHHHHHHHHHH--HTT--S-HHHHHHHHHHTTSSHHHHHHHHHHH
T ss_pred             ChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHH--HhCCCCcHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence              2223334556899999999999999999883  23334567788888888887776665554433

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=4.4e-07  Score=92.90  Aligned_cols=192  Identities=13%  Similarity=0.085  Sum_probs=113.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |.....++|.+..+..|..++..+. -...+.++|++|+||||+|+.++..+.....   ..|..+        .....+
T Consensus        14 P~~f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C--------~sC~~i   84 (484)
T PRK14956         14 PQFFRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNEC--------TSCLEI   84 (484)
T ss_pred             CCCHHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCC--------cHHHHH
Confidence            3445789999999999999887542 2346899999999999999999987643211   111111        000011


Q ss_pred             HHHHHHHHhcC---CCC-CCchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hhh
Q 009306          261 RQQLLSTLLND---GNV-KNFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQV  332 (538)
Q Consensus       261 ~~~l~~~l~~~---~~~-~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~~  332 (538)
                      .......+...   ... ...+.++...+... ..++.-++|||+++..  ....+++..+.....+..+|++|.. ..+
T Consensus        85 ~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI  164 (484)
T PRK14956         85 TKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKI  164 (484)
T ss_pred             HccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhc
Confidence            00000000000   000 01111122222111 2345669999999744  5677777776654455655555543 333


Q ss_pred             hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          333 LANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       333 ~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      ...+ .....|.+.+++.++..+.+...+..  .......+....|++.++|.+.
T Consensus       165 ~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~--Egi~~e~eAL~~Ia~~S~Gd~R  217 (484)
T PRK14956        165 PETILSRCQDFIFKKVPLSVLQDYSEKLCKI--ENVQYDQEGLFWIAKKGDGSVR  217 (484)
T ss_pred             cHHHHhhhheeeecCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCChHH
Confidence            3222 22357999999999999998887632  2234457788999999999984

>PRK05642 DNA replication initiation factor; Validated

Probab=98.71  E-value=4.3e-07  Score=86.09  Aligned_cols=154  Identities=19%  Similarity=0.194  Sum_probs=93.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      ...+.|+|++|+|||+|++++++.+......++|+.. .+         +...                  ...+.+.+.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~-~~---------~~~~------------------~~~~~~~~~   96 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL-AE---------LLDR------------------GPELLDNLE   96 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH-HH---------HHhh------------------hHHHHHhhh
Confidence            3568999999999999999999877655445666651 11         1110                  011222232


Q ss_pred             CCCeEEEEecCCCh---HHH-HHHhcCcCC-CCCCCEEEEeccchh-h--------hhhcCCCeeEEcCCCCHHHHHHHH
Q 009306          291 RKKVLIVFDDVDHP---RQI-KILVGRLDL-FASGSRIIITTRDRQ-V--------LANCGVDEVYQMEELVHDDALRLF  356 (538)
Q Consensus       291 ~k~~LlVlDdv~~~---~~~-~~l~~~l~~-~~~~~~iiiTtR~~~-~--------~~~~~~~~~~~l~~L~~~ea~~Lf  356 (538)
                      +-. +|||||++..   ..+ +.+...+.. ...|..+|+|++... -        .+.+....++++++++.++-.+++
T Consensus        97 ~~d-~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il  175 (234)
T PRK05642         97 QYE-LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRAL  175 (234)
T ss_pred             hCC-EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHH
Confidence            222 7889999522   222 223322221 134677888887531 1        122223467899999999999999


Q ss_pred             HhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          357 SRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       357 ~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ..++...  .-...++...-+++.+.|..-.+..+-..|
T Consensus       176 ~~ka~~~--~~~l~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        176 QLRASRR--GLHLTDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             HHHHHHc--CCCCCHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            8666322  233457788888888888876665555544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=7.8e-07  Score=92.45  Aligned_cols=198  Identities=17%  Similarity=0.109  Sum_probs=110.3

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce---eeEEEEee-hhhhhh--cCCh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF---SGSYFARN-VREAEE--TCRL  257 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f---~~~~~~~~-~~~~~~--~~~~  257 (538)
                      |..-..++|.+...+.|...+..+. -...+.++|++|+||||+|+.++..+...-   ...|..+. +.....  ...+
T Consensus        10 P~~~~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv   88 (472)
T PRK14962         10 PKTFSEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDV   88 (472)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCcc
Confidence            3445789999988888888776432 235689999999999999999998753210   00000000 000000  0000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-  329 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-  329 (538)
                      ..        +...  .....+... .+.+.     ..+++-++|+|+++..  .....++..+...+....+|++|.+ 
T Consensus        89 ~e--------l~aa--~~~gid~iR-~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~  157 (472)
T PRK14962         89 IE--------LDAA--SNRGIDEIR-KIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNL  157 (472)
T ss_pred             EE--------EeCc--ccCCHHHHH-HHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCCh
Confidence            00        0000  000011111 11111     1245569999999754  3456666665543444555544443 


Q ss_pred             hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHHHHh
Q 009306          330 RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLGRYL  395 (538)
Q Consensus       330 ~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~~~L  395 (538)
                      ..+...+ .....+++.+++.++....+...+..  .......+....|++.++|. ..++..+-.+.
T Consensus       158 ~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~--egi~i~~eal~~Ia~~s~GdlR~aln~Le~l~  223 (472)
T PRK14962        158 EKVPPTIISRCQVIEFRNISDELIIKRLQEVAEA--EGIEIDREALSFIAKRASGGLRDALTMLEQVW  223 (472)
T ss_pred             HhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            2332222 23468899999999999998887632  22244567788899888655 56766665543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.71  E-value=8.1e-07  Score=91.97  Aligned_cols=180  Identities=16%  Similarity=0.162  Sum_probs=112.2

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce---------------------eeE
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF---------------------SGS  242 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f---------------------~~~  242 (538)
                      |....++||.+..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+-..+                     ..+
T Consensus         9 P~~f~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv   87 (491)
T PRK14964          9 PSSFKDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDV   87 (491)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCE
Confidence            3445789999999999988886542 245789999999999999999987542211                     111


Q ss_pred             EEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCC
Q 009306          243 YFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFAS  319 (538)
Q Consensus       243 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~  319 (538)
                      +.+.    .....+... .+.+...                 .... ..++.-++|+|+++..  .....++..+....+
T Consensus        88 ~eid----aas~~~vdd-IR~Iie~-----------------~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~  145 (491)
T PRK14964         88 IEID----AASNTSVDD-IKVILEN-----------------SCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAP  145 (491)
T ss_pred             EEEe----cccCCCHHH-HHHHHHH-----------------HHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCC
Confidence            1111    000111111 1111111                 1000 1234558999999644  456777777766566


Q ss_pred             CCEEEEeccc-hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          320 GSRIIITTRD-RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       320 ~~~iiiTtR~-~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      +..+|++|.+ ..+...+ .....+++.+++.++..+.+...+..  .......+.+..|++.++|.+..+
T Consensus       146 ~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~--Egi~i~~eAL~lIa~~s~GslR~a  214 (491)
T PRK14964        146 HVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKK--ENIEHDEESLKLIAENSSGSMRNA  214 (491)
T ss_pred             CeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHH
Confidence            7777766643 3333222 23467899999999999999887732  233455777889999999988533

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.70  E-value=9.6e-07  Score=92.15  Aligned_cols=192  Identities=15%  Similarity=0.106  Sum_probs=112.2

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee-------eEEEEee-hhhhhh--
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS-------GSYFARN-VREAEE--  253 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~-------~~~~~~~-~~~~~~--  253 (538)
                      |....+++|.+..++.|...+..+. -.+.+.++|++|+||||+|+.+++.+-....       ..|..+. +.....  
T Consensus        17 P~~f~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~   95 (507)
T PRK06645         17 PSNFAELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHN   95 (507)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCC
Confidence            3445778999999999988776432 3457899999999999999999987643210       0111110 000000  


Q ss_pred             cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec
Q 009306          254 TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       254 ~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                      ...+..        +...  .....++....+...    ..+++-++|||+++..  ..+..++..+....+.+.+|++|
T Consensus        96 h~Dv~e--------idaa--s~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aT  165 (507)
T PRK06645         96 HPDIIE--------IDAA--SKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFAT  165 (507)
T ss_pred             CCcEEE--------eecc--CCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEe
Confidence            000000        0000  001112221111111    2345668999999754  45677776665545566655444


Q ss_pred             -cchhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          328 -RDRQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       328 -R~~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                       +...+...+ .....+++.+++.++..+.+...+...  ......+....|++.++|.+.-+
T Consensus       166 te~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~e--gi~ie~eAL~~Ia~~s~GslR~a  226 (507)
T PRK06645        166 TEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQE--NLKTDIEALRIIAYKSEGSARDA  226 (507)
T ss_pred             CChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence             444443333 234678999999999999999887322  23345677788999999987443

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

Probab=98.70  E-value=3.5e-08  Score=90.14  Aligned_cols=50  Identities=24%  Similarity=0.413  Sum_probs=35.6

Q ss_pred             CceeccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          189 DLVGVRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .|+||+.++++|...|.. .....+.+.|+|++|+|||+|.++++.++...
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            489999999999999942 33457889999999999999999999987776

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.70  E-value=5.1e-07  Score=85.68  Aligned_cols=155  Identities=13%  Similarity=0.157  Sum_probs=93.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.+.|+|++|+|||+|+..+++........+.|+.. ...   .   .....                     +.+.+
T Consensus        44 ~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~-~~~---~---~~~~~---------------------~~~~~   95 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPL-DKR---A---WFVPE---------------------VLEGM   95 (235)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEH-HHH---h---hhhHH---------------------HHHHh
Confidence            34579999999999999999999876654444555541 110   0   00000                     11111


Q ss_pred             cCCCeEEEEecCCCh---HHH-HHHhcCcCCC-CCC-CEEEEeccch---------hhhhhcCCCeeEEcCCCCHHHHHH
Q 009306          290 TRKKVLIVFDDVDHP---RQI-KILVGRLDLF-ASG-SRIIITTRDR---------QVLANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~---~~~-~~l~~~l~~~-~~~-~~iiiTtR~~---------~~~~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      .. --+|+|||++..   ..+ +.+...+... ..| .++|+||+..         .+...+....++++++++.++-.+
T Consensus        96 ~~-~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~  174 (235)
T PRK08084         96 EQ-LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQ  174 (235)
T ss_pred             hh-CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHH
Confidence            11 248899999542   222 1222211110 123 4789998754         222333445689999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ++.+++..  ..-...++...-+++.+.|..-.+..+...+
T Consensus       175 ~l~~~a~~--~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        175 ALQLRARL--RGFELPEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             HHHHHHHH--cCCCCCHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            99886622  2244567888889999988876655544433

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.69  E-value=5.5e-07  Score=95.72  Aligned_cols=196  Identities=14%  Similarity=0.085  Sum_probs=111.5

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceee---EEEEe-ehhhhhhcCChHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG---SYFAR-NVREAEETCRLGD  259 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~---~~~~~-~~~~~~~~~~~~~  259 (538)
                      |.....++|.+..++.|..++..+. -...+.++|+.|+||||+|+.++..+-.....   .|-.+ .+....... ..+
T Consensus        12 P~tFddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~-~~D   89 (709)
T PRK08691         12 PKTFADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGR-YVD   89 (709)
T ss_pred             CCCHHHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccC-ccc
Confidence            3445789999999999999987532 24568999999999999999999865322100   00000 000000000 000


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHH---H-hcCCCeEEEEecCCChH--HHHHHhcCcCCCCCCCEEEEeccch-hh
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSR---R-LTRKKVLIVFDDVDHPR--QIKILVGRLDLFASGSRIIITTRDR-QV  332 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~---~-l~~k~~LlVlDdv~~~~--~~~~l~~~l~~~~~~~~iiiTtR~~-~~  332 (538)
                      ++     .+...  .....+...+.+..   . ..+++-++|||+++...  ....|+..+......+.+|++|.+. .+
T Consensus        90 vl-----EidaA--s~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL  162 (709)
T PRK08691         90 LL-----EIDAA--SNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKV  162 (709)
T ss_pred             eE-----EEecc--ccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCcccc
Confidence            00     00000  00111111111111   0 12455699999997543  3555666555445567777776544 22


Q ss_pred             hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          333 LANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       333 ~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      ...+ .....+.+.+++.++..+.+.+.+-.  .......+.+..|++.++|.+.-+..
T Consensus       163 ~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~k--Egi~id~eAL~~Ia~~A~GslRdAln  219 (709)
T PRK08691        163 PVTVLSRCLQFVLRNMTAQQVADHLAHVLDS--EKIAYEPPALQLLGRAAAGSMRDALS  219 (709)
T ss_pred             chHHHHHHhhhhcCCCCHHHHHHHHHHHHHH--cCCCcCHHHHHHHHHHhCCCHHHHHH
Confidence            2111 22246788999999999999887732  22334567788999999999854433

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.68  E-value=9e-07  Score=92.98  Aligned_cols=182  Identities=14%  Similarity=0.101  Sum_probs=110.4

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce---------------------eeE
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF---------------------SGS  242 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f---------------------~~~  242 (538)
                      |....++||-+..++.|..++..+. -...+.++|++|+||||+|+.+++.+-..-                     +..
T Consensus        12 P~~f~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~   90 (509)
T PRK14958         12 PRCFQEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDL   90 (509)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceE
Confidence            3445789999999999999997532 245678999999999999999998653210                     111


Q ss_pred             EEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCC
Q 009306          243 YFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASG  320 (538)
Q Consensus       243 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~  320 (538)
                      +.+.    ......+..+ +.++..+..                .-..++.-++|||+++..  .....++..+....++
T Consensus        91 ~eid----aas~~~v~~i-R~l~~~~~~----------------~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~  149 (509)
T PRK14958         91 FEVD----AASRTKVEDT-RELLDNIPY----------------APTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSH  149 (509)
T ss_pred             EEEc----ccccCCHHHH-HHHHHHHhh----------------ccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCC
Confidence            1111    0001111111 111111110                001234568999999753  5566777766655667


Q ss_pred             CEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          321 SRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       321 ~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      +++|++|.+. .+...+ .....+++.+++.++....+...+-..  ......+....+++.++|.+.-+.
T Consensus       150 ~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~e--gi~~~~~al~~ia~~s~GslR~al  218 (509)
T PRK14958        150 VKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEE--NVEFENAALDLLARAANGSVRDAL  218 (509)
T ss_pred             eEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCcHHHHH
Confidence            7777665443 222221 223578899999999888777665222  223446677889999999885443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.68  E-value=4.5e-06  Score=83.54  Aligned_cols=195  Identities=17%  Similarity=0.151  Sum_probs=114.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc----eeeEEEEeehhhhhhcCChHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH----FSGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~----f~~~~~~~~~~~~~~~~~~~~  259 (538)
                      |.....++|.+...+.|...+..+. -...+.|+|+.|+||||+|..++..+-..    +.......       ...--.
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~-------~~~~c~   90 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLAD-------PDPASP   90 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCC-------CCCCCH
Confidence            3456789999999999999887542 34568999999999999999999876442    11000000       000000


Q ss_pred             HHHHHHHH-------Hhc---CCC----CCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCC
Q 009306          260 LRQQLLST-------LLN---DGN----VKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFA  318 (538)
Q Consensus       260 l~~~l~~~-------l~~---~~~----~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~  318 (538)
                      ..+.+...       +..   ...    ....+++.. .+.+.+     .++.-++|||+++..  .....++..+....
T Consensus        91 ~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR-~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp  169 (351)
T PRK09112         91 VWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIR-RVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPP  169 (351)
T ss_pred             HHHHHHcCCCCCEEEeecccccccccccccCCHHHHH-HHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCC
Confidence            11111111       000   000    001122221 222222     245669999999743  45666766665544


Q ss_pred             CCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          319 SGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       319 ~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      .+..+|++|... .+++.. .....+.+.+++.++..+++......   .. ...+.+..+++.++|.|.....+
T Consensus       170 ~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~---~~-~~~~~~~~i~~~s~G~pr~Al~l  240 (351)
T PRK09112        170 ARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSS---QG-SDGEITEALLQRSKGSVRKALLL  240 (351)
T ss_pred             CCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcc---cC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            555555555433 333332 22358999999999999999874311   11 33566788999999999755433

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.67  E-value=9e-07  Score=89.79  Aligned_cols=169  Identities=14%  Similarity=0.099  Sum_probs=105.2

Q ss_pred             CCceeccchhHHHHHhhhcCCC--------CceEEEEeccCCCchhHHHHHHHHhhccce--------------------
Q 009306          188 EDLVGVRLPMKEIESLLRTGST--------NVYKLGIWGIGGIGKTTIAGAIFNKISRHF--------------------  239 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~--------~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--------------------  239 (538)
                      +.++|.+..++.|...+..+..        -.+.+.++|++|+|||++|+.++..+-...                    
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~h   84 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTH   84 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            4688999989999888875421        246688999999999999999988653321                    


Q ss_pred             eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhc
Q 009306          240 SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVG  312 (538)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~  312 (538)
                      +...++..   .                     .....+++.. .+.+.+     .+++-++|||+++..  .....++.
T Consensus        85 pD~~~i~~---~---------------------~~~i~i~~iR-~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk  139 (394)
T PRK07940         85 PDVRVVAP---E---------------------GLSIGVDEVR-ELVTIAARRPSTGRWRIVVIEDADRLTERAANALLK  139 (394)
T ss_pred             CCEEEecc---c---------------------cccCCHHHHH-HHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHH
Confidence            11111110   0                     0001111111 111111     234458889999754  44556666


Q ss_pred             CcCCCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          313 RLDLFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       313 ~l~~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      .+....++..+|++|.+. .+.+.+ .....+.+++++.++..+.+....       ....+.+..++..++|.|...
T Consensus       140 ~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~-------~~~~~~a~~la~~s~G~~~~A  210 (394)
T PRK07940        140 AVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRD-------GVDPETARRAARASQGHIGRA  210 (394)
T ss_pred             HhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhc-------CCCHHHHHHHHHHcCCCHHHH
Confidence            665545667666666554 444332 234689999999999999887543       122456788999999999643

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.67  E-value=2.9e-07  Score=93.58  Aligned_cols=174  Identities=17%  Similarity=0.212  Sum_probs=101.2

Q ss_pred             CCCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          186 ENEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ...++.|++.++++|.+.+..           +....+-+.|+|++|+|||+||+.+++.....|-..   .        
T Consensus       120 ~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v---~--------  188 (364)
T TIGR01242       120 SYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRV---V--------  188 (364)
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEec---c--------
Confidence            345789999999999886642           112245699999999999999999999876553211   1        


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH-HhcCCCeEEEEecCCChH----------------HHHHHhcCcCCC
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR-RLTRKKVLIVFDDVDHPR----------------QIKILVGRLDLF  317 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~-~l~~k~~LlVlDdv~~~~----------------~~~~l~~~l~~~  317 (538)
                        ...+.......          .......+.+ .-...+.+|+|||++...                .+..++..+..+
T Consensus       189 --~~~l~~~~~g~----------~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~  256 (364)
T TIGR01242       189 --GSELVRKYIGE----------GARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGF  256 (364)
T ss_pred             --hHHHHHHhhhH----------HHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCC
Confidence              00111110000          0011111111 123467899999986431                122233222221


Q ss_pred             --CCCCEEEEeccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 --ASGSRIIITTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 --~~~~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                        ..+..||.||.....+     ........+.++..+.++..++|..+..+......   .....+++.+.|..
T Consensus       257 ~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~---~~~~~la~~t~g~s  328 (364)
T TIGR01242       257 DPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAED---VDLEAIAKMTEGAS  328 (364)
T ss_pred             CCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCcc---CCHHHHHHHcCCCC
Confidence              2466788888754322     11133567899999999999999988744332221   12456777777764

Many proteins may score above the trusted cutoff because an internal

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.67  E-value=1.4e-06  Score=92.75  Aligned_cols=194  Identities=12%  Similarity=0.112  Sum_probs=111.7

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce----eeE----EEEe-ehhhhhhcC
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF----SGS----YFAR-NVREAEETC  255 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f----~~~----~~~~-~~~~~~~~~  255 (538)
                      ...+++||-+..++.|..++..+. -...+.++|+.|+||||+|+.+++.+-..-    .+.    |-.+ .+.......
T Consensus        13 ~~f~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~   91 (618)
T PRK14951         13 RSFSEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGR   91 (618)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCC
Confidence            445789999999999999887542 345679999999999999999988653210    000    0000 000000000


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEecc
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTR  328 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR  328 (538)
                      .. ++.     .+...  ....+++..+.+ +..     .++.-++|||+++..  .....++..+.....+..+|++|.
T Consensus        92 h~-D~~-----eldaa--s~~~Vd~iReli-~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Tt  162 (618)
T PRK14951         92 FV-DYT-----ELDAA--SNRGVDEVQQLL-EQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATT  162 (618)
T ss_pred             CC-cee-----ecCcc--cccCHHHHHHHH-HHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEEC
Confidence            00 000     00000  001111211111 111     234458999999754  456777777665556666666654


Q ss_pred             c-hhhhhh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          329 D-RQVLAN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       329 ~-~~~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      + ..+... ......+++++++.++..+.+.+.+..  .......+....|++.++|.+.-+..
T Consensus       163 d~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~--egi~ie~~AL~~La~~s~GslR~al~  224 (618)
T PRK14951        163 DPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAA--ENVPAEPQALRLLARAARGSMRDALS  224 (618)
T ss_pred             CchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            3 333322 223468999999999999999877622  22234567788999999998754433

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.67  E-value=1.1e-06  Score=89.36  Aligned_cols=184  Identities=14%  Similarity=0.117  Sum_probs=112.2

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc----ee-----------------eEE
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH----FS-----------------GSY  243 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~----f~-----------------~~~  243 (538)
                      ..-..++|.+..++.|...+..+. -.+.+.++|++|+||||+|+.++..+...    +.                 ...
T Consensus        11 ~~~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~   89 (355)
T TIGR02397        11 QTFEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVI   89 (355)
T ss_pred             CcHhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEE
Confidence            344678999999999999887532 34578899999999999999999875422    10                 011


Q ss_pred             EEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCC
Q 009306          244 FARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGS  321 (538)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~  321 (538)
                      ++..    ...... ...+.+...+...                -..+++-++|+|+++..  .....++..+....+.+
T Consensus        90 ~~~~----~~~~~~-~~~~~l~~~~~~~----------------p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~  148 (355)
T TIGR02397        90 EIDA----ASNNGV-DDIREILDNVKYA----------------PSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHV  148 (355)
T ss_pred             Eeec----cccCCH-HHHHHHHHHHhcC----------------cccCCceEEEEeChhhcCHHHHHHHHHHHhCCccce
Confidence            1110    000000 0011111111100                01234458999999754  44566666665445566


Q ss_pred             EEEEeccchh-hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHH
Q 009306          322 RIIITTRDRQ-VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLG  392 (538)
Q Consensus       322 ~iiiTtR~~~-~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~  392 (538)
                      .+|++|.+.. +...+ .....+++.+++.++..+++...+-..  ......+.+..+++.++|.|..+....
T Consensus       149 ~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~--g~~i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       149 VFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKE--GIKIEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             eEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCChHHHHHHH
Confidence            6666665443 22222 223578899999999999998876322  223446788899999999996655444

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.

>PF13173 AAA_14: AAA domain

Probab=98.64  E-value=2.5e-07  Score=78.98  Aligned_cols=119  Identities=15%  Similarity=0.099  Sum_probs=73.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      +++.|.|+.|+|||||+++++.... .-...+++.......     ....               ..+ ....+.+....
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi~~~~~~~-----~~~~---------------~~~-~~~~~~~~~~~   60 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL-PPENILYINFDDPRD-----RRLA---------------DPD-LLEYFLELIKP   60 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc-ccccceeeccCCHHH-----HHHh---------------hhh-hHHHHHHhhcc
Confidence            5789999999999999999998765 222344443111100     0000               000 12222333334


Q ss_pred             CCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhc------CCCeeEEcCCCCHHHH
Q 009306          292 KKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANC------GVDEVYQMEELVHDDA  352 (538)
Q Consensus       292 k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~------~~~~~~~l~~L~~~ea  352 (538)
                      ++.+|+||++.....|...+..+....++.+|++|+.....+..-      +....+++.||+..|-
T Consensus        61 ~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             CCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            678999999987776666665554445678999999887655321      2234689999998774

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.63  E-value=1.3e-06  Score=91.69  Aligned_cols=196  Identities=13%  Similarity=0.078  Sum_probs=112.1

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhh--cCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEE--TCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~--~~~~~  258 (538)
                      .....++|.+..++.|...+..+ .-...+.++|+.|+||||+|+.++..+.....   ..|-.+ .+.....  ..++.
T Consensus        13 ~~f~diiGq~~~v~~L~~~i~~~-rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dli   91 (546)
T PRK14957         13 QSFAEVAGQQHALNSLVHALETQ-KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLI   91 (546)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceE
Confidence            34478899999999999888753 23456789999999999999999986542110   000000 0000000  00000


Q ss_pred             HHHHHHHHHHhcCCCCC-CchhhcHHHHHHH-hcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc-hhhh
Q 009306          259 DLRQQLLSTLLNDGNVK-NFLNTDLNFQSRR-LTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD-RQVL  333 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~-l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~  333 (538)
                      .+        ....... .........+... ..+++-++|||+++.  ......++..+......+.+|++|.+ ..+.
T Consensus        92 ei--------daas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil  163 (546)
T PRK14957         92 EI--------DAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIP  163 (546)
T ss_pred             Ee--------ecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhh
Confidence            00        0000000 1111111111111 234566999999974  35567777776655566666655543 3333


Q ss_pred             hh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHH
Q 009306          334 AN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVL  391 (538)
Q Consensus       334 ~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~  391 (538)
                      .. ......+++.+++.++..+.+...+-..  ...........+++.++|.+. ++..+
T Consensus       164 ~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~e--gi~~e~~Al~~Ia~~s~GdlR~alnlL  221 (546)
T PRK14957        164 VTILSRCIQLHLKHISQADIKDQLKIILAKE--NINSDEQSLEYIAYHAKGSLRDALSLL  221 (546)
T ss_pred             hhHHHheeeEEeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            22 2234689999999999998888765221  234456777889999999774 44444

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.63  E-value=5.8e-07  Score=95.84  Aligned_cols=194  Identities=14%  Similarity=0.096  Sum_probs=112.9

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhh--cCCh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEE--TCRL  257 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~--~~~~  257 (538)
                      |.....+||.+..++.|...+..+. -...+.++|+.|+||||+|+.++..+-....   ..|-.+ .+.....  ..++
T Consensus        12 P~~f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~   90 (647)
T PRK07994         12 PQTFAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDL   90 (647)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCc
Confidence            3445789999999999998887542 2455789999999999999999987543210   000000 0000000  0000


Q ss_pred             HHHHHHHHHHHhcCCCCC-CchhhcHHHHHH-HhcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hh
Q 009306          258 GDLRQQLLSTLLNDGNVK-NFLNTDLNFQSR-RLTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QV  332 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~-~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~  332 (538)
                      ..        +....... ..+.++...+.. -..++.-++|||+++.  ......|+..+.....+.++|++|.+. .+
T Consensus        91 ie--------idaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kL  162 (647)
T PRK07994         91 IE--------IDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  162 (647)
T ss_pred             ee--------ecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCcccc
Confidence            00        00000000 111111111111 1234566999999974  456777777776556677766665544 33


Q ss_pred             hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          333 LANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       333 ~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...+ .....+.+.+++.++..+.+...+-..  ......+....|++.++|.+.-.
T Consensus       163 l~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e--~i~~e~~aL~~Ia~~s~Gs~R~A  217 (647)
T PRK07994        163 PVTILSRCLQFHLKALDVEQIRQQLEHILQAE--QIPFEPRALQLLARAADGSMRDA  217 (647)
T ss_pred             chHHHhhheEeeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            3222 234689999999999999998765221  22344667788999999988533

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.62  E-value=3.5e-06  Score=83.83  Aligned_cols=176  Identities=15%  Similarity=0.226  Sum_probs=110.3

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-----eeeEEEEeehhhhhhcCChHHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----FSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      ..++|.+..++.+...+..+ .-.+...++|+.|+||||+|+.++..+-..     ++....+...  ......... .+
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~-~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~--~~~~i~v~~-ir   79 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKN-RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPI--NKKSIGVDD-IR   79 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcC-CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccc--cCCCCCHHH-HH
Confidence            46789888888999888643 235678899999999999999999865321     2222122100  001111111 12


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCC--ChHHHHHHhcCcCCCCCCCEEEEeccchhh-hhhc-CC
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVD--HPRQIKILVGRLDLFASGSRIIITTRDRQV-LANC-GV  338 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~-~~~~-~~  338 (538)
                      .+...+...                -..+++-++|+|+++  +......++..+....+++.+|++|.+... ++.+ ..
T Consensus        80 ~~~~~~~~~----------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SR  143 (313)
T PRK05564         80 NIIEEVNKK----------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSR  143 (313)
T ss_pred             HHHHHHhcC----------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhh
Confidence            222211110                012345577888875  456678888888776778888888866533 2222 23


Q ss_pred             CeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          339 DEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       339 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      ...+++.+++.++....+.+...      ....+.+..++..++|.|.-+.
T Consensus       144 c~~~~~~~~~~~~~~~~l~~~~~------~~~~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        144 CQIYKLNRLSKEEIEKFISYKYN------DIKEEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             ceeeeCCCcCHHHHHHHHHHHhc------CCCHHHHHHHHHHcCCCHHHHH
Confidence            46899999999999998876541      1234557788999999986443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.59  E-value=1.2e-06  Score=90.80  Aligned_cols=167  Identities=13%  Similarity=0.188  Sum_probs=101.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+.|+|..|+|||+|++++++.+....  ..++++.          ...+...+...+....       .....+++.
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~----------~~~f~~~~~~~l~~~~-------~~~~~~~~~  203 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS----------GDEFARKAVDILQKTH-------KEIEQFKNE  203 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE----------HHHHHHHHHHHHHHhh-------hHHHHHHHH
Confidence            45689999999999999999999765432  2334443          2234444444333210       112223333


Q ss_pred             hcCCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccch-hh--------hhhcCCCeeEEcCCCCHHHHHH
Q 009306          289 LTRKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRDR-QV--------LANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~~-~~--------~~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      +. ..-+|||||+...    ...+.+...+.. ...+..||+|+... ..        ...+...-++.+++++.++..+
T Consensus       204 ~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~  282 (450)
T PRK14087        204 IC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATA  282 (450)
T ss_pred             hc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHH
Confidence            33 3458899999532    223333322221 13455788887533 12        2223344578899999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ++.+++-.........++.+.-|++.++|.|-.+.-+...+
T Consensus       283 iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l  323 (450)
T PRK14087        283 IIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRL  323 (450)
T ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            99998732221124668889999999999998877665443

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

Probab=98.59  E-value=1e-06  Score=95.99  Aligned_cols=173  Identities=24%  Similarity=0.344  Sum_probs=102.6

Q ss_pred             CCCCCceeccchhH---HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMK---EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~---~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      ...+.|+|++..+.   .|...+..  +....+.|+|++|+||||||+.+++.....|.   .+...     ...+..+ 
T Consensus        25 ~tldd~vGQe~ii~~~~~L~~~i~~--~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~---~lna~-----~~~i~di-   93 (725)
T PRK13341         25 RTLEEFVGQDHILGEGRLLRRAIKA--DRVGSLILYGPPGVGKTTLARIIANHTRAHFS---SLNAV-----LAGVKDL-   93 (725)
T ss_pred             CcHHHhcCcHHHhhhhHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHhcCcce---eehhh-----hhhhHHH-
Confidence            34467899998874   46666654  34556899999999999999999987654441   12110     0111111 


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHh--cCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEe--ccchh--hh
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRL--TRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIIT--TRDRQ--VL  333 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiT--tR~~~--~~  333 (538)
                      +..                 .....+.+  .+++.+|+|||++.  ..+.+.+...+.   .+..++|+  |.+..  +.
T Consensus        94 r~~-----------------i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~aTTenp~~~l~  153 (725)
T PRK13341         94 RAE-----------------VDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIGATTENPYFEVN  153 (725)
T ss_pred             HHH-----------------HHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEEecCCChHhhhh
Confidence            111                 11111111  24567999999964  445556665442   34444443  33321  11


Q ss_pred             hhc-CCCeeEEcCCCCHHHHHHHHHhhhcC-----CCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          334 ANC-GVDEVYQMEELVHDDALRLFSRHAFG-----GDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       334 ~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~-----~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ..+ .....+.+++|+.++...++.+.+-.     +.......++....+++.+.|+.--+
T Consensus       154 ~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~l  214 (725)
T PRK13341        154 KALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSL  214 (725)
T ss_pred             hHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHH
Confidence            111 12357899999999999999876621     12223456777889999999986433

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.58  E-value=3e-06  Score=77.63  Aligned_cols=88  Identities=17%  Similarity=0.234  Sum_probs=62.0

Q ss_pred             CCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCC
Q 009306          291 RKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHP  366 (538)
Q Consensus       291 ~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  366 (538)
                      +.+-++|+||++..  ...+.++..+....+.+.+|++|++. .+...+ .....+++.+++.++..+.+.+..      
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~g------  168 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQG------  168 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHcC------
Confidence            45568999999754  44666766666555667777777654 222222 234689999999999999998761      


Q ss_pred             CCchHHHHHHHHHHhcCCcH
Q 009306          367 HESHTELACKTIKYARGVPL  386 (538)
Q Consensus       367 ~~~~~~~~~~i~~~~~G~PL  386 (538)
                        ...+.+..+++.++|.|.
T Consensus       169 --i~~~~~~~i~~~~~g~~r  186 (188)
T TIGR00678       169 --ISEEAAELLLALAGGSPG  186 (188)
T ss_pred             --CCHHHHHHHHHHcCCCcc
Confidence              235678899999999985

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.

>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=98.57  E-value=5.2e-07  Score=78.60  Aligned_cols=54  Identities=28%  Similarity=0.323  Sum_probs=40.3

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +|++..+..+...+...  ..+.+.|+|++|+|||+|++.+++.+......++++.
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            47788888888887642  3457999999999999999999998753333344443

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.57  E-value=3.1e-06  Score=93.34  Aligned_cols=193  Identities=10%  Similarity=0.057  Sum_probs=111.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhhc-CChH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEET-CRLG  258 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~~-~~~~  258 (538)
                      |.....+||.+..++.|...+..+. -...+.++|+.|+||||+|+.+++.+.....   ..|-.+ .+...... ....
T Consensus        11 P~~f~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~   89 (824)
T PRK07764         11 PATFAEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSL   89 (824)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCC
Confidence            3444789999999999999987532 2456889999999999999999987642110   001000 00000000 0000


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHH-----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-h
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-R  330 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~  330 (538)
                      ++.     .+...  ....+++... +++.     ..++.-++|||+++..  .....|+..+.....++.+|++|.+ .
T Consensus        90 dv~-----eidaa--s~~~Vd~iR~-l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~  161 (824)
T PRK07764         90 DVT-----EIDAA--SHGGVDDARE-LRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPD  161 (824)
T ss_pred             cEE-----Eeccc--ccCCHHHHHH-HHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChh
Confidence            000     00000  0011122111 1111     2345558899999754  5566777777665667776666543 3


Q ss_pred             hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          331 QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       331 ~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      .++..+ .....|++..++.++..+++.+.+-..  ......+....+++.++|.+..
T Consensus       162 kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~E--Gv~id~eal~lLa~~sgGdlR~  217 (824)
T PRK07764        162 KVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQE--GVPVEPGVLPLVIRAGGGSVRD  217 (824)
T ss_pred             hhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHH
Confidence            444433 234689999999999999888765221  2234566778899999998843

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.56  E-value=3.9e-06  Score=89.09  Aligned_cols=202  Identities=14%  Similarity=0.065  Sum_probs=113.5

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhhc-CChH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEET-CRLG  258 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~~-~~~~  258 (538)
                      |....+++|.+..++.|..++..+ .-...+.++|+.|+||||+|+.++..+.....   ..|-.+ .+...... ....
T Consensus         9 P~~f~eivGq~~i~~~L~~~i~~~-r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~   87 (584)
T PRK14952          9 PATFAEVVGQEHVTEPLSSALDAG-RINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSI   87 (584)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCc
Confidence            344578999999999999998753 23456789999999999999999987542110   000000 00000000 0000


Q ss_pred             HHHHHHHHHHhcCCCCC-CchhhcHHHHHHH-hcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc-hhhh
Q 009306          259 DLRQQLLSTLLNDGNVK-NFLNTDLNFQSRR-LTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD-RQVL  333 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~-l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~  333 (538)
                      ++.     .+....... ..+.++.+.+... ..+++-++|||+++.  ......|+..+.....+..+|++|.+ ..+.
T Consensus        88 dvi-----eidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll  162 (584)
T PRK14952         88 DVV-----ELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVL  162 (584)
T ss_pred             eEE-----EeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhH
Confidence            000     000000000 1111111111111 123455899999974  45567777777655566766655543 4444


Q ss_pred             hhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHHHH
Q 009306          334 ANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVLGR  393 (538)
Q Consensus       334 ~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~~~  393 (538)
                      ..+ .....+++.+++.++..+.+...+...  ......+....|++.++|.+. ++..+-.
T Consensus       163 ~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~e--gi~i~~~al~~Ia~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        163 PTIRSRTHHYPFRLLPPRTMRALIARICEQE--GVVVDDAVYPLVIRAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HHHHHhceEEEeeCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            332 234689999999999999888766322  223446677888999999874 4444433

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.55  E-value=3.8e-06  Score=85.63  Aligned_cols=182  Identities=16%  Similarity=0.181  Sum_probs=108.3

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc--------eeeEEEEeehhhhhhcC
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--------FSGSYFARNVREAEETC  255 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--------f~~~~~~~~~~~~~~~~  255 (538)
                      |..-..++|.+..++.+...+..+ .-.+.+.++|++|+|||++|+.+++.+...        |...++..+   .....
T Consensus        13 P~~~~~iig~~~~~~~l~~~i~~~-~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~---~~~~~   88 (367)
T PRK14970         13 PQTFDDVVGQSHITNTLLNAIENN-HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELD---AASNN   88 (367)
T ss_pred             CCcHHhcCCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEec---cccCC
Confidence            344577899999999999988753 234578899999999999999998876431        111111110   00001


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEecc-chhh
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTR-DRQV  332 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR-~~~~  332 (538)
                      .. .-...+...+...                -..+++-++++|+++..  ..+..+...+......+.+|+++. ...+
T Consensus        89 ~~-~~i~~l~~~~~~~----------------p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl  151 (367)
T PRK14970         89 SV-DDIRNLIDQVRIP----------------PQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKI  151 (367)
T ss_pred             CH-HHHHHHHHHHhhc----------------cccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccC
Confidence            11 1111222111100                01234558999999643  345666554443344555555553 2222


Q ss_pred             hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          333 LANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       333 ~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...+ .....+++++++.++....+...+...  ......+.+..+++.++|.+-.+
T Consensus       152 ~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~--g~~i~~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        152 IPTILSRCQIFDFKRITIKDIKEHLAGIAVKE--GIKFEDDALHIIAQKADGALRDA  206 (367)
T ss_pred             CHHHHhcceeEecCCccHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHhCCCCHHHH
Confidence            2221 223578999999999999888876322  22345678889999999977543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.55  E-value=2.5e-06  Score=87.55  Aligned_cols=200  Identities=13%  Similarity=0.116  Sum_probs=112.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc--eeeEEEEeehhhhhhcCChHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--FSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      |.....++|.+..++.|..++..+. -...+.++|++|+||||+|+.+++.+...  +...-|.....   .+.+.-...
T Consensus        12 P~~~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~---~~c~~c~~c   87 (397)
T PRK14955         12 PKKFADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVT---EPCGECESC   87 (397)
T ss_pred             CCcHhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCC---CCCCCCHHH
Confidence            3445789999999999988887542 24458899999999999999999876431  00000000000   000000000


Q ss_pred             HHHHHHHhc-----CCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-c
Q 009306          262 QQLLSTLLN-----DGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-R  328 (538)
Q Consensus       262 ~~l~~~l~~-----~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R  328 (538)
                      +.+......     ........++... +.+.+     .+.+-++|+|+++..  ..+..++..+....+.+.+|++| +
T Consensus        88 ~~~~~~~~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~  166 (397)
T PRK14955         88 RDFDAGTSLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTE  166 (397)
T ss_pred             HHHhcCCCCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence            000000000     0000011122221 22222     234558899999754  45666766665545566666555 3


Q ss_pred             chhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          329 DRQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       329 ~~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      ...+...+ .....+++.+++.++..+.+...+-  ........+.+..+++.++|.+--+..
T Consensus       167 ~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~--~~g~~i~~~al~~l~~~s~g~lr~a~~  227 (397)
T PRK14955        167 LHKIPATIASRCQRFNFKRIPLEEIQQQLQGICE--AEGISVDADALQLIGRKAQGSMRDAQS  227 (397)
T ss_pred             hHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            33333222 1224788999999999998887762  222345678889999999998854433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.54  E-value=2.1e-06  Score=90.34  Aligned_cols=198  Identities=16%  Similarity=0.133  Sum_probs=110.9

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      |.....++|++..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+...-    |..    .. ..+--...+.
T Consensus        12 P~~F~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~----~~~----~~-~Cg~C~sCr~   81 (605)
T PRK05896         12 PHNFKQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKAINCLN----PKD----GD-CCNSCSVCES   81 (605)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCCC----CCC----CC-CCcccHHHHH
Confidence            4455789999999999999886532 346789999999999999999998764211    100    00 0000000000


Q ss_pred             HHHH-------HhcCCCCC-CchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hh
Q 009306          264 LLST-------LLNDGNVK-NFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQ  331 (538)
Q Consensus       264 l~~~-------l~~~~~~~-~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~  331 (538)
                      +...       +....... ..++.....+... ...++-++|+|+++..  .....|+..+.....+..+|++|.. ..
T Consensus        82 i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~K  161 (605)
T PRK05896         82 INTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQK  161 (605)
T ss_pred             HHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHh
Confidence            0000       00000000 0111111111110 1123347999999753  4556666655544455666555533 33


Q ss_pred             hhhh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHHHH
Q 009306          332 VLAN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVLGR  393 (538)
Q Consensus       332 ~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~~~  393 (538)
                      +... ......+++.+++.++....+...+-.  .......+.+..+++.++|.+. |+..+-.
T Consensus       162 Ll~TI~SRcq~ieF~~Ls~~eL~~~L~~il~k--egi~Is~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        162 IPLTIISRCQRYNFKKLNNSELQELLKSIAKK--EKIKIEDNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             hhHHHHhhhhhcccCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            3322 223467899999999999988886622  2223446778899999999774 4444443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.53  E-value=6.3e-06  Score=87.97  Aligned_cols=195  Identities=16%  Similarity=0.152  Sum_probs=114.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---------eEEEEeehhhhhh-
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---------GSYFARNVREAEE-  253 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---------~~~~~~~~~~~~~-  253 (538)
                      |.....++|.+..++.|...+..+. -...+.++|+.|+||||+|+.+++.+-....         .+.+-..+..... 
T Consensus        20 P~~f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g   98 (598)
T PRK09111         20 PQTFDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEG   98 (598)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcC
Confidence            3445789999999999999887542 3456899999999999999999987643221         0000000000000 


Q ss_pred             -cCChHHHHHHHHHHHhcCCCCCCchhh---cHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEe
Q 009306          254 -TCRLGDLRQQLLSTLLNDGNVKNFLNT---DLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIIT  326 (538)
Q Consensus       254 -~~~~~~l~~~l~~~l~~~~~~~~~~~~---~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiT  326 (538)
                       ..++..+        ....  ...+++   +...+... ...++-++|||+++..  .....|+..+....+++.+|++
T Consensus        99 ~h~Dv~e~--------~a~s--~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~  168 (598)
T PRK09111         99 RHVDVLEM--------DAAS--HTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFA  168 (598)
T ss_pred             CCCceEEe--------cccc--cCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEE
Confidence             0000000        0000  011222   11111110 1234458999999654  4566777666655667777665


Q ss_pred             c-cchhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          327 T-RDRQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       327 t-R~~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      | ....+...+ .....+++.+++.++....+.+.+-  ........+.+..|++.++|.+.-+...
T Consensus       169 tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~--kegi~i~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        169 TTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAA--KEGVEVEDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             eCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            5 333333332 2346889999999999999988762  2223345677889999999998655433

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.53  E-value=3.2e-06  Score=89.46  Aligned_cols=196  Identities=10%  Similarity=0.099  Sum_probs=114.2

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee--e-EEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS--G-SYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~-~~~~~~~~~~~~~~~~~~l  260 (538)
                      |....+++|.+..++.|...+..+ .-...+.++|+.|+||||+|+.+++.+-....  . .|-.+            ..
T Consensus        12 P~sf~dIiGQe~v~~~L~~ai~~~-ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C------------~s   78 (624)
T PRK14959         12 PQTFAEVAGQETVKAILSRAAQEN-RVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTC------------EQ   78 (624)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCccc------------HH
Confidence            334467899998888888888753 22467889999999999999999987642110  0 00000            00


Q ss_pred             HHHHHHHH----hcCC-CCCCchhhcHHHHHHH-----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEecc
Q 009306          261 RQQLLSTL----LNDG-NVKNFLNTDLNFQSRR-----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTR  328 (538)
Q Consensus       261 ~~~l~~~l----~~~~-~~~~~~~~~~~~l~~~-----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR  328 (538)
                      .+.+....    .... .....+++.. .+.+.     ..+++-+||||+++..  .....|+..+........+|++|.
T Consensus        79 C~~i~~g~hpDv~eId~a~~~~Id~iR-~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt  157 (624)
T PRK14959         79 CRKVTQGMHVDVVEIDGASNRGIDDAK-RLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATT  157 (624)
T ss_pred             HHHHhcCCCCceEEEecccccCHHHHH-HHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecC
Confidence            00000000    0000 0000111111 11111     1345669999999754  456667666654345566666555


Q ss_pred             c-hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc-HHHHHHHHHh
Q 009306          329 D-RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP-LALEVLGRYL  395 (538)
Q Consensus       329 ~-~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-Lal~~~~~~L  395 (538)
                      + ..+...+ .....+++.+++.++..+.+...+...  ......+.+..+++.++|.+ .++..+...+
T Consensus       158 ~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~e--gi~id~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        158 EPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGRE--GVDYDPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             ChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            4 3333222 223578999999999999988766322  22345678889999999976 6777766544

>PRK06620 hypothetical protein; Validated

Probab=98.53  E-value=1.8e-06  Score=80.53  Aligned_cols=138  Identities=11%  Similarity=0.073  Sum_probs=85.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      +.+.|+|++|+|||+|++.+++....     .++...   .  .     ..                        +.. .
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~-----~~~~~~---~--~-----~~------------------------~~~-~   84 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNA-----YIIKDI---F--F-----NE------------------------EIL-E   84 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCC-----EEcchh---h--h-----ch------------------------hHH-h
Confidence            56999999999999999988776432     222200   0  0     00                        001 1


Q ss_pred             CCeEEEEecCCChHH--HHHHhcCcCCCCCCCEEEEeccchh-------hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcC
Q 009306          292 KKVLIVFDDVDHPRQ--IKILVGRLDLFASGSRIIITTRDRQ-------VLANCGVDEVYQMEELVHDDALRLFSRHAFG  362 (538)
Q Consensus       292 k~~LlVlDdv~~~~~--~~~l~~~l~~~~~~~~iiiTtR~~~-------~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~  362 (538)
                      ..-+++|||++...+  +-.+...+.  ..|..+|+|++...       ..+.+....++++++++.++..+++.+.+..
T Consensus        85 ~~d~lliDdi~~~~~~~lf~l~N~~~--e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~  162 (214)
T PRK06620         85 KYNAFIIEDIENWQEPALLHIFNIIN--EKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSI  162 (214)
T ss_pred             cCCEEEEeccccchHHHHHHHHHHHH--hcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHH
Confidence            234788999975432  222222222  34668889887442       2223334458999999999988888887621


Q ss_pred             CCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          363 GDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       363 ~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                        ..-...++...-+++.+.|.--.+.-+-.
T Consensus       163 --~~l~l~~ev~~~L~~~~~~d~r~l~~~l~  191 (214)
T PRK06620        163 --SSVTISRQIIDFLLVNLPREYSKIIEILE  191 (214)
T ss_pred             --cCCCCCHHHHHHHHHHccCCHHHHHHHHH
Confidence              22345577888888888877655544433

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.50  E-value=3.1e-06  Score=86.51  Aligned_cols=174  Identities=16%  Similarity=0.210  Sum_probs=99.1

Q ss_pred             CCCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          186 ENEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ..+++.|++.++++|.+.+..           +....+-+.|+|++|+|||++|++++++....|-   .+. ..     
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i---~v~-~~-----  199 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFI---RVV-GS-----  199 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEE---Eee-hH-----
Confidence            345788999999999886532           1233556999999999999999999998654321   111 11     


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH-HhcCCCeEEEEecCCCh-------------HH---HHHHhcCcCCC
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR-RLTRKKVLIVFDDVDHP-------------RQ---IKILVGRLDLF  317 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~-~l~~k~~LlVlDdv~~~-------------~~---~~~l~~~l~~~  317 (538)
                          .+.    ....+.     . ......+.+ .-...+.+|+|||++..             +.   +..++..+..+
T Consensus       200 ----~l~----~~~~g~-----~-~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~  265 (389)
T PRK03992        200 ----ELV----QKFIGE-----G-ARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGF  265 (389)
T ss_pred             ----HHh----Hhhccc-----h-HHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhcccc
Confidence                111    110000     0 011111111 12356789999999753             11   22222222221


Q ss_pred             --CCCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 --ASGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 --~~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                        ..+..||.||.....+..     ...+..+++++.+.++-.++|..+..+......   .....+++.+.|.-
T Consensus       266 ~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~---~~~~~la~~t~g~s  337 (389)
T PRK03992        266 DPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADD---VDLEELAELTEGAS  337 (389)
T ss_pred             CCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCc---CCHHHHHHHcCCCC
Confidence              235567777765433221     123567999999999999999988743222211   12456677776653

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.49  E-value=1.4e-06  Score=93.75  Aligned_cols=197  Identities=14%  Similarity=0.116  Sum_probs=113.2

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      .....++|.+..++.|..++..+. -...+.++|+.|+||||+|+.+++.+.......-.        ...+.-...+.+
T Consensus        13 ~~~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~--------~~c~~c~~c~~i   83 (585)
T PRK14950         13 QTFAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKG--------RPCGTCEMCRAI   83 (585)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC--------CCCccCHHHHHH
Confidence            344789999999999988887542 34567899999999999999999876421100000        000000111111


Q ss_pred             HHHHhcC----CC-CCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hh
Q 009306          265 LSTLLND----GN-VKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQ  331 (538)
Q Consensus       265 ~~~l~~~----~~-~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~  331 (538)
                      .......    .. .....++.. .+.+.+     ..++-++|||+++..  +..+.|+..+....+...+|+++.+ ..
T Consensus        84 ~~~~~~d~~~i~~~~~~~vd~ir-~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~k  162 (585)
T PRK14950         84 AEGSAVDVIEMDAASHTSVDDAR-EIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHK  162 (585)
T ss_pred             hcCCCCeEEEEeccccCCHHHHH-HHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhh
Confidence            1100000    00 001111111 111221     234568999999744  5566776666544556666665543 33


Q ss_pred             hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          332 VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       332 ~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      +...+ .....+++..++..+....+...+..  .......+.+..+++.++|.+..+.....
T Consensus       163 ll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~--egl~i~~eal~~La~~s~Gdlr~al~~Le  223 (585)
T PRK14950        163 VPATILSRCQRFDFHRHSVADMAAHLRKIAAA--EGINLEPGALEAIARAATGSMRDAENLLQ  223 (585)
T ss_pred             hhHHHHhccceeeCCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            33322 22357889999999999988877632  22234567788999999999965544433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.49  E-value=1.2e-06  Score=87.45  Aligned_cols=156  Identities=17%  Similarity=0.226  Sum_probs=90.3

Q ss_pred             cccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          178 RLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       178 ~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      +.....|.....++|.+...+.+..++..+ .-..++.++|++|+|||++|+.+++.....+   ..+. ...    ...
T Consensus        11 w~~kyrP~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lll~G~~G~GKT~la~~l~~~~~~~~---~~i~-~~~----~~~   81 (316)
T PHA02544         11 WEQKYRPSTIDECILPAADKETFKSIVKKG-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEV---LFVN-GSD----CRI   81 (316)
T ss_pred             ceeccCCCcHHHhcCcHHHHHHHHHHHhcC-CCCeEEEeeCcCCCCHHHHHHHHHHHhCccc---eEec-cCc----ccH
Confidence            334445556688999999999999988753 2356777799999999999999998763321   2222 111    111


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh---HHHHHHhcCcCCCCCCCEEEEeccchhhh-
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP---RQIKILVGRLDLFASGSRIIITTRDRQVL-  333 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~~~~l~~~l~~~~~~~~iiiTtR~~~~~-  333 (538)
                      .. .+..+.......               .....+-+|||||++..   +....+...+.....++++|+||.....+ 
T Consensus        82 ~~-i~~~l~~~~~~~---------------~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~  145 (316)
T PHA02544         82 DF-VRNRLTRFASTV---------------SLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGII  145 (316)
T ss_pred             HH-HHHHHHHHHHhh---------------cccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhch
Confidence            11 111111110000               01134568999999754   22333333333345677888888654221 


Q ss_pred             hhc-CCCeeEEcCCCCHHHHHHHHHh
Q 009306          334 ANC-GVDEVYQMEELVHDDALRLFSR  358 (538)
Q Consensus       334 ~~~-~~~~~~~l~~L~~~ea~~Lf~~  358 (538)
                      +.+ .....+.++..+.++..+++..
T Consensus       146 ~~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544        146 EPLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             HHHHhhceEEEeCCCCHHHHHHHHHH
Confidence            111 1234677888888888776554

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.49  E-value=4.4e-06  Score=86.64  Aligned_cols=162  Identities=17%  Similarity=0.134  Sum_probs=97.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+.|+|++|+|||+|+.++++.+...++  .++|+.          ...+...+...+...     ..    ....+.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~----------~~~f~~~~~~~~~~~-----~~----~~f~~~  190 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT----------SEKFLNDLVDSMKEG-----KL----NEFREK  190 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE----------HHHHHHHHHHHHhcc-----cH----HHHHHH
Confidence            456999999999999999999998766543  344444          122333443333211     11    123333


Q ss_pred             hcCCCeEEEEecCCCh---H-HHHHHhcCcCC-CCCCCEEEEecc-chhhh--------hhcCCCeeEEcCCCCHHHHHH
Q 009306          289 LTRKKVLIVFDDVDHP---R-QIKILVGRLDL-FASGSRIIITTR-DRQVL--------ANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~---~-~~~~l~~~l~~-~~~~~~iiiTtR-~~~~~--------~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      ...+.-+|+|||++..   . .-+.+...+.. ...+..+|+||. .+.-+        ..+....++++++.+.+.-.+
T Consensus       191 ~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~  270 (440)
T PRK14088        191 YRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKK  270 (440)
T ss_pred             HHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHH
Confidence            3345668999999632   1 11222222110 123557888874 33222        122334578999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      ++.+.+..  ......++.+..|++.+.|+.-.|.-+-.
T Consensus       271 IL~~~~~~--~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~  307 (440)
T PRK14088        271 IARKMLEI--EHGELPEEVLNFVAENVDDNLRRLRGAII  307 (440)
T ss_pred             HHHHHHHh--cCCCCCHHHHHHHHhccccCHHHHHHHHH
Confidence            99988732  23345578889999999888765554443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.49  E-value=3.4e-06  Score=89.27  Aligned_cols=196  Identities=13%  Similarity=0.092  Sum_probs=109.7

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~~~~~~~l  260 (538)
                      .....++|.+..++.|..++..+. -...+.++|++|+||||+|+.++..+-....   ..|-.+ .+....... ..++
T Consensus        13 ~~f~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~-~~d~   90 (527)
T PRK14969         13 KSFSELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGR-FVDL   90 (527)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCC-CCce
Confidence            344778999999999998887532 2456789999999999999999987632110   000000 000000000 0000


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhh
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVL  333 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~  333 (538)
                      .     .+...  .....++....+...    ..+++-++|+|+++..  .....++..+......+.+|++|.+. .+.
T Consensus        91 ~-----ei~~~--~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil  163 (527)
T PRK14969         91 I-----EVDAA--SNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIP  163 (527)
T ss_pred             e-----Eeecc--ccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCc
Confidence            0     00000  001111111111110    1245569999999854  44666776666545566666655443 222


Q ss_pred             hhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHH
Q 009306          334 ANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVL  391 (538)
Q Consensus       334 ~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~  391 (538)
                      ..+ .....+++++++.++..+.+...+-..  ......+.+..+++.++|.+. ++..+
T Consensus       164 ~tI~SRc~~~~f~~l~~~~i~~~L~~il~~e--gi~~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        164 VTVLSRCLQFNLKQMPPPLIVSHLQHILEQE--NIPFDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             hhHHHHHHHHhcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            121 113578899999999998887765221  123456677889999999885 44443

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

Probab=98.48  E-value=7.3e-06  Score=77.45  Aligned_cols=188  Identities=14%  Similarity=0.152  Sum_probs=114.8

Q ss_pred             cccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc--ceeeEEEEeehhhhhhcCCh
Q 009306          180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR--HFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       180 ~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~--~f~~~~~~~~~~~~~~~~~~  257 (538)
                      ....|+..+.++|.+..++.|...+..  ...+....+||+|.|||+-|..++.++-.  -|++++--.+.   +...+.
T Consensus        28 eKYrPkt~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lna---SderGi  102 (346)
T KOG0989|consen   28 EKYRPKTFDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNA---SDERGI  102 (346)
T ss_pred             HHhCCCcHHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcc---cccccc
Confidence            334566678899999999999988875  45677999999999999999999987533  34444332221   111121


Q ss_pred             HHHHHHH--HHHHhcCCCCCCchhhcHHHHHHHhcCCC-eEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchhh
Q 009306          258 GDLRQQL--LSTLLNDGNVKNFLNTDLNFQSRRLTRKK-VLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQV  332 (538)
Q Consensus       258 ~~l~~~l--~~~l~~~~~~~~~~~~~~~~l~~~l~~k~-~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~  332 (538)
                      .-.-..+  ++++.....  ....         -..++ -+||||+++..  +.|.++...+..+....+.|+.+..-..
T Consensus       103 svvr~Kik~fakl~~~~~--~~~~---------~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsr  171 (346)
T KOG0989|consen  103 SVVREKIKNFAKLTVLLK--RSDG---------YPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSR  171 (346)
T ss_pred             cchhhhhcCHHHHhhccc--cccC---------CCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhh
Confidence            1000000  000000000  0000         00123 48899999865  5577777777766777776655543322


Q ss_pred             h-hhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          333 L-ANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       333 ~-~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      . ..+ ....-+..++|..++...-+...+  ....-..+.+..+.|++.++|--
T Consensus       172 ii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia--~~E~v~~d~~al~~I~~~S~GdL  224 (346)
T KOG0989|consen  172 IIRPLVSRCQKFRFKKLKDEDIVDRLEKIA--SKEGVDIDDDALKLIAKISDGDL  224 (346)
T ss_pred             CChHHHhhHHHhcCCCcchHHHHHHHHHHH--HHhCCCCCHHHHHHHHHHcCCcH
Confidence            1 111 122467899999999988888877  33334556778899999998864

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.47  E-value=1e-05  Score=86.59  Aligned_cols=198  Identities=14%  Similarity=0.124  Sum_probs=110.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc--eeeEEEEeehhh-hhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--FSGSYFARNVRE-AEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--f~~~~~~~~~~~-~~~~~~~~~l  260 (538)
                      |.....++|.+..++.|...+..+ .-...+.++|+.|+||||+|+.+++.+-..  .....|.....+ .........+
T Consensus        12 P~~f~eivGQe~i~~~L~~~i~~~-ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~   90 (620)
T PRK14954         12 PSKFADITAQEHITHTIQNSLRMD-RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDF   90 (620)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcC-CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHH
Confidence            344578999999999999988743 234558899999999999999999876431  100011110000 0000000000


Q ss_pred             HHHH---HHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-cch
Q 009306          261 RQQL---LSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-RDR  330 (538)
Q Consensus       261 ~~~l---~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R~~  330 (538)
                      ...-   +..+.+.  ....+++....+...    ..+.+-++|+||++..  .....|+..+....+.+.+|++| +..
T Consensus        91 ~~g~~~n~~~~d~~--s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~  168 (620)
T PRK14954         91 DAGTSLNISEFDAA--SNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELH  168 (620)
T ss_pred             hccCCCCeEEeccc--ccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChh
Confidence            0000   0000000  001122222221111    1234458899999754  44667776666544556655554 333


Q ss_pred             hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          331 QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       331 ~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      .+...+ .....+++.+++.++....+.+.+..  .......+.+..+++.++|..-
T Consensus       169 kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~--egi~I~~eal~~La~~s~Gdlr  223 (620)
T PRK14954        169 KIPATIASRCQRFNFKRIPLDEIQSQLQMICRA--EGIQIDADALQLIARKAQGSMR  223 (620)
T ss_pred             hhhHHHHhhceEEecCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHhCCCHH
Confidence            443332 34578999999999999888876522  1233457788899999999765

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.47  E-value=1.5e-05  Score=83.37  Aligned_cols=193  Identities=11%  Similarity=0.069  Sum_probs=110.4

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-----eeeEEEEeehhhhhh--cCCh
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----FSGSYFARNVREAEE--TCRL  257 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f~~~~~~~~~~~~~~--~~~~  257 (538)
                      .....++|.+..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+...     .++.. ..++.....  ..++
T Consensus        13 ~~f~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~-c~nc~~i~~g~~~d~   90 (486)
T PRK14953         13 KFFKEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGK-CENCVEIDKGSFPDL   90 (486)
T ss_pred             CcHHHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCc-cHHHHHHhcCCCCcE
Confidence            344678999999999999887542 34567889999999999999999875321     01100 000000000  0000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-cc
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-RD  329 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R~  329 (538)
                      ..        +....  ....+. ...+.+..     .+++-++|+|+++..  .....++..+....+...+|++| +.
T Consensus        91 ~e--------idaas--~~gvd~-ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~  159 (486)
T PRK14953         91 IE--------IDAAS--NRGIDD-IRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEY  159 (486)
T ss_pred             EE--------EeCcc--CCCHHH-HHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCH
Confidence            00        00000  011111 11122221     245569999999754  44566666665444455555554 33


Q ss_pred             hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHH
Q 009306          330 RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLG  392 (538)
Q Consensus       330 ~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~  392 (538)
                      ..+...+ .....+.+.+++.++....+...+-..  ......+.+..+++.++|.+..+..+.
T Consensus       160 ~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~e--gi~id~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        160 DKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEE--KIEYEEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             HHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            3333221 234578999999999999888876322  223456778889999999876544443

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.47  E-value=4.8e-06  Score=86.01  Aligned_cols=162  Identities=19%  Similarity=0.190  Sum_probs=96.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+.|+|++|+|||+|++++++.+....+  .++|+. .         ..+...+...+...     .    ...+.+.
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~-~---------~~~~~~~~~~~~~~-----~----~~~~~~~  196 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS-S---------EKFTNDFVNALRNN-----K----MEEFKEK  196 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE-H---------HHHHHHHHHHHHcC-----C----HHHHHHH
Confidence            456899999999999999999998766542  344443 1         12222333333211     1    1222333


Q ss_pred             hcCCCeEEEEecCCCh----HHHHHHhcCcCCC-CCCCEEEEeccch-hhh--------hhcCCCeeEEcCCCCHHHHHH
Q 009306          289 LTRKKVLIVFDDVDHP----RQIKILVGRLDLF-ASGSRIIITTRDR-QVL--------ANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~----~~~~~l~~~l~~~-~~~~~iiiTtR~~-~~~--------~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      +.+ .-+|+|||++..    ...+.+...+... ..+..+|+|+... ..+        ..+.....+.+++.+.++-.+
T Consensus       197 ~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~  275 (405)
T TIGR00362       197 YRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLA  275 (405)
T ss_pred             HHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHH
Confidence            332 348999999642    1122232222111 2355688877542 212        222233578999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHH
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRY  394 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~  394 (538)
                      ++.+.+..  ......++....+++.+.|..-.|+-+...
T Consensus       276 il~~~~~~--~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~  313 (405)
T TIGR00362       276 ILQKKAEE--EGLELPDEVLEFIAKNIRSNVRELEGALNR  313 (405)
T ss_pred             HHHHHHHH--cCCCCCHHHHHHHHHhcCCCHHHHHHHHHH
Confidence            99998732  334456788889999999988765544433

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).

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

Probab=98.46  E-value=1.8e-06  Score=83.04  Aligned_cols=175  Identities=21%  Similarity=0.310  Sum_probs=103.7

Q ss_pred             CCCCCceeccchhHH---HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKE---IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~---l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      ..-.++||.+..+.+   |.+++.  .+..+.+.+||++|+||||||+.++..-+.+-  ..|+..........++..++
T Consensus       135 ktL~dyvGQ~hlv~q~gllrs~ie--q~~ipSmIlWGppG~GKTtlArlia~tsk~~S--yrfvelSAt~a~t~dvR~if  210 (554)
T KOG2028|consen  135 KTLDDYVGQSHLVGQDGLLRSLIE--QNRIPSMILWGPPGTGKTTLARLIASTSKKHS--YRFVELSATNAKTNDVRDIF  210 (554)
T ss_pred             chHHHhcchhhhcCcchHHHHHHH--cCCCCceEEecCCCCchHHHHHHHHhhcCCCc--eEEEEEeccccchHHHHHHH
Confidence            344567777765544   233333  34677899999999999999999998655442  33444221111122222222


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCC--ChHHHHHHhcCcCCCCCCCEEEE--eccchhh---hh
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVD--HPRQIKILVGRLDLFASGSRIII--TTRDRQV---LA  334 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~~~iii--TtR~~~~---~~  334 (538)
                      ++-    ..               ...+..++.+|.+|+|.  +..|-+.|++..   .+|.-++|  ||-++..   ..
T Consensus       211 e~a----q~---------------~~~l~krkTilFiDEiHRFNksQQD~fLP~V---E~G~I~lIGATTENPSFqln~a  268 (554)
T KOG2028|consen  211 EQA----QN---------------EKSLTKRKTILFIDEIHRFNKSQQDTFLPHV---ENGDITLIGATTENPSFQLNAA  268 (554)
T ss_pred             HHH----HH---------------HHhhhcceeEEEeHHhhhhhhhhhhccccee---ccCceEEEecccCCCccchhHH
Confidence            221    10               12345788999999995  556677777665   35665555  4555432   12


Q ss_pred             hcCCCeeEEcCCCCHHHHHHHHHhhhc---CCCC---C-C----CchHHHHHHHHHHhcCCc
Q 009306          335 NCGVDEVYQMEELVHDDALRLFSRHAF---GGDH---P-H----ESHTELACKTIKYARGVP  385 (538)
Q Consensus       335 ~~~~~~~~~l~~L~~~ea~~Lf~~~~~---~~~~---~-~----~~~~~~~~~i~~~~~G~P  385 (538)
                      .+....++.|+.|+.++...++.+-.-   ....   + +    ..+..+.+-++..|.|-.
T Consensus       269 LlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDa  330 (554)
T KOG2028|consen  269 LLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDA  330 (554)
T ss_pred             HHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchH
Confidence            223456889999999999999887321   1111   1 1    234556677777787765

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.45  E-value=3.7e-06  Score=87.93  Aligned_cols=161  Identities=16%  Similarity=0.150  Sum_probs=97.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+.|+|++|+|||+|++++++.+...++  .++|+. .         ..+...+...+...     .    ...+.+.
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~-~---------~~~~~~~~~~~~~~-----~----~~~~~~~  208 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVT-S---------EKFTNDFVNALRNN-----T----MEEFKEK  208 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEE-H---------HHHHHHHHHHHHcC-----c----HHHHHHH
Confidence            456899999999999999999998876643  244443 1         12222333332211     1    1223333


Q ss_pred             hcCCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccchh---------hhhhcCCCeeEEcCCCCHHHHHH
Q 009306          289 LTRKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRDRQ---------VLANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~~~---------~~~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      +. +.-+|+|||++..    ...+.+...+.. ...+..+|+|+....         +...+....++++++++.++-.+
T Consensus       209 ~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~  287 (450)
T PRK00149        209 YR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIA  287 (450)
T ss_pred             Hh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHH
Confidence            33 3458999999532    112233222111 123556888775431         12233334578999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      ++...+-.  ......++....|++.+.|..-.|.-+-.
T Consensus       288 il~~~~~~--~~~~l~~e~l~~ia~~~~~~~R~l~~~l~  324 (450)
T PRK00149        288 ILKKKAEE--EGIDLPDEVLEFIAKNITSNVRELEGALN  324 (450)
T ss_pred             HHHHHHHH--cCCCCCHHHHHHHHcCcCCCHHHHHHHHH
Confidence            99998732  23445678899999999998876544433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.44  E-value=2.3e-05  Score=82.13  Aligned_cols=195  Identities=12%  Similarity=0.080  Sum_probs=113.2

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eee--EEEEee-hhhhhh--cCCh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSG--SYFARN-VREAEE--TCRL  257 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~--~~~~~~-~~~~~~--~~~~  257 (538)
                      |..-..++|-+...+.|...+..+. -.+.+.++|+.|+||||+|+.++..+-.. ...  .|..+. +.....  ...+
T Consensus        10 P~~fdeiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv   88 (535)
T PRK08451         10 PKHFDELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDI   88 (535)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeE
Confidence            3445789999999999999887542 35567899999999999999999875321 000  011100 000000  0000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-  330 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-  330 (538)
                      ..        +...  .....++..+.+...    ..+++-++|||+++..  +....++..+....+.+++|++|.+. 
T Consensus        89 ~e--------ldaa--s~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~  158 (535)
T PRK08451         89 IE--------MDAA--SNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPL  158 (535)
T ss_pred             EE--------eccc--cccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChh
Confidence            00        0000  000111222211110    0134458899999754  45667776666556677777777654 


Q ss_pred             hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          331 QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       331 ~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      .+...+ .....+++.+++.++..+.+...+-..  ......+.+..+++.++|.+.-+..+
T Consensus       159 kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~E--Gi~i~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        159 KLPATILSRTQHFRFKQIPQNSIISHLKTILEKE--GVSYEPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             hCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCcHHHHHHH
Confidence            222211 224688999999999999988766222  22345678889999999998544443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.42  E-value=2.7e-06  Score=82.28  Aligned_cols=131  Identities=14%  Similarity=0.149  Sum_probs=69.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      ....+.++|++|+||||+|+.++..+....  ....++..        ....+    .....+     .........+. 
T Consensus        41 ~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~--------~~~~l----~~~~~g-----~~~~~~~~~~~-  102 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEV--------ERADL----VGEYIG-----HTAQKTREVIK-  102 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEe--------cHHHh----hhhhcc-----chHHHHHHHHH-
Confidence            345688999999999999999988653211  11112210        00011    111100     00011111111 


Q ss_pred             HhcCCCeEEEEecCCC----------hHHHHHHhcCcCCCCCCCEEEEeccchhh---h---hhc--CCCeeEEcCCCCH
Q 009306          288 RLTRKKVLIVFDDVDH----------PRQIKILVGRLDLFASGSRIIITTRDRQV---L---ANC--GVDEVYQMEELVH  349 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~~----------~~~~~~l~~~l~~~~~~~~iiiTtR~~~~---~---~~~--~~~~~~~l~~L~~  349 (538)
                      .  ...-+|+||+++.          .+.++.++..+........+|+++.....   .   +.+  .....+.+++++.
T Consensus       103 ~--a~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~  180 (261)
T TIGR02881       103 K--ALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTV  180 (261)
T ss_pred             h--ccCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCH
Confidence            1  1235889999974          23456666555433334455555543221   0   011  1234688999999


Q ss_pred             HHHHHHHHhhh
Q 009306          350 DDALRLFSRHA  360 (538)
Q Consensus       350 ~ea~~Lf~~~~  360 (538)
                      +|..+++.+.+
T Consensus       181 ~el~~Il~~~~  191 (261)
T TIGR02881       181 EELMEIAERMV  191 (261)
T ss_pred             HHHHHHHHHHH
Confidence            99999998776

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.41  E-value=4.4e-06  Score=93.27  Aligned_cols=194  Identities=13%  Similarity=0.130  Sum_probs=105.9

Q ss_pred             HHHHHHHhhhccccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------e
Q 009306          167 LIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------S  240 (538)
Q Consensus       167 ~i~~i~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~  240 (538)
                      .+++...++.....   +..-+.++||+.++..+...|....  ..-+.|+|++|+|||++|..++.++....      .
T Consensus       169 ~l~~~~~~L~~~~r---~~~ld~~iGr~~ei~~~i~~l~r~~--~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~  243 (852)
T TIGR03345       169 ALDQYTTDLTAQAR---EGKIDPVLGRDDEIRQMIDILLRRR--QNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRN  243 (852)
T ss_pred             hHHHHhhhHHHHhc---CCCCCcccCCHHHHHHHHHHHhcCC--cCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccC
Confidence            44444444433332   2344789999999999999887532  23467999999999999999999875431      1


Q ss_pred             eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh--cCCCeEEEEecCCChH-------HHH---
Q 009306          241 GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL--TRKKVLIVFDDVDHPR-------QIK---  308 (538)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~-------~~~---  308 (538)
                      ..+|..+..........                 ....+..+..+.+.+  .+++++|+||+++...       +.+   
T Consensus       244 ~~i~~l~l~~l~ag~~~-----------------~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n  306 (852)
T TIGR03345       244 VRLLSLDLGLLQAGASV-----------------KGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAAN  306 (852)
T ss_pred             CeEEEeehhhhhccccc-----------------chHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHH
Confidence            22332222111000000                 001111111111111  2468999999985431       111   


Q ss_pred             HHhcCcCCCCCCCEEEEeccchhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhhcC--CCCCCCchHHHHHHHHH
Q 009306          309 ILVGRLDLFASGSRIIITTRDRQVLAN-------CGVDEVYQMEELVHDDALRLFSRHAFG--GDHPHESHTELACKTIK  379 (538)
Q Consensus       309 ~l~~~l~~~~~~~~iiiTtR~~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~~~~~~i~~  379 (538)
                      .+.+.+.  ....++|-+|.....-+.       ....+.+.+++++.++..+++....-.  ....-....+....+++
T Consensus       307 ~Lkp~l~--~G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~  384 (852)
T TIGR03345       307 LLKPALA--RGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVE  384 (852)
T ss_pred             HhhHHhh--CCCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHH
Confidence            2334432  234566666654322111       123368999999999999997544311  11122334566666777


Q ss_pred             HhcCC
Q 009306          380 YARGV  384 (538)
Q Consensus       380 ~~~G~  384 (538)
                      .+.++
T Consensus       385 ls~ry  389 (852)
T TIGR03345       385 LSHRY  389 (852)
T ss_pred             Hcccc
Confidence            77654

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

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

Probab=98.40  E-value=4.6e-06  Score=92.29  Aligned_cols=193  Identities=12%  Similarity=0.143  Sum_probs=104.6

Q ss_pred             HHHHHHHhhhccccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-----e-e
Q 009306          167 LIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----F-S  240 (538)
Q Consensus       167 ~i~~i~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f-~  240 (538)
                      .+++...++.....   +..-+.++||+.++..+.+.|....  ..-+.++|++|+|||++|+.++.++...     + .
T Consensus       164 ~l~~~~~~l~~~~r---~~~l~~~igr~~ei~~~~~~L~~~~--~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~  238 (731)
T TIGR02639       164 ALEKYTVDLTEKAK---NGKIDPLIGREDELERTIQVLCRRK--KNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKN  238 (731)
T ss_pred             HHHHHhhhHHHHHh---cCCCCcccCcHHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcC
Confidence            34444444433332   2334679999999999999887542  3347899999999999999999987432     1 2


Q ss_pred             eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh-----------HHHH
Q 009306          241 GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP-----------RQIK  308 (538)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~-----------~~~~  308 (538)
                      ..+|..+...         +...       .. .....+.....+.+.+ ..++.+|+||+++..           +...
T Consensus       239 ~~~~~~~~~~---------l~a~-------~~-~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~  301 (731)
T TIGR02639       239 AKIYSLDMGS---------LLAG-------TK-YRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASN  301 (731)
T ss_pred             CeEEEecHHH---------Hhhh-------cc-ccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHH
Confidence            3344332111         1100       00 0011122222222222 246789999998632           1223


Q ss_pred             HHhcCcCCCCCCCEEEEeccchhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhhcC--CCCCCCchHHHHHHHHH
Q 009306          309 ILVGRLDLFASGSRIIITTRDRQVLAN-------CGVDEVYQMEELVHDDALRLFSRHAFG--GDHPHESHTELACKTIK  379 (538)
Q Consensus       309 ~l~~~l~~~~~~~~iiiTtR~~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~~~~~~i~~  379 (538)
                      .+.+.+.  ....++|-+|....+-..       ......+++++++.++..+++....-.  .........+....+++
T Consensus       302 ~L~~~l~--~g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~  379 (731)
T TIGR02639       302 LLKPALS--SGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVE  379 (731)
T ss_pred             HHHHHHh--CCCeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHH
Confidence            3444433  223455555543221111       112357899999999999999865421  11122334555556665


Q ss_pred             HhcC
Q 009306          380 YARG  383 (538)
Q Consensus       380 ~~~G  383 (538)
                      .++.
T Consensus       380 ls~r  383 (731)
T TIGR02639       380 LSAR  383 (731)
T ss_pred             hhhc
Confidence            5543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.39  E-value=1.1e-05  Score=86.87  Aligned_cols=196  Identities=13%  Similarity=0.123  Sum_probs=111.1

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh----cCChHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE----TCRLGD  259 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~----~~~~~~  259 (538)
                      |.....++|.+..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+-.......+-. +..+..    ...+..
T Consensus        14 P~~f~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~p-C~~C~~~~~~~~Dvie   91 (725)
T PRK07133         14 PKTFDDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEP-CQECIENVNNSLDIIE   91 (725)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCc-hhHHHHhhcCCCcEEE
Confidence            3445778999999999999887542 3556789999999999999999987532111000000 000000    000000


Q ss_pred             HHHHHHHHHhcCCCCC-CchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-cchhhhh
Q 009306          260 LRQQLLSTLLNDGNVK-NFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-RDRQVLA  334 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R~~~~~~  334 (538)
                              +....... ..++++...+... ..+++-++|+|+++..  .....|+..+........+|++| ....+..
T Consensus        92 --------idaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~  163 (725)
T PRK07133         92 --------MDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPL  163 (725)
T ss_pred             --------EeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhH
Confidence                    00000000 0111111111111 1245569999999743  45667776666545555555544 4444433


Q ss_pred             hc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHH
Q 009306          335 NC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVL  391 (538)
Q Consensus       335 ~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~  391 (538)
                      .+ .....+++.+++.++..+.+...+-..  ......+.+..+++.++|.+. |+..+
T Consensus       164 TI~SRcq~ieF~~L~~eeI~~~L~~il~ke--gI~id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        164 TILSRVQRFNFRRISEDEIVSRLEFILEKE--NISYEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             HHHhhceeEEccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            32 234689999999999999888765221  223445678889999999774 44433

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

Probab=98.38  E-value=1.3e-05  Score=80.00  Aligned_cols=172  Identities=16%  Similarity=0.226  Sum_probs=107.4

Q ss_pred             CCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccceee--EEEEeehhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG--SYFARNVREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~--~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..+..++||+.++..+.+++..  ..+....+-|.|-+|.|||.+...++.........  .+++.+..    -.....+
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~s----l~~~~ai  222 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTS----LTEASAI  222 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeecc----ccchHHH
Confidence            3457899999999999998865  33456678999999999999999998877665543  46665322    2344556


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcC--CCeEEEEecCCChHH--HHHHhcCcCCC-CCCCEEEEeccch-----
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR--KKVLIVFDDVDHPRQ--IKILVGRLDLF-ASGSRIIITTRDR-----  330 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~--k~~LlVlDdv~~~~~--~~~l~~~l~~~-~~~~~iiiTtR~~-----  330 (538)
                      +..+++.+...........+....+.+...+  ..+|+|+|+.|....  -..+...+.|- -+++++|+.--..     
T Consensus       223 F~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlT  302 (529)
T KOG2227|consen  223 FKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLT  302 (529)
T ss_pred             HHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHH
Confidence            6666666633333332224444445444433  368999999976532  11111111111 2466655443221     


Q ss_pred             -hhhhhcC-----CCeeEEcCCCCHHHHHHHHHhhh
Q 009306          331 -QVLANCG-----VDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       331 -~~~~~~~-----~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                       ..+..+.     ....+..+|.+.++..++|..+.
T Consensus       303 dR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl  338 (529)
T KOG2227|consen  303 DRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRL  338 (529)
T ss_pred             HHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHH
Confidence             2222222     23578899999999999999998

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.36  E-value=1.2e-05  Score=84.96  Aligned_cols=161  Identities=12%  Similarity=0.157  Sum_probs=96.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+.|+|..|+|||.|+.++++.....+  ..++|+.          ...+...+...+...         ....+++.
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit----------aeef~~el~~al~~~---------~~~~f~~~  374 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS----------SEEFTNEFINSIRDG---------KGDSFRRR  374 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee----------HHHHHHHHHHHHHhc---------cHHHHHHH
Confidence            34589999999999999999999876533  2344544          222333333332211         11223333


Q ss_pred             hcCCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccch---------hhhhhcCCCeeEEcCCCCHHHHHH
Q 009306          289 LTRKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRDR---------QVLANCGVDEVYQMEELVHDDALR  354 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~~---------~~~~~~~~~~~~~l~~L~~~ea~~  354 (538)
                      +. +.-+|||||++..    ..-+.|+..+.. ...+..|||||...         .+...+....+++|.+.+.+.-.+
T Consensus       375 y~-~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~a  453 (617)
T PRK14086        375 YR-EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIA  453 (617)
T ss_pred             hh-cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHH
Confidence            33 2358899999532    111223222211 13456788888653         222333445688999999999999


Q ss_pred             HHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          355 LFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       355 Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      ++.+++.  .......++++.-|++.+.++.-.|.-+..
T Consensus       454 IL~kka~--~r~l~l~~eVi~yLa~r~~rnvR~LegaL~  490 (617)
T PRK14086        454 ILRKKAV--QEQLNAPPEVLEFIASRISRNIRELEGALI  490 (617)
T ss_pred             HHHHHHH--hcCCCCCHHHHHHHHHhccCCHHHHHHHHH
Confidence            9998873  233455678888888888877655544433

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.36  E-value=2.9e-05  Score=82.57  Aligned_cols=194  Identities=10%  Similarity=0.077  Sum_probs=113.4

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-----eeeEEEEeehhhhhhcCChH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----FSGSYFARNVREAEETCRLG  258 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f~~~~~~~~~~~~~~~~~~~  258 (538)
                      |..-..++|-+..++.|...+..+ .-.+.+.++|+.|+||||+|+.++..+-..     .++.. ...+........+.
T Consensus        12 P~~f~diiGqe~iv~~L~~~i~~~-~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~-C~~C~~i~~~~~~d   89 (563)
T PRK06647         12 PRDFNSLEGQDFVVETLKHSIESN-KIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGE-CSSCKSIDNDNSLD   89 (563)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCcc-chHHHHHHcCCCCC
Confidence            344578999999999999998754 235678899999999999999999875421     01100 00000000000000


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHH---HH-HhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-h
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQ---SR-RLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-Q  331 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l---~~-~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~  331 (538)
                       +.     .+.+.  .....++.....   .. -..+++-++|+|+++..  .....++..+....+...+|++|.+. .
T Consensus        90 -v~-----~idga--s~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~k  161 (563)
T PRK06647         90 -VI-----EIDGA--SNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHK  161 (563)
T ss_pred             -eE-----EecCc--ccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHH
Confidence             00     00000  001112211111   11 11345568999999654  45677777776555666666666443 3


Q ss_pred             hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          332 VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       332 ~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      +...+ .....+++.+++.++..+.+...+...  ......+.+..+++.++|.+..+.
T Consensus       162 L~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~e--gi~id~eAl~lLa~~s~GdlR~al  218 (563)
T PRK06647        162 LPATIKSRCQHFNFRLLSLEKIYNMLKKVCLED--QIKYEDEALKWIAYKSTGSVRDAY  218 (563)
T ss_pred             hHHHHHHhceEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHH
Confidence            33222 224578999999999999888776332  233457788889999999885443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=1.9e-05  Score=81.96  Aligned_cols=198  Identities=12%  Similarity=0.102  Sum_probs=110.5

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee----eEEEEe-ehhhhhhcCChHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS----GSYFAR-NVREAEETCRLGD  259 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~----~~~~~~-~~~~~~~~~~~~~  259 (538)
                      ..-.+++|.+..++.|...+..+. -.+.+.++|++|+||||+|+.++..+-..-.    ..|-.+ ++.......... 
T Consensus        14 ~~~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d-   91 (451)
T PRK06305         14 QTFSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLD-   91 (451)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCc-
Confidence            344789999999999999887532 2456889999999999999999987543200    000000 000000000000 


Q ss_pred             HHHHHHHHHhcCCCCC-CchhhcHHHHHH-HhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hhhhh
Q 009306          260 LRQQLLSTLLNDGNVK-NFLNTDLNFQSR-RLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQVLA  334 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~-~~~~~~~~~l~~-~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~~  334 (538)
                      +     ..+.+..... ..+......+.. .....+-++|+|+++..  .....+...+....++..+|++|.+ ..+..
T Consensus        92 ~-----~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~  166 (451)
T PRK06305         92 V-----LEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPG  166 (451)
T ss_pred             e-----EEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcch
Confidence            0     0000000000 011111111110 01245668999999744  4456666665544456666666643 33322


Q ss_pred             hc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHH
Q 009306          335 NC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVL  391 (538)
Q Consensus       335 ~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~  391 (538)
                      .+ .....+++.+++.++..+.+...+-.  .......+.+..+++.++|.+. ++..+
T Consensus       167 tI~sRc~~v~f~~l~~~el~~~L~~~~~~--eg~~i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        167 TILSRCQKMHLKRIPEETIIDKLALIAKQ--EGIETSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             HHHHhceEEeCCCCCHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            22 23467899999999999988876522  2233457788899999999874 44433

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.35  E-value=2.6e-05  Score=80.74  Aligned_cols=153  Identities=12%  Similarity=0.123  Sum_probs=90.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      ...+.|+|++|+|||+|++++++.+......+.|+.          ...+...+...+...     .    ...++..+ 
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~----------~~~f~~~~~~~l~~~-----~----~~~f~~~~-  200 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVR----------SELFTEHLVSAIRSG-----E----MQRFRQFY-  200 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEee----------HHHHHHHHHHHHhcc-----h----HHHHHHHc-
Confidence            356899999999999999999998765444455554          112222333333211     1    12233333 


Q ss_pred             CCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccc-hh--------hhhhcCCCeeEEcCCCCHHHHHHHH
Q 009306          291 RKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRD-RQ--------VLANCGVDEVYQMEELVHDDALRLF  356 (538)
Q Consensus       291 ~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~-~~--------~~~~~~~~~~~~l~~L~~~ea~~Lf  356 (538)
                      ...-+|+|||++..    ...+.+...+.. ...+..||+||.. +.        +...+.....+.+.+++.++..+++
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL  280 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFL  280 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHH
Confidence            34458899998532    112222222110 1245678888854 21        1222333468899999999999999


Q ss_pred             HhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          357 SRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       357 ~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .+.+-.  ......++...-+++.+.|+-
T Consensus       281 ~~k~~~--~~~~l~~evl~~la~~~~~di  307 (445)
T PRK12422        281 ERKAEA--LSIRIEETALDFLIEALSSNV  307 (445)
T ss_pred             HHHHHH--cCCCCCHHHHHHHHHhcCCCH
Confidence            988732  223455677777877777664

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

Probab=98.35  E-value=8.9e-07  Score=75.70  Aligned_cols=89  Identities=22%  Similarity=0.412  Sum_probs=47.8

Q ss_pred             ccEEEcCcccccccchHHHHHHHHhhC-------CCee-Ee---------eC-CCCCCCcchHHHHHHHHhcceEEEEec
Q 009306           18 YDVFLSFGGEDTRESFTSHLYSALSRE-------TVET-FI---------DD-DLRRGDEISQSLLDAIEASSISIIIFS   79 (538)
Q Consensus        18 ~dvFiSy~~~D~~~~~~~~l~~~l~~~-------g~~~-~~---------d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S   79 (538)
                      |+|||||++.|.. ..+..|...+...       .+.. |.         +. +....+.|...|.+.|.+|+++|+++|
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            5799999999933 3777777777663       2211 11         11 222345789999999999999999999


Q ss_pred             cCcccchhhHHHHHHHHHHHhhcCCeEEEEEE
Q 009306           80 ESYASSRWCLDELLKILECKKEYAQIVVPVFY  111 (538)
Q Consensus        80 ~~y~~s~~c~~El~~~~~~~~~~~~~v~pv~~  111 (538)
                      ++-..|.|+..|+..+++    .+.+|+-|.+
T Consensus        80 ~~T~~s~wV~~EI~~A~~----~~~~Ii~V~~  107 (130)
T PF08937_consen   80 PNTAKSKWVNWEIEYALK----KGKPIIGVYL  107 (130)
T ss_dssp             TT----HHHHHHHHHHTT----T---EEEEET
T ss_pred             CCcccCcHHHHHHHHHHH----CCCCEEEEEC
Confidence            999999999999998886    3455666653

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.33  E-value=5.5e-05  Score=81.44  Aligned_cols=191  Identities=16%  Similarity=0.118  Sum_probs=110.1

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceee----EEEEe-ehhhhhhc--CCh
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG----SYFAR-NVREAEET--CRL  257 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~----~~~~~-~~~~~~~~--~~~  257 (538)
                      ..-..++|.+..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+-.....    .|-.+ .+......  ..+
T Consensus        14 ~~f~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~   92 (614)
T PRK14971         14 STFESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNI   92 (614)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCce
Confidence            344789999999999999887532 34568899999999999999998865311000    00000 00000000  000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-cch
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-RDR  330 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R~~  330 (538)
                      ..        +...  .....++....+.+.    ..+++-++|||+++..  .....|+..+.....++.+|++| ...
T Consensus        93 ~~--------ld~~--~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~  162 (614)
T PRK14971         93 HE--------LDAA--SNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKH  162 (614)
T ss_pred             EE--------eccc--ccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCch
Confidence            00        0000  001111111111110    1234458899999754  45677777666545566665554 444


Q ss_pred             hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          331 QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       331 ~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      .+...+ .....+++.+++.++....+.+.+...  .-....+.+..+++.++|...-+
T Consensus       163 kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~e--gi~i~~~al~~La~~s~gdlr~a  219 (614)
T PRK14971        163 KILPTILSRCQIFDFNRIQVADIVNHLQYVASKE--GITAEPEALNVIAQKADGGMRDA  219 (614)
T ss_pred             hchHHHHhhhheeecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            444332 234689999999999999998766222  23345667889999999977543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.31  E-value=7e-05  Score=80.63  Aligned_cols=196  Identities=16%  Similarity=0.136  Sum_probs=110.4

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      .....++|.+..++.|..++..+. -.+.+.++|+.|+||||+|+.++..+-.......-.       ...+.-...+.+
T Consensus        13 ~~f~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~-------~~Cg~C~~C~~i   84 (620)
T PRK14948         13 QRFDELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTP-------EPCGKCELCRAI   84 (620)
T ss_pred             CcHhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCC-------CCCcccHHHHHH
Confidence            344678999999999999887542 235688999999999999999998764321000000       000000011111


Q ss_pred             HHHHhc-----CCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hh
Q 009306          265 LSTLLN-----DGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQ  331 (538)
Q Consensus       265 ~~~l~~-----~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~  331 (538)
                      ......     .......++...+.+ +.+     .+++-++|||+++..  +....|+..+........+|++|.+ ..
T Consensus        85 ~~g~h~D~~ei~~~~~~~vd~IReii-~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~  163 (620)
T PRK14948         85 AAGNALDVIEIDAASNTGVDNIRELI-ERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQR  163 (620)
T ss_pred             hcCCCccEEEEeccccCCHHHHHHHH-HHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhh
Confidence            100000     000001111111111 111     234458999999754  4566777666544445555555443 33


Q ss_pred             hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          332 VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       332 ~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      ++..+ .....+++.+++.++....+...+..  .......+.+..+++.++|.+..+..+
T Consensus       164 llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~k--egi~is~~al~~La~~s~G~lr~A~~l  222 (620)
T PRK14948        164 VLPTIISRCQRFDFRRIPLEAMVQHLSEIAEK--ESIEIEPEALTLVAQRSQGGLRDAESL  222 (620)
T ss_pred             hhHHHHhheeEEEecCCCHHHHHHHHHHHHHH--hCCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            33332 23467889999999998888776522  122344567889999999988654433

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=2.5e-05  Score=83.70  Aligned_cols=198  Identities=13%  Similarity=0.095  Sum_probs=110.5

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~~~~~~~l  260 (538)
                      ....+++|.+..++.|...+..+ .-...+.++|+.|+||||+|+.++..+-..-.   ..|-.+ .+.......... +
T Consensus        13 ~~f~~iiGq~~v~~~L~~~i~~~-~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d-~   90 (576)
T PRK14965         13 QTFSDLTGQEHVSRTLQNAIDTG-RVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVD-V   90 (576)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCC-e
Confidence            44578999999999999988753 23456789999999999999999987532100   000000 000000000000 0


Q ss_pred             HHHHHHHHhcCCCCC-CchhhcHHHHHHH-hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hhhhhh
Q 009306          261 RQQLLSTLLNDGNVK-NFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQVLAN  335 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~-~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~~~  335 (538)
                      .     .+.+..... .++.++...+... ...+.-++|||+++..  .....|+..+....++..+|++|.+ ..+...
T Consensus        91 ~-----eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~t  165 (576)
T PRK14965         91 F-----EIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPIT  165 (576)
T ss_pred             e-----eeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHH
Confidence            0     000000000 1111111111110 1234458899999754  4566777666654566666655543 334333


Q ss_pred             c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc-HHHHHH
Q 009306          336 C-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP-LALEVL  391 (538)
Q Consensus       336 ~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P-Lal~~~  391 (538)
                      + .....+++.+++.++....+...+-.  .......+.+..+++.++|.. .++..+
T Consensus       166 I~SRc~~~~f~~l~~~~i~~~L~~i~~~--egi~i~~~al~~la~~a~G~lr~al~~L  221 (576)
T PRK14965        166 ILSRCQRFDFRRIPLQKIVDRLRYIADQ--EGISISDAALALVARKGDGSMRDSLSTL  221 (576)
T ss_pred             HHHhhhhhhcCCCCHHHHHHHHHHHHHH--hCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            2 23457889999999999888776522  223345677888999999976 455444

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.28  E-value=3.3e-05  Score=82.42  Aligned_cols=190  Identities=14%  Similarity=0.072  Sum_probs=108.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEe-ehhhhhhc--CCh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFAR-NVREAEET--CRL  257 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~-~~~~~~~~--~~~  257 (538)
                      |.....++|.+..++.|...+..+. -.+.+.++|+.|+||||+|+.++..+-..-.   ..|-.+ .+......  .++
T Consensus        12 P~~f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv   90 (559)
T PRK05563         12 PQTFEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDV   90 (559)
T ss_pred             CCcHHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCe
Confidence            3445789999999999999987543 3566788999999999999999986532110   000000 00000000  000


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEec-cc
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITT-RD  329 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTt-R~  329 (538)
                      ..        +....  ....++.. .+.+.     ..++.-++|||+++..  .....++..+.....+..+|++| ..
T Consensus        91 ~e--------idaas--~~~vd~ir-~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~  159 (559)
T PRK05563         91 IE--------IDAAS--NNGVDEIR-DIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEP  159 (559)
T ss_pred             EE--------eeccc--cCCHHHHH-HHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            00        00000  01111111 11111     1245568899999754  45667776665444555555544 33


Q ss_pred             hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          330 RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       330 ~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      ..+...+ .....+++.+++.++..+.+...+-..  ......+.+..+++.++|.+..
T Consensus       160 ~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~e--gi~i~~~al~~ia~~s~G~~R~  216 (559)
T PRK05563        160 HKIPATILSRCQRFDFKRISVEDIVERLKYILDKE--GIEYEDEALRLIARAAEGGMRD  216 (559)
T ss_pred             hhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHH
Confidence            3333222 234578899999999999888776222  2234467788889999988753

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.28  E-value=8.8e-06  Score=91.19  Aligned_cols=193  Identities=13%  Similarity=0.123  Sum_probs=103.4

Q ss_pred             HHHHHHHhhhccccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-----e-e
Q 009306          167 LIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-----F-S  240 (538)
Q Consensus       167 ~i~~i~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-----f-~  240 (538)
                      .+++...++......   ...+.++||+.+++.+.+.|....  ..-+.++|++|+|||++|..++.++...     . .
T Consensus       161 ~l~~~~~~l~~~a~~---~~~~~~igr~~ei~~~~~~L~r~~--~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~  235 (821)
T CHL00095        161 TLEEFGTNLTKEAID---GNLDPVIGREKEIERVIQILGRRT--KNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILED  235 (821)
T ss_pred             HHHHHHHHHHHHHHc---CCCCCCCCcHHHHHHHHHHHcccc--cCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcC
Confidence            445544444443211   223568999999999999997542  2346799999999999999999986532     1 2


Q ss_pred             eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-hcCCCeEEEEecCCChH----------HHHH
Q 009306          241 GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-LTRKKVLIVFDDVDHPR----------QIKI  309 (538)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~~----------~~~~  309 (538)
                      ..+|..+....         +       .+... ....++.+..+.+. ...++++|+||+++..-          ....
T Consensus       236 ~~i~~l~~~~l---------~-------ag~~~-~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~l  298 (821)
T CHL00095        236 KLVITLDIGLL---------L-------AGTKY-RGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANI  298 (821)
T ss_pred             CeEEEeeHHHH---------h-------ccCCC-ccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHH
Confidence            33443322111         0       01100 01122222222222 23568899999985321          1223


Q ss_pred             HhcCcCCCCCCCEEEEeccchhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhh--cCCCCCCCchHHHHHHHHHH
Q 009306          310 LVGRLDLFASGSRIIITTRDRQVLAN-------CGVDEVYQMEELVHDDALRLFSRHA--FGGDHPHESHTELACKTIKY  380 (538)
Q Consensus       310 l~~~l~~~~~~~~iiiTtR~~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~--~~~~~~~~~~~~~~~~i~~~  380 (538)
                      +.+.+.  ....++|.+|.....-..       ......+.++..+.++..+++....  +..........+....+++.
T Consensus       299 Lkp~l~--rg~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~l  376 (821)
T CHL00095        299 LKPALA--RGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKL  376 (821)
T ss_pred             hHHHHh--CCCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            333332  233556666654433111       1223567889999999888876532  10101111334555666666


Q ss_pred             hcC
Q 009306          381 ARG  383 (538)
Q Consensus       381 ~~G  383 (538)
                      ++|
T Consensus       377 s~~  379 (821)
T CHL00095        377 SDQ  379 (821)
T ss_pred             hhc
Confidence            654

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.25  E-value=1.7e-05  Score=82.58  Aligned_cols=159  Identities=19%  Similarity=0.308  Sum_probs=89.8

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccce-----eeEEEEeehhhh
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-----SGSYFARNVREA  251 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-----~~~~~~~~~~~~  251 (538)
                      .++.|.+.+++++.+.+..           +-...+-+.|+|++|+|||++|+++++.+...+     ...+|+. +.. 
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~-v~~-  259 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLN-IKG-  259 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEe-ccc-
Confidence            5577899988888776431           122345699999999999999999999876542     1233433 110 


Q ss_pred             hhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCChH--------------HHHHHhcCcCC
Q 009306          252 EETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHPR--------------QIKILVGRLDL  316 (538)
Q Consensus       252 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~~--------------~~~~l~~~l~~  316 (538)
                            ..+    +....+.  ....+.......++.. .+++++|+||+++...              .+..++..+..
T Consensus       260 ------~eL----l~kyvGe--te~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDg  327 (512)
T TIGR03689       260 ------PEL----LNKYVGE--TERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDG  327 (512)
T ss_pred             ------hhh----cccccch--HHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcc
Confidence                  000    0000000  0011111222222221 3578999999997421              12334443332


Q ss_pred             CC--CCCEEEEeccchhhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          317 FA--SGSRIIITTRDRQVLA-----NCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       317 ~~--~~~~iiiTtR~~~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ..  .+..||.||.....+.     ....+..++++..+.++..++|..+.
T Consensus       328 l~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l  378 (512)
T TIGR03689       328 VESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYL  378 (512)
T ss_pred             cccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHh
Confidence            22  3444566664443322     11345678999999999999999886

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.24  E-value=2.4e-05  Score=87.63  Aligned_cols=170  Identities=12%  Similarity=0.114  Sum_probs=92.6

Q ss_pred             HHHHHHHhhhccccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------e
Q 009306          167 LIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------S  240 (538)
Q Consensus       167 ~i~~i~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~  240 (538)
                      .+++.-.++.....+   ..-+.++||+.++..+.+.|....  ...+.++|++|+|||+||..++.++....      .
T Consensus       160 ~l~~~~~~l~~~~r~---~~l~~vigr~~ei~~~i~iL~r~~--~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~  234 (857)
T PRK10865        160 ALKKYTIDLTERAEQ---GKLDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKG  234 (857)
T ss_pred             HHHHHhhhHHHHHhc---CCCCcCCCCHHHHHHHHHHHhcCC--cCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCC
Confidence            344444444333322   234679999999999999887532  33477999999999999999999875421      1


Q ss_pred             eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh--cCCCeEEEEecCCChH----------HHH
Q 009306          241 GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL--TRKKVLIVFDDVDHPR----------QIK  308 (538)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~----------~~~  308 (538)
                      ..+|..+.........                . ....+.....+.+.+  ...+++|++|+++...          .-.
T Consensus       235 ~~~~~l~l~~l~ag~~----------------~-~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~  297 (857)
T PRK10865        235 RRVLALDMGALVAGAK----------------Y-RGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGN  297 (857)
T ss_pred             CEEEEEehhhhhhccc----------------h-hhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHH
Confidence            2233222211100000                0 011111111121211  2468999999996432          223


Q ss_pred             HHhcCcCCCCCCCEEEEeccchhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          309 ILVGRLDLFASGSRIIITTRDRQVLAN-------CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       309 ~l~~~l~~~~~~~~iiiTtR~~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      .+.+.+.  ....++|-+|........       ....+.+.+...+.++...++....
T Consensus       298 ~lkp~l~--~g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        298 MLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             Hhcchhh--cCCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHh
Confidence            3334432  234556655554432111       1122356677778899998886654

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

Probab=98.23  E-value=0.0001  Score=68.27  Aligned_cols=181  Identities=14%  Similarity=0.165  Sum_probs=104.3

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCC--CchhhcHHHHH
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK--NFLNTDLNFQS  286 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~--~~~~~~~~~l~  286 (538)
                      ++.+++.++|.-|.|||.+++++..-+...--.++.+.     .+..+...+...+...+...+...  ...++....+.
T Consensus        49 d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~-----~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~  123 (269)
T COG3267          49 DGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVID-----KPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELA  123 (269)
T ss_pred             cCCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEec-----CcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHH
Confidence            45668999999999999999965554433222222322     234455566666666665522211  22233333333


Q ss_pred             HHh-cCCC-eEEEEecCCCh-----HHHHHHhcCcCCCCCCCEEEEeccch-------hhhhhcC-CCee-EEcCCCCHH
Q 009306          287 RRL-TRKK-VLIVFDDVDHP-----RQIKILVGRLDLFASGSRIIITTRDR-------QVLANCG-VDEV-YQMEELVHD  350 (538)
Q Consensus       287 ~~l-~~k~-~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~iiiTtR~~-------~~~~~~~-~~~~-~~l~~L~~~  350 (538)
                      ... ++++ ..+++|+..+.     +.++.|...-......-+|+..-..+       .++...+ ...+ |+++|++.+
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~  203 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEA  203 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChH
Confidence            333 4555 89999998543     33444433322222222344333211       1111111 1123 899999999


Q ss_pred             HHHHHHHhhhcCCCCCCC-chHHHHHHHHHHhcCCcHHHHHHHHH
Q 009306          351 DALRLFSRHAFGGDHPHE-SHTELACKTIKYARGVPLALEVLGRY  394 (538)
Q Consensus       351 ea~~Lf~~~~~~~~~~~~-~~~~~~~~i~~~~~G~PLal~~~~~~  394 (538)
                      +...++..+.-+...+.+ ...+....+.....|.|.+++.++..
T Consensus       204 ~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~  248 (269)
T COG3267         204 ETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLATL  248 (269)
T ss_pred             HHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHHH
Confidence            999999888754433333 34556778899999999999888764

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.23  E-value=3e-05  Score=87.26  Aligned_cols=154  Identities=12%  Similarity=0.124  Sum_probs=87.4

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~~  259 (538)
                      .-+.++||+.++..+...|....  ...+.++|++|+|||+++..++.++...+      ...+|..+...         
T Consensus       171 ~~~~~igr~~ei~~~~~~l~r~~--~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~---------  239 (852)
T TIGR03346       171 KLDPVIGRDEEIRRTIQVLSRRT--KNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGA---------  239 (852)
T ss_pred             CCCcCCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHH---------
Confidence            34679999999999999987543  23467899999999999999999875431      22233322111         


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHh--cCCCeEEEEecCCChH----------HHHHHhcCcCCCCCCCEEEEec
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRL--TRKKVLIVFDDVDHPR----------QIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                      +..       +.. .....+.....+.+.+  .+++.+|+||+++...          ....+.+.+.  ....++|-+|
T Consensus       240 l~a-------~~~-~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~--~g~i~~IgaT  309 (852)
T TIGR03346       240 LIA-------GAK-YRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALA--RGELHCIGAT  309 (852)
T ss_pred             Hhh-------cch-hhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhh--cCceEEEEeC
Confidence            100       000 0011122222222222  2468999999996431          1233333332  2234555555


Q ss_pred             cchhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          328 RDRQVLAN-------CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       328 R~~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      .....-..       ......+.++..+.++..+++....
T Consensus       310 t~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       310 TLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             cHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence            44432111       1123467899999999999887653

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.

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

Probab=98.22  E-value=2.3e-05  Score=79.83  Aligned_cols=174  Identities=15%  Similarity=0.168  Sum_probs=98.1

Q ss_pred             CCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          187 NEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      -.++.|.+...++|.+.+..           +-...+-+.|+|++|+|||+||+.+++.....|-   .+. ..      
T Consensus       144 ~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi---~i~-~s------  213 (398)
T PTZ00454        144 YSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFI---RVV-GS------  213 (398)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEE---EEe-hH------
Confidence            35688999888888875531           1234567999999999999999999987654431   111 00      


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------H---HHHHHhcCcCCC--
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------R---QIKILVGRLDLF--  317 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~---~~~~l~~~l~~~--  317 (538)
                         .+    .....+.     ........+.......|.+|+||+++..             .   .+..++..+..+  
T Consensus       214 ---~l----~~k~~ge-----~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~  281 (398)
T PTZ00454        214 ---EF----VQKYLGE-----GPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQ  281 (398)
T ss_pred             ---HH----HHHhcch-----hHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCC
Confidence               11    1111000     0011111222223467899999998642             0   122333333221  


Q ss_pred             CCCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 ASGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 ~~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      ..+..||+||.....+..     ......++++..+.++-.++|..+..+.....   .-....+++.+.|..
T Consensus       282 ~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~---dvd~~~la~~t~g~s  351 (398)
T PTZ00454        282 TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSE---EVDLEDFVSRPEKIS  351 (398)
T ss_pred             CCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCc---ccCHHHHHHHcCCCC
Confidence            235667888765533321     13456789999999998888887663221111   112456667776654

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=98.22  E-value=0.00024  Score=70.26  Aligned_cols=192  Identities=11%  Similarity=0.107  Sum_probs=109.6

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc---------------eeeEEEEeehhhhh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH---------------FSGSYFARNVREAE  252 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~---------------f~~~~~~~~~~~~~  252 (538)
                      ..++|.+...+.+...+..+. -.+...++|+.|+||+++|..++..+-..               ++...|+...... 
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~-   81 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQH-   81 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccc-
Confidence            468899999999999887542 24679999999999999999999865321               2333443310000 


Q ss_pred             hcCChHHHHHHHHHHHh--cCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEE
Q 009306          253 ETCRLGDLRQQLLSTLL--NDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRI  323 (538)
Q Consensus       253 ~~~~~~~l~~~l~~~l~--~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~i  323 (538)
                      ......   .......+  ........+++. ..+.+.+     .+.+-++|+|+++..  .....++..+...+ .+.+
T Consensus        82 ~g~~~~---~~~~~~~~~~~~~~~~I~id~i-r~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~f  156 (314)
T PRK07399         82 QGKLIT---ASEAEEAGLKRKAPPQIRLEQI-REIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTL  156 (314)
T ss_pred             cccccc---hhhhhhccccccccccCcHHHH-HHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeE
Confidence            000000   00000111  000000111121 2223333     235568999999754  45667776665544 4555


Q ss_pred             EEec-cchhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          324 IITT-RDRQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       324 iiTt-R~~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      |++| ....+++.+ .....+++.+++.++..+.+.....  ..   ........++..++|.|.....+
T Consensus       157 ILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~--~~---~~~~~~~~l~~~a~Gs~~~al~~  221 (314)
T PRK07399        157 ILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGD--EE---ILNINFPELLALAQGSPGAAIAN  221 (314)
T ss_pred             EEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhc--cc---cchhHHHHHHHHcCCCHHHHHHH
Confidence            5555 444444443 2346899999999999999988651  11   11112357899999999655443

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

Probab=98.22  E-value=7.6e-05  Score=71.67  Aligned_cols=198  Identities=15%  Similarity=0.137  Sum_probs=115.7

Q ss_pred             CCceecc---chhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhcccee------eEEEEeehhhhhhcCCh
Q 009306          188 EDLVGVR---LPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS------GSYFARNVREAEETCRL  257 (538)
Q Consensus       188 ~~~vGR~---~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~------~~~~~~~~~~~~~~~~~  257 (538)
                      +.+||-.   ..++.|.++|.. .....+.+.|+|.+|+|||++++.++..+...++      .++.+.    .....+.
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq----~P~~p~~  109 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQ----MPPEPDE  109 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEe----cCCCCCh
Confidence            4455544   345566666664 3344677999999999999999999986554432      233333    5566778


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC-CCeEEEEecCCCh-----HHHHHHhcCcCCCCC---CCEEEEecc
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR-KKVLIVFDDVDHP-----RQIKILVGRLDLFAS---GSRIIITTR  328 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~-k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~---~~~iiiTtR  328 (538)
                      ..+...++..++...............+...++. +.-+||||++.+.     ..-+.++..+...++   =+-|.+-|+
T Consensus       110 ~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~  189 (302)
T PF05621_consen  110 RRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTR  189 (302)
T ss_pred             HHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccH
Confidence            8899999999887655555555555555555543 4458999999653     222222222221122   234555555


Q ss_pred             chhhhhhc-----CCCeeEEcCCCCHH-HHHHHHHhhh--cC-CCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          329 DRQVLANC-----GVDEVYQMEELVHD-DALRLFSRHA--FG-GDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       329 ~~~~~~~~-----~~~~~~~l~~L~~~-ea~~Lf~~~~--~~-~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      +...+-..     +....+.++....+ +...|+....  .. .....-...+++..|++.++|+.--+.
T Consensus       190 ~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~  259 (302)
T PF05621_consen  190 EAYRALRTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELS  259 (302)
T ss_pred             HHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHH
Confidence            43221111     11345667776654 4445543332  11 112223457889999999999974443

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

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

Probab=98.21  E-value=8.5e-05  Score=69.08  Aligned_cols=56  Identities=18%  Similarity=0.345  Sum_probs=42.7

Q ss_pred             CCCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +...+.++|.+.+.+.|.+....  .+....-+.+||..|.|||+|++++.+++....
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~G   80 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQG   80 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcC
Confidence            34557899999999998764432  122344588899999999999999999877654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.20  E-value=7.3e-05  Score=74.28  Aligned_cols=93  Identities=11%  Similarity=0.176  Sum_probs=63.2

Q ss_pred             CCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCC
Q 009306          292 KKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPH  367 (538)
Q Consensus       292 k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  367 (538)
                      ++-++|||+++.  ......++..+..-.+++.+|++|.+. .+++.+ .....+.+.+++.+++.+.+....  .    
T Consensus       106 ~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~--~----  179 (328)
T PRK05707        106 GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQAL--P----  179 (328)
T ss_pred             CCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhc--c----
Confidence            344567899974  456777777776656677777777665 344333 234678999999999999997653  1    


Q ss_pred             CchHHHHHHHHHHhcCCcHHHHH
Q 009306          368 ESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       368 ~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      ....+.+..++..++|.|+....
T Consensus       180 ~~~~~~~~~~l~la~Gsp~~A~~  202 (328)
T PRK05707        180 ESDERERIELLTLAGGSPLRALQ  202 (328)
T ss_pred             cCChHHHHHHHHHcCCCHHHHHH
Confidence            12234456778999999964433

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=98.19  E-value=0.00037  Score=69.92  Aligned_cols=104  Identities=15%  Similarity=0.102  Sum_probs=68.4

Q ss_pred             CeEEEEecCCCh--------HHHHHHhcCcCCCCCCCEEEEeccchhhhhhc------CCCeeEEcCCCCHHHHHHHHHh
Q 009306          293 KVLIVFDDVDHP--------RQIKILVGRLDLFASGSRIIITTRDRQVLANC------GVDEVYQMEELVHDDALRLFSR  358 (538)
Q Consensus       293 ~~LlVlDdv~~~--------~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~------~~~~~~~l~~L~~~ea~~Lf~~  358 (538)
                      +-+|||||+...        ..+..+...+.. ++-.+||++|-+......+      ...+.+.|...+.+-|.++...
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~-~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~  227 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQ-NNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLS  227 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHh-cCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHH
Confidence            458999998421        112222222221 3456888888776443322      2446788999999999999999


Q ss_pred             hhcCCCCC------------------CCchHHHHHHHHHHhcCCcHHHHHHHHHhcC
Q 009306          359 HAFGGDHP------------------HESHTELACKTIKYARGVPLALEVLGRYLYG  397 (538)
Q Consensus       359 ~~~~~~~~------------------~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~  397 (538)
                      +.......                  ...........++.+||--.-|+.+++.++.
T Consensus       228 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiks  284 (431)
T PF10443_consen  228 QLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKS  284 (431)
T ss_pred             HhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHc
Confidence            88332110                  0134455677889999999999999998865

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.19  E-value=5e-05  Score=74.11  Aligned_cols=128  Identities=14%  Similarity=0.132  Sum_probs=70.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      .+.|+|++|+|||++|+.++..+....  ....|+...        ...+    ...+.+..     .......+ +.  
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~--------~~~l----~~~~~g~~-----~~~~~~~~-~~--  119 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVT--------RDDL----VGQYIGHT-----APKTKEIL-KR--  119 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEec--------HHHH----hHhhcccc-----hHHHHHHH-HH--
Confidence            588999999999999988887654321  111222200        0111    11111110     01111111 11  


Q ss_pred             CCCeEEEEecCCCh-----------HHHHHHhcCcCCCCCCCEEEEeccchhhhhhc--------CCCeeEEcCCCCHHH
Q 009306          291 RKKVLIVFDDVDHP-----------RQIKILVGRLDLFASGSRIIITTRDRQVLANC--------GVDEVYQMEELVHDD  351 (538)
Q Consensus       291 ~k~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~--------~~~~~~~l~~L~~~e  351 (538)
                      ..+-+|+||+++..           +....+...+.....+.+||+++.....-...        .....+++++++.+|
T Consensus       120 a~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~ed  199 (284)
T TIGR02880       120 AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAE  199 (284)
T ss_pred             ccCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHH
Confidence            13468999999632           22445555544434566677766543221111        123578999999999


Q ss_pred             HHHHHHhhh
Q 009306          352 ALRLFSRHA  360 (538)
Q Consensus       352 a~~Lf~~~~  360 (538)
                      ..+++...+
T Consensus       200 l~~I~~~~l  208 (284)
T TIGR02880       200 LLVIAGLML  208 (284)
T ss_pred             HHHHHHHHH
Confidence            999988876

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.

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

Probab=98.14  E-value=6.8e-05  Score=75.41  Aligned_cols=155  Identities=17%  Similarity=0.194  Sum_probs=92.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ....+.|||+.|.|||.|++++++......+...++.        .........+...+..         ......++..
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y--------~~se~f~~~~v~a~~~---------~~~~~Fk~~y  174 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVY--------LTSEDFTNDFVKALRD---------NEMEKFKEKY  174 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEe--------ccHHHHHHHHHHHHHh---------hhHHHHHHhh
Confidence            4667999999999999999999998877766332222        1122222333332221         1122333443


Q ss_pred             cCCCeEEEEecCCCh----HHHHHHhcCcCCC-CCCCEEEEeccch---------hhhhhcCCCeeEEcCCCCHHHHHHH
Q 009306          290 TRKKVLIVFDDVDHP----RQIKILVGRLDLF-ASGSRIIITTRDR---------QVLANCGVDEVYQMEELVHDDALRL  355 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~----~~~~~l~~~l~~~-~~~~~iiiTtR~~---------~~~~~~~~~~~~~l~~L~~~ea~~L  355 (538)
                        .--++++||++-.    ..-+.+...+... ..|..||+|++..         .+.+.+....++++.+++.+....+
T Consensus       175 --~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~ai  252 (408)
T COG0593         175 --SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAI  252 (408)
T ss_pred             --ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHH
Confidence              3348899999532    2233333322211 3455899998543         2233344557899999999999999


Q ss_pred             HHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          356 FSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       356 f~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      +.+++  ........++...-+++....+-
T Consensus       253 L~kka--~~~~~~i~~ev~~~la~~~~~nv  280 (408)
T COG0593         253 LRKKA--EDRGIEIPDEVLEFLAKRLDRNV  280 (408)
T ss_pred             HHHHH--HhcCCCCCHHHHHHHHHHhhccH
Confidence            99976  23333444566666666555543

>CHL00176 ftsH cell division protein; Validated

Probab=98.13  E-value=7.6e-05  Score=80.44  Aligned_cols=172  Identities=17%  Similarity=0.201  Sum_probs=97.9

Q ss_pred             CCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          187 NEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      ..++.|.+...+++.+.+..          +....+-+.|+|++|+|||+||++++.+....|   +.+. ..       
T Consensus       182 f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~---i~is-~s-------  250 (638)
T CHL00176        182 FRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPF---FSIS-GS-------  250 (638)
T ss_pred             HHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCe---eecc-HH-------
Confidence            35678888777766655421          112245699999999999999999998753321   1111 11       


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC--C
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF--A  318 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~--~  318 (538)
                        .+....    .+     .........+.......+++|+|||++..                ..+..++..+..+  .
T Consensus       251 --~f~~~~----~g-----~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~  319 (638)
T CHL00176        251 --EFVEMF----VG-----VGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGN  319 (638)
T ss_pred             --HHHHHh----hh-----hhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCC
Confidence              111100    00     01111222333444568899999999643                1133343333322  2


Q ss_pred             CCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcC
Q 009306          319 SGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARG  383 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G  383 (538)
                      .+..||.+|.....+..     ...+..+.++..+.++-.+++..++..   ...........+++.+.|
T Consensus       320 ~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~---~~~~~d~~l~~lA~~t~G  386 (638)
T CHL00176        320 KGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARN---KKLSPDVSLELIARRTPG  386 (638)
T ss_pred             CCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhh---cccchhHHHHHHHhcCCC
Confidence            35566666655433221     134567889999999999999888733   111223345677888777

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

Probab=98.11  E-value=4.5e-05  Score=83.68  Aligned_cols=152  Identities=14%  Similarity=0.199  Sum_probs=86.4

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      +.++||+.++..+.+.|....  ..-+.|+|++|+|||++|+.++.++....      ...+|..+         +..+ 
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~--~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~---------~~~l-  253 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLD---------IGSL-  253 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEecc---------HHHH-
Confidence            569999999999999887632  23367899999999999999998753321      22233221         1111 


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------HHHH-HHhcCcCCCCCCCEEEEeccc
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------RQIK-ILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------~~~~-~l~~~l~~~~~~~~iiiTtR~  329 (538)
                         +   .+.. .....+.....+.+.+ ...+.+|+||+++..          .+.. .+.+.+.  ....++|-+|..
T Consensus       254 ---l---aG~~-~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~--~g~i~vIgATt~  324 (758)
T PRK11034        254 ---L---AGTK-YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTY  324 (758)
T ss_pred             ---h---cccc-hhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh--CCCeEEEecCCh
Confidence               1   0000 0011222222222222 346789999999632          1121 2333332  223455555544


Q ss_pred             hhhhhh-------cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          330 RQVLAN-------CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       330 ~~~~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ..+...       .+..+.+.+++++.++..+++....
T Consensus       325 ~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        325 QEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             HHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence            332111       1123578999999999999998654

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

Probab=98.11  E-value=3e-05  Score=79.57  Aligned_cols=173  Identities=19%  Similarity=0.217  Sum_probs=97.8

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .++.|.+.++++|.+.+..           +-...+.+.|+|++|+|||++|+.+++.....|-   .+.. .       
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi---~V~~-s-------  251 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFL---RVVG-S-------  251 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEE---EEec-c-------
Confidence            5678999999999886642           1123456889999999999999999998765542   1110 0       


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----------------HHHHHhcCcCCC--C
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----------------QIKILVGRLDLF--A  318 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----------------~~~~l~~~l~~~--~  318 (538)
                        .+...    ..+.     ........+.....+.+.+|+||+++...                .+-.++..+..+  .
T Consensus       252 --eL~~k----~~Ge-----~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~  320 (438)
T PTZ00361        252 --ELIQK----YLGD-----GPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSR  320 (438)
T ss_pred             --hhhhh----hcch-----HHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhccc
Confidence              01000    0000     00011111122224578899999985321                112222222211  2


Q ss_pred             CCCEEEEeccchhhhhhc-----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          319 SGSRIIITTRDRQVLANC-----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~~~~-----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .+..||++|.....+...     .....++++..+.++..++|..+...-.....   -....++..+.|.-
T Consensus       321 ~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~d---vdl~~la~~t~g~s  389 (438)
T PTZ00361        321 GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAED---VDLEEFIMAKDELS  389 (438)
T ss_pred             CCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcC---cCHHHHHHhcCCCC
Confidence            356788888755443221     23567899999999999999987632211111   12345666666554

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.10  E-value=4.6e-05  Score=82.29  Aligned_cols=50  Identities=20%  Similarity=0.294  Sum_probs=39.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |...+.++|++..+..+.+.+..  .....+.|+|++|+||||||+.++...
T Consensus       150 p~~~~~iiGqs~~~~~l~~~ia~--~~~~~vlL~Gp~GtGKTTLAr~i~~~~  199 (615)
T TIGR02903       150 PRAFSEIVGQERAIKALLAKVAS--PFPQHIILYGPPGVGKTTAARLALEEA  199 (615)
T ss_pred             cCcHHhceeCcHHHHHHHHHHhc--CCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            34446799999999988777643  234569999999999999999988754

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.

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

Probab=98.10  E-value=0.00027  Score=72.34  Aligned_cols=222  Identities=16%  Similarity=0.119  Sum_probs=124.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCC
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRK  292 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k  292 (538)
                      ++.|.|+.++||||+++.+.......   .+++...........+.+....                     +.+.-..+
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~---~iy~~~~d~~~~~~~l~d~~~~---------------------~~~~~~~~   94 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE---IIYINFDDLRLDRIELLDLLRA---------------------YIELKERE   94 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcc---eEEEEecchhcchhhHHHHHHH---------------------HHHhhccC
Confidence            89999999999999997777665544   4444421111111111111111                     11111126


Q ss_pred             CeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhh-----c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCC
Q 009306          293 KVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLAN-----C-GVDEVYQMEELVHDDALRLFSRHAFGGDHP  366 (538)
Q Consensus       293 ~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~-----~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  366 (538)
                      +.+|+||.|.....|...+..+...++. +|++|+.+...+..     + +....+++-||+..|-..+-....    ..
T Consensus        95 ~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~~~~~~----~~  169 (398)
T COG1373          95 KSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKLKGEEI----EP  169 (398)
T ss_pred             CceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhhccccc----ch
Confidence            7899999999999888887776655555 88888877644322     1 345678999999999887543111    00


Q ss_pred             CCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHHhhcCCCCcHHHHHHHhH-hCCCHHhHHHhhccc-ccc
Q 009306          367 HESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISY-DGLDDKEQNIFLDIA-CFF  444 (538)
Q Consensus       367 ~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~l~~~~~~~v~~~l~~s~-~~L~~~~k~~l~~la-~f~  444 (538)
                      . . ....-+-.-.+||.|.++..-...-.  ........+.          .++.+..- ... ...+.++..++ -.+
T Consensus       170 ~-~-~~~~f~~Yl~~GGfP~~v~~~~~~~~--~~~~~~~~~~----------~Di~~~~~~~~~-~~~k~i~~~l~~~~g  234 (398)
T COG1373         170 S-K-LELLFEKYLETGGFPESVKADLSEKK--LKEYLDTILK----------RDIIERGKIENA-DLMKRILRFLASNIG  234 (398)
T ss_pred             h-H-HHHHHHHHHHhCCCcHHHhCcchhhH--HHHHHHHHHH----------HHHHHHcCcccH-HHHHHHHHHHHhhcC
Confidence            0 1 11123334557999987754332111  0011111110          01111110 011 34455554444 445


Q ss_pred             CCCCHHHHHHHH-HhCCCChHHHHHHHhhCCceeE
Q 009306          445 IDEDRDTATKFL-DDCEFFATSAIEVLVDKHLITI  478 (538)
Q Consensus       445 ~~~~~~~l~~l~-~~~~~~~~~~l~~L~~~~Li~~  478 (538)
                      ..++...+...+ ..+......+++.|.+.-++..
T Consensus       235 ~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~  269 (398)
T COG1373         235 SPISYSSLARELKGISKDTIRKYLSYLEDAFLLFL  269 (398)
T ss_pred             CccCHHHHHHHHhccchHHHHHHHHHHHHhhheEE
Confidence            568889988888 4454556678888888888773

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.07  E-value=9e-05  Score=78.53  Aligned_cols=180  Identities=17%  Similarity=0.185  Sum_probs=98.0

Q ss_pred             CCCceeccchhHHHHHhhh---c-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          187 NEDLVGVRLPMKEIESLLR---T-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~---~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      -++++|.+...+++.+++.   .       +....+-+.++|++|+|||+||+.++......|    +....        
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~----~~i~~--------  121 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPF----FSISG--------  121 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCe----eeccH--------
Confidence            3567888877766665443   1       122345589999999999999999998754332    11110        


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----------------HHHHHhcCcCCC--C
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----------------QIKILVGRLDLF--A  318 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----------------~~~~l~~~l~~~--~  318 (538)
                       ..+..    ...+     .........+.......|.+|+|||++...                .+..++..+..+  .
T Consensus       122 -~~~~~----~~~g-----~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~  191 (495)
T TIGR01241       122 -SDFVE----MFVG-----VGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTN  191 (495)
T ss_pred             -HHHHH----HHhc-----ccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCC
Confidence             11111    0000     011111222223334678999999996421                122333333222  2


Q ss_pred             CCCEEEEeccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHH
Q 009306          319 SGSRIIITTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVL  391 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~  391 (538)
                      .+..||.||.....+     .....+..+.++..+.++-.+++..+.......   .......+++.+.|. +--|..+
T Consensus       192 ~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~---~~~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       192 TGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA---PDVDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             CCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC---cchhHHHHHHhCCCCCHHHHHHH
Confidence            244456666544221     112345688999999999999998876332211   122345788888774 3444443

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.

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

Probab=98.07  E-value=6.3e-05  Score=73.31  Aligned_cols=168  Identities=18%  Similarity=0.275  Sum_probs=100.8

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceE-EEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYK-LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~-v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      ..+.|.+|+.++..+..++...+...+. +.|+|.+|.|||.+.+++.+....   ..+|+.+    -.......+..++
T Consensus         4 l~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~---~~vw~n~----~ecft~~~lle~I   76 (438)
T KOG2543|consen    4 LEPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL---ENVWLNC----VECFTYAILLEKI   76 (438)
T ss_pred             cccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC---cceeeeh----HHhccHHHHHHHH
Confidence            3478899999999999999876554444 589999999999999999987632   3568773    3346667777777


Q ss_pred             HHHHhcC-CCCC---C---chhhcHHHHHH--Hhc--CCCeEEEEecCCChHHHH-----HHhcCcCCCCCCCEEEEecc
Q 009306          265 LSTLLND-GNVK---N---FLNTDLNFQSR--RLT--RKKVLIVFDDVDHPRQIK-----ILVGRLDLFASGSRIIITTR  328 (538)
Q Consensus       265 ~~~l~~~-~~~~---~---~~~~~~~~l~~--~l~--~k~~LlVlDdv~~~~~~~-----~l~~~l~~~~~~~~iiiTtR  328 (538)
                      +.+.... .+..   .   ........+.+  ...  ++.++|||||++...+.+     .+............+|+++-
T Consensus        77 L~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~  156 (438)
T KOG2543|consen   77 LNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSA  156 (438)
T ss_pred             HHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEec
Confidence            7776421 1111   1   11111222222  122  358999999997654422     22111111112233333332


Q ss_pred             c---hhhhhhcCCC--eeEEcCCCCHHHHHHHHHhhh
Q 009306          329 D---RQVLANCGVD--EVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       329 ~---~~~~~~~~~~--~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      .   .......+..  -++.++..+.+|..+++.+.-
T Consensus       157 ~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~  193 (438)
T KOG2543|consen  157 PSCEKQYLINTGTLEIVVLHFPQYSVEETQVILSRDN  193 (438)
T ss_pred             cccHHHhhcccCCCCceEEecCCCCHHHHHHHHhcCC
Confidence            2   2223222322  356789999999999987643

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

Probab=98.05  E-value=0.00011  Score=71.09  Aligned_cols=171  Identities=19%  Similarity=0.249  Sum_probs=99.7

Q ss_pred             CceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          189 DLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      ..=|-+.++++|.+...-           +-+..+-|.++|++|.|||-||++++++....|     +..++        
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtF-----Irvvg--------  218 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATF-----IRVVG--------  218 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceE-----EEecc--------
Confidence            445677777777765432           223456699999999999999999999876543     33111        


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------------HHHHHHhcCcCCCCC-
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------------RQIKILVGRLDLFAS-  319 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~~~-  319 (538)
                      ..+.+..    .+.      -..+...+.+.. ...|.+|.+|++|..                ..+-.|+..+..|.+ 
T Consensus       219 SElVqKY----iGE------GaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~  288 (406)
T COG1222         219 SELVQKY----IGE------GARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPR  288 (406)
T ss_pred             HHHHHHH----hcc------chHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCC
Confidence            1122221    111      111222222222 357899999999642                123344555555544 


Q ss_pred             -CCEEEEeccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          320 -GSRIIITTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       320 -~~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                       +.+||..|...+.+     ..-..++.++++.-+.+.-.++|.-|..+=+...+   --.+.+++.+.|.-
T Consensus       289 ~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~d---vd~e~la~~~~g~s  357 (406)
T COG1222         289 GNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADD---VDLELLARLTEGFS  357 (406)
T ss_pred             CCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccC---cCHHHHHHhcCCCc
Confidence             56888877655443     22245678999977777777788777632221111   11456677777764

>CHL00181 cbbX CbbX; Provisional

Probab=98.03  E-value=0.00019  Score=69.99  Aligned_cols=129  Identities=12%  Similarity=0.142  Sum_probs=71.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc-e-eeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH-F-SGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~-f-~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.++|++|+|||++|+.++...... + ...-|+...        ...    +.....+..     .......+.+  
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~--------~~~----l~~~~~g~~-----~~~~~~~l~~--  120 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVT--------RDD----LVGQYIGHT-----APKTKEVLKK--  120 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEec--------HHH----HHHHHhccc-----hHHHHHHHHH--
Confidence            348899999999999999998864321 1 111122200        111    111111110     0111111211  


Q ss_pred             cCCCeEEEEecCCCh-----------HHHHHHhcCcCCCCCCCEEEEeccchhhhhh------c--CCCeeEEcCCCCHH
Q 009306          290 TRKKVLIVFDDVDHP-----------RQIKILVGRLDLFASGSRIIITTRDRQVLAN------C--GVDEVYQMEELVHD  350 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~------~--~~~~~~~l~~L~~~  350 (538)
                       ...-+|+||+++..           +....+...+.....+.+||+++........      +  .....+.+++++.+
T Consensus       121 -a~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~  199 (287)
T CHL00181        121 -AMGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPE  199 (287)
T ss_pred             -ccCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHH
Confidence             12359999999642           3345555544443455667777654322110      1  23457899999999


Q ss_pred             HHHHHHHhhh
Q 009306          351 DALRLFSRHA  360 (538)
Q Consensus       351 ea~~Lf~~~~  360 (538)
                      |..+++...+
T Consensus       200 el~~I~~~~l  209 (287)
T CHL00181        200 ELLQIAKIML  209 (287)
T ss_pred             HHHHHHHHHH
Confidence            9999998887

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

Probab=98.01  E-value=5.1e-05  Score=64.85  Aligned_cols=23  Identities=35%  Similarity=0.472  Sum_probs=21.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |.|+|++|+|||++|+.+++.+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTT
T ss_pred             CEEECcCCCCeeHHHHHHHhhcc
Confidence            57999999999999999999875

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 ....

>CHL00195 ycf46 Ycf46; Provisional

Probab=98.00  E-value=0.00014  Score=75.85  Aligned_cols=175  Identities=16%  Similarity=0.151  Sum_probs=94.6

Q ss_pred             CCceeccchhHHHHHhh---hc-----CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHH
Q 009306          188 EDLVGVRLPMKEIESLL---RT-----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L---~~-----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~  259 (538)
                      .++-|.+...+.+....   ..     +-...+-+.++|++|+|||.+|+.++......|    +..+...         
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~----~~l~~~~---------  294 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPL----LRLDVGK---------  294 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCE----EEEEhHH---------
Confidence            45778776665555421   10     223456799999999999999999999865432    1111110         


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH--------------HHHHHhcCcCCCCCCCEEEE
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR--------------QIKILVGRLDLFASGSRIII  325 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--------------~~~~l~~~l~~~~~~~~iii  325 (538)
                          +.....+     .........+...-...|++|+||++|..-              .+..++..+.....+.-||.
T Consensus       295 ----l~~~~vG-----ese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIa  365 (489)
T CHL00195        295 ----LFGGIVG-----ESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVA  365 (489)
T ss_pred             ----hcccccC-----hHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEE
Confidence                0000000     001111111222223578999999996320              11222222222233455666


Q ss_pred             eccchhhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          326 TTRDRQVLA-----NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       326 TtR~~~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      ||.+...+.     ....+..+.++..+.++-.++|..+..+.. +..........+++.+.|..
T Consensus       366 TTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~-~~~~~~~dl~~La~~T~GfS  429 (489)
T CHL00195        366 TANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFR-PKSWKKYDIKKLSKLSNKFS  429 (489)
T ss_pred             ecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcC-CCcccccCHHHHHhhcCCCC
Confidence            776553221     123567888999999999999988873322 11111223567777777764

>PRK08116 hypothetical protein; Validated

Probab=97.95  E-value=5.8e-05  Score=72.96  Aligned_cols=102  Identities=26%  Similarity=0.352  Sum_probs=56.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      ..+.|+|.+|+|||.||.++++.+..+...++|+.          ...++..+........      ......+.+.+.+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~----------~~~ll~~i~~~~~~~~------~~~~~~~~~~l~~  178 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN----------FPQLLNRIKSTYKSSG------KEDENEIIRSLVN  178 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE----------HHHHHHHHHHHHhccc------cccHHHHHHHhcC
Confidence            45899999999999999999998776544455554          2223333333322110      0111223334444


Q ss_pred             CCeEEEEecCC--Ch--HHHHHHhcCcC-CCCCCCEEEEeccch
Q 009306          292 KKVLIVFDDVD--HP--RQIKILVGRLD-LFASGSRIIITTRDR  330 (538)
Q Consensus       292 k~~LlVlDdv~--~~--~~~~~l~~~l~-~~~~~~~iiiTtR~~  330 (538)
                      -. ||||||+.  ..  .....+...+. ....+..+||||...
T Consensus       179 ~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        179 AD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            44 89999993  22  12222322222 113456788888644

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

Probab=97.94  E-value=1.2e-05  Score=76.45  Aligned_cols=93  Identities=18%  Similarity=0.149  Sum_probs=57.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC-C--C---chhhcH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV-K--N---FLNTDL  282 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~-~--~---~~~~~~  282 (538)
                      ....++|.|++|+|||||++.+++.+.. +|+..+|+..+.+  ....+.++++.+...+...... .  .   ......
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~e--r~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~   92 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDE--RPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVL   92 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccC--CCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHH
Confidence            3456899999999999999999998754 5788888774433  1346777777773322211111 1  0   111112


Q ss_pred             HHHHHH-hcCCCeEEEEecCCCh
Q 009306          283 NFQSRR-LTRKKVLIVFDDVDHP  304 (538)
Q Consensus       283 ~~l~~~-l~~k~~LlVlDdv~~~  304 (538)
                      ...... -.++++++++|++...
T Consensus        93 ~~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          93 EKAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHHCCCCEEEEEECHHHh
Confidence            222222 2478999999998543

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.

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

Probab=97.92  E-value=7e-05  Score=71.30  Aligned_cols=80  Identities=16%  Similarity=0.217  Sum_probs=48.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc----cceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS----RHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQS  286 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~----~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~  286 (538)
                      .|++.++||||.|||+|++++++++.    ..|..+.-+.    .    ...+++.+-++.-+      ..+..+...+.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liE----i----nshsLFSKWFsESg------KlV~kmF~kI~  242 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIE----I----NSHSLFSKWFSESG------KLVAKMFQKIQ  242 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEE----E----ehhHHHHHHHhhhh------hHHHHHHHHHH
Confidence            57899999999999999999999643    3454444443    1    11222222222222      23444555566


Q ss_pred             HHhcCCC--eEEEEecCCCh
Q 009306          287 RRLTRKK--VLIVFDDVDHP  304 (538)
Q Consensus       287 ~~l~~k~--~LlVlDdv~~~  304 (538)
                      +.+.++.  +++.+|+|++.
T Consensus       243 ELv~d~~~lVfvLIDEVESL  262 (423)
T KOG0744|consen  243 ELVEDRGNLVFVLIDEVESL  262 (423)
T ss_pred             HHHhCCCcEEEEEeHHHHHH
Confidence            6665555  56678999754

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

Probab=97.91  E-value=0.00025  Score=73.55  Aligned_cols=187  Identities=17%  Similarity=0.191  Sum_probs=112.4

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc----ee--eEEEEeehhhhhhcCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH----FS--GSYFARNVREAEETCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~----f~--~~~~~~~~~~~~~~~~~~  258 (538)
                      ....+++|.+..+..|...+..+. -......+|+.|+||||+|+.++..+-..    ..  +.|..+  ...... ...
T Consensus        13 ~~F~evvGQe~v~~~L~nal~~~r-i~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~C--k~I~~g-~~~   88 (515)
T COG2812          13 KTFDDVVGQEHVVKTLSNALENGR-IAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISC--KEINEG-SLI   88 (515)
T ss_pred             ccHHHhcccHHHHHHHHHHHHhCc-chhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhh--HhhhcC-Ccc
Confidence            344778999999999999887532 24457789999999999999999854221    11  111111  111111 000


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCC--ChHHHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVD--HPRQIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ++..     +.....  ..+++..+ +.+..     .++.=+.|||+|+  +...+.+++..+..-.++...|+.|.+..
T Consensus        89 DviE-----iDaASn--~gVddiR~-i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~  160 (515)
T COG2812          89 DVIE-----IDAASN--TGVDDIRE-IIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQ  160 (515)
T ss_pred             cchh-----hhhhhc--cChHHHHH-HHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcC
Confidence            0000     000000  11222111 22222     2344588999996  44678889888876667777776666552


Q ss_pred             h-h-hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          332 V-L-ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       332 ~-~-~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      - . +-+...+.|.++.++.++....+...+  ....-..+.+....+++..+|..
T Consensus       161 Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~--~~E~I~~e~~aL~~ia~~a~Gs~  214 (515)
T COG2812         161 KIPNTILSRCQRFDFKRLDLEEIAKHLAAIL--DKEGINIEEDALSLIARAAEGSL  214 (515)
T ss_pred             cCchhhhhccccccccCCCHHHHHHHHHHHH--HhcCCccCHHHHHHHHHHcCCCh
Confidence            2 2 122334689999999999999988877  33334455677777888887765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.91  E-value=0.00014  Score=80.79  Aligned_cols=173  Identities=17%  Similarity=0.164  Sum_probs=94.1

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      +++.|.+..++.+.+++..           +-...+.+.|+|++|+|||+||+.+++.....|   +.+. ..+....  
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~---i~i~-~~~i~~~--  251 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYF---ISIN-GPEIMSK--  251 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeE---EEEe-cHHHhcc--
Confidence            4588999999988876632           112345689999999999999999998765432   2222 1110000  


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCCC-CCCE
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLFA-SGSR  322 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~~-~~~~  322 (538)
                                 ..     ..........+.......+.+|+|||++..             .....+...+.... .+..
T Consensus       252 -----------~~-----g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~v  315 (733)
T TIGR01243       252 -----------YY-----GESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRV  315 (733)
T ss_pred             -----------cc-----cHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCE
Confidence                       00     000111112222233456789999998542             11233333333222 2333


Q ss_pred             EEE-eccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          323 III-TTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       323 iii-TtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      ++| +|.....+ ..+    .....+.++..+.++-.+++..+.-.....   .......+++.+.|..
T Consensus       316 ivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~---~d~~l~~la~~t~G~~  381 (733)
T TIGR01243       316 IVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLA---EDVDLDKLAEVTHGFV  381 (733)
T ss_pred             EEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCc---cccCHHHHHHhCCCCC
Confidence            444 44433211 111    234578888889999888888665221111   1223567778887764

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.90  E-value=0.00058  Score=67.35  Aligned_cols=91  Identities=14%  Similarity=0.136  Sum_probs=63.6

Q ss_pred             CCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhcC-CCeeEEcCCCCHHHHHHHHHhhhcCCCCCC
Q 009306          292 KKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANCG-VDEVYQMEELVHDDALRLFSRHAFGGDHPH  367 (538)
Q Consensus       292 k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  367 (538)
                      +.-++|||+++..  ....+++..+..-.+++.+|++|.+. .+++.+. ....+.+.+++.+++.+.+....       
T Consensus       113 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~-------  185 (319)
T PRK08769        113 IAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQG-------  185 (319)
T ss_pred             CcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHcC-------
Confidence            4558999999754  55677777776656777777777653 4444432 34678999999999999887532       


Q ss_pred             CchHHHHHHHHHHhcCCcHHHHH
Q 009306          368 ESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       368 ~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                       .....+..++..++|.|+....
T Consensus       186 -~~~~~a~~~~~l~~G~p~~A~~  207 (319)
T PRK08769        186 -VSERAAQEALDAARGHPGLAAQ  207 (319)
T ss_pred             -CChHHHHHHHHHcCCCHHHHHH
Confidence             1133466789999999975533

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.90  E-value=5.3e-05  Score=81.08  Aligned_cols=56  Identities=20%  Similarity=0.221  Sum_probs=45.2

Q ss_pred             ccCCCCCCCceeccchhHHHHHhhhcCC---CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          181 DTFHSENEDLVGVRLPMKEIESLLRTGS---TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       181 ~~~~~~~~~~vGR~~~l~~l~~~L~~~~---~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|.....++|.+..++++..++....   ...++++|+|++|+||||+++.++..+.
T Consensus        77 KyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~  135 (637)
T TIGR00602        77 KYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG  135 (637)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3445666889999999999999987532   3356799999999999999999998654

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

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

Probab=97.88  E-value=1.8e-05  Score=69.56  Aligned_cols=64  Identities=17%  Similarity=0.359  Sum_probs=55.5

Q ss_pred             cEEEcCccccc-ccchHHHHHHHHhhC-CCeeEeeC-CCC--CCCcchHHHHHHHHhcceEEEEeccCc
Q 009306           19 DVFLSFGGEDT-RESFTSHLYSALSRE-TVETFIDD-DLR--RGDEISQSLLDAIEASSISIIIFSESY   82 (538)
Q Consensus        19 dvFiSy~~~D~-~~~~~~~l~~~l~~~-g~~~~~d~-~~~--~g~~~~~~i~~~i~~s~~~i~v~S~~y   82 (538)
                      -|||||++... ...+|..|...|+.. |+.|.+|. +..  ++..+..++.+.+++++.+|+|+||.|
T Consensus         2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~   70 (150)
T PF08357_consen    2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY   70 (150)
T ss_pred             eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence            49999998543 447799999999999 99999998 664  477899999999999999999999654

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 [].

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.88  E-value=0.00039  Score=69.48  Aligned_cols=146  Identities=12%  Similarity=0.117  Sum_probs=87.9

Q ss_pred             Ccee-ccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc---------------------eeeEEEEe
Q 009306          189 DLVG-VRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH---------------------FSGSYFAR  246 (538)
Q Consensus       189 ~~vG-R~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~---------------------f~~~~~~~  246 (538)
                      .++| -+..++.|...+..+ .-.....++|+.|+|||++|+.++..+-..                     ++...++.
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~-~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~   84 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKN-RLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVA   84 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEec
Confidence            4566 666677777777643 235567999999999999999998865321                     11111111


Q ss_pred             ehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCC
Q 009306          247 NVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP--RQIKILVGRLDLFASG  320 (538)
Q Consensus       247 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~  320 (538)
                      .                        ......+++..+.+...    ..+.+-++|+|+++..  .....++..+...+++
T Consensus        85 ~------------------------~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~  140 (329)
T PRK08058         85 P------------------------DGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGG  140 (329)
T ss_pred             c------------------------ccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCC
Confidence            0                        00001112222211111    1234458999999744  4567777777765677


Q ss_pred             CEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhh
Q 009306          321 SRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRH  359 (538)
Q Consensus       321 ~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~  359 (538)
                      +.+|++|.+. .+.+.+ .....+++.+++.++..+.+...
T Consensus       141 ~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        141 TTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             ceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            7777777654 333333 23468999999999998888653

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.84  E-value=8.5e-05  Score=63.88  Aligned_cols=35  Identities=29%  Similarity=0.300  Sum_probs=27.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.+.|+|++|+||||+++.++..+......++++.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~   37 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYID   37 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEEC
Confidence            46899999999999999999998766543344443

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.83  E-value=0.00057  Score=64.78  Aligned_cols=36  Identities=22%  Similarity=0.231  Sum_probs=29.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...+.++|.+|+|||+|+.++++.+......++++.
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it  134 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT  134 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            346899999999999999999998766555555554

>PRK08181 transposase; Validated

Probab=97.82  E-value=8e-05  Score=71.62  Aligned_cols=35  Identities=29%  Similarity=0.268  Sum_probs=27.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .-+.|+|++|+|||.||.++++....+...+.|+.
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~  141 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR  141 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeee
Confidence            34899999999999999999987765544455554

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.82  E-value=0.00023  Score=79.23  Aligned_cols=173  Identities=17%  Similarity=0.198  Sum_probs=95.9

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .++.|.+...+.|.+.+.-           +....+-+.++|++|+|||+||+++++.....|   +.+. ..       
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~f---i~v~-~~-------  521 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANF---IAVR-GP-------  521 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCE---EEEe-hH-------
Confidence            4567888777777665431           112345589999999999999999999865443   1111 10       


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--------------HHHHHHhcCcCCC--CCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--------------RQIKILVGRLDLF--ASG  320 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--------------~~~~~l~~~l~~~--~~~  320 (538)
                            .+++...+     .............-...+.+|+||+++..              ..+..++..+...  ..+
T Consensus       522 ------~l~~~~vG-----ese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~  590 (733)
T TIGR01243       522 ------EILSKWVG-----ESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSN  590 (733)
T ss_pred             ------HHhhcccC-----cHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCC
Confidence                  11111111     01111111222222457899999998642              1233344433321  234


Q ss_pred             CEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          321 SRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       321 ~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .-||.||.....+..     -..+..+.++..+.++-.++|..+..+.....   ......+++.+.|.-
T Consensus       591 v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~---~~~l~~la~~t~g~s  657 (733)
T TIGR01243       591 VVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAE---DVDLEELAEMTEGYT  657 (733)
T ss_pred             EEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCc---cCCHHHHHHHcCCCC
Confidence            456666655433221     13456888999999999999977652221111   112456777777764

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.

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

Probab=97.82  E-value=0.0002  Score=66.28  Aligned_cols=172  Identities=16%  Similarity=0.227  Sum_probs=99.7

Q ss_pred             CCceeccchhHHH---HHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          188 EDLVGVRLPMKEI---ESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       188 ~~~vGR~~~l~~l---~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ++.||.+....+.   .+.|..    +....+-|..+|++|.|||.+|++++++.+.-|    .....            
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp~----l~vka------------  184 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPL----LLVKA------------  184 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCce----EEech------------
Confidence            5788888766544   344543    334577899999999999999999998865432    11100            


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHH-hcCCCeEEEEecCCCh--------------HHHHHHhcCcCCC--CCCCEE
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRR-LTRKKVLIVFDDVDHP--------------RQIKILVGRLDLF--ASGSRI  323 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~--------------~~~~~l~~~l~~~--~~~~~i  323 (538)
                       .+++....+      +....+..+.++ -+..|+++.||++|..              +.+.+++..+...  +.|...
T Consensus       185 -t~liGehVG------dgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvt  257 (368)
T COG1223         185 -TELIGEHVG------DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVT  257 (368)
T ss_pred             -HHHHHHHhh------hHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEE
Confidence             111111111      111111222222 2457999999998642              3355666555433  345555


Q ss_pred             EEeccchhhhhhc---CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          324 IITTRDRQVLANC---GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       324 iiTtR~~~~~~~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      |-.|.+...+...   .....++..--+.+|-..++...+  ..-|.+.... .+.++++++|..
T Consensus       258 IaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~--k~~Plpv~~~-~~~~~~~t~g~S  319 (368)
T COG1223         258 IAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYA--KKFPLPVDAD-LRYLAAKTKGMS  319 (368)
T ss_pred             EeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHH--HhCCCccccC-HHHHHHHhCCCC
Confidence            6556555443321   234567778888899999998887  2333322222 567777777764

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.81  E-value=3.8e-05  Score=76.41  Aligned_cols=92  Identities=16%  Similarity=0.161  Sum_probs=57.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCC-CCCC--ch---hhcH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDG-NVKN--FL---NTDL  282 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~-~~~~--~~---~~~~  282 (538)
                      ..+..+|+|++|+|||||++.+++.+.. +|+..+|+..+.+.  ...+.++++.+...+.... +...  ..   ....
T Consensus       168 kGQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER--~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~i  245 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDER--PEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVI  245 (416)
T ss_pred             cCceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCc--hhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHH
Confidence            3445899999999999999999997765 58888898865542  2356667777653222111 1110  00   0111


Q ss_pred             HHHHHH-hcCCCeEEEEecCCC
Q 009306          283 NFQSRR-LTRKKVLIVFDDVDH  303 (538)
Q Consensus       283 ~~l~~~-l~~k~~LlVlDdv~~  303 (538)
                      +.-... ..++.++|++|++..
T Consensus       246 e~Ae~~~e~G~dVlL~iDsItR  267 (416)
T PRK09376        246 EKAKRLVEHGKDVVILLDSITR  267 (416)
T ss_pred             HHHHHHHHcCCCEEEEEEChHH
Confidence            111111 257899999999954

>PRK12377 putative replication protein; Provisional

Probab=97.78  E-value=0.0001  Score=70.03  Aligned_cols=36  Identities=22%  Similarity=0.202  Sum_probs=29.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...+.|+|++|+|||+||.++++.+......+.|+.
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            356899999999999999999998876655556654

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.78  E-value=0.001  Score=64.22  Aligned_cols=25  Identities=36%  Similarity=0.458  Sum_probs=21.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+.|.|++|+|||+||+.++.....
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~lg~   47 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARKRDR   47 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            4789999999999999999986543

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).

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.76  E-value=0.0014  Score=65.45  Aligned_cols=89  Identities=13%  Similarity=0.165  Sum_probs=62.6

Q ss_pred             CCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCC
Q 009306          291 RKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHP  366 (538)
Q Consensus       291 ~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  366 (538)
                      ++.=++|||+++.  ......++..+..-.++..+|++|.+. .+++.+ ...+.+.+.+++.+++.+.+....      
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~------  180 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREV------  180 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHcc------
Confidence            4555899999974  456778888777666677776666654 455443 234578899999999999886542      


Q ss_pred             CCchHHHHHHHHHHhcCCcH
Q 009306          367 HESHTELACKTIKYARGVPL  386 (538)
Q Consensus       367 ~~~~~~~~~~i~~~~~G~PL  386 (538)
                       ....+.+..++..++|.|.
T Consensus       181 -~~~~~~a~~~~~la~G~~~  199 (334)
T PRK07993        181 -TMSQDALLAALRLSAGAPG  199 (334)
T ss_pred             -CCCHHHHHHHHHHcCCCHH
Confidence             1223446788999999995

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

Probab=97.75  E-value=0.00048  Score=67.88  Aligned_cols=151  Identities=23%  Similarity=0.248  Sum_probs=81.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh--cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHH
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE--TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQS  286 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~--~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~  286 (538)
                      ...+.++|||++|+|||.+|++++.+....|    ......+...  .-.....+++++..                 ..
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~~----i~vsa~eL~sk~vGEsEk~IR~~F~~-----------------A~  204 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIEP----IVMSAGELESENAGEPGKLIRQRYRE-----------------AA  204 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCCe----EEEEHHHhhcCcCCcHHHHHHHHHHH-----------------HH
Confidence            3467899999999999999999999876543    2221211111  01122222222221                 11


Q ss_pred             HH--hcCCCeEEEEecCCCh------------HHH--HHHhcCcC--------------CCCCCCEEEEeccchhhhhh-
Q 009306          287 RR--LTRKKVLIVFDDVDHP------------RQI--KILVGRLD--------------LFASGSRIIITTRDRQVLAN-  335 (538)
Q Consensus       287 ~~--l~~k~~LlVlDdv~~~------------~~~--~~l~~~l~--------------~~~~~~~iiiTtR~~~~~~~-  335 (538)
                      +.  -+.++++|+||++|..            .++  ..|+..+.              ....+..||.||.....+.. 
T Consensus       205 ~~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpA  284 (413)
T PLN00020        205 DIIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAP  284 (413)
T ss_pred             HHhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHh
Confidence            11  1468999999998631            111  23332211              12345667888866543221 


Q ss_pred             -c---CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          336 -C---GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       336 -~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                       .   ..+..|  ..-+.++-.+++..+. +.....   .....++++...|-|+
T Consensus       285 LlRpGRfDk~i--~lPd~e~R~eIL~~~~-r~~~l~---~~dv~~Lv~~f~gq~~  333 (413)
T PLN00020        285 LIRDGRMEKFY--WAPTREDRIGVVHGIF-RDDGVS---REDVVKLVDTFPGQPL  333 (413)
T ss_pred             HcCCCCCCcee--CCCCHHHHHHHHHHHh-ccCCCC---HHHHHHHHHcCCCCCc
Confidence             1   122333  4456677777777665 222222   3556677777777765

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.73  E-value=0.0022  Score=63.41  Aligned_cols=89  Identities=9%  Similarity=0.135  Sum_probs=63.1

Q ss_pred             CCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhcC-CCeeEEcCCCCHHHHHHHHHhhhcCCCCC
Q 009306          291 RKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANCG-VDEVYQMEELVHDDALRLFSRHAFGGDHP  366 (538)
Q Consensus       291 ~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  366 (538)
                      ++.=++|||+++..  ....+++..+..-.++..+|++|.+. .+++.+. ....+.+.+++.+++.+.+....  .   
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~--~---  180 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQS--S---  180 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHh--c---
Confidence            34458889999754  56778888777666777777777654 4454432 34688999999999999988764  1   


Q ss_pred             CCchHHHHHHHHHHhcCCcH
Q 009306          367 HESHTELACKTIKYARGVPL  386 (538)
Q Consensus       367 ~~~~~~~~~~i~~~~~G~PL  386 (538)
                        .....+..++..++|.|+
T Consensus       181 --~~~~~~~~~~~l~~g~p~  198 (325)
T PRK06871        181 --AEISEILTALRINYGRPL  198 (325)
T ss_pred             --cChHHHHHHHHHcCCCHH
Confidence              112245677889999995

>PRK04132 replication factor C small subunit; Provisional

Probab=97.71  E-value=0.00092  Score=73.76  Aligned_cols=153  Identities=14%  Similarity=0.156  Sum_probs=92.6

Q ss_pred             Eec--cCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCC
Q 009306          216 IWG--IGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRK  292 (538)
Q Consensus       216 I~G--~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k  292 (538)
                      +.|  |.++||||+|..+++++-. .+...+...+.   ++..+.. ..+.+...+......              -..+
T Consensus       569 ~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNA---Sd~rgid-~IR~iIk~~a~~~~~--------------~~~~  630 (846)
T PRK04132        569 IGGNLPTVLHNTTAALALARELFGENWRHNFLELNA---SDERGIN-VIREKVKEFARTKPI--------------GGAS  630 (846)
T ss_pred             hcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeC---CCcccHH-HHHHHHHHHHhcCCc--------------CCCC
Confidence            347  8899999999999998632 23222222222   2222332 233333322211110              0123


Q ss_pred             CeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCC
Q 009306          293 KVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHE  368 (538)
Q Consensus       293 ~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  368 (538)
                      .-++|||+++..  .....|...+......+++|+++.+. .+...+ .....+++.+++.++..+.+...+...  ...
T Consensus       631 ~KVvIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~E--gi~  708 (846)
T PRK04132        631 FKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENE--GLE  708 (846)
T ss_pred             CEEEEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhc--CCC
Confidence            469999999865  46677777766556677777766554 333332 234689999999999998887765221  122


Q ss_pred             chHHHHHHHHHHhcCCcHHH
Q 009306          369 SHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       369 ~~~~~~~~i~~~~~G~PLal  388 (538)
                      ..++....++..++|.+...
T Consensus       709 i~~e~L~~Ia~~s~GDlR~A  728 (846)
T PRK04132        709 LTEEGLQAILYIAEGDMRRA  728 (846)
T ss_pred             CCHHHHHHHHHHcCCCHHHH
Confidence            34678889999999988443

>TIGR00767 rho transcription termination factor Rho

Probab=97.70  E-value=6.4e-05  Score=75.18  Aligned_cols=93  Identities=15%  Similarity=0.117  Sum_probs=58.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC-C-Cc----hhhcH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV-K-NF----LNTDL  282 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~-~-~~----~~~~~  282 (538)
                      ..+.++|+|++|.|||||++.+++.+... |+..+|+..+.+  ....+.++++.+...+....-. . ..    .....
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgE--R~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDE--RPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCC--CCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            34569999999999999999999987665 888888875433  2346777888774432221111 1 00    11111


Q ss_pred             HHHHHH-hcCCCeEEEEecCCCh
Q 009306          283 NFQSRR-LTRKKVLIVFDDVDHP  304 (538)
Q Consensus       283 ~~l~~~-l~~k~~LlVlDdv~~~  304 (538)
                      +..... -.+++++|++|++...
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHH
Confidence            112222 2578999999999644

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

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.68  E-value=0.0041  Score=61.32  Aligned_cols=105  Identities=13%  Similarity=0.178  Sum_probs=68.7

Q ss_pred             CCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhcC-CCeeEEcCCCCHHHHHHHHHhhhcCCCCCC
Q 009306          292 KKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANCG-VDEVYQMEELVHDDALRLFSRHAFGGDHPH  367 (538)
Q Consensus       292 k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  367 (538)
                      +.=++|||+++..  ....+++..+..-.+++.+|++|.+. .+++.+. ....+.+.+++.+++.+.+....      .
T Consensus       108 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~------~  181 (319)
T PRK06090        108 GYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQG------I  181 (319)
T ss_pred             CceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcC------C
Confidence            3458899999754  56777887777666777776666554 4555443 34688999999999999887542      1


Q ss_pred             CchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 009306          368 ESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSK  409 (538)
Q Consensus       368 ~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~  409 (538)
                      +    ....++..++|.|+....+   +.......++..+..
T Consensus       182 ~----~~~~~l~l~~G~p~~A~~~---~~~~~~~~~~~~~~~  216 (319)
T PRK06090        182 T----VPAYALKLNMGSPLKTLAM---MKEGGLEKYHKLERQ  216 (319)
T ss_pred             c----hHHHHHHHcCCCHHHHHHH---hCCCcHHHHHHHHHH
Confidence            1    1356788999999855443   333333444434433

>PRK09183 transposase/IS protein; Provisional

Probab=97.67  E-value=0.00018  Score=69.16  Aligned_cols=35  Identities=26%  Similarity=0.239  Sum_probs=26.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+.|+|++|+|||+||..++.........+.|+.
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~  137 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT  137 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            45889999999999999999887544433344443

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

Probab=97.66  E-value=0.00063  Score=70.25  Aligned_cols=173  Identities=15%  Similarity=0.146  Sum_probs=95.1

Q ss_pred             CCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          187 NEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      ..++=|.+..+.+|.+++..          +-...+-|.+|||+|+|||.||++++.++.-.|     +.    .+.   
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf-----~~----isA---  256 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPF-----LS----ISA---  256 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCce-----Ee----ecc---
Confidence            35677999999999887643          112356699999999999999999999875443     22    000   


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCC------
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLF------  317 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~------  317 (538)
                           -++.+.+.+     .+.+...+...+.....|++++||++|..             ..+..|+..+...      
T Consensus       257 -----peivSGvSG-----ESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~  326 (802)
T KOG0733|consen  257 -----PEIVSGVSG-----ESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTK  326 (802)
T ss_pred             -----hhhhcccCc-----ccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccC
Confidence                 011112111     12222233333444678999999999742             1133444333322      


Q ss_pred             CCCCEEEEe-ccchhhhhhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC
Q 009306          318 ASGSRIIIT-TRDRQVLANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV  384 (538)
Q Consensus       318 ~~~~~iiiT-tR~~~~~~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~  384 (538)
                      +.+.-||-+ +|-..+-+.+    +.++.+.|.--+..+-.+++...+-+-.....   =..++|++.+-|.
T Consensus       327 g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~---~d~~qlA~lTPGf  395 (802)
T KOG0733|consen  327 GDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGD---FDFKQLAKLTPGF  395 (802)
T ss_pred             CCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCC---cCHHHHHhcCCCc
Confidence            222333333 3433332222    24567778777777666766666532221111   1134566666665

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

Probab=97.65  E-value=0.00024  Score=64.62  Aligned_cols=55  Identities=25%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             ccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          181 DTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       181 ~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...|..-.+.||-++-++.+.-...++  +.+-+.|.||+|+||||-+..+++++-.
T Consensus        20 KYrP~~l~dIVGNe~tv~rl~via~~g--nmP~liisGpPG~GKTTsi~~LAr~LLG   74 (333)
T KOG0991|consen   20 KYRPSVLQDIVGNEDTVERLSVIAKEG--NMPNLIISGPPGTGKTTSILCLARELLG   74 (333)
T ss_pred             hhCchHHHHhhCCHHHHHHHHHHHHcC--CCCceEeeCCCCCchhhHHHHHHHHHhC
Confidence            344555578899999998888776643  4666899999999999999999987543

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

Probab=97.64  E-value=0.00027  Score=74.42  Aligned_cols=156  Identities=19%  Similarity=0.296  Sum_probs=90.1

Q ss_pred             CCCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          187 NEDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      ..+.+|.+...+.+.+.|.-    +.-..++++++||+|+|||+|++.++..+...|-. +-+-.+++.+.         
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            35679999999999888753    23346799999999999999999999988776531 11211211111         


Q ss_pred             HHHHHHhcCCCCCCchh----hcHHHHHHHhcCCCeEEEEecCCCh----------HHHHHHhcCcC-CCC--------C
Q 009306          263 QLLSTLLNDGNVKNFLN----TDLNFQSRRLTRKKVLIVFDDVDHP----------RQIKILVGRLD-LFA--------S  319 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~----~~~~~l~~~l~~k~~LlVlDdv~~~----------~~~~~l~~~l~-~~~--------~  319 (538)
                           +.+...  ..+.    .....+++ .+.+.-+++||++|..          ..++.|-+..+ .|.        .
T Consensus       392 -----IRGHRR--TYIGamPGrIiQ~mkk-a~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yD  463 (782)
T COG0466         392 -----IRGHRR--TYIGAMPGKIIQGMKK-AGVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYD  463 (782)
T ss_pred             -----hccccc--cccccCChHHHHHHHH-hCCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccc
Confidence                 001100  1111    11222222 2445668999999742          11333322211 111        1


Q ss_pred             CCEEE-Eeccch-h-h-hhhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          320 GSRII-ITTRDR-Q-V-LANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       320 ~~~ii-iTtR~~-~-~-~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      -|.|+ |+|-+. . + .+.++..+++++.+.+.+|-.++-.++.
T Consensus       464 LS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         464 LSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             hhheEEEeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence            24443 333322 1 1 2344566899999999999999888876

>PRK06526 transposase; Provisional

Probab=97.63  E-value=0.00012  Score=70.05  Aligned_cols=33  Identities=21%  Similarity=0.160  Sum_probs=25.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      .-+.|+|++|+|||+||..++.........+.|
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f  131 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF  131 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCchhh
Confidence            458999999999999999999876554333344

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

Probab=97.62  E-value=0.001  Score=69.98  Aligned_cols=160  Identities=16%  Similarity=0.103  Sum_probs=87.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      .+-|.|.|+.|+|||+|++++++.+... +-.+.++.+..  .....+..+++-+-                 +.+.+.+
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~--l~~~~~e~iQk~l~-----------------~vfse~~  491 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCST--LDGSSLEKIQKFLN-----------------NVFSEAL  491 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechh--ccchhHHHHHHHHH-----------------HHHHHHH
Confidence            4569999999999999999999987643 33344444221  11222333333222                 2233456


Q ss_pred             cCCCeEEEEecCCChH---------------HHHHHh----cCcCCCCCCCEEEEeccchhhh-----hhcCCCeeEEcC
Q 009306          290 TRKKVLIVFDDVDHPR---------------QIKILV----GRLDLFASGSRIIITTRDRQVL-----ANCGVDEVYQME  345 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~---------------~~~~l~----~~l~~~~~~~~iiiTtR~~~~~-----~~~~~~~~~~l~  345 (538)
                      ...|-+|||||++...               -+..++    ......+....+|.|.....-+     ...-...+..|+
T Consensus       492 ~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~  571 (952)
T KOG0735|consen  492 WYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALP  571 (952)
T ss_pred             hhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecC
Confidence            6789999999996321               112222    1111112222344444333211     111234567899


Q ss_pred             CCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHH
Q 009306          346 ELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVL  391 (538)
Q Consensus       346 ~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~  391 (538)
                      .+...+-.++++....  ........+...-+..+|+|. |.-+.++
T Consensus       572 ap~~~~R~~IL~~~~s--~~~~~~~~~dLd~ls~~TEGy~~~DL~if  616 (952)
T KOG0735|consen  572 APAVTRRKEILTTIFS--KNLSDITMDDLDFLSVKTEGYLATDLVIF  616 (952)
T ss_pred             CcchhHHHHHHHHHHH--hhhhhhhhHHHHHHHHhcCCccchhHHHH
Confidence            9998888888776652  222333344455577888775 4444443

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.62  E-value=0.0013  Score=66.94  Aligned_cols=125  Identities=21%  Similarity=0.245  Sum_probs=74.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-  288 (538)
                      ....+.+.|++|+|||+||..++..  ..|+.+-.++    ....-++                   +......++++. 
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~--S~FPFvKiiS----pe~miG~-------------------sEsaKc~~i~k~F  591 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS--SDFPFVKIIS----PEDMIGL-------------------SESAKCAHIKKIF  591 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh--cCCCeEEEeC----hHHccCc-------------------cHHHHHHHHHHHH
Confidence            4567889999999999999998864  6677554443    1111111                   111222222222 


Q ss_pred             ---hcCCCeEEEEecCCChH------------HHHHHhcCcCCCCC-CCE--EEEeccchhhhhhcC----CCeeEEcCC
Q 009306          289 ---LTRKKVLIVFDDVDHPR------------QIKILVGRLDLFAS-GSR--IIITTRDRQVLANCG----VDEVYQMEE  346 (538)
Q Consensus       289 ---l~~k~~LlVlDdv~~~~------------~~~~l~~~l~~~~~-~~~--iiiTtR~~~~~~~~~----~~~~~~l~~  346 (538)
                         .+..--+||+||++..-            .++.+.-.+....| |-+  |+-||....++..++    ....+.++.
T Consensus       592 ~DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpn  671 (744)
T KOG0741|consen  592 EDAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPN  671 (744)
T ss_pred             HHhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCc
Confidence               23344689999996432            23333333332233 223  556677777887775    345789999


Q ss_pred             CCH-HHHHHHHHhh
Q 009306          347 LVH-DDALRLFSRH  359 (538)
Q Consensus       347 L~~-~ea~~Lf~~~  359 (538)
                      ++. ++..+.++..
T Consensus       672 l~~~~~~~~vl~~~  685 (744)
T KOG0741|consen  672 LTTGEQLLEVLEEL  685 (744)
T ss_pred             cCchHHHHHHHHHc
Confidence            988 7777777664

>PRK06921 hypothetical protein; Provisional

Probab=97.62  E-value=0.00016  Score=69.69  Aligned_cols=36  Identities=22%  Similarity=0.251  Sum_probs=29.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ...+.++|++|+|||+|+.++++.+..+ ...++|+.
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            4568999999999999999999987765 44556665

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

Probab=97.59  E-value=0.00027  Score=74.19  Aligned_cols=156  Identities=19%  Similarity=0.259  Sum_probs=88.7

Q ss_pred             CCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      ++.+|+++..+.+.+++.-    ++-+.++++++||+|+|||++|+.++..+...|.. +-+   +...+...+      
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfR-fSv---GG~tDvAeI------  480 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFR-FSV---GGMTDVAEI------  480 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEE-Eec---cccccHHhh------
Confidence            4579999999999888753    44567899999999999999999999987766531 111   111111000      


Q ss_pred             HHHHHhcCCCCCCchhhcHHHHHHHh---cCCCeEEEEecCCCh----------HHHHHHhcCc---------CCCCCCC
Q 009306          264 LLSTLLNDGNVKNFLNTDLNFQSRRL---TRKKVLIVFDDVDHP----------RQIKILVGRL---------DLFASGS  321 (538)
Q Consensus       264 l~~~l~~~~~~~~~~~~~~~~l~~~l---~~k~~LlVlDdv~~~----------~~~~~l~~~l---------~~~~~~~  321 (538)
                           .+..  ...+...-..+.+.|   +...-|+.||+||..          ..++.+-+..         +---.-|
T Consensus       481 -----kGHR--RTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLS  553 (906)
T KOG2004|consen  481 -----KGHR--RTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLS  553 (906)
T ss_pred             -----cccc--eeeeccCChHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchh
Confidence                 0100  011111212222222   334558889999742          1122221111         1001236


Q ss_pred             EEEEeccchhh----hhhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          322 RIIITTRDRQV----LANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       322 ~iiiTtR~~~~----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      +|++....+.+    .+..+..++++|.+...+|-+.+-.++.
T Consensus       554 kVLFicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  554 KVLFICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             heEEEEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhh
Confidence            66554433211    1223445789999999999998887776

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.59  E-value=0.00018  Score=67.95  Aligned_cols=49  Identities=22%  Similarity=0.240  Sum_probs=38.9

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|.++|..+-....++.|+|++|+|||++|.+++.........++|+.
T Consensus        10 ~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         10 KMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3456666655566788999999999999999999987766666778876

>PRK10536 hypothetical protein; Provisional

Probab=97.58  E-value=0.00042  Score=65.29  Aligned_cols=54  Identities=13%  Similarity=0.089  Sum_probs=39.6

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh-h-ccceeeEEEE
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK-I-SRHFSGSYFA  245 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~-~-~~~f~~~~~~  245 (538)
                      ..+.+|......+..++..    ..++.++|++|.|||+||.+++.. + ...|...+..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~----~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~  110 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES----KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVT  110 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc----CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEe
Confidence            4567787777777777753    348999999999999999998884 3 3445544443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.57  E-value=0.0041  Score=70.29  Aligned_cols=51  Identities=22%  Similarity=0.337  Sum_probs=39.8

Q ss_pred             CCCceeccchhHHHHHhhhcC------CC-CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          187 NEDLVGVRLPMKEIESLLRTG------ST-NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~------~~-~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...++|.+..++.+...+...      .. ....+.++|++|+|||++|+.++.....
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~  621 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFD  621 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            356899999999998877541      11 1356889999999999999999987643

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.

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

Probab=97.56  E-value=7.6e-05  Score=67.40  Aligned_cols=35  Identities=34%  Similarity=0.353  Sum_probs=27.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .-+.|+|++|+|||.||.+++++...+-..+.|+.
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~   82 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFIT   82 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEee
Confidence            45999999999999999999987666545566665

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.55  E-value=0.00027  Score=65.21  Aligned_cols=108  Identities=16%  Similarity=0.164  Sum_probs=61.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEE-eehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA-RNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~-~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      ++.|+|++|+||||++..+...+.......++. .+..+.... ..    ..+.    ...............++..+..
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~~-~~----~~~i----~q~~vg~~~~~~~~~i~~aLr~   73 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVHE-SK----RSLI----NQREVGLDTLSFENALKAALRQ   73 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCcccccc-Cc----ccee----eecccCCCccCHHHHHHHHhcC
Confidence            689999999999999999888765443333332 211110000 00    0000    0001111223345566777777


Q ss_pred             CCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhh
Q 009306          292 KKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQV  332 (538)
Q Consensus       292 k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~  332 (538)
                      .+=+|++|++.+.+.+.......   ..|..++.|+-....
T Consensus        74 ~pd~ii~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~  111 (198)
T cd01131          74 DPDVILVGEMRDLETIRLALTAA---ETGHLVMSTLHTNSA  111 (198)
T ss_pred             CcCEEEEcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcH
Confidence            88899999998777665544332   235556666655543

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.

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=97.55  E-value=0.0044  Score=62.01  Aligned_cols=44  Identities=14%  Similarity=0.382  Sum_probs=34.8

Q ss_pred             chhHHHHHhhhcCC-CCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          195 LPMKEIESLLRTGS-TNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       195 ~~l~~l~~~L~~~~-~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+.|.+.+.... ....+|+|.|.=|+|||++.+.+.+.+...
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            34456666666533 567889999999999999999999988776

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 [].

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.54  E-value=0.0012  Score=60.57  Aligned_cols=59  Identities=20%  Similarity=0.294  Sum_probs=43.6

Q ss_pred             CCCCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEE
Q 009306          185 SENEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSY  243 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~  243 (538)
                      ..-..++|-+.+.+.|.+.-..  .+-...-|.+||..|.|||+|++++.+.+...+...+
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLV  117 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADEGLRLV  117 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhcCCeEE
Confidence            3446789999998888764322  1222344899999999999999999999887765533

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.53  E-value=0.0009  Score=69.91  Aligned_cols=152  Identities=16%  Similarity=0.206  Sum_probs=85.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+-|.++||||+|||++|+++++.-...|-.+   .         +     .++++...+.     +.........+.
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsv---k---------g-----pEL~sk~vGe-----SEr~ir~iF~kA  523 (693)
T KOG0730|consen  466 SPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSV---K---------G-----PELFSKYVGE-----SERAIREVFRKA  523 (693)
T ss_pred             CCCceEEEECCCCcchHHHHHHHhhhhcCCeeec---c---------C-----HHHHHHhcCc-----hHHHHHHHHHHH
Confidence            4567799999999999999999999866554211   1         0     0111111111     111122222233


Q ss_pred             hcCCCeEEEEecCCCh-------------HHHHHHhcCcCCCCCCCEEEEe--c-cchhhhhh-c---CCCeeEEcCCCC
Q 009306          289 LTRKKVLIVFDDVDHP-------------RQIKILVGRLDLFASGSRIIIT--T-RDRQVLAN-C---GVDEVYQMEELV  348 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~~~~~~iiiT--t-R~~~~~~~-~---~~~~~~~l~~L~  348 (538)
                      -+..+++|.||++|..             ..+..++..++.......|+|.  | |...+-.. +   +.++.+.++.-+
T Consensus       524 R~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD  603 (693)
T KOG0730|consen  524 RQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPD  603 (693)
T ss_pred             hhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCcc
Confidence            3456799999998743             2245555555544444444433  2 33222111 1   356788888888


Q ss_pred             HHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          349 HDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       349 ~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .+--.++|..++-+  -+.... -...++++.+.|.-
T Consensus       604 ~~aR~~Ilk~~~kk--mp~~~~-vdl~~La~~T~g~S  637 (693)
T KOG0730|consen  604 LEARLEILKQCAKK--MPFSED-VDLEELAQATEGYS  637 (693)
T ss_pred             HHHHHHHHHHHHhc--CCCCcc-ccHHHHHHHhccCC
Confidence            88889999988822  222111 23456677676664

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.53  E-value=0.01  Score=59.21  Aligned_cols=88  Identities=15%  Similarity=0.180  Sum_probs=60.1

Q ss_pred             CCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc-hhhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCC
Q 009306          292 KKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD-RQVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPH  367 (538)
Q Consensus       292 k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  367 (538)
                      +.-++|||+++.  ......++..+..-.+++.+|++|.+ ..+++.+ .....+.+.+++.++..+.+....     ..
T Consensus       132 ~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~-----~~  206 (342)
T PRK06964        132 GARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG-----VA  206 (342)
T ss_pred             CceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC-----CC
Confidence            445889999974  46677888877766677776665554 4555443 234688999999999999997652     11


Q ss_pred             CchHHHHHHHHHHhcCCcHHHH
Q 009306          368 ESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       368 ~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      +     ...++..++|.|+...
T Consensus       207 ~-----~~~~l~~~~Gsp~~Al  223 (342)
T PRK06964        207 D-----ADALLAEAGGAPLAAL  223 (342)
T ss_pred             h-----HHHHHHHcCCCHHHHH
Confidence            1     2235778899996443

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.51  E-value=0.0023  Score=67.45  Aligned_cols=202  Identities=16%  Similarity=0.163  Sum_probs=121.6

Q ss_pred             CCCCceeccchhHHHHHhhhc--CC-CCceEEEEeccCCCchhHHHHHHHHhhcc-----ceeeE--EEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLLRT--GS-TNVYKLGIWGIGGIGKTTIAGAIFNKISR-----HFSGS--YFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~--~~-~~~~~v~I~G~~GiGKTtLa~~~~~~~~~-----~f~~~--~~~~~~~~~~~~~  255 (538)
                      .+..+-+|+.+..+|...+..  .. +....+-|.|.+|.|||..+..+.+.+..     .-+..  +.+.    .-.-.
T Consensus       394 vp~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveIN----gm~l~  469 (767)
T KOG1514|consen  394 VPESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEIN----GLRLA  469 (767)
T ss_pred             ccccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEc----ceeec
Confidence            567789999999999998865  22 33558899999999999999999986541     11222  2232    11234


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc-----CCCeEEEEecCCChHH--HHHHhcCcCCC-CCCCEEEEec
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT-----RKKVLIVFDDVDHPRQ--IKILVGRLDLF-ASGSRIIITT  327 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~-----~k~~LlVlDdv~~~~~--~~~l~~~l~~~-~~~~~iiiTt  327 (538)
                      ....+...|...+.+...   ......+.+..+..     .++++|++|++|.+-.  -+.+...+.|- .++++++|.+
T Consensus       470 ~~~~~Y~~I~~~lsg~~~---~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~  546 (767)
T KOG1514|consen  470 SPREIYEKIWEALSGERV---TWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIA  546 (767)
T ss_pred             CHHHHHHHHHHhcccCcc---cHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEE
Confidence            466677777776655432   23333444444443     4668999999976532  23333333333 3577766654


Q ss_pred             cch------h-----hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCC-CCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          328 RDR------Q-----VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHP-HESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       328 R~~------~-----~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~-~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      -..      .     +...+ .-..+.+.|.+..+..+++..+.-+-... ....+-.+++++...|..=.|+...-+..
T Consensus       547 IaNTmdlPEr~l~nrvsSRl-g~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic~RA~  625 (767)
T KOG1514|consen  547 IANTMDLPERLLMNRVSSRL-GLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDICRRAA  625 (767)
T ss_pred             ecccccCHHHHhccchhhhc-cceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence            322      1     11111 23567889999999999998887333222 12233345566666666666666555544

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

Probab=97.50  E-value=0.0024  Score=70.93  Aligned_cols=50  Identities=18%  Similarity=0.294  Sum_probs=38.8

Q ss_pred             CCCceeccchhHHHHHhhhcC------CC-CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          187 NEDLVGVRLPMKEIESLLRTG------ST-NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~------~~-~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++|.+..++.+...+...      .+ ....+.++|++|+|||+||+.++..+.
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            356899999999888776531      11 234678999999999999999998773

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

Probab=97.49  E-value=0.0025  Score=70.74  Aligned_cols=184  Identities=17%  Similarity=0.210  Sum_probs=96.9

Q ss_pred             hhhHHHHHHHHhhhccccccCC-----------CCCCCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHH
Q 009306          163 PESALIEEIVNAILKRLDDTFH-----------SENEDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTI  227 (538)
Q Consensus       163 ~e~~~i~~i~~~~~~~~~~~~~-----------~~~~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtL  227 (538)
                      +|+..+....+-+..-......           ....+.+|.+...+.|.++|..    +......++++|++|+||||+
T Consensus       286 ~e~~~~~~yl~~~~~~pw~~~~~~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl  365 (784)
T PRK10787        286 AEATVVRGYIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSL  365 (784)
T ss_pred             chHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHH
Confidence            4777777766655442111111           1234689999999999887763    223456799999999999999


Q ss_pred             HHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChHH-
Q 009306          228 AGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQ-  306 (538)
Q Consensus       228 a~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~-  306 (538)
                      ++.++..+...|-..-+ ...      .+...+...- ....+     .........+... ....-+++||+++.... 
T Consensus       366 ~~~ia~~l~~~~~~i~~-~~~------~d~~~i~g~~-~~~~g-----~~~G~~~~~l~~~-~~~~~villDEidk~~~~  431 (784)
T PRK10787        366 GQSIAKATGRKYVRMAL-GGV------RDEAEIRGHR-RTYIG-----SMPGKLIQKMAKV-GVKNPLFLLDEIDKMSSD  431 (784)
T ss_pred             HHHHHHHhCCCEEEEEc-CCC------CCHHHhccch-hccCC-----CCCcHHHHHHHhc-CCCCCEEEEEChhhcccc
Confidence            99999876554422111 111      1111110000 00000     0111112222221 22334789999964311 


Q ss_pred             -----HHHHhcCcCC---------------CCCCCEEEEeccchhhhhh-cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          307 -----IKILVGRLDL---------------FASGSRIIITTRDRQVLAN-CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       307 -----~~~l~~~l~~---------------~~~~~~iiiTtR~~~~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                           ...+...+..               .-.+..+|.|+....+.+. ++...++++.+++.+|-.++..++.
T Consensus       432 ~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        432 MRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             cCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence                 2333332221               0123444555543322111 1334678999999999999887776

>TIGR00763 lon ATP-dependent protease La

Probab=97.49  E-value=0.00092  Score=74.70  Aligned_cols=52  Identities=29%  Similarity=0.420  Sum_probs=39.9

Q ss_pred             CCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          188 EDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ..++|.+...+.+.+++..    +....+.+.++|++|+|||++|+.++..+...|
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~  375 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKF  375 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCe
Confidence            4578888888888776532    222345799999999999999999999876544

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.49  E-value=0.0028  Score=71.35  Aligned_cols=51  Identities=18%  Similarity=0.325  Sum_probs=38.9

Q ss_pred             CCCceeccchhHHHHHhhhcC------CC-CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          187 NEDLVGVRLPMKEIESLLRTG------ST-NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~------~~-~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...++|.+..++.+...+...      .+ ....+.++|++|+|||+||+.++..+..
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~  624 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFD  624 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhc
Confidence            356899999999888876531      11 1246889999999999999999986543

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

Probab=97.48  E-value=0.00064  Score=65.06  Aligned_cols=37  Identities=30%  Similarity=0.271  Sum_probs=29.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...-+.++|++|+|||.||.++.+++......+.|+.
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            3445999999999999999999999884444555554

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.48  E-value=0.00019  Score=66.98  Aligned_cols=45  Identities=24%  Similarity=0.236  Sum_probs=36.1

Q ss_pred             HhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          202 SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       202 ~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|..+-....++.|+|++|+|||+++.+++.........++|+.
T Consensus         3 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~   47 (209)
T TIGR02237         3 ELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID   47 (209)
T ss_pred             hhhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            345555566789999999999999999999987665556778877

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

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

Probab=97.46  E-value=0.00022  Score=72.57  Aligned_cols=46  Identities=22%  Similarity=0.226  Sum_probs=37.2

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++++.+..++.+...|..+    +.+.++|++|+|||++|+.++..+..
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~  220 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTG  220 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcC
Confidence            45677788888888888643    34889999999999999999987643

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.46  E-value=0.0015  Score=57.99  Aligned_cols=138  Identities=17%  Similarity=0.233  Sum_probs=71.8

Q ss_pred             eccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc--------------------eeeEEEEeehhhh
Q 009306          192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--------------------FSGSYFARNVREA  251 (538)
Q Consensus       192 GR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--------------------f~~~~~~~~~~~~  251 (538)
                      |-+..++.|...+..+ .-...+.++|+.|+||+++|..++..+-..                    ++...++.... .
T Consensus         1 gq~~~~~~L~~~~~~~-~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~-~   78 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSG-RLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDK-K   78 (162)
T ss_dssp             S-HHHHHHHHHHHHCT-C--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTT-S
T ss_pred             CcHHHHHHHHHHHHcC-CcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEeccc-c
Confidence            4455566677766543 235568999999999999999999864321                    22222222000 0


Q ss_pred             hhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc
Q 009306          252 EETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       252 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                      ...-.. +-.+.+...+...                ...++.=++||||++.  .+...+|+..+.....++.+|++|.+
T Consensus        79 ~~~i~i-~~ir~i~~~~~~~----------------~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~  141 (162)
T PF13177_consen   79 KKSIKI-DQIREIIEFLSLS----------------PSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNN  141 (162)
T ss_dssp             SSSBSH-HHHHHHHHHCTSS-----------------TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-
T ss_pred             cchhhH-HHHHHHHHHHHHH----------------HhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECC
Confidence            000011 1111222211111                0123455899999975  45677777777666778888888876


Q ss_pred             hh-hhhhc-CCCeeEEcCCCC
Q 009306          330 RQ-VLANC-GVDEVYQMEELV  348 (538)
Q Consensus       330 ~~-~~~~~-~~~~~~~l~~L~  348 (538)
                      .. +++.. .....+.+.+++
T Consensus       142 ~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  142 PSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             GGGS-HHHHTTSEEEEE----
T ss_pred             hHHChHHHHhhceEEecCCCC
Confidence            63 33333 233566776654

...

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.45  E-value=0.0014  Score=63.16  Aligned_cols=173  Identities=20%  Similarity=0.196  Sum_probs=100.8

Q ss_pred             CCCceeccchhHHHHHhhhcC--CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhh--hcCChHHHHH
Q 009306          187 NEDLVGVRLPMKEIESLLRTG--STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAE--ETCRLGDLRQ  262 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~--~~~~~~~l~~  262 (538)
                      ...++|-.++-+.+..++...  -++...+.|.||.|.|||+|......+ .+.+...+.++.....-  +...+..+.+
T Consensus        23 ~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~-~q~~~E~~l~v~Lng~~~~dk~al~~I~r  101 (408)
T KOG2228|consen   23 HINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSD-IQENGENFLLVRLNGELQTDKIALKGITR  101 (408)
T ss_pred             CcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhh-HHhcCCeEEEEEECccchhhHHHHHHHHH
Confidence            357899999999999888651  123456899999999999998877666 33444333433332221  2234555556


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhc------CCCeEEEEecCCCh----HH--HHHHhc-CcCCCCCCCEEEEeccc
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLT------RKKVLIVFDDVDHP----RQ--IKILVG-RLDLFASGSRIIITTRD  329 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~------~k~~LlVlDdv~~~----~~--~~~l~~-~l~~~~~~~~iiiTtR~  329 (538)
                      ++..++........+..+....+...|.      ..++++|+|++|--    .|  +-.++. .-....|-+-|-+|||-
T Consensus       102 ql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrl  181 (408)
T KOG2228|consen  102 QLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRL  181 (408)
T ss_pred             HHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccc
Confidence            6555543332222344444444444442      24588999988632    11  122211 11112445567788886


Q ss_pred             hh-------hhhhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          330 RQ-------VLANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       330 ~~-------~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ..       |-.......++-++.++-++-.++++...
T Consensus       182 d~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  182 DILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             cHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence            52       22223333466778899999999988876

>cd01394 radB RadB

Probab=97.43  E-value=0.00036  Score=65.54  Aligned_cols=50  Identities=22%  Similarity=0.232  Sum_probs=38.7

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +..|..+|..+-....++.|+|++|+||||+|.+++.........++|+.
T Consensus         5 i~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394           5 CKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             hhHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            34566677655566788999999999999999999988765555666765

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.41  E-value=0.00068  Score=66.70  Aligned_cols=36  Identities=28%  Similarity=0.354  Sum_probs=29.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+-+.|+|+.|+|||.||.++++.+......+.|+.
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~  191 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLH  191 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            456999999999999999999999876544555654

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.40  E-value=0.00086  Score=66.56  Aligned_cols=35  Identities=20%  Similarity=0.278  Sum_probs=29.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+.|+|++|+|||+||.++++.+......++|+.
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            55999999999999999999998766655566665

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.39  E-value=0.0055  Score=57.53  Aligned_cols=207  Identities=12%  Similarity=0.137  Sum_probs=115.5

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc------ceeeEEEEeehhh-----------
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR------HFSGSYFARNVRE-----------  250 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~------~f~~~~~~~~~~~-----------  250 (538)
                      +.+.+++..-..+..+..  .++.+-+.++|++|.||-|.+..+.+++-.      +-+...|......           
T Consensus        13 ~~l~~~~e~~~~Lksl~~--~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~y   90 (351)
T KOG2035|consen   13 DELIYHEELANLLKSLSS--TGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNY   90 (351)
T ss_pred             hhcccHHHHHHHHHHhcc--cCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccc
Confidence            446667666666666554  234566899999999999999988875422      1223333321111           


Q ss_pred             ---h-hh--cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCe-EEEEecCCCh--HHHHHHhcCcCCCCCCC
Q 009306          251 ---A-EE--TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKV-LIVFDDVDHP--RQIKILVGRLDLFASGS  321 (538)
Q Consensus       251 ---~-~~--~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~-LlVlDdv~~~--~~~~~l~~~l~~~~~~~  321 (538)
                         . +.  ...-.-+.+.++.++++...++..            ..+++ ++||-.+|+.  +.-.++...+......+
T Consensus        91 HlEitPSDaG~~DRvViQellKevAQt~qie~~------------~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~  158 (351)
T KOG2035|consen   91 HLEITPSDAGNYDRVVIQELLKEVAQTQQIETQ------------GQRPFKVVVINEADELTRDAQHALRRTMEKYSSNC  158 (351)
T ss_pred             eEEeChhhcCcccHHHHHHHHHHHHhhcchhhc------------cccceEEEEEechHhhhHHHHHHHHHHHHHHhcCc
Confidence               0 00  111123455555555544332211            12333 6677777654  22333333333335678


Q ss_pred             EEEEeccch-hhhhhcC-CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcC--
Q 009306          322 RIIITTRDR-QVLANCG-VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYG--  397 (538)
Q Consensus       322 ~iiiTtR~~-~~~~~~~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~--  397 (538)
                      |+|+...+- .+..... ..-.++++..+++|....+++.+-+  ..-....+++.+|+++++|+-.---++...++-  
T Consensus       159 RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~k--E~l~lp~~~l~rIa~kS~~nLRrAllmlE~~~~~n  236 (351)
T KOG2035|consen  159 RLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKK--EGLQLPKELLKRIAEKSNRNLRRALLMLEAVRVNN  236 (351)
T ss_pred             eEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHH--hcccCcHHHHHHHHHHhcccHHHHHHHHHHHHhcc
Confidence            887764332 1222221 2246889999999999999988733  233344889999999999985333233332221  


Q ss_pred             C---------CHHHHHHHHHHh
Q 009306          398 K---------RREVWENAKSKW  410 (538)
Q Consensus       398 ~---------~~~~~~~~l~~l  410 (538)
                      .         +..+|+-.+.+.
T Consensus       237 ~~~~a~~~~i~~~dWe~~i~e~  258 (351)
T KOG2035|consen  237 EPFTANSQVIPKPDWEIYIQEI  258 (351)
T ss_pred             ccccccCCCCCCccHHHHHHHH
Confidence            1         235677777654

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

Probab=97.38  E-value=0.0022  Score=67.71  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=47.5

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      .+..+++.++|++|+||||||..+++.-.  | .++=+.    +++......+-..+...+.......            
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkqaG--Y-sVvEIN----ASDeRt~~~v~~kI~~avq~~s~l~------------  383 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQAG--Y-SVVEIN----ASDERTAPMVKEKIENAVQNHSVLD------------  383 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHhcC--c-eEEEec----ccccccHHHHHHHHHHHHhhccccc------------
Confidence            34578999999999999999999887521  1 122222    3334444444455544443321100            


Q ss_pred             HhcCCCeEEEEecCCCh
Q 009306          288 RLTRKKVLIVFDDVDHP  304 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~~~  304 (538)
                       ...+|..||+|++|..
T Consensus       384 -adsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  384 -ADSRPVCLVIDEIDGA  399 (877)
T ss_pred             -cCCCcceEEEecccCC
Confidence             1268899999999753

>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=97.38  E-value=0.00065  Score=63.68  Aligned_cols=34  Identities=24%  Similarity=0.456  Sum_probs=29.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .++|.|.+|+|||||+..+.......|..++...
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t   48 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLIT   48 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEe
Confidence            4889999999999999999999989996665554

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

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.37  E-value=0.0011  Score=63.08  Aligned_cols=50  Identities=18%  Similarity=0.152  Sum_probs=38.1

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +..|.++|..+-+...++.|+|++|+|||+|+.+++.....+-..++|+.
T Consensus        11 i~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~   60 (234)
T PRK06067         11 NEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVIT   60 (234)
T ss_pred             CHHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEE
Confidence            34566667666667788999999999999999999776544555677766

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.37  E-value=0.0015  Score=65.33  Aligned_cols=142  Identities=17%  Similarity=0.157  Sum_probs=80.4

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee---------------------eEEEEeeh
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS---------------------GSYFARNV  248 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---------------------~~~~~~~~  248 (538)
                      ++|-+.....+..+..........+.++|++|+||||+|..+++.+-...+                     ....+.  
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~--   80 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELN--   80 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEec--
Confidence            566667777777777643333446999999999999999999997653321                     111211  


Q ss_pred             hhhhhcCC---hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEE
Q 009306          249 REAEETCR---LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRI  323 (538)
Q Consensus       249 ~~~~~~~~---~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~i  323 (538)
                        .+....   ..+..+.+........                ..++.-+++||+++..  +...++...+........+
T Consensus        81 --~s~~~~~~i~~~~vr~~~~~~~~~~----------------~~~~~kviiidead~mt~~A~nallk~lEep~~~~~~  142 (325)
T COG0470          81 --PSDLRKIDIIVEQVRELAEFLSESP----------------LEGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRF  142 (325)
T ss_pred             --ccccCCCcchHHHHHHHHHHhccCC----------------CCCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEE
Confidence              111111   1222222222211110                0245569999999865  3456666666665677888


Q ss_pred             EEeccch-hhhhhcC-CCeeEEcCCCCHHH
Q 009306          324 IITTRDR-QVLANCG-VDEVYQMEELVHDD  351 (538)
Q Consensus       324 iiTtR~~-~~~~~~~-~~~~~~l~~L~~~e  351 (538)
                      |++|.+. .+.+.+. ....+++.+.+..+
T Consensus       143 il~~n~~~~il~tI~SRc~~i~f~~~~~~~  172 (325)
T COG0470         143 ILITNDPSKILPTIRSRCQRIRFKPPSRLE  172 (325)
T ss_pred             EEEcCChhhccchhhhcceeeecCCchHHH
Confidence            8877643 3333322 23466777643333

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

Probab=97.37  E-value=0.0012  Score=71.39  Aligned_cols=118  Identities=17%  Similarity=0.250  Sum_probs=69.8

Q ss_pred             CCCceeccchhHHHHHhhhc-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHH
Q 009306          187 NEDLVGVRLPMKEIESLLRT-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~  259 (538)
                      ...++|.+..+..+.+.+..       .......+...||.|+|||.||++++..+-..=...+-++ .++.        
T Consensus       490 ~~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~D-MSEy--------  560 (786)
T COG0542         490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRID-MSEY--------  560 (786)
T ss_pred             hcceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeec-hHHH--------
Confidence            35789999999988877653       1223567788999999999999999987643222222222 1111        


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCe-EEEEecCC--ChHHHHHHhcCc
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKV-LIVFDDVD--HPRQIKILVGRL  314 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~-LlVlDdv~--~~~~~~~l~~~l  314 (538)
                      .-+.-.+.+.+.++.-...++ ...+-+..+++|| +|.||+++  +++-...|+..+
T Consensus       561 ~EkHsVSrLIGaPPGYVGyee-GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVl  617 (786)
T COG0542         561 MEKHSVSRLIGAPPGYVGYEE-GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVL  617 (786)
T ss_pred             HHHHHHHHHhCCCCCCceecc-ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHh
Confidence            112223344444333222222 3334455567777 88899996  455555555444

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

Probab=97.36  E-value=0.0031  Score=65.36  Aligned_cols=129  Identities=19%  Similarity=0.238  Sum_probs=76.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      ..-|.+|||+|+|||-||++++++-...|     +..       .+.     +++....+.     +.........+.-.
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEag~NF-----isV-------KGP-----ELlNkYVGE-----SErAVR~vFqRAR~  602 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEAGANF-----ISV-------KGP-----ELLNKYVGE-----SERAVRQVFQRARA  602 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhccCce-----Eee-------cCH-----HHHHHHhhh-----HHHHHHHHHHHhhc
Confidence            34589999999999999999999876664     220       111     122222111     11122222223335


Q ss_pred             CCCeEEEEecCCCh-------------HHHHHHhcCcCCCC--CCCEEEEeccchhhh-----hhcCCCeeEEcCCCCHH
Q 009306          291 RKKVLIVFDDVDHP-------------RQIKILVGRLDLFA--SGSRIIITTRDRQVL-----ANCGVDEVYQMEELVHD  350 (538)
Q Consensus       291 ~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~~--~~~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~  350 (538)
                      ..|++|.||++|..             ..+..|+..+....  .|.-||-.|..+++.     ..-+.+..+-++.-+.+
T Consensus       603 saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~  682 (802)
T KOG0733|consen  603 SAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAE  682 (802)
T ss_pred             CCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHH
Confidence            68999999999743             23455555554332  344555555433332     22234567778888999


Q ss_pred             HHHHHHHhhhc
Q 009306          351 DALRLFSRHAF  361 (538)
Q Consensus       351 ea~~Lf~~~~~  361 (538)
                      |-.+++....-
T Consensus       683 eR~~ILK~~tk  693 (802)
T KOG0733|consen  683 ERVAILKTITK  693 (802)
T ss_pred             HHHHHHHHHhc
Confidence            99999988874

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.35  E-value=0.0093  Score=59.29  Aligned_cols=85  Identities=13%  Similarity=0.201  Sum_probs=50.9

Q ss_pred             CeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCC
Q 009306          293 KVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHE  368 (538)
Q Consensus       293 ~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  368 (538)
                      +-++|+|+++.  ......+...+.....+..+|++|.+.. +.+.+ .....+.+.+++.+++.+.+....     .. 
T Consensus       114 ~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~~-----~~-  187 (325)
T PRK08699        114 LRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRERG-----VA-  187 (325)
T ss_pred             ceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhcC-----CC-
Confidence            34556788864  3445555555544345676777777653 33332 234678899999999999886542     11 


Q ss_pred             chHHHHHHHHHHhcCCcHH
Q 009306          369 SHTELACKTIKYARGVPLA  387 (538)
Q Consensus       369 ~~~~~~~~i~~~~~G~PLa  387 (538)
                      ...    ..+..++|-|+.
T Consensus       188 ~~~----~~l~~~~g~p~~  202 (325)
T PRK08699        188 EPE----ERLAFHSGAPLF  202 (325)
T ss_pred             cHH----HHHHHhCCChhh
Confidence            111    123568898954

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

Probab=97.34  E-value=0.0013  Score=62.01  Aligned_cols=49  Identities=20%  Similarity=0.169  Sum_probs=37.1

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~  246 (538)
                      ..|..+|..+-....++.|+|++|+|||+||..++.......      ..++|+.
T Consensus         6 ~~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~   60 (226)
T cd01393           6 KALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID   60 (226)
T ss_pred             HHHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEe
Confidence            345566655556678899999999999999999988754444      5667776

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.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.32  E-value=0.0017  Score=69.25  Aligned_cols=46  Identities=24%  Similarity=0.406  Sum_probs=37.3

Q ss_pred             CCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          187 NEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .++++|.+..++.+...+...  ....+.|+|++|+|||++|+.+++.
T Consensus        64 f~~iiGqs~~i~~l~~al~~~--~~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCGP--NPQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHH
Confidence            357899999999998776533  3345789999999999999999864

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.30  E-value=0.00053  Score=62.77  Aligned_cols=110  Identities=15%  Similarity=0.049  Sum_probs=60.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC--CCchhhcHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV--KNFLNTDLNFQSRRL  289 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~--~~~~~~~~~~l~~~l  289 (538)
                      .++.|+|+.|.||||++..++.+...+...++++. .. ........    .+.+.++.....  .....+....+.+ .
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k-~~-~d~~~~~~----~i~~~lg~~~~~~~~~~~~~~~~~~~~-~   75 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFK-PA-IDDRYGEG----KVVSRIGLSREAIPVSSDTDIFELIEE-E   75 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEe-cc-ccccccCC----cEecCCCCcccceEeCChHHHHHHHHh-h
Confidence            46789999999999999999998766544444442 10 01111111    122222211000  0122333333333 2


Q ss_pred             cCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          290 TRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       290 ~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      .++.-+||+|++.-  .+++..+...+.  ..|..||+|.++.
T Consensus        76 ~~~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~  116 (190)
T PRK04296         76 GEKIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDT  116 (190)
T ss_pred             CCCCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecCc
Confidence            33556999999853  344444443322  4688899998874

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

Probab=97.29  E-value=0.0002  Score=61.93  Aligned_cols=46  Identities=24%  Similarity=0.260  Sum_probs=32.5

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ||+...++++.+.+..-......|.|+|.+|+||+++|+.++..-.
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~   46 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSG   46 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcC
Confidence            5677777777776654223445589999999999999998887543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.28  E-value=0.0011  Score=58.57  Aligned_cols=33  Identities=24%  Similarity=0.293  Sum_probs=27.2

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.|+|++|+||||++..++.........++|+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            689999999999999999988766555566665

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=0.0017  Score=64.43  Aligned_cols=98  Identities=20%  Similarity=0.222  Sum_probs=59.7

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcC-CCC
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLND-GNV  274 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~-~~~  274 (538)
                      -+.++.+.|..+--...++.|-|.+|||||||..+++.++.... .+.|+..      ..++..+ +--...++.. .+.
T Consensus        78 g~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVsG------EES~~Qi-klRA~RL~~~~~~l  149 (456)
T COG1066          78 GIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVSG------EESLQQI-KLRADRLGLPTNNL  149 (456)
T ss_pred             ChHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEeC------CcCHHHH-HHHHHHhCCCccce
Confidence            45567777765444567899999999999999999999998776 6677652      1122221 1122223211 111


Q ss_pred             CCchhhcHHHHHHHh-cCCCeEEEEecC
Q 009306          275 KNFLNTDLNFQSRRL-TRKKVLIVFDDV  301 (538)
Q Consensus       275 ~~~~~~~~~~l~~~l-~~k~~LlVlDdv  301 (538)
                      ....+...+.+.+.+ +.++-++|+|.+
T Consensus       150 ~l~aEt~~e~I~~~l~~~~p~lvVIDSI  177 (456)
T COG1066         150 YLLAETNLEDIIAELEQEKPDLVVIDSI  177 (456)
T ss_pred             EEehhcCHHHHHHHHHhcCCCEEEEecc
Confidence            122223333444444 368899999998

>TIGR01817 nifA Nif-specific regulatory protein

Probab=97.25  E-value=0.0047  Score=66.28  Aligned_cols=52  Identities=21%  Similarity=0.288  Sum_probs=41.5

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .....++|....++++.+.+..-......|.|+|++|+|||++|+.+++.-.
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~  244 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSP  244 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCC
Confidence            3457899999999999887765333444589999999999999999987643

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.25  E-value=0.0034  Score=68.51  Aligned_cols=127  Identities=17%  Similarity=0.171  Sum_probs=71.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      +-+.|+|++|+|||++|+.++.+....|   +.+. ...         +...    ..+     .........+......
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~~~~f---~~is-~~~---------~~~~----~~g-----~~~~~~~~~f~~a~~~  243 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEAKVPF---FTIS-GSD---------FVEM----FVG-----VGASRVRDMFEQAKKA  243 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHcCCCE---EEEe-hHH---------hHHh----hhc-----ccHHHHHHHHHHHHhc
Confidence            3489999999999999999998765443   1121 110         0000    000     0011111122222345


Q ss_pred             CCeEEEEecCCChH----------------HHHHHhcCcCCCC--CCCEEEEeccchhhhhh-----cCCCeeEEcCCCC
Q 009306          292 KKVLIVFDDVDHPR----------------QIKILVGRLDLFA--SGSRIIITTRDRQVLAN-----CGVDEVYQMEELV  348 (538)
Q Consensus       292 k~~LlVlDdv~~~~----------------~~~~l~~~l~~~~--~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~  348 (538)
                      .|++|+||++|...                .+..++..+..+.  .+.-+|.||.....+..     -..++.+.++..+
T Consensus       244 ~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd  323 (644)
T PRK10733        244 APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPD  323 (644)
T ss_pred             CCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCC
Confidence            78999999996531                2333433333222  23445556665543221     1345678899999


Q ss_pred             HHHHHHHHHhhh
Q 009306          349 HDDALRLFSRHA  360 (538)
Q Consensus       349 ~~ea~~Lf~~~~  360 (538)
                      .++-.+++..+.
T Consensus       324 ~~~R~~Il~~~~  335 (644)
T PRK10733        324 VRGREQILKVHM  335 (644)
T ss_pred             HHHHHHHHHHHh
Confidence            988889888876

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.24  E-value=0.0016  Score=65.83  Aligned_cols=50  Identities=20%  Similarity=0.285  Sum_probs=38.6

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.+|.+.|..+-....++.|.|.+|+|||||+.+++.........++|+.
T Consensus        68 i~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs  117 (372)
T cd01121          68 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS  117 (372)
T ss_pred             CHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            45666677655556778999999999999999999988766545566665

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.23  E-value=0.0032  Score=59.83  Aligned_cols=50  Identities=12%  Similarity=0.135  Sum_probs=38.8

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +..|.++|..+-+...++.|.|++|+|||+||.++..........++|+.
T Consensus         7 i~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877         7 IPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             cHhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            34566677666667789999999999999999998876545556677766

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.

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

Probab=97.22  E-value=0.0046  Score=68.23  Aligned_cols=49  Identities=14%  Similarity=0.218  Sum_probs=38.7

Q ss_pred             CCceeccchhHHHHHhhhcC-------CCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRTG-------STNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~-------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++|.+..++.|...+...       ......+.++|++|+|||+||+.++..+.
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~  513 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999988877531       11234688999999999999999998773

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.21  E-value=0.00089  Score=67.35  Aligned_cols=108  Identities=15%  Similarity=0.149  Sum_probs=61.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe-ehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR-NVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~-~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ...+.|+|+.|+||||+.+.+...+.......++.. +..+..        .... ..+................++..+
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~--------~~~~-~~~i~q~evg~~~~~~~~~l~~~l  192 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYV--------HRNK-RSLINQREVGLDTLSFANALRAAL  192 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhh--------ccCc-cceEEccccCCCCcCHHHHHHHhh
Confidence            357999999999999999999887665444444432 111110        0000 000001111111223456677778


Q ss_pred             cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          290 TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      +..+=.|++|++.+.+.....+...   ..|..++.|.-..
T Consensus       193 r~~pd~i~vgEird~~~~~~~l~aa---~tGh~v~~T~Ha~  230 (343)
T TIGR01420       193 REDPDVILIGEMRDLETVELALTAA---ETGHLVFGTLHTN  230 (343)
T ss_pred             ccCCCEEEEeCCCCHHHHHHHHHHH---HcCCcEEEEEcCC
Confidence            8899999999998877665533321   2354455554443

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.20  E-value=0.0022  Score=71.95  Aligned_cols=50  Identities=24%  Similarity=0.295  Sum_probs=38.7

Q ss_pred             CCceeccchhHHHHHhhhc-------CCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRT-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..++|.+..++.+.+.+..       ......++.++|++|+|||.||+.++..+-.
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~  622 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYG  622 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhC
Confidence            5689999999888877642       1122346889999999999999999987643

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.

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

Probab=97.20  E-value=0.011  Score=64.17  Aligned_cols=154  Identities=15%  Similarity=0.171  Sum_probs=88.6

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-ee-----eEEEEeehhhhhhcCChHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FS-----GSYFARNVREAEETCRLGD  259 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~-----~~~~~~~~~~~~~~~~~~~  259 (538)
                      .-+.++||+.|++.+.+.|.....+.+  .++|.+|+|||+++.-++.++... .+     ..++-.+...         
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~KNNP--vLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~---------  236 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRTKNNP--VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGS---------  236 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccCCCCC--eEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHH---------
Confidence            346789999999999999986544443  467999999999999999986543 11     1222211111         


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh-----------HHHHHHhcCcCCCCCCCEEEEec
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP-----------RQIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                             -..+. .-....++....+.+.+ +..+++|.+|.++..           +....+.+.+.+ +.--.|-.||
T Consensus       237 -------LvAGa-kyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR-GeL~~IGATT  307 (786)
T COG0542         237 -------LVAGA-KYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR-GELRCIGATT  307 (786)
T ss_pred             -------Hhccc-cccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc-CCeEEEEecc
Confidence                   11111 11133333333333333 345899999998532           122333344431 2222345566


Q ss_pred             cchhh------hhhcCCCeeEEcCCCCHHHHHHHHHhh
Q 009306          328 RDRQV------LANCGVDEVYQMEELVHDDALRLFSRH  359 (538)
Q Consensus       328 R~~~~------~~~~~~~~~~~l~~L~~~ea~~Lf~~~  359 (538)
                      -++.-      ...-...+.+.+...+.+++..++...
T Consensus       308 ~~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         308 LDEYRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             HHHHHHHhhhchHHHhcCceeeCCCCCHHHHHHHHHHH
Confidence            44411      011123467889999999999988764

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.20  E-value=0.0013  Score=62.60  Aligned_cols=48  Identities=19%  Similarity=0.212  Sum_probs=35.2

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~  246 (538)
                      .|..+|..+-....++.|+|++|+|||+||..++......      ...++|+.
T Consensus         7 ~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~   60 (235)
T cd01123           7 ALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID   60 (235)
T ss_pred             hhHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEe
Confidence            4555666555667889999999999999999998653322      25677776

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 .

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.19  E-value=0.0015  Score=58.96  Aligned_cols=37  Identities=35%  Similarity=0.591  Sum_probs=31.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++.|+|++|+||||+|+.++..+...+...+++.
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~   42 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLD   42 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            3458999999999999999999999877766666664

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=97.19  E-value=0.0022  Score=67.60  Aligned_cols=54  Identities=24%  Similarity=0.280  Sum_probs=40.8

Q ss_pred             CCCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|....+++--...++++..||..   +....+++.|+||+|+||||.++.+++++.
T Consensus        14 ~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg   70 (519)
T PF03215_consen   14 APKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG   70 (519)
T ss_pred             CCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            334445555556788888888875   233467899999999999999999999864

>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=97.14  E-value=0.00035  Score=58.76  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=21.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +|+|.|++|+||||+|+.+++++
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            58999999999999999999876

...

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.14  E-value=0.0054  Score=66.12  Aligned_cols=178  Identities=16%  Similarity=0.187  Sum_probs=104.1

Q ss_pred             CCCCceeccchhHHHHHh---hhc-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESL---LRT-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~---L~~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      .-.++.|-+...++|++.   |..       +..-++-+.|+||+|.|||-||++++-+-.     +-|+....      
T Consensus       309 ~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAg-----VPF~svSG------  377 (774)
T KOG0731|consen  309 KFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAG-----VPFFSVSG------  377 (774)
T ss_pred             ccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccC-----Cceeeech------
Confidence            346788888766666654   432       222356699999999999999999997633     22333111      


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-----------------HHHHHHhcCcCCCC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-----------------RQIKILVGRLDLFA  318 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-----------------~~~~~l~~~l~~~~  318 (538)
                        .++.+.+    .+.     ............-.+.|++|.+|++|..                 ..+..++..++.+.
T Consensus       378 --SEFvE~~----~g~-----~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~  446 (774)
T KOG0731|consen  378 --SEFVEMF----VGV-----GASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFE  446 (774)
T ss_pred             --HHHHHHh----ccc-----chHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCc
Confidence              1111111    000     0011111112222467899999988632                 23666666666555


Q ss_pred             CCCEE--EEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          319 SGSRI--IITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       319 ~~~~i--iiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      ....|  +-+|...+++..     -+.++.+.++.-+...-.++|..++...... ....+++. ++..+-|++=|
T Consensus       447 ~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~-~e~~dl~~-~a~~t~gf~ga  520 (774)
T KOG0731|consen  447 TSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLD-DEDVDLSK-LASLTPGFSGA  520 (774)
T ss_pred             CCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCC-cchhhHHH-HHhcCCCCcHH
Confidence            44433  334444444322     2356778899999999999999998433322 34455555 88889888744

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.13  E-value=0.0011  Score=58.20  Aligned_cols=117  Identities=14%  Similarity=0.126  Sum_probs=60.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHH----HHhcC-----CCCC---Cchhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLS----TLLND-----GNVK---NFLNT  280 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~----~l~~~-----~~~~---~~~~~  280 (538)
                      .|-|++..|.||||+|...+-+...+-..+.++...... ...+-...++.+-.    ..+..     .+..   .....
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~-~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~a~~   82 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGYRVGVVQFLKGG-WKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAAAAE   82 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEEeCCC-CccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHHHHH
Confidence            577888889999999999998876665555554422221 11222233333200    00000     0000   11112


Q ss_pred             cHHHHHHHhcC-CCeEEEEecCCCh-----HHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          281 DLNFQSRRLTR-KKVLIVFDDVDHP-----RQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       281 ~~~~l~~~l~~-k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      .....++.+.. .-=|||||++-..     -..+.+...+....++..+|+|.|+.
T Consensus        83 ~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          83 GWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            23333444443 4459999998322     12233333333335688999999986

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.12  E-value=0.0037  Score=70.40  Aligned_cols=50  Identities=18%  Similarity=0.332  Sum_probs=38.4

Q ss_pred             CCCceeccchhHHHHHhhhc---C---CC-CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          187 NEDLVGVRLPMKEIESLLRT---G---ST-NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~---~---~~-~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++|.+..++.+...+..   +   .+ ....+.++|++|+|||+||+.+++.+-
T Consensus       508 ~~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~  564 (821)
T CHL00095        508 HKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFF  564 (821)
T ss_pred             cCcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhc
Confidence            36789999999998877642   1   11 134577899999999999999998764

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.12  E-value=0.0018  Score=64.47  Aligned_cols=101  Identities=15%  Similarity=0.140  Sum_probs=57.6

Q ss_pred             HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee-eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCc-
Q 009306          200 IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS-GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNF-  277 (538)
Q Consensus       200 l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~-~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~-  277 (538)
                      +.+.+..-+ ..+.++|+|++|+|||||++.+++.+....+ ..+++..+  ........++.+.+...+......... 
T Consensus       123 vID~l~PiG-kGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lI--gER~~EV~df~~~i~~~Vvast~de~~~  199 (380)
T PRK12608        123 VVDLVAPIG-KGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLI--DERPEEVTDMRRSVKGEVYASTFDRPPD  199 (380)
T ss_pred             hhhheeecC-CCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEe--cCCCCCHHHHHHHHhhhEEeecCCCCHH
Confidence            445554322 3345799999999999999999998766543 22232222  223456677777776655432211111 


Q ss_pred             ----hhhcHHHHHHHh--cCCCeEEEEecCCC
Q 009306          278 ----LNTDLNFQSRRL--TRKKVLIVFDDVDH  303 (538)
Q Consensus       278 ----~~~~~~~l~~~l--~~k~~LlVlDdv~~  303 (538)
                          .........+.+  .+++++||+|++..
T Consensus       200 ~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr  231 (380)
T PRK12608        200 EHIRVAELVLERAKRLVEQGKDVVILLDSLTR  231 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHH
Confidence                111111122222  47899999999854

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

Probab=97.10  E-value=0.0064  Score=64.62  Aligned_cols=151  Identities=19%  Similarity=0.187  Sum_probs=83.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.+.++|++|.|||.||++++......|-.+..-             +    +++...+     ..............
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~-------------~----l~sk~vG-----esek~ir~~F~~A~  332 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGS-------------E----LLSKWVG-----ESEKNIRELFEKAR  332 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCH-------------H----Hhccccc-----hHHHHHHHHHHHHH
Confidence            455799999999999999999999765554322110             1    1111000     11111122222333


Q ss_pred             cCCCeEEEEecCCCh-------------HHHHHHhcCcCCCCC--CCEEEEeccchhhhhhc-----CCCeeEEcCCCCH
Q 009306          290 TRKKVLIVFDDVDHP-------------RQIKILVGRLDLFAS--GSRIIITTRDRQVLANC-----GVDEVYQMEELVH  349 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~~~--~~~iiiTtR~~~~~~~~-----~~~~~~~l~~L~~  349 (538)
                      +..+++|.+|+++..             ..+..++..+.....  +..||-+|-....+...     ..+..+.++.-+.
T Consensus       333 ~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~  412 (494)
T COG0464         333 KLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDL  412 (494)
T ss_pred             cCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCH
Confidence            578999999999632             223344433332222  33445555444333211     3456888999999


Q ss_pred             HHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcC
Q 009306          350 DDALRLFSRHAFGGDHPHESHTELACKTIKYARG  383 (538)
Q Consensus       350 ~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G  383 (538)
                      ++..+.|..+.-..... -...-....+++.+.|
T Consensus       413 ~~r~~i~~~~~~~~~~~-~~~~~~~~~l~~~t~~  445 (494)
T COG0464         413 EERLEIFKIHLRDKKPP-LAEDVDLEELAEITEG  445 (494)
T ss_pred             HHHHHHHHHHhcccCCc-chhhhhHHHHHHHhcC
Confidence            99999999988322221 1112234455555555

>PRK14974 cell division protein FtsY; Provisional

Probab=97.10  E-value=0.0035  Score=62.27  Aligned_cols=29  Identities=21%  Similarity=0.318  Sum_probs=25.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +..+++++|++|+||||++..++..+...
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~  167 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKN  167 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            36789999999999999999998877654

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.09  E-value=0.025  Score=55.92  Aligned_cols=48  Identities=19%  Similarity=0.116  Sum_probs=35.1

Q ss_pred             eEEcCCCCHHHHHHHHHhhhcCCCCCC-CchHHHHHHHHHHhcCCcHHH
Q 009306          341 VYQMEELVHDDALRLFSRHAFGGDHPH-ESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       341 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~-~~~~~~~~~i~~~~~G~PLal  388 (538)
                      .+++++++.+|+..++....-.+-... ...+...+++.-..+|||.-+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHh
Confidence            789999999999999988774333322 344556667777779999654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PHA00729 NTP-binding motif containing protein

Probab=97.08  E-value=0.0018  Score=60.04  Aligned_cols=27  Identities=30%  Similarity=0.304  Sum_probs=23.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +...+.|+|.+|+||||||..+++++.
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            334689999999999999999998753

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=97.08  E-value=0.0072  Score=60.35  Aligned_cols=47  Identities=21%  Similarity=0.187  Sum_probs=38.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++|+...++.+.+.+..-......|.|+|.+|+||+++|+.+...
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            56899999999988877653333445999999999999999988864

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

Probab=97.07  E-value=0.0014  Score=64.59  Aligned_cols=50  Identities=20%  Similarity=0.164  Sum_probs=38.6

Q ss_pred             hHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...|..+|. .+-+..+++-|+|++|+||||||..++.........++|+.
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          40 SLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             CHHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            345566665 55566788999999999999999999887655556677776

RecA couples ATP hydrolysis to DNA strand exchange.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.07  E-value=0.00077  Score=66.82  Aligned_cols=49  Identities=14%  Similarity=0.281  Sum_probs=41.4

Q ss_pred             CceeccchhHHHHHhhhcC----CCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          189 DLVGVRLPMKEIESLLRTG----STNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~~----~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++|.+..+.++.+++...    ....++++|+|++|+||||||..++..+..
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            7999999999999888651    234688999999999999999999987644

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

>PRK09354 recA recombinase A; Provisional

Probab=97.06  E-value=0.0014  Score=64.96  Aligned_cols=99  Identities=19%  Similarity=0.148  Sum_probs=58.8

Q ss_pred             hHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHH---HHHhcCC
Q 009306          197 MKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLL---STLLNDG  272 (538)
Q Consensus       197 l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~---~~l~~~~  272 (538)
                      ...|..+|. .+-+..+++-|+|++|+||||||..++......-..++|+..-....    . ...+.+.   ..+....
T Consensus        45 i~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~----~-~~a~~lGvdld~lli~q  119 (349)
T PRK09354         45 SLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALD----P-VYAKKLGVDIDNLLVSQ  119 (349)
T ss_pred             cHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchH----H-HHHHHcCCCHHHeEEec
Confidence            345666776 55567789999999999999999999887666666777876322111    1 1222221   1111111


Q ss_pred             CCCCchhhcHHHHHHHhc-CCCeEEEEecCC
Q 009306          273 NVKNFLNTDLNFQSRRLT-RKKVLIVFDDVD  302 (538)
Q Consensus       273 ~~~~~~~~~~~~l~~~l~-~k~~LlVlDdv~  302 (538)
                        ....++....+...+. +..-+||+|.+.
T Consensus       120 --p~~~Eq~l~i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        120 --PDTGEQALEIADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             --CCCHHHHHHHHHHHhhcCCCCEEEEeChh
Confidence              1234444444444443 456789999874

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.06  E-value=0.0065  Score=60.89  Aligned_cols=37  Identities=22%  Similarity=0.253  Sum_probs=28.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++++|+|++|+||||++..++..+..+-..+.++.
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~  276 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFIT  276 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEe
Confidence            3578999999999999999999987765433344443

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

Probab=97.05  E-value=0.016  Score=55.10  Aligned_cols=172  Identities=17%  Similarity=0.199  Sum_probs=92.6

Q ss_pred             CCceeccchhHHHHHhhh----------cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          188 EDLVGVRLPMKEIESLLR----------TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~----------~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      .++-|.+...+.|.+...          .....-+-|.++|++|.|||-||++++-+-...|    |-..         .
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnSTF----FSvS---------S  199 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANSTF----FSVS---------S  199 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCCce----EEee---------h
Confidence            567788888887776421          1222356799999999999999999998754332    2211         1


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh---------HHH----HHHhcCcC---CCCCC
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP---------RQI----KILVGRLD---LFASG  320 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~---------~~~----~~l~~~l~---~~~~~  320 (538)
                      .++...   .++       .-+.+...+.+.. .++|-+|.+|++|..         +..    ..|+-.+.   ....|
T Consensus       200 SDLvSK---WmG-------ESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~g  269 (439)
T KOG0739|consen  200 SDLVSK---WMG-------ESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDG  269 (439)
T ss_pred             HHHHHH---Hhc-------cHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCc
Confidence            111111   111       1122233333332 468999999999743         111    12222222   11234


Q ss_pred             CEEEEeccchhhhhhc---CCCeeEEcCCCCHHHHH-HHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          321 SRIIITTRDRQVLANC---GVDEVYQMEELVHDDAL-RLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       321 ~~iiiTtR~~~~~~~~---~~~~~~~l~~L~~~ea~-~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .-|+-.|.-+.++...   +....+-+ ||.+..|. .+|.-+.  ++.+....+...+++.+++.|..
T Consensus       270 vLVLgATNiPw~LDsAIRRRFekRIYI-PLPe~~AR~~MF~lhl--G~tp~~LT~~d~~eL~~kTeGyS  335 (439)
T KOG0739|consen  270 VLVLGATNIPWVLDSAIRRRFEKRIYI-PLPEAHARARMFKLHL--GDTPHVLTEQDFKELARKTEGYS  335 (439)
T ss_pred             eEEEecCCCchhHHHHHHHHhhcceec-cCCcHHHhhhhheecc--CCCccccchhhHHHHHhhcCCCC
Confidence            4455455544444322   12223333 34444444 4555555  55566666777888888888864

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.04  E-value=0.005  Score=63.44  Aligned_cols=29  Identities=24%  Similarity=0.345  Sum_probs=25.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...++.++|++|+||||++..++..+...
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~  122 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKK  122 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            46789999999999999999999887655

>PRK08118 topology modulation protein; Reviewed

Probab=97.04  E-value=0.0005  Score=61.49  Aligned_cols=24  Identities=38%  Similarity=0.583  Sum_probs=21.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|.|+|++|+||||||+.+++.+.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~   26 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLN   26 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            489999999999999999999764

>PRK04328 hypothetical protein; Provisional

Probab=97.04  E-value=0.0048  Score=59.08  Aligned_cols=49  Identities=12%  Similarity=0.102  Sum_probs=37.3

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|.++|..+-+...++.|.|++|.|||+|+.+++.+.......++|+.
T Consensus        10 ~~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         10 PGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             hhHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            3566667655566778999999999999999998877545555666765

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.03  E-value=0.017  Score=56.82  Aligned_cols=52  Identities=15%  Similarity=0.115  Sum_probs=37.5

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      ...+.++=.......+...+..+    +.|.|.|++|+||||+|+.++..+...+-
T Consensus        42 ~~d~~y~f~~~~~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~lA~~l~~~~~   93 (327)
T TIGR01650        42 DIDPAYLFDKATTKAICAGFAYD----RRVMVQGYHGTGKSTHIEQIAARLNWPCV   93 (327)
T ss_pred             CCCCCccCCHHHHHHHHHHHhcC----CcEEEEeCCCChHHHHHHHHHHHHCCCeE
Confidence            34445555555666676666532    34999999999999999999998765543

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=97.02  E-value=0.006  Score=60.89  Aligned_cols=46  Identities=22%  Similarity=0.157  Sum_probs=34.8

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++|+...++++.+.+..-......|.|+|.+|+||+++|+.+...-
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s   46 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLS   46 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhc
Confidence            4677777777777665433334458999999999999999888753

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>TIGR02012 tigrfam_recA protein RecA

Probab=97.01  E-value=0.0016  Score=64.07  Aligned_cols=50  Identities=20%  Similarity=0.179  Sum_probs=38.5

Q ss_pred             hHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...|..+|. .+-+..+++.|+|++|+||||||..++......-..++|+.
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId   90 (321)
T TIGR02012        40 SLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   90 (321)
T ss_pred             CHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Confidence            345566665 55567789999999999999999998887665555667775

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.

>PTZ00494 tuzin-like protein; Provisional

Probab=97.00  E-value=0.046  Score=55.14  Aligned_cols=180  Identities=11%  Similarity=0.042  Sum_probs=97.5

Q ss_pred             HHHHHhhhcccccc------CCCCCCCceeccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccceee
Q 009306          169 EEIVNAILKRLDDT------FHSENEDLVGVRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSG  241 (538)
Q Consensus       169 ~~i~~~~~~~~~~~------~~~~~~~~vGR~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~  241 (538)
                      .-.++.+.+..++.      .+.....+|.|+.+=..+.+.|.. +....++++++|.-|+|||+|++....+   ..-.
T Consensus       346 ~~Av~TLsk~~~~~~~~~~~a~a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrk---E~~p  422 (664)
T PTZ00494        346 RTAIETLSKAARPRKEEGMLAAAAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRV---EGVA  422 (664)
T ss_pred             HHHHHHhhcccCCCcccccccccccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHH---cCCC
Confidence            33445555554443      245678899999999999888876 4456899999999999999999976543   2233


Q ss_pred             EEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHH-------HHhcCCCeEEEE--ecCCChHHHHHHhc
Q 009306          242 SYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQS-------RRLTRKKVLIVF--DDVDHPRQIKILVG  312 (538)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~-------~~l~~k~~LlVl--Ddv~~~~~~~~l~~  312 (538)
                      .+|+. ++      ...+.++.+...++-.. . ....++++.+.       ....++.-+||+  =+-.+..-+-.-.-
T Consensus       423 aV~VD-VR------g~EDtLrsVVKALgV~n-v-e~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLREGssL~RVYnE~v  493 (664)
T PTZ00494        423 LVHVD-VG------GTEDTLRSVVRALGVSN-V-EVCGDLLGFVEEAMRGATVKASDGVPFLVMRLREGSDLGRVYGEVV  493 (664)
T ss_pred             eEEEE-ec------CCcchHHHHHHHhCCCC-h-hhhccHHHHHHHHHHHHHHhcCCCCCEEEEEeccCCcHHHHHHHHH
Confidence            45554 22      22223344444443321 1 11122222222       122344445554  33333322111111


Q ss_pred             CcCCCCCCCEEEEeccchhhh---hhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          313 RLDLFASGSRIIITTRDRQVL---ANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       313 ~l~~~~~~~~iiiTtR~~~~~---~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      .+..-..-|+|++----+.+-   ..+..-..|-+++++.++|.++.....
T Consensus       494 aLacDrRlCHvv~EVplESLT~~n~~LPRLDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        494 SLVSDCQACHIVLAVPMKALTPLNVSSRRLDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             HHHccchhheeeeechHhhhchhhccCccceeEecCCcCHHHHHHHHhccc
Confidence            111223457777643322210   011123578999999999999776554

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.98  E-value=0.017  Score=59.39  Aligned_cols=43  Identities=21%  Similarity=0.298  Sum_probs=34.0

Q ss_pred             cchhHHHHHhhh-----cCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          194 RLPMKEIESLLR-----TGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       194 ~~~l~~l~~~L~-----~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+.++..||.     ...-+.+++.|+||+|+||||..+.++..+.
T Consensus        88 kkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg  135 (634)
T KOG1970|consen   88 KKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELG  135 (634)
T ss_pred             HHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhC
Confidence            346677777877     3344577999999999999999999998754

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

Probab=96.96  E-value=0.0026  Score=61.37  Aligned_cols=101  Identities=14%  Similarity=0.086  Sum_probs=58.2

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCC
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK  275 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~  275 (538)
                      .++.|..++..   ....+.|.|+.|+||||+++.+...+.......+.+.+..+..    +..+     .++.-.   .
T Consensus        68 ~~~~l~~~~~~---~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~----~~~~-----~q~~v~---~  132 (264)
T cd01129          68 NLEIFRKLLEK---PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ----IPGI-----NQVQVN---E  132 (264)
T ss_pred             HHHHHHHHHhc---CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec----CCCc-----eEEEeC---C
Confidence            33444455542   2347999999999999999998887654322334443222111    1000     000000   0


Q ss_pred             CchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHh
Q 009306          276 NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       276 ~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      ..-......++..++..+-.|+++++.+.+....+.
T Consensus       133 ~~~~~~~~~l~~~lR~~PD~i~vgEiR~~e~a~~~~  168 (264)
T cd01129         133 KAGLTFARGLRAILRQDPDIIMVGEIRDAETAEIAV  168 (264)
T ss_pred             cCCcCHHHHHHHHhccCCCEEEeccCCCHHHHHHHH
Confidence            111134566677788889999999998887665444

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.96  E-value=0.0026  Score=61.61  Aligned_cols=37  Identities=24%  Similarity=0.347  Sum_probs=28.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++.++|++|+||||++..++..+......+.++.
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~  107 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAA  107 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEe
Confidence            4678999999999999999999987765543444443

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.

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

Probab=96.96  E-value=0.002  Score=61.65  Aligned_cols=55  Identities=27%  Similarity=0.392  Sum_probs=39.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLS  266 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~  266 (538)
                      ..+.++|.|.+|.|||||++.+++.++.+|...+++..+.+-  .....++.+.+..
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer--~~Ev~e~~~~~~~  122 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGER--TREGNDLYHEMKE  122 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccC--cHHHHHHHHHHHh
Confidence            345589999999999999999999988777766776655432  2334445555543

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.95  E-value=0.0042  Score=64.65  Aligned_cols=51  Identities=20%  Similarity=0.217  Sum_probs=39.2

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      -+..|.++|..+-....++.|.|++|+|||||+.+++.........++|+.
T Consensus        65 Gi~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs  115 (446)
T PRK11823         65 GIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVS  115 (446)
T ss_pred             CcHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            445677777655556778999999999999999999988764444566665

>PRK06696 uridine kinase; Validated

Probab=96.95  E-value=0.0012  Score=62.11  Aligned_cols=46  Identities=28%  Similarity=0.363  Sum_probs=35.3

Q ss_pred             ccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          193 VRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       193 R~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      |...+++|.+.+.. ..+...+|+|.|.+|+||||||+.++..+...
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~   49 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKKR   49 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            55566666665543 33467899999999999999999999987543

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.94  E-value=0.0038  Score=57.23  Aligned_cols=113  Identities=25%  Similarity=0.285  Sum_probs=52.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh--ccceeeEEEEeehhhhhh--cCChHHH-------HHHHHHHHhcCCCCCCch
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI--SRHFSGSYFARNVREAEE--TCRLGDL-------RQQLLSTLLNDGNVKNFL  278 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~--~~~f~~~~~~~~~~~~~~--~~~~~~l-------~~~l~~~l~~~~~~~~~~  278 (538)
                      ...++.+.|++|.|||.||.+.+-+.  ...|...++....-+...  ..-+.++       ...+...+....     .
T Consensus        18 ~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~-----~   92 (205)
T PF02562_consen   18 NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELF-----G   92 (205)
T ss_dssp             H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS------
T ss_pred             hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHh-----C
Confidence            34579999999999999999888643  355777777654332111  1111111       111222221110     0


Q ss_pred             hhcHHHHH----------HHhcC---CCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          279 NTDLNFQS----------RRLTR---KKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       279 ~~~~~~l~----------~~l~~---k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ....+.+.          ..+++   ...+||+|++.+  ..++..++..   .+.+|++|++--..
T Consensus        93 ~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR---~g~~skii~~GD~~  156 (205)
T PF02562_consen   93 KEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTR---IGEGSKIIITGDPS  156 (205)
T ss_dssp             TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTT---B-TT-EEEEEE---
T ss_pred             hHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHcc---cCCCcEEEEecCce
Confidence            11111111          12333   346999999954  4567776544   37899999986443

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.94  E-value=0.0046  Score=58.46  Aligned_cols=49  Identities=20%  Similarity=0.214  Sum_probs=36.5

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|.++|..+-....++.|.|++|+|||+|+.+++.........++|+.
T Consensus         7 ~~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881         7 EGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             hhHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            4455666555556778999999999999999998765444455667776

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.93  E-value=0.0038  Score=58.94  Aligned_cols=49  Identities=14%  Similarity=0.086  Sum_probs=33.8

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|...+..+-+...++.|.|++|+||||||.+++.....+...++|+.
T Consensus        11 ~~ld~~l~ggi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         11 DELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             eeeehhhCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            3444455444455668999999999999999887776544444556655

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.93  E-value=0.0081  Score=61.36  Aligned_cols=151  Identities=19%  Similarity=0.194  Sum_probs=79.8

Q ss_pred             CCceeccc---hhHHHHHhhhcC-------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          188 EDLVGVRL---PMKEIESLLRTG-------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       188 ~~~vGR~~---~l~~l~~~L~~~-------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      +++-|.+.   |++++.+.|...       +.=.+-|.++|++|.|||-||++++-+-.-.    +|....++.      
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP----FF~~sGSEF------  373 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP----FFYASGSEF------  373 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC----eEeccccch------
Confidence            45667765   455555666542       1124569999999999999999998764322    233211111      


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCCCCCCEEE
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLFASGSRII  324 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~~~~~~ii  324 (538)
                      .    +++-.        .......+.....-.+-|++|.||++|..             ..+..++..++.|.++.-||
T Consensus       374 d----Em~VG--------vGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiI  441 (752)
T KOG0734|consen  374 D----EMFVG--------VGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGII  441 (752)
T ss_pred             h----hhhhc--------ccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceE
Confidence            1    11100        00111122222233567999999999742             23666777777666655444


Q ss_pred             Ee--ccchhhhh-hc----CCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          325 IT--TRDRQVLA-NC----GVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       325 iT--tR~~~~~~-~~----~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      |.  |.-++.+. .+    +.+..+.++.-+..--.++|..+.
T Consensus       442 vigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl  484 (752)
T KOG0734|consen  442 VIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYL  484 (752)
T ss_pred             EEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHH
Confidence            43  22222221 11    234456666555544445555444

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.92  E-value=0.0047  Score=55.44  Aligned_cols=29  Identities=24%  Similarity=0.269  Sum_probs=24.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      +++.++|.+|+||||+|++++..+++.-.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~i~   30 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQEIW   30 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHhhh
Confidence            46889999999999999999998776543

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.91  E-value=0.017  Score=64.02  Aligned_cols=49  Identities=24%  Similarity=0.249  Sum_probs=38.5

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++|+...++.+.+.+..-......|.|+|++|+|||++|+.++..-.
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~  424 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSG  424 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcC
Confidence            4799999999888776654223344599999999999999999987543

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

Probab=96.90  E-value=0.025  Score=52.40  Aligned_cols=51  Identities=27%  Similarity=0.417  Sum_probs=36.6

Q ss_pred             CceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          189 DLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +.=|.+-+.+++.+...-           +-+..+-+.++|++|+|||.||+++++.....|
T Consensus       156 diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~f  217 (408)
T KOG0727|consen  156 DIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  217 (408)
T ss_pred             ccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchhe
Confidence            344666666666654321           334567799999999999999999998766554

>KOG3928 consensus Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]

Probab=96.87  E-value=0.019  Score=57.01  Aligned_cols=57  Identities=16%  Similarity=0.024  Sum_probs=38.1

Q ss_pred             CeeEEcCCCCHHHHHHHHHhhhcCCCCC-CCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          339 DEVYQMEELVHDDALRLFSRHAFGGDHP-HESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       339 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~-~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ..++++++++.+|+.++.....-.+-.. ....++.-+++.-..+|||--++.++.++
T Consensus       403 f~pi~v~nYt~~E~~~~i~YYl~~nwl~kkv~~Ee~~kql~fLSngNP~l~~~lca~~  460 (461)
T KOG3928|consen  403 FVPIEVENYTLDEFEALIDYYLQSNWLLKKVPGEENIKQLYFLSNGNPSLMERLCAFL  460 (461)
T ss_pred             cCccccCCCCHHHHHHHHHHHHHhhHHHhhcCcccchhhhhhhcCCCHHHHHHHHHhc
Confidence            3468899999999999887765211100 00114456778888899997777776655

>PRK07667 uridine kinase; Provisional

Probab=96.87  E-value=0.0019  Score=59.23  Aligned_cols=42  Identities=24%  Similarity=0.436  Sum_probs=32.1

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ++.|.+.+..-.+...+|+|.|.+|+||||+|..+...+...
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~~~   44 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMKQE   44 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            344555555544556899999999999999999999977543

>PRK07261 topology modulation protein; Provisional

Probab=96.86  E-value=0.004  Score=55.89  Aligned_cols=23  Identities=35%  Similarity=0.551  Sum_probs=20.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|.|+|++|+||||||+.++..+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            38999999999999999998764

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.85  E-value=0.0012  Score=56.84  Aligned_cols=37  Identities=35%  Similarity=0.567  Sum_probs=28.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccc-ee-eEEEEeehh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRH-FS-GSYFARNVR  249 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~-f~-~~~~~~~~~  249 (538)
                      -++|+|++|+||||++..+++.++.. |. +.+|..-++
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVR   45 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeee
Confidence            48999999999999999999988766 54 344444333

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.84  E-value=0.025  Score=60.26  Aligned_cols=50  Identities=20%  Similarity=0.342  Sum_probs=41.4

Q ss_pred             CCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          187 NEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++|+...++++.+.+..-......|.|+|..|+|||++|+.+...-.
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~  235 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASP  235 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC
Confidence            46799999999999888776444455699999999999999999998643

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.84  E-value=0.011  Score=53.54  Aligned_cols=125  Identities=16%  Similarity=0.192  Sum_probs=62.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHh---cCC-----------CCC
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLL---NDG-----------NVK  275 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~---~~~-----------~~~  275 (538)
                      ...+++|.|+.|.|||||++.++..... ..+.+++... ..      ......+-..++   ...           ...
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~~~-~~G~i~~~g~-~~------~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~   98 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDLKP-QQGEITLDGV-PV------SDLEKALSSLISVLNQRPYLFDTTLRNNLGRR   98 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccCCC-CCCEEEECCE-EH------HHHHHHHHhhEEEEccCCeeecccHHHhhccc
Confidence            3457999999999999999999875433 2334444311 00      000000000000   000           000


Q ss_pred             -CchhhcHHHHHHHhcCCCeEEEEecCC---ChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEc
Q 009306          276 -NFLNTDLNFQSRRLTRKKVLIVFDDVD---HPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQM  344 (538)
Q Consensus       276 -~~~~~~~~~l~~~l~~k~~LlVlDdv~---~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l  344 (538)
                       ..-+...-.+.+.+..++-++++|+..   +....+.+...+.....+..||++|.+......  .++++.+
T Consensus        99 LS~G~~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~--~d~~~~l  169 (178)
T cd03247          99 FSGGERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIEH--MDKILFL  169 (178)
T ss_pred             CCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHHh--CCEEEEE
Confidence             111222233445566788899999873   222222222222211236678888888766543  3455544

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>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=96.84  E-value=0.0014  Score=57.27  Aligned_cols=36  Identities=25%  Similarity=0.328  Sum_probs=30.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+|.|+|.+|+||||||+++..++......++++.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFARGIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEec
Confidence            357999999999999999999999988777777775

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 ....

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

Probab=96.83  E-value=0.0037  Score=59.00  Aligned_cols=125  Identities=19%  Similarity=0.126  Sum_probs=67.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEee-hhhhhhcCChHHHHHHHHHHHhcCC------CCC-Cchhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARN-VREAEETCRLGDLRQQLLSTLLNDG------NVK-NFLNTD  281 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~-~~~~~~~~~~~~l~~~l~~~l~~~~------~~~-~~~~~~  281 (538)
                      ...+++|+|.+|+|||||++.+..-.......+.|-.. +.... .........+++...+...      +-. ..-+..
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~-~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQ  116 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLS-KEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQ  116 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcc-hhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhh
Confidence            34579999999999999999998765544333333210 00000 1122334445555544221      111 112222


Q ss_pred             HHHHHHHhcCCCeEEEEecCCCh------HHHHHHhcCcCCCCCCCEEEEeccchhhhhhc
Q 009306          282 LNFQSRRLTRKKVLIVFDDVDHP------RQIKILVGRLDLFASGSRIIITTRDRQVLANC  336 (538)
Q Consensus       282 ~~~l~~~l~~k~~LlVlDdv~~~------~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~  336 (538)
                      .-.+.+.+.-+|-++|.|+.-+.      .++-.++..+.. ..+...++.|-+-.+...+
T Consensus       117 Ri~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~-~~~lt~lFIsHDL~vv~~i  176 (268)
T COG4608         117 RIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQE-ELGLTYLFISHDLSVVRYI  176 (268)
T ss_pred             hHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHH-HhCCeEEEEEEEHHhhhhh
Confidence            33455667889999999987332      233333332221 2356677777777666554

>TIGR00416 sms DNA repair protein RadA

Probab=96.82  E-value=0.0054  Score=63.87  Aligned_cols=52  Identities=19%  Similarity=0.221  Sum_probs=40.1

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .-+..|.++|..+-....++.|.|.+|+|||||+.+++.........++|+.
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            3456677777666566788999999999999999999887765544566765

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)).

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=96.81  E-value=0.029  Score=51.94  Aligned_cols=147  Identities=20%  Similarity=0.332  Sum_probs=81.9

Q ss_pred             eccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          192 GVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       192 GR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |-+.++++|.+.+.-           +-...+-+.++|++|.|||-||+++++..     .+.|+. ++.       ..+
T Consensus       151 gLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht-----~c~fir-vsg-------sel  217 (404)
T KOG0728|consen  151 GLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT-----DCTFIR-VSG-------SEL  217 (404)
T ss_pred             cHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc-----ceEEEE-ech-------HHH
Confidence            345566666554432           12345568999999999999999998753     333443 211       122


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------H---HHHHHhcCcCCC--CCCCE
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------R---QIKILVGRLDLF--ASGSR  322 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~---~~~~l~~~l~~~--~~~~~  322 (538)
                      .+..+..-.      .-..++.-.-   -...|.+|..|++|+.             +   ..-.++..+..|  ..+.+
T Consensus       218 vqk~igegs------rmvrelfvma---rehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknik  288 (404)
T KOG0728|consen  218 VQKYIGEGS------RMVRELFVMA---REHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIK  288 (404)
T ss_pred             HHHHhhhhH------HHHHHHHHHH---HhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceE
Confidence            222211100      0011111111   1356889999998642             1   122344444433  34677


Q ss_pred             EEEeccchhhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          323 IIITTRDRQVLA-----NCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       323 iiiTtR~~~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ||+.|...+++.     .-..++-++.++-+.+.-.+++.-+.
T Consensus       289 vimatnridild~allrpgridrkiefp~p~e~ar~~ilkihs  331 (404)
T KOG0728|consen  289 VIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHS  331 (404)
T ss_pred             EEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhh
Confidence            888776544432     22455678888888887778777665

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.81  E-value=0.0087  Score=55.03  Aligned_cols=46  Identities=17%  Similarity=0.136  Sum_probs=30.9

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      +.+.+...+..   +.+++.|+|++|.||||+++.+...+...-..+++
T Consensus         6 Q~~a~~~~l~~---~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~   51 (196)
T PF13604_consen    6 QREAVRAILTS---GDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIG   51 (196)
T ss_dssp             HHHHHHHHHHC---TCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEE
T ss_pred             HHHHHHHHHhc---CCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEE
Confidence            34445555542   34578899999999999999988876665333333

>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=96.81  E-value=0.0021  Score=59.01  Aligned_cols=35  Identities=17%  Similarity=0.208  Sum_probs=27.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +++.++|+.|+||||.+.+++.+++.+-..+..++
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhccccceeec
Confidence            68999999999999999999988776644455554

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 ....

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.79  E-value=0.0021  Score=61.71  Aligned_cols=49  Identities=20%  Similarity=0.202  Sum_probs=33.9

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc--c----ceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS--R----HFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~--~----~f~~~~~~~  246 (538)
                      ..|.++|..+-....+.=|+|++|+|||+||..++-...  .    .-..++|++
T Consensus        25 ~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyid   79 (256)
T PF08423_consen   25 KSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYID   79 (256)
T ss_dssp             HHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEE
T ss_pred             HHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEe
Confidence            456667754444566788999999999999998876432  1    123467776

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 ....

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.79  E-value=0.0076  Score=54.23  Aligned_cols=23  Identities=22%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      ...+++|.|+.|+|||||.+.+.
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~~il   42 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVNEGL   42 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHh
Confidence            34579999999999999999885

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>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=96.78  E-value=0.006  Score=53.04  Aligned_cols=105  Identities=17%  Similarity=0.171  Sum_probs=56.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ...+++|.|+.|.|||||++.++..... ..+.+++.......--..                 . ..-+...-.+.+.+
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~~~~-~~G~i~~~~~~~i~~~~~-----------------l-S~G~~~rv~laral   85 (144)
T cd03221          25 PGDRIGLVGRNGAGKSTLLKLIAGELEP-DEGIVTWGSTVKIGYFEQ-----------------L-SGGEKMRLALAKLL   85 (144)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCCCC-CceEEEECCeEEEEEEcc-----------------C-CHHHHHHHHHHHHH
Confidence            3457999999999999999998875432 234444431100000000                 0 11112222344555


Q ss_pred             cCCCeEEEEecCC---ChHHHHHHhcCcCCCCCCCEEEEeccchhhhhh
Q 009306          290 TRKKVLIVFDDVD---HPRQIKILVGRLDLFASGSRIIITTRDRQVLAN  335 (538)
Q Consensus       290 ~~k~~LlVlDdv~---~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~  335 (538)
                      ..++-++++|+..   +....+.+...+...  +..||++|.+......
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~~  132 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLDQ  132 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHHH
Confidence            6778899999873   222222332222211  2467888877655443

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.

>PRK06762 hypothetical protein; Provisional

Probab=96.78  E-value=0.0081  Score=53.59  Aligned_cols=24  Identities=38%  Similarity=0.448  Sum_probs=22.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+++|+|++|+||||+|+.++..+
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999999886

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

Probab=96.73  E-value=0.0077  Score=54.09  Aligned_cols=129  Identities=19%  Similarity=0.287  Sum_probs=62.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC---------CCchhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV---------KNFLNT  280 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~---------~~~~~~  280 (538)
                      ....++|.|+.|.|||||.+.++..... ..+.+++.... ... .......+.+ ..+......         -..-+.
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~~~~-~~G~i~~~g~~-~~~-~~~~~~~~~i-~~~~~~~~~~~~t~~e~lLS~G~~  102 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRLYDP-TSGEILIDGVD-LRD-LDLESLRKNI-AYVPQDPFLFSGTIRENILSGGQR  102 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCCCC-CCCEEEECCEE-hhh-cCHHHHHhhE-EEEcCCchhccchHHHHhhCHHHH
Confidence            3457999999999999999999876443 33444443210 000 0000000000 000000000         000111


Q ss_pred             cHHHHHHHhcCCCeEEEEecCC---ChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEc
Q 009306          281 DLNFQSRRLTRKKVLIVFDDVD---HPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQM  344 (538)
Q Consensus       281 ~~~~l~~~l~~k~~LlVlDdv~---~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l  344 (538)
                      ..-.+...+..++-++++|+-.   +....+.+...+.....+..||++|.+......  .++++.+
T Consensus       103 ~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~--~d~~~~l  167 (171)
T cd03228         103 QRIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIRD--ADRIIVL  167 (171)
T ss_pred             HHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHHHh--CCEEEEE
Confidence            2223445566788899999873   222222222222111235678888887766544  3455544

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>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=96.70  E-value=0.0042  Score=53.77  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|.++|++|+||||+|+.+.....
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

...

>CHL00206 ycf2 Ycf2; Provisional

Probab=96.70  E-value=0.017  Score=67.96  Aligned_cols=27  Identities=11%  Similarity=0.099  Sum_probs=23.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+-|.++|++|+|||.||++++.+..
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es~ 1655 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNSY 1655 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhcC
Confidence            355699999999999999999998743

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.68  E-value=0.01  Score=53.06  Aligned_cols=126  Identities=20%  Similarity=0.131  Sum_probs=62.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehh---hhhhcCCh--HHHHHHHHHHHhcCCCCC-CchhhcHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVR---EAEETCRL--GDLRQQLLSTLLNDGNVK-NFLNTDLN  283 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~---~~~~~~~~--~~l~~~l~~~l~~~~~~~-~~~~~~~~  283 (538)
                      ....++|.|+.|.|||||++.++...... .+.+++...+   -..+...+  ..+.+.+...    .... ..-+...-
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~-~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~----~~~~LS~G~~~rv  100 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWPWG-SGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP----WDDVLSGGEQQRL  100 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCCC-CceEEECCCceEEEECCCCccccccHHHHhhcc----CCCCCCHHHHHHH
Confidence            34579999999999999999998764322 2222221100   00111111  1222222110    1111 22222333


Q ss_pred             HHHHHhcCCCeEEEEecCC---ChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEc
Q 009306          284 FQSRRLTRKKVLIVFDDVD---HPRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQM  344 (538)
Q Consensus       284 ~l~~~l~~k~~LlVlDdv~---~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l  344 (538)
                      .+.+.+..++-++++|+-.   +....+.+...+...  +..+|++|.+......  .++++.+
T Consensus       101 ~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~~~--~d~i~~l  160 (166)
T cd03223         101 AFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLWKF--HDRVLDL  160 (166)
T ss_pred             HHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHHhh--CCEEEEE
Confidence            4455566788899999863   222222222222211  3567888877655432  3445544

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.67  E-value=0.041  Score=55.58  Aligned_cols=150  Identities=19%  Similarity=0.197  Sum_probs=79.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      .|-..++||||.|||++..++++.+.-  +  ++.-.+......   .+ ++.|+..                      .
T Consensus       235 KRGYLLYGPPGTGKSS~IaAmAn~L~y--d--IydLeLt~v~~n---~d-Lr~LL~~----------------------t  284 (457)
T KOG0743|consen  235 KRGYLLYGPPGTGKSSFIAAMANYLNY--D--IYDLELTEVKLD---SD-LRHLLLA----------------------T  284 (457)
T ss_pred             hccceeeCCCCCCHHHHHHHHHhhcCC--c--eEEeeeccccCc---HH-HHHHHHh----------------------C
Confidence            456899999999999999999987542  2  222211111111   11 2222211                      2


Q ss_pred             CCCeEEEEecCCChHH--------------------HHHHhcCcC--CCCC-CCEE-EEeccchhhhhh--c---CCCee
Q 009306          291 RKKVLIVFDDVDHPRQ--------------------IKILVGRLD--LFAS-GSRI-IITTRDRQVLAN--C---GVDEV  341 (538)
Q Consensus       291 ~k~~LlVlDdv~~~~~--------------------~~~l~~~l~--~~~~-~~~i-iiTtR~~~~~~~--~---~~~~~  341 (538)
                      ..+-+|||.|+|..-+                    +--|+..+.  |..+ +-|| |+||.....+..  +   +.+-.
T Consensus       285 ~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmh  364 (457)
T KOG0743|consen  285 PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMH  364 (457)
T ss_pred             CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeE
Confidence            3556888888864210                    112333332  2223 2355 455554433221  1   23345


Q ss_pred             EEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          342 YQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       342 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      +.+.-=+.+....|+.+..... .    ...++.+|.+...|.-+.=..++..|
T Consensus       365 I~mgyCtf~~fK~La~nYL~~~-~----~h~L~~eie~l~~~~~~tPA~V~e~l  413 (457)
T KOG0743|consen  365 IYMGYCTFEAFKTLASNYLGIE-E----DHRLFDEIERLIEETEVTPAQVAEEL  413 (457)
T ss_pred             EEcCCCCHHHHHHHHHHhcCCC-C----CcchhHHHHHHhhcCccCHHHHHHHH
Confidence            6788888888888888877221 1    23455566655566544444555544

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.67  E-value=0.0064  Score=55.11  Aligned_cols=123  Identities=16%  Similarity=0.169  Sum_probs=61.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeeh--hhhhh---cCChHHHHHHHHHHHhcCCC-----CC-Cch
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNV--REAEE---TCRLGDLRQQLLSTLLNDGN-----VK-NFL  278 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~--~~~~~---~~~~~~l~~~l~~~l~~~~~-----~~-~~~  278 (538)
                      ...+++|.|+.|.|||||++.++..... ..+.+++...  .....   ...+. ...+++..++....     .. ..-
T Consensus        24 ~G~~~~l~G~nGsGKStLl~~i~G~~~~-~~G~v~~~g~~~~~~~~~~~~~~i~-~~~q~l~~~gl~~~~~~~~~~LS~G  101 (180)
T cd03214          24 AGEIVGILGPNGAGKSTLLKTLAGLLKP-SSGEILLDGKDLASLSPKELARKIA-YVPQALELLGLAHLADRPFNELSGG  101 (180)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC-CCcEEEECCEECCcCCHHHHHHHHh-HHHHHHHHcCCHhHhcCCcccCCHH
Confidence            3457999999999999999999875433 3444444311  10000   00111 11113333221110     01 111


Q ss_pred             hhcHHHHHHHhcCCCeEEEEecCC---ChHHHHHHhcCcCCC-CC-CCEEEEeccchhhhh
Q 009306          279 NTDLNFQSRRLTRKKVLIVFDDVD---HPRQIKILVGRLDLF-AS-GSRIIITTRDRQVLA  334 (538)
Q Consensus       279 ~~~~~~l~~~l~~k~~LlVlDdv~---~~~~~~~l~~~l~~~-~~-~~~iiiTtR~~~~~~  334 (538)
                      +...-.+.+.+...+-++++|+..   +....+.+...+... .. +..||++|.+.....
T Consensus       102 ~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~  162 (180)
T cd03214         102 ERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            222333445566788899999873   222233332222211 22 567888887765543

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.66  E-value=0.0078  Score=53.47  Aligned_cols=118  Identities=15%  Similarity=0.043  Sum_probs=60.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHH---hcC-----CCCC---Cchhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTL---LND-----GNVK---NFLNT  280 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l---~~~-----~~~~---~~~~~  280 (538)
                      ..+-|++..|.||||.|..++.+...+-..++.+...... ...+-...++.+.-.+   +..     .+..   .....
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~ra~~~g~~v~ivQFlKg~-~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~   84 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALRALGHGKKVGVIQFIKGA-WPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKA   84 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCC-cccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHH
Confidence            4677888899999999999998866554444333222111 1112222222221000   000     0000   11222


Q ss_pred             cHHHHHHHhcCC-CeEEEEecCCCh-----HHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          281 DLNFQSRRLTRK-KVLIVFDDVDHP-----RQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       281 ~~~~l~~~l~~k-~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ..+..++.+... -=+||||++-..     -..+.+...+...+++..||+|-|+.
T Consensus        85 ~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        85 AWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            334444555444 459999998321     11222222333335788999999986

Alternate name: corrinoid adenosyltransferase.

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

Probab=96.64  E-value=0.035  Score=58.84  Aligned_cols=174  Identities=20%  Similarity=0.179  Sum_probs=93.0

Q ss_pred             CceeccchhHHHHHhhhcCC-----------CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          189 DLVGVRLPMKEIESLLRTGS-----------TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~~~-----------~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      ++-|.....+.|++.+.-..           .-..-|.++|++|+|||-||.+++....-+     |++.       .++
T Consensus       668 digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~-----fisv-------KGP  735 (952)
T KOG0735|consen  668 DIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLR-----FISV-------KGP  735 (952)
T ss_pred             ecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCee-----EEEe-------cCH
Confidence            44555555555665554221           112348999999999999999988764332     3331       121


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCC--CCCCE
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLF--ASGSR  322 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~--~~~~~  322 (538)
                           ++++...+.     +.+.......+.-..+|+++.+|++|+.             ..+..++..+...  -.|.-
T Consensus       736 -----ElL~KyIGa-----SEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~  805 (952)
T KOG0735|consen  736 -----ELLSKYIGA-----SEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVY  805 (952)
T ss_pred             -----HHHHHHhcc-----cHHHHHHHHHHhhccCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEE
Confidence                 233333222     1122222233333569999999999753             2345555554421  23555


Q ss_pred             EEE-eccchhh----hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          323 III-TTRDRQV----LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       323 iii-TtR~~~~----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      |+- |||..-+    +..-+.++.+.-+.-+..|-+++|....-.  ... ...-..+.++.++.|..-|
T Consensus       806 i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s--~~~-~~~vdl~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  806 ILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNS--LLK-DTDVDLECLAQKTDGFTGA  872 (952)
T ss_pred             EEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhc--cCC-ccccchHHHhhhcCCCchh
Confidence            554 4454422    111123445555666777777877766511  111 1122356677788887643

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.63  E-value=0.012  Score=51.45  Aligned_cols=24  Identities=38%  Similarity=0.495  Sum_probs=21.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++.|+|.+|+||||||+.+...+.
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999998765

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.61  E-value=0.0043  Score=65.52  Aligned_cols=101  Identities=13%  Similarity=0.084  Sum_probs=63.1

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcC---
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLND---  271 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~---  271 (538)
                      .-+..|.++|..+-....++.|.|++|+|||||+.+++.....+-..++|+..      ......+.+..- .++-.   
T Consensus       247 tGi~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~------eEs~~~i~~~~~-~lg~~~~~  319 (484)
T TIGR02655       247 SGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAY------EESRAQLLRNAY-SWGIDFEE  319 (484)
T ss_pred             CChHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEe------eCCHHHHHHHHH-HcCCChHH
Confidence            34567778887766777889999999999999999999987666556666652      223333333321 11110   


Q ss_pred             ------------CCCCCchhhcHHHHHHHhcC-CCeEEEEecCC
Q 009306          272 ------------GNVKNFLNTDLNFQSRRLTR-KKVLIVFDDVD  302 (538)
Q Consensus       272 ------------~~~~~~~~~~~~~l~~~l~~-k~~LlVlDdv~  302 (538)
                                  .+.....+.....+.+.+.. ++-++|+|.+.
T Consensus       320 ~~~~g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       320 MEQQGLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             HhhCCcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence                        01112234455555555543 56789999874

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.61  E-value=0.009  Score=56.93  Aligned_cols=95  Identities=16%  Similarity=0.149  Sum_probs=60.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEE-EeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF-ARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~-~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ....|.|+|+.|+||||-...+.+.+-.++...+. +.+         +-+..-+--..+........+.....+.++..
T Consensus       124 ~~GLILVTGpTGSGKSTTlAamId~iN~~~~~HIlTIED---------PIE~vh~skkslI~QREvG~dT~sF~~aLraA  194 (353)
T COG2805         124 PRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIED---------PIEYVHESKKSLINQREVGRDTLSFANALRAA  194 (353)
T ss_pred             CCceEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEecC---------chHhhhcchHhhhhHHHhcccHHHHHHHHHHH
Confidence            34579999999999998777777776655544333 221         11111111111222223335566677888999


Q ss_pred             hcCCCeEEEEecCCChHHHHHHhcC
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILVGR  313 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~~~  313 (538)
                      |+.-|=+|++-+..+.+.+..-+.+
T Consensus       195 LReDPDVIlvGEmRD~ETi~~ALtA  219 (353)
T COG2805         195 LREDPDVILVGEMRDLETIRLALTA  219 (353)
T ss_pred             hhcCCCEEEEeccccHHHHHHHHHH
Confidence            9999999999999888877655544

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.57  E-value=0.0046  Score=61.57  Aligned_cols=49  Identities=16%  Similarity=0.163  Sum_probs=34.7

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc--cc----eeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS--RH----FSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~--~~----f~~~~~~~  246 (538)
                      ..|.++|..+-....+.-|+|++|+|||+|+.+++-...  ..    -..++|++
T Consensus       113 ~~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyId  167 (344)
T PLN03187        113 QALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYID  167 (344)
T ss_pred             HhHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEE
Confidence            455666765556677888999999999999999875321  11    23567776

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.56  E-value=0.0068  Score=54.66  Aligned_cols=119  Identities=15%  Similarity=0.057  Sum_probs=62.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHH-HH---HhcC-----CCCC---Cch
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLL-ST---LLND-----GNVK---NFL  278 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~-~~---l~~~-----~~~~---~~~  278 (538)
                      ...+.|+|..|-||||.|..++.+...+-..+..+...... ...+-...++.+. -.   .+..     .+..   ...
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~-~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~~  100 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGA-WSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAAA  100 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCC-CccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHHH
Confidence            34689999999999999999998766554444444322221 1112222222210 00   0000     0000   111


Q ss_pred             hhcHHHHHHHhcC-CCeEEEEecCCCh-----HHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          279 NTDLNFQSRRLTR-KKVLIVFDDVDHP-----RQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       279 ~~~~~~l~~~l~~-k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ....+..++.+.. +-=+||||++-..     -..+.+...+...+++..||+|-|+.
T Consensus       101 ~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        101 REGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            2233444455544 4459999998321     11233333333335788999999976

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.55  E-value=0.058  Score=48.17  Aligned_cols=79  Identities=9%  Similarity=0.036  Sum_probs=41.7

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC--
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR--  291 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~--  291 (538)
                      +.|.|.+|+|||++|.+++...   ...++|+..    ....+ .++.+.+.. .....+......+....+.+.+..  
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~---~~~~~y~at----~~~~d-~em~~rI~~-H~~~R~~~w~t~E~~~~l~~~l~~~~   72 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL---GGPVTYIAT----AEAFD-DEMAERIAR-HRKRRPAHWRTIETPRDLVSALKELD   72 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc---CCCeEEEEc----cCcCC-HHHHHHHHH-HHHhCCCCceEeecHHHHHHHHHhcC
Confidence            6789999999999999998762   234555541    11222 123333332 222222222222333334444422  


Q ss_pred             CCeEEEEecC
Q 009306          292 KKVLIVFDDV  301 (538)
Q Consensus       292 k~~LlVlDdv  301 (538)
                      +.-.++||.+
T Consensus        73 ~~~~VLIDcl   82 (169)
T cd00544          73 PGDVVLIDCL   82 (169)
T ss_pred             CCCEEEEEcH
Confidence            3447999986

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.52  E-value=0.012  Score=55.46  Aligned_cols=38  Identities=13%  Similarity=-0.040  Sum_probs=29.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ....++.|.|.+|+|||+++.+++.....+...++|+.
T Consensus        62 ~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         62 KPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            45668999999999999999999887655555566655

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.52  E-value=0.0017  Score=59.26  Aligned_cols=94  Identities=20%  Similarity=0.166  Sum_probs=51.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhc-CCCC-CCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN-DGNV-KNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~-~~~~-~~~~~~~~~~l~~~  288 (538)
                      ...++|.|+.|+|||||++.++..+.... ..+.+.+..+.....      .... .+.. .... ..........+...
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~~~~-~~i~ied~~E~~~~~------~~~~-~~~~~~~~~~~~~~~~~~~~l~~~   96 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIPPDE-RIITIEDTAELQLPH------PNWV-RLVTRPGNVEGSGEVTMADLLRSA   96 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCCCC-CEEEECCccccCCCC------CCEE-EEEEecCCCCCCCccCHHHHHHHH
Confidence            45799999999999999999998765432 333333211111000      0000 0000 0000 01112334555666


Q ss_pred             hcCCCeEEEEecCCChHHHHHHhc
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILVG  312 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~~  312 (538)
                      ++..|-.++++++.+.+.+..+..
T Consensus        97 lR~~pd~i~igEir~~ea~~~~~a  120 (186)
T cd01130          97 LRMRPDRIIVGEVRGGEALDLLQA  120 (186)
T ss_pred             hccCCCEEEEEccCcHHHHHHHHH
Confidence            777889999999988776654443

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.

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

Probab=96.51  E-value=0.002  Score=54.57  Aligned_cols=22  Identities=50%  Similarity=0.771  Sum_probs=20.6

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |+|.|++|+||||+|+.+..++
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999985

...

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

Probab=96.50  E-value=0.0075  Score=53.70  Aligned_cols=119  Identities=16%  Similarity=0.183  Sum_probs=59.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ....++|.|+.|.|||||.+.++..... ..+.+++.... .. ........+.   .++.... -..-+...-.+.+.+
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~i~G~~~~-~~G~v~~~g~~-~~-~~~~~~~~~~---~i~~~~q-LS~G~~qrl~laral   97 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGLYKP-DSGEILVDGKE-VS-FASPRDARRA---GIAMVYQ-LSVGERQMVEIARAL   97 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC-CCeEEEECCEE-CC-cCCHHHHHhc---CeEEEEe-cCHHHHHHHHHHHHH
Confidence            3457999999999999999999875432 34445543210 00 0011111000   0110000 011122233344556


Q ss_pred             cCCCeEEEEecCC---ChHHHHHHhcCcCCC-CCCCEEEEeccchhhhhh
Q 009306          290 TRKKVLIVFDDVD---HPRQIKILVGRLDLF-ASGSRIIITTRDRQVLAN  335 (538)
Q Consensus       290 ~~k~~LlVlDdv~---~~~~~~~l~~~l~~~-~~~~~iiiTtR~~~~~~~  335 (538)
                      ...+-++++|+..   +....+.+...+... ..+..||++|.+......
T Consensus        98 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~~  147 (163)
T cd03216          98 ARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVFE  147 (163)
T ss_pred             hcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            6778899999873   222222222222111 236678888888764443

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.50  E-value=0.0025  Score=66.63  Aligned_cols=51  Identities=24%  Similarity=0.294  Sum_probs=41.9

Q ss_pred             CCceeccchhHHHHHhhh----cCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          188 EDLVGVRLPMKEIESLLR----TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~----~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+++|.+..++.+.+.|.    ......+++.++||+|.||||||+.++..+...
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~  130 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERV  130 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhC
Confidence            368999999999998883    233456899999999999999999999865443

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.50  E-value=0.015  Score=52.44  Aligned_cols=36  Identities=28%  Similarity=0.213  Sum_probs=27.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+||||+|+.++..+........++
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            345899999999999999999999875433334444

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.50  E-value=0.037  Score=56.25  Aligned_cols=25  Identities=28%  Similarity=0.161  Sum_probs=22.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|+|++|+||||++..++...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4679999999999999999999764

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.50  E-value=0.02  Score=51.03  Aligned_cols=58  Identities=12%  Similarity=0.204  Sum_probs=37.1

Q ss_pred             hcHHHHHHHhcCCCeEEEEec----CCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcC
Q 009306          280 TDLNFQSRRLTRKKVLIVFDD----VDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCG  337 (538)
Q Consensus       280 ~~~~~l~~~l~~k~~LlVlDd----v~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~  337 (538)
                      +....+.+.+-++|-+++-|+    +|..-.++.+.-.-.....|..|++.|-+..+...+.
T Consensus       143 QQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         143 QQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             HHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhcc
Confidence            334455666778999999996    4444444333211111245889999999998877764

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.50  E-value=0.0077  Score=57.95  Aligned_cols=48  Identities=21%  Similarity=0.214  Sum_probs=37.9

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|..+|..+-+..+++=|+|+.|+||||+|.+++-........++|++
T Consensus        48 ~LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~aq~~g~~a~fID   95 (279)
T COG0468          48 ALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKPGGKAAFID   95 (279)
T ss_pred             hHHHHhcCCcccceEEEEecCCCcchhhHHHHHHHHhhcCCCeEEEEe
Confidence            344555555566788889999999999999999887666666788887

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.49  E-value=0.012  Score=53.11  Aligned_cols=116  Identities=16%  Similarity=0.108  Sum_probs=58.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeeh--hhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNV--REAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      ...+++|.|+.|.|||||++.++...... .+.+.+...  .-..+...                  -..-+...-.+.+
T Consensus        24 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~-~G~i~~~g~~i~~~~q~~~------------------LSgGq~qrv~lar   84 (177)
T cd03222          24 EGEVIGIVGPNGTGKTTAVKILAGQLIPN-GDNDEWDGITPVYKPQYID------------------LSGGELQRVAIAA   84 (177)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCCCCC-CcEEEECCEEEEEEcccCC------------------CCHHHHHHHHHHH
Confidence            34579999999999999999988754332 233333210  00000000                  0111122233445


Q ss_pred             HhcCCCeEEEEecCC---ChHHHHHHhcCcCCC-CC-CCEEEEeccchhhhhhcCCCeeEEcC
Q 009306          288 RLTRKKVLIVFDDVD---HPRQIKILVGRLDLF-AS-GSRIIITTRDRQVLANCGVDEVYQME  345 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~---~~~~~~~l~~~l~~~-~~-~~~iiiTtR~~~~~~~~~~~~~~~l~  345 (538)
                      .+..++-++++|+-.   +....+.+...+... .. +..||++|.+......+. ++++.+.
T Consensus        85 al~~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~~~~~-d~i~~l~  146 (177)
T cd03222          85 ALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLDYLS-DRIHVFE  146 (177)
T ss_pred             HHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHHHHhC-CEEEEEc
Confidence            566788899999873   222222222111111 12 356778887765554321 3444443

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.48  E-value=0.022  Score=54.96  Aligned_cols=115  Identities=17%  Similarity=0.148  Sum_probs=61.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCC-----CCCCchhhcHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDG-----NVKNFLNTDLNFQ  285 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~-----~~~~~~~~~~~~l  285 (538)
                      ...++|.|++|.|||||.+.++..+... .+.+++... ..........+... ...+....     +....... ...+
T Consensus       111 ~~~~~i~g~~g~GKttl~~~l~~~~~~~-~G~i~~~g~-~v~~~d~~~ei~~~-~~~~~q~~~~~r~~v~~~~~k-~~~~  186 (270)
T TIGR02858       111 VLNTLIISPPQCGKTTLLRDLARILSTG-ISQLGLRGK-KVGIVDERSEIAGC-VNGVPQHDVGIRTDVLDGCPK-AEGM  186 (270)
T ss_pred             eeEEEEEcCCCCCHHHHHHHHhCccCCC-CceEEECCE-EeecchhHHHHHHH-hcccccccccccccccccchH-HHHH
Confidence            4679999999999999999999876543 223333210 00000001111111 00010000     00011111 1112


Q ss_pred             HHHh-cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhh
Q 009306          286 SRRL-TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQV  332 (538)
Q Consensus       286 ~~~l-~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~  332 (538)
                      ...+ ...|-++++|++...+.+..+...+.   .|..+|+||-+..+
T Consensus       187 ~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~  231 (270)
T TIGR02858       187 MMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDV  231 (270)
T ss_pred             HHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHH
Confidence            2222 35788999999987776766665542   47789999887654

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>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=96.47  E-value=0.0079  Score=54.09  Aligned_cols=34  Identities=21%  Similarity=0.272  Sum_probs=26.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++.++|++|+||||++..++..+...-..+..+.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~   35 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA   35 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            5789999999999999999988766533334443

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.

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.026  Score=59.76  Aligned_cols=176  Identities=18%  Similarity=0.179  Sum_probs=95.8

Q ss_pred             CCCCceeccchhHHHHHhh---hcC-------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLL---RTG-------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L---~~~-------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      ...+.-|.+...+++.+.+   ...       ..-++-+.++|++|.|||.||++++.+..-.|-   +++ .       
T Consensus       148 ~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf---~iS-G-------  216 (596)
T COG0465         148 TFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFF---SIS-G-------  216 (596)
T ss_pred             ChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCce---ecc-c-------
Confidence            3467788887666666544   321       122556899999999999999999987543321   111 0       


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCCCC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLFAS  319 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~~~  319 (538)
                        .++.+.+    .+     ...........+..++.|++|++|.+|..                ..+..++..++.++.
T Consensus       217 --S~FVemf----VG-----vGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~  285 (596)
T COG0465         217 --SDFVEMF----VG-----VGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGG  285 (596)
T ss_pred             --hhhhhhh----cC-----CCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCC
Confidence              0000000    00     01111122233344567899999998632                245666666666664


Q ss_pred             CCEEE-E-eccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          320 GSRII-I-TTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       320 ~~~ii-i-TtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      +.-|| + .|..++++     ..-+.++.+.++..+...-.+++.-++-.......  -+ ...+++.+-|.-.
T Consensus       286 ~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~--Vd-l~~iAr~tpGfsG  356 (596)
T COG0465         286 NEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAED--VD-LKKIARGTPGFSG  356 (596)
T ss_pred             CCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCc--CC-HHHHhhhCCCccc
Confidence            33233 2 23333333     22235567778887877777888766632222211  11 2237777777653

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.47  E-value=0.022  Score=57.84  Aligned_cols=27  Identities=22%  Similarity=0.214  Sum_probs=23.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+++.++|+.|+||||.+..++..+.
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            357899999999999999999998765

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

Probab=96.47  E-value=0.0023  Score=58.79  Aligned_cols=26  Identities=35%  Similarity=0.530  Sum_probs=23.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +|+|.|++|+||||+|+.+...+...
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCcc
Confidence            58999999999999999999987644

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 ....

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.038  Score=59.12  Aligned_cols=50  Identities=26%  Similarity=0.333  Sum_probs=33.2

Q ss_pred             CceeccchhHHHHHhhh----------cCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          189 DLVGVRLPMKEIESLLR----------TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~----------~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ++=|-+.-..+|.+-+.          .+-....-|.++|++|.|||-||++++-+..-.
T Consensus       673 DVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL~  732 (953)
T KOG0736|consen  673 DVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSLN  732 (953)
T ss_pred             cccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhceee
Confidence            34455555555554332          222223358999999999999999999876544

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.47  E-value=0.027  Score=56.72  Aligned_cols=29  Identities=21%  Similarity=0.264  Sum_probs=24.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++++|++|+||||++..++.+....
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~  164 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMR  164 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            35689999999999999999999876544

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.46  E-value=0.012  Score=52.93  Aligned_cols=27  Identities=33%  Similarity=0.406  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|+.|.|||||.+.++....
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (173)
T cd03246          27 PGESLAIIGPSGSGKSTLARLILGLLR   53 (173)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccC
Confidence            345799999999999999999987543

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

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

Probab=96.46  E-value=0.19  Score=53.34  Aligned_cols=133  Identities=15%  Similarity=0.209  Sum_probs=67.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc---------eeeEEEEeehhhhhhcCCh------------HHHHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH---------FSGSYFARNVREAEETCRL------------GDLRQQLLSTLL  269 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~---------f~~~~~~~~~~~~~~~~~~------------~~l~~~l~~~l~  269 (538)
                      ...|+|+|+.|+|||||.+.+.......         -...+|-...........+            ..-.+.++..++
T Consensus       348 g~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~  427 (530)
T COG0488         348 GDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFG  427 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcC
Confidence            3459999999999999999996643322         1111221111010000011            223333333333


Q ss_pred             cCCCCC-Cc------hhhcHHHHHHHhcCCCeEEEEecCCC---hHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCC
Q 009306          270 NDGNVK-NF------LNTDLNFQSRRLTRKKVLIVFDDVDH---PRQIKILVGRLDLFASGSRIIITTRDRQVLANCGVD  339 (538)
Q Consensus       270 ~~~~~~-~~------~~~~~~~l~~~l~~k~~LlVlDdv~~---~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~  339 (538)
                      -..+.. ..      -+...-.+...+-.++=++|||+--+   .+.++.+...+..  -.+.||+.|-++..+..+. .
T Consensus       428 F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~--f~Gtvl~VSHDr~Fl~~va-~  504 (530)
T COG0488         428 FTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLD--FEGTVLLVSHDRYFLDRVA-T  504 (530)
T ss_pred             CChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHh--CCCeEEEEeCCHHHHHhhc-c
Confidence            221111 11      11222334455567888999997632   2334444333332  2345888899998877764 4


Q ss_pred             eeEEcCC
Q 009306          340 EVYQMEE  346 (538)
Q Consensus       340 ~~~~l~~  346 (538)
                      +++.+.+
T Consensus       505 ~i~~~~~  511 (530)
T COG0488         505 RIWLVED  511 (530)
T ss_pred             eEEEEcC
Confidence            5666654

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.46  E-value=0.0099  Score=53.55  Aligned_cols=23  Identities=35%  Similarity=0.543  Sum_probs=20.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|.|.|++|.||||+|+.+++++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999984

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=96.45  E-value=0.06  Score=50.17  Aligned_cols=147  Identities=20%  Similarity=0.298  Sum_probs=77.4

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .++=|-+.++++|.+.+--           +-...+-+..+||+|.|||-+|++.+.+....|-     .       -.+
T Consensus       171 sDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFL-----K-------LAg  238 (424)
T KOG0652|consen  171 SDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFL-----K-------LAG  238 (424)
T ss_pred             cccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHH-----H-------hcc
Confidence            3445666666666554311           1123455889999999999999998877544331     1       000


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH----hcCCCeEEEEecCCCh----------------HHHHHHhcCcCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR----LTRKKVLIVFDDVDHP----------------RQIKILVGRLDL  316 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~----l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~  316 (538)
                      + .+.+.+             +.+....++..    -...|.+|.+|+++..                ...-.++..+..
T Consensus       239 P-QLVQMf-------------IGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDG  304 (424)
T KOG0652|consen  239 P-QLVQMF-------------IGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDG  304 (424)
T ss_pred             h-HHHhhh-------------hcchHHHHHHHHHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcC
Confidence            0 111111             11111112211    1357899999988531                113344555555


Q ss_pred             CCCC--CEEEEeccchhh-----hhhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          317 FASG--SRIIITTRDRQV-----LANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       317 ~~~~--~~iiiTtR~~~~-----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      |.+.  .+||..|..-.+     +.+-.-++-++++--+.+.-.++++-+.
T Consensus       305 Fss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHs  355 (424)
T KOG0652|consen  305 FSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHS  355 (424)
T ss_pred             CCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhh
Confidence            5554  456655543322     2333345567776666666566666555

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.44  E-value=0.02  Score=55.62  Aligned_cols=38  Identities=13%  Similarity=-0.090  Sum_probs=30.0

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ....++.|.|++|+||||++.+++...... ...++|+.
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            345678999999999999999998876544 45666765

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.44  E-value=0.41  Score=46.95  Aligned_cols=165  Identities=9%  Similarity=0.087  Sum_probs=91.6

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc---------ee-eEEEEeehhhhhhcCChHHHHHHHHHH
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH---------FS-GSYFARNVREAEETCRLGDLRQQLLST  267 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~---------f~-~~~~~~~~~~~~~~~~~~~l~~~l~~~  267 (538)
                      +.+...+..+ .-.++..++|+.|.||+++|..++..+-..         .+ ...++. ..  ........+ +.+...
T Consensus         6 ~~l~~~i~~~-~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d-~~--g~~i~vd~I-r~l~~~   80 (299)
T PRK07132          6 KFLDNSATQN-KISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFD-IF--DKDLSKSEF-LSAINK   80 (299)
T ss_pred             HHHHHHHHhC-CCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEec-cC--CCcCCHHHH-HHHHHH
Confidence            3444444432 235678899999999999999999876211         11 111111 00  001111111 112221


Q ss_pred             HhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccc-hhhhhhc-CCCeeEE
Q 009306          268 LLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRD-RQVLANC-GVDEVYQ  343 (538)
Q Consensus       268 l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~~~~-~~~~~~~  343 (538)
                      +....               .-.+.+=++|+|+++..  .....++..+...++++.+|++|.+ ..+++.+ .....++
T Consensus        81 ~~~~~---------------~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~  145 (299)
T PRK07132         81 LYFSS---------------FVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFN  145 (299)
T ss_pred             hccCC---------------cccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEE
Confidence            11100               00135668899998754  4466777777665677777765544 4444442 3457899


Q ss_pred             cCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          344 MEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       344 l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      +.+++.++..+.+....        ..++.+..++..++|.=-|+..
T Consensus       146 f~~l~~~~l~~~l~~~~--------~~~~~a~~~a~~~~~~~~a~~~  184 (299)
T PRK07132        146 VKEPDQQKILAKLLSKN--------KEKEYNWFYAYIFSNFEQAEKY  184 (299)
T ss_pred             CCCCCHHHHHHHHHHcC--------CChhHHHHHHHHcCCHHHHHHH
Confidence            99999999998877541        1234455666666662234443

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.42  E-value=0.012  Score=58.60  Aligned_cols=49  Identities=22%  Similarity=0.262  Sum_probs=36.0

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~  246 (538)
                      ..+..+|..+-....++-|+|++|+|||+++.+++......      -..++|+.
T Consensus        89 ~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~  143 (317)
T PRK04301         89 KELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID  143 (317)
T ss_pred             HHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe
Confidence            45566666555567789999999999999999998764322      13577776

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.41  E-value=0.0059  Score=61.47  Aligned_cols=95  Identities=17%  Similarity=0.156  Sum_probs=54.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee---eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS---GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~---~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      ...+.|+|+.|+||||+++.++..+....+   .++.+.+..+    ..+..+.. ....+. ..............++.
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE----~~~~~~~~-~~~~v~-Q~~v~~~~~~~~~~l~~  207 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIE----FVYDEIET-ISASVC-QSEIPRHLNNFAAGVRN  207 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCce----Eecccccc-ccceee-eeeccccccCHHHHHHH
Confidence            457999999999999999999987643322   2333322111    11111000 000000 01111122334566777


Q ss_pred             HhcCCCeEEEEecCCChHHHHHHh
Q 009306          288 RLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      .++..|-.+++.++.+.+.....+
T Consensus       208 aLR~~Pd~i~vGEiRd~et~~~al  231 (358)
T TIGR02524       208 ALRRKPHAILVGEARDAETISAAL  231 (358)
T ss_pred             HhccCCCEEeeeeeCCHHHHHHHH
Confidence            888899999999998888775444

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.

>TIGR01069 mutS2 MutS2 family protein

Probab=96.41  E-value=0.0043  Score=68.76  Aligned_cols=24  Identities=25%  Similarity=0.018  Sum_probs=21.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+.++|+|+.|.||||+.+.+.-.
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHHH
Confidence            468999999999999999988764

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.40  E-value=0.037  Score=57.14  Aligned_cols=36  Identities=17%  Similarity=0.121  Sum_probs=27.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc--cceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS--RHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~--~~f~~~~~~~  246 (538)
                      .+++.++|++|+||||++..++..+.  .....+.++.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            45899999999999999999988765  2333445544

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.39  E-value=0.08  Score=54.28  Aligned_cols=36  Identities=19%  Similarity=0.141  Sum_probs=27.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...++.++|++|+||||++..++..++.+...+..+
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV  134 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLV  134 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            357899999999999999999998766543333433

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.38  E-value=0.015  Score=57.77  Aligned_cols=49  Identities=22%  Similarity=0.262  Sum_probs=35.8

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~  246 (538)
                      ..+..+|..+-....++-|+|++|+|||+|+.+++......      -..++|+.
T Consensus        82 ~~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~  136 (310)
T TIGR02236        82 KELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID  136 (310)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE
Confidence            44556666555567888999999999999999998764321      12677776

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.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.37  E-value=0.03  Score=51.96  Aligned_cols=63  Identities=22%  Similarity=0.349  Sum_probs=39.0

Q ss_pred             hcHHHHHHHhcCCCeEEEEecC----CCh--HHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEcC
Q 009306          280 TDLNFQSRRLTRKKVLIVFDDV----DHP--RQIKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQME  345 (538)
Q Consensus       280 ~~~~~l~~~l~~k~~LlVlDdv----~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l~  345 (538)
                      +..-.+.+.+...|-+|+.|+-    |..  ..+-.++..+.. ..|..||+.|-+..++..+  ++++.+.
T Consensus       148 qQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~-~~g~tii~VTHd~~lA~~~--dr~i~l~  216 (226)
T COG1136         148 QQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNK-ERGKTIIMVTHDPELAKYA--DRVIELK  216 (226)
T ss_pred             HHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHH-hcCCEEEEEcCCHHHHHhC--CEEEEEe
Confidence            3345566778889999999975    322  223233322211 2367899999999888865  3555543

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.37  E-value=0.0066  Score=55.74  Aligned_cols=30  Identities=33%  Similarity=0.463  Sum_probs=26.6

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.+|+|.|.+|+||||+|+.++..+...
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHHhCcC
Confidence            346789999999999999999999988765

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.37  E-value=0.004  Score=58.09  Aligned_cols=23  Identities=17%  Similarity=0.047  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .+.+.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            47899999999999999999874

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG3910 Predicted ATPase [General function prediction only]

Probab=96.37  E-value=0.027  Score=49.99  Aligned_cols=24  Identities=33%  Similarity=0.234  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..++..|+|..|+|||||...++-
T Consensus        36 ~apIT~i~GENGsGKSTLLEaiA~   59 (233)
T COG3910          36 RAPITFITGENGSGKSTLLEAIAA   59 (233)
T ss_pred             cCceEEEEcCCCccHHHHHHHHHh
Confidence            466889999999999999999876

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=96.37  E-value=0.0089  Score=60.17  Aligned_cols=100  Identities=19%  Similarity=0.265  Sum_probs=56.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+-+-|||..|.|||.|.-.+|+.+...-...            ..+..++..+-+.+.....    ....+..+.+.+
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R------------~HFh~Fm~~vh~~l~~~~~----~~~~l~~va~~l  124 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRR------------VHFHEFMLDVHSRLHQLRG----QDDPLPQVADEL  124 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCCcccccc------------ccccHHHHHHHHHHHHHhC----CCccHHHHHHHH
Confidence            356689999999999999999998765421111            1222333333333322211    122234455566


Q ss_pred             cCCCeEEEEecC--CChH---HHHHHhcCcCCCCCCCEEEEec
Q 009306          290 TRKKVLIVFDDV--DHPR---QIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       290 ~~k~~LlVlDdv--~~~~---~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                      .++..||.||++  .+..   .+..++..+.  ..|..+|.||
T Consensus       125 ~~~~~lLcfDEF~V~DiaDAmil~rLf~~l~--~~gvvlVaTS  165 (362)
T PF03969_consen  125 AKESRLLCFDEFQVTDIADAMILKRLFEALF--KRGVVLVATS  165 (362)
T ss_pred             HhcCCEEEEeeeeccchhHHHHHHHHHHHHH--HCCCEEEecC
Confidence            677779999987  3332   3444444432  3455555544

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>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=96.36  E-value=0.0054  Score=59.17  Aligned_cols=35  Identities=17%  Similarity=0.067  Sum_probs=23.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|.|+|.||+||||+|+++...+...-..+.++.
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~   36 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEEKGKEVVIIS   36 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEc
Confidence            47899999999999999999997765433344443

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.34  E-value=0.0031  Score=64.93  Aligned_cols=46  Identities=17%  Similarity=0.141  Sum_probs=39.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..++||+..++.+...+..+..    +.|.|++|+|||+||+.++.....
T Consensus        20 ~~i~gre~vI~lll~aalag~h----VLL~GpPGTGKT~LAraLa~~~~~   65 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGES----VFLLGPPGIAKSLIARRLKFAFQN   65 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCCC----EEEECCCChhHHHHHHHHHHHhcc
Confidence            5699999999999887765433    899999999999999999987543

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.34  E-value=0.0019  Score=58.93  Aligned_cols=21  Identities=24%  Similarity=-0.027  Sum_probs=18.7

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ++.|+|+.|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            368999999999999999884

>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=96.34  E-value=0.003  Score=47.20  Aligned_cols=23  Identities=30%  Similarity=0.472  Sum_probs=21.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +++|.|.+|+||||+++.+.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999886

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.34  E-value=0.014  Score=57.69  Aligned_cols=50  Identities=12%  Similarity=0.166  Sum_probs=35.8

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh--c----cceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI--S----RHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~--~----~~f~~~~~~~  246 (538)
                      ...|..+|..+-....++-|+|++|+|||+|+.+++-..  .    ..-..++|++
T Consensus        82 ~~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYId  137 (313)
T TIGR02238        82 SQALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID  137 (313)
T ss_pred             CHHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEE
Confidence            345666777655667889999999999999999887532  1    1123567776

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.

>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=96.32  E-value=0.003  Score=61.38  Aligned_cols=121  Identities=17%  Similarity=0.172  Sum_probs=67.3

Q ss_pred             CceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHH
Q 009306          189 DLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTL  268 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l  268 (538)
                      .+.-.....+.+.++|...-.....+.|.|+.|+||||++..+...+...-...+-+.+..+....              
T Consensus       105 ~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~--------------  170 (270)
T PF00437_consen  105 DLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLP--------------  170 (270)
T ss_dssp             CCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--S--------------
T ss_pred             hccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeec--------------
Confidence            333333344555556654322456799999999999999999998776652233333322111100              


Q ss_pred             hcCCCCC----CchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEE-EEecc
Q 009306          269 LNDGNVK----NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRI-IITTR  328 (538)
Q Consensus       269 ~~~~~~~----~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~i-iiTtR  328 (538)
                       ......    .........+...|+..+=.|+++++.+.+....+...    ..|..+ +-|..
T Consensus       171 -~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~~e~~~~~~a~----~tGh~~~~tT~H  230 (270)
T PF00437_consen  171 -GPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIRDPEAAEAIQAA----NTGHLGSLTTLH  230 (270)
T ss_dssp             -CSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-SCHHHHHHHHH----HTT-EEEEEEEE
T ss_pred             -ccceEEEEeecCcccHHHHHHHHhcCCCCcccccccCCHhHHHHHHhh----ccCCceeeeeee
Confidence             000000    12334456677778888999999999888777764433    346666 44443

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 ....

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

Probab=96.32  E-value=0.011  Score=49.51  Aligned_cols=60  Identities=22%  Similarity=0.351  Sum_probs=52.5

Q ss_pred             cEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccC
Q 009306           19 DVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSES   81 (538)
Q Consensus        19 dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~   81 (538)
                      .|||.|+ +|  ..++..+...|+..|+.+.+-. ....|..+.+.+.+.+.+|+..|++++|+
T Consensus         1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpD   61 (125)
T PF10137_consen    1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPD   61 (125)
T ss_pred             CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEccc
Confidence            4899997 66  5789999999998888877655 66889999999999999999999999994

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

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.32  E-value=0.033  Score=52.02  Aligned_cols=48  Identities=21%  Similarity=0.333  Sum_probs=33.4

Q ss_pred             ceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          190 LVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .=|-..++++|.+....           +-+..+-|.++|++|.|||-+|++++++...
T Consensus       179 vggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtda  237 (435)
T KOG0729|consen  179 VGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDA  237 (435)
T ss_pred             ccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCc
Confidence            34555666666554321           2234556899999999999999999998643

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.30  E-value=0.016  Score=53.82  Aligned_cols=26  Identities=31%  Similarity=0.252  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||++.++...
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~G~~   52 (207)
T PRK13539         27 AGEALVLTGPNGSGKTTLLRLIAGLL   52 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45579999999999999999998753

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.29  E-value=0.034  Score=55.62  Aligned_cols=37  Identities=22%  Similarity=0.195  Sum_probs=28.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++++|+|+.|+||||++..++..+..+...+.++.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lIt  241 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFIT  241 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            4678999999999999999999987654433445554

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.28  E-value=0.0082  Score=59.46  Aligned_cols=94  Identities=16%  Similarity=0.130  Sum_probs=51.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC-ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC-RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~-~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ....++|+|+.|+|||||++.+...+.... ..+.+.+..+..... ....+       ...........-...+.+...
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~~~~~-~iv~ied~~El~~~~~~~~~l-------~~~~~~~~~~~~~~~~~l~~~  214 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEIPKDE-RIITIEDTREIFLPHPNYVHL-------FYSKGGQGLAKVTPKDLLQSC  214 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccCCccc-cEEEEcCccccCCCCCCEEEE-------EecCCCCCcCccCHHHHHHHH
Confidence            345699999999999999999998765432 233333222211110 00000       000000001111234456667


Q ss_pred             hcCCCeEEEEecCCChHHHHHHh
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      ++..+-.|++|++...+.++.+.
T Consensus       215 Lr~~pd~ii~gE~r~~e~~~~l~  237 (308)
T TIGR02788       215 LRMRPDRIILGELRGDEAFDFIR  237 (308)
T ss_pred             hcCCCCeEEEeccCCHHHHHHHH
Confidence            78888999999998876655443

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.28  E-value=0.019  Score=55.97  Aligned_cols=37  Identities=16%  Similarity=0.125  Sum_probs=28.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc-e-eeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH-F-SGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f-~~~~~~~  246 (538)
                      ..++++|+|++|+||||++..++..+... . ..+.++.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            35689999999999999999999877644 2 3344444

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

Probab=96.27  E-value=0.0092  Score=60.83  Aligned_cols=23  Identities=39%  Similarity=0.518  Sum_probs=20.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...++|.|++|+||||||+.+.-
T Consensus       362 G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         362 GEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             CceEEEECCCCccHHHHHHHHHc
Confidence            34699999999999999999875

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.27  E-value=0.0023  Score=52.50  Aligned_cols=25  Identities=36%  Similarity=0.654  Sum_probs=21.6

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      |.|+|++|+|||+||..++..+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~   25 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKH   25 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999876654

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

>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=96.27  E-value=0.0035  Score=52.39  Aligned_cols=31  Identities=32%  Similarity=0.499  Sum_probs=21.7

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      +.|+|.+|+|||++|+.++..+...|..+-+
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~f~RIq~   32 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLSFKRIQF   32 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT--EEEEE-
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCceeEEEe
Confidence            6799999999999999999998888765443

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.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.27  E-value=0.024  Score=50.95  Aligned_cols=35  Identities=29%  Similarity=0.320  Sum_probs=25.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ....++|.|+.|.|||||++.++..... ..+.+++
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~~~~-~~G~i~~   59 (173)
T cd03230          25 KGEIYGLLGPNGAGKTTLIKIILGLLKP-DSGEIKV   59 (173)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCCC-CCeEEEE
Confidence            3457999999999999999998875432 2344444

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.26  E-value=0.0059  Score=53.56  Aligned_cols=37  Identities=27%  Similarity=0.266  Sum_probs=30.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++.++|.+|.||||||.++..++......++.++
T Consensus        22 ~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LD   58 (197)
T COG0529          22 KGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLD   58 (197)
T ss_pred             CCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            4568999999999999999999999877765555554

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.25  E-value=0.0061  Score=58.75  Aligned_cols=41  Identities=15%  Similarity=0.164  Sum_probs=32.1

Q ss_pred             cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          206 TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       206 ~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+-+...++.|+|++|+|||++|.+++.....+-..++|+.
T Consensus        31 GGip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        31 GGIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CCeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            34455678999999999999999999876555555677776

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08233 hypothetical protein; Provisional

Probab=96.25  E-value=0.0037  Score=56.65  Aligned_cols=26  Identities=27%  Similarity=0.369  Sum_probs=23.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|+|.|++|+||||||+.++..+.
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            36899999999999999999998764

>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=96.25  E-value=0.032  Score=48.87  Aligned_cols=88  Identities=20%  Similarity=0.150  Sum_probs=45.1

Q ss_pred             EeccCCCchhHHHHHHHHhhccceeeEEEEee---hhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC-
Q 009306          216 IWGIGGIGKTTIAGAIFNKISRHFSGSYFARN---VREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR-  291 (538)
Q Consensus       216 I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~---~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~-  291 (538)
                      |.|+||+||||+|+.++.++.     ...++.   ++.......  .+...+-..+.....  ...+-....+...+.. 
T Consensus         1 i~G~PgsGK~t~~~~la~~~~-----~~~is~~~llr~~~~~~s--~~g~~i~~~l~~g~~--vp~~~v~~ll~~~l~~~   71 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYG-----LVHISVGDLLREEIKSDS--ELGKQIQEYLDNGEL--VPDELVIELLKERLEQP   71 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHT-----SEEEEHHHHHHHHHHTTS--HHHHHHHHHHHTTSS----HHHHHHHHHHHHHSG
T ss_pred             CcCCCCCChHHHHHHHHHhcC-----cceechHHHHHHHHhhhh--HHHHHHHHHHHhhcc--chHHHHHHHHHHHHhhh
Confidence            689999999999999998752     223331   111111111  111222222221111  2233344555555533 


Q ss_pred             -CCeEEEEecC-CChHHHHHHhc
Q 009306          292 -KKVLIVFDDV-DHPRQIKILVG  312 (538)
Q Consensus       292 -k~~LlVlDdv-~~~~~~~~l~~  312 (538)
                       ...-+|||++ .+..+.+.+..
T Consensus        72 ~~~~g~ildGfPrt~~Qa~~l~~   94 (151)
T PF00406_consen   72 PCNRGFILDGFPRTLEQAEALEE   94 (151)
T ss_dssp             GTTTEEEEESB-SSHHHHHHHHH
T ss_pred             cccceeeeeeccccHHHHHHHHH
Confidence             2456889999 45666666654

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 ....

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.24  E-value=0.011  Score=57.07  Aligned_cols=47  Identities=21%  Similarity=0.194  Sum_probs=39.3

Q ss_pred             HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          200 IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       200 l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      |.+.|..+-+..+++.|+|.+|+|||+++.++..+.......++|+.
T Consensus        12 lD~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          12 LDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             hHHHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            44455555567889999999999999999999999888888888876

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.23  E-value=0.032  Score=53.15  Aligned_cols=40  Identities=23%  Similarity=0.116  Sum_probs=30.9

Q ss_pred             CCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          207 GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       207 ~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      +-....++.|.|.+|.|||+++.+++...... -..++|++
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s   49 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS   49 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe
Confidence            44456789999999999999999998876554 44566655

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.22  E-value=0.0082  Score=60.58  Aligned_cols=93  Identities=17%  Similarity=0.101  Sum_probs=54.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+.|+|+.|+||||+++.+...+....+  ..+-+.+..+... .....+..      ........+.......++..+
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~-~~~~~~~~------~~q~evg~~~~~~~~~l~~aL  222 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYIL-GSPDDLLP------PAQSQIGRDVDSFANGIRLAL  222 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhcc-CCCceeec------ccccccCCCccCHHHHHHHhh
Confidence            36889999999999999999887654322  2333332211110 00000000      000111122234456777888


Q ss_pred             cCCCeEEEEecCCChHHHHHHh
Q 009306          290 TRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      +..|=.|+++++.+.+..+..+
T Consensus       223 R~~PD~I~vGEiRd~et~~~al  244 (372)
T TIGR02525       223 RRAPKIIGVGEIRDLETFQAAV  244 (372)
T ss_pred             ccCCCEEeeCCCCCHHHHHHHH
Confidence            8899999999999888776543

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

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

Probab=96.21  E-value=0.011  Score=60.64  Aligned_cols=26  Identities=23%  Similarity=0.281  Sum_probs=22.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+.++|++|+|||+||+.++..+..
T Consensus       109 ~~iLl~Gp~GtGKT~lAr~lA~~l~~  134 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQTLARILDV  134 (412)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            45899999999999999999987643

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.16  E-value=0.032  Score=48.77  Aligned_cols=23  Identities=26%  Similarity=0.580  Sum_probs=20.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++.|+|++|+||||+|+.+....
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            37899999999999999998874

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.16  E-value=0.0049  Score=57.41  Aligned_cols=26  Identities=38%  Similarity=0.624  Sum_probs=23.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|+|.|++|+|||||++.++..+
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            56789999999999999999999876

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.14  E-value=0.018  Score=61.49  Aligned_cols=53  Identities=15%  Similarity=0.123  Sum_probs=40.2

Q ss_pred             cchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          194 RLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       194 ~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..-+..|.++|..+-+...++.|.|.+|+|||+|+.+++.....+ -..+.|+.
T Consensus        14 ~TGI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis   67 (509)
T PRK09302         14 PTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVT   67 (509)
T ss_pred             cCCchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            334556667776666677899999999999999999998765555 45666765

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=96.13  E-value=0.091  Score=57.81  Aligned_cols=49  Identities=20%  Similarity=0.307  Sum_probs=38.3

Q ss_pred             CCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          187 NEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+.++|....++++.+.+..-......|.|+|.+|+||+++|+.+.+.-
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s  372 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNES  372 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhC
Confidence            4678999988888877665422333458999999999999999998754

>PTZ00301 uridine kinase; Provisional

Probab=96.13  E-value=0.0048  Score=57.20  Aligned_cols=28  Identities=29%  Similarity=0.546  Sum_probs=23.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+|+|.|++|+||||||+.+..++...
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~~~   30 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELMAH   30 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHHhh
Confidence            3579999999999999999998876443

>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=96.12  E-value=0.006  Score=52.62  Aligned_cols=23  Identities=30%  Similarity=0.382  Sum_probs=21.2

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |.|+|++|+|||+||+.+++.+.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~   24 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLG   24 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh
Confidence            78999999999999999999873

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.

>PRK04040 adenylate kinase; Provisional

Probab=96.11  E-value=0.0062  Score=55.51  Aligned_cols=25  Identities=28%  Similarity=0.494  Sum_probs=22.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+|+|+|++|+||||+++.+..++.
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            4799999999999999999999874

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.10  E-value=0.01  Score=56.84  Aligned_cols=26  Identities=27%  Similarity=0.492  Sum_probs=22.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +|.++|++|+||||+|+.++..+...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~~   26 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSEK   26 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            37899999999999999999877543

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PRK03839 putative kinase; Provisional

Probab=96.10  E-value=0.005  Score=55.83  Aligned_cols=24  Identities=33%  Similarity=0.560  Sum_probs=21.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|.|.|++|+||||+++.+++++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999999864

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=96.10  E-value=0.013  Score=51.69  Aligned_cols=125  Identities=20%  Similarity=0.198  Sum_probs=62.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      ..+++|.|+.|.|||||++.++..+.. ..+.+++.... .. ......    ....+.-.... ..-+...-.+...+.
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~~~~-~~G~i~~~~~~-~~-~~~~~~----~~~~i~~~~ql-S~G~~~r~~l~~~l~   96 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGLLKP-TSGEILIDGKD-IA-KLPLEE----LRRRIGYVPQL-SGGQRQRVALARALL   96 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC-CccEEEECCEE-cc-cCCHHH----HHhceEEEeeC-CHHHHHHHHHHHHHh
Confidence            357999999999999999999876543 34445544210 00 000001    11111100000 111222233445556


Q ss_pred             CCCeEEEEecCC---ChHHHHHHhcCcCCC-CCCCEEEEeccchhhhhhcCCCeeEEc
Q 009306          291 RKKVLIVFDDVD---HPRQIKILVGRLDLF-ASGSRIIITTRDRQVLANCGVDEVYQM  344 (538)
Q Consensus       291 ~k~~LlVlDdv~---~~~~~~~l~~~l~~~-~~~~~iiiTtR~~~~~~~~~~~~~~~l  344 (538)
                      ..+-++++|+..   +......+...+... ..+..++++|.+......+ .++++.+
T Consensus        97 ~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~~-~d~i~~l  153 (157)
T cd00267          97 LNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAELA-ADRVIVL  153 (157)
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHh-CCEEEEE
Confidence            678899999984   222222222222111 2246788888777665553 2344443

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.10  E-value=0.016  Score=60.84  Aligned_cols=99  Identities=16%  Similarity=0.159  Sum_probs=57.6

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCC
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKN  276 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~  276 (538)
                      ++.+..++..   ...++.|+|+.|+||||+...+...+.......+-+.+..+    ..+..+     .+.    ....
T Consensus       231 ~~~l~~~~~~---~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE----~~~~~~-----~q~----~v~~  294 (486)
T TIGR02533       231 LSRFERLIRR---PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVE----YQIEGI-----GQI----QVNP  294 (486)
T ss_pred             HHHHHHHHhc---CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCee----eecCCC-----ceE----EEcc
Confidence            3444444432   23479999999999999999888776543223333332111    011000     000    0011


Q ss_pred             ch-hhcHHHHHHHhcCCCeEEEEecCCChHHHHHHh
Q 009306          277 FL-NTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       277 ~~-~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      .. ......++..|+..|=.|++.++.+.+......
T Consensus       295 ~~g~~f~~~lr~~LR~dPDvI~vGEiRd~eta~~a~  330 (486)
T TIGR02533       295 KIGLTFAAGLRAILRQDPDIIMVGEIRDLETAQIAI  330 (486)
T ss_pred             ccCccHHHHHHHHHhcCCCEEEEeCCCCHHHHHHHH
Confidence            11 234567778888999999999998887655544

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.10  E-value=0.0092  Score=56.09  Aligned_cols=41  Identities=24%  Similarity=0.386  Sum_probs=29.6

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .++.+.+....++..+|+|+|+||.|||||..++...++..
T Consensus        16 ~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~   56 (266)
T PF03308_consen   16 RELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRER   56 (266)
T ss_dssp             HHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhc
Confidence            34444444434467799999999999999999999987765

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.

>TIGR00235 udk uridine kinase

Probab=96.09  E-value=0.0058  Score=56.82  Aligned_cols=28  Identities=36%  Similarity=0.538  Sum_probs=24.4

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +...+++|.|++|+|||||++.++..+.
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3567899999999999999999998654

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

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

Probab=96.09  E-value=0.041  Score=50.38  Aligned_cols=25  Identities=24%  Similarity=0.310  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|.|||||++.++..
T Consensus        32 ~Ge~~~l~G~nGsGKSTLl~~l~G~   56 (192)
T cd03232          32 PGTLTALMGESGAGKTTLLDVLAGR   56 (192)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457999999999999999999864

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00035 Rad51 protein; Provisional

Probab=96.07  E-value=0.019  Score=57.47  Aligned_cols=39  Identities=18%  Similarity=0.214  Sum_probs=31.2

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...|.++|..+-....++.|+|++|+|||+|+..++-..
T Consensus       104 ~~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~  142 (337)
T PTZ00035        104 STQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTC  142 (337)
T ss_pred             cHHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHh
Confidence            345667777666667889999999999999999887543

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.07  E-value=0.0073  Score=51.27  Aligned_cols=40  Identities=18%  Similarity=0.157  Sum_probs=28.3

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++-+.|...-....++.|.|.-|.||||+++.++..+.
T Consensus         8 t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~lg   47 (133)
T TIGR00150         8 MDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLG   47 (133)
T ss_pred             HHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3344444433223445799999999999999999998753

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.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.06  E-value=0.024  Score=56.21  Aligned_cols=39  Identities=26%  Similarity=0.250  Sum_probs=31.1

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -...|..+|..+-....++.|+|++|+|||+|+..++..
T Consensus        81 g~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~  119 (316)
T TIGR02239        81 GSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVT  119 (316)
T ss_pred             CCHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHH
Confidence            345666777665566788999999999999999998863

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).

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.06  E-value=0.0057  Score=54.94  Aligned_cols=26  Identities=23%  Similarity=0.362  Sum_probs=23.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|.|+|++|+||||+|+.++.++.
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999999863

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.05  E-value=0.032  Score=52.72  Aligned_cols=52  Identities=21%  Similarity=0.368  Sum_probs=33.6

Q ss_pred             HHHHHHHhcCCCeEEEEecC----CCh--HHHHHHhcCcCCCCCCCEEEEeccchhhhhh
Q 009306          282 LNFQSRRLTRKKVLIVFDDV----DHP--RQIKILVGRLDLFASGSRIIITTRDRQVLAN  335 (538)
Q Consensus       282 ~~~l~~~l~~k~~LlVlDdv----~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~  335 (538)
                      ...+.+.|...+=|++||+-    |..  ..+-.++..+.  ..|..||++|-+-.....
T Consensus       147 RV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~--~eg~tIl~vtHDL~~v~~  204 (254)
T COG1121         147 RVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELR--QEGKTVLMVTHDLGLVMA  204 (254)
T ss_pred             HHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHH--HCCCEEEEEeCCcHHhHh
Confidence            34556778889999999974    322  23444444443  338889999988755443

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=96.05  E-value=0.043  Score=52.40  Aligned_cols=26  Identities=35%  Similarity=0.493  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||++.++...
T Consensus        24 ~Ge~~~i~G~NGsGKSTLlk~L~G~~   49 (246)
T cd03237          24 ESEVIGILGPNGIGKTTFIKMLAGVL   49 (246)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999998754

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=96.04  E-value=0.46  Score=49.24  Aligned_cols=25  Identities=24%  Similarity=0.391  Sum_probs=21.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      -..++++|+.|+|||||.+.++-.+
T Consensus       416 ~srvAlVGPNG~GKsTLlKl~~gdl  440 (614)
T KOG0927|consen  416 DSRVALVGPNGAGKSTLLKLITGDL  440 (614)
T ss_pred             ccceeEecCCCCchhhhHHHHhhcc
Confidence            3458999999999999999888753

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

Probab=96.02  E-value=0.049  Score=59.74  Aligned_cols=25  Identities=28%  Similarity=0.343  Sum_probs=21.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|+|.+|+|||||++.+..-
T Consensus       498 ~Ge~vaIvG~SGsGKSTL~KLL~gl  522 (709)
T COG2274         498 PGEKVAIVGRSGSGKSTLLKLLLGL  522 (709)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3456999999999999999988763

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.02  E-value=0.019  Score=56.81  Aligned_cols=36  Identities=25%  Similarity=0.397  Sum_probs=28.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++++|++|+||||++..++..++..-..+..+
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li  148 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLA  148 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEE
Confidence            467899999999999999999998876553333333

>cd01858 NGP_1 NGP-1

Probab=96.01  E-value=0.045  Score=48.28  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=19.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++++|++|+|||||...+...
T Consensus       103 ~~v~~~G~~nvGKStliN~l~~~  125 (157)
T cd01858         103 ISVGFIGYPNVGKSSIINTLRSK  125 (157)
T ss_pred             eEEEEEeCCCCChHHHHHHHhcC
Confidence            45789999999999999998763

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.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.00  E-value=0.0085  Score=56.08  Aligned_cols=24  Identities=21%  Similarity=0.014  Sum_probs=21.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..++++|+|+.|.||||+.+.++-
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            456789999999999999998887

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.00  E-value=0.01  Score=54.72  Aligned_cols=24  Identities=25%  Similarity=0.141  Sum_probs=21.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++++|+|+.|.|||||++.++...
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHH
Confidence            789999999999999999988643

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.99  E-value=0.033  Score=51.36  Aligned_cols=25  Identities=28%  Similarity=0.372  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|.|+.|.|||||.+.++..
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          25 KGEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457999999999999999998875

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.98  E-value=0.0088  Score=56.56  Aligned_cols=31  Identities=26%  Similarity=0.253  Sum_probs=26.6

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +...+++|.|++|.|||||++.++..++...
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~~~   61 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQDG   61 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhhcc
Confidence            4578899999999999999999998776543

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.98  E-value=0.0084  Score=53.71  Aligned_cols=36  Identities=19%  Similarity=0.114  Sum_probs=27.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc-cceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS-RHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~-~~f~~~~~~~  246 (538)
                      ...+.+.|++|+|||.||+.++..+. ......+-+.
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d   39 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRID   39 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEE
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHh
Confidence            34688999999999999999999877 4444344443

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=95.98  E-value=0.06  Score=47.93  Aligned_cols=34  Identities=26%  Similarity=0.301  Sum_probs=25.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      ...+.|+|+.|+|||||.+.++--.+..-..+.|
T Consensus        28 Ge~~~i~G~NG~GKTtLLRilaGLl~p~~G~v~~   61 (209)
T COG4133          28 GEALQITGPNGAGKTTLLRILAGLLRPDAGEVYW   61 (209)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcccCCCCCeEEe
Confidence            3468899999999999999998755544333444

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.97  E-value=0.055  Score=51.46  Aligned_cols=24  Identities=17%  Similarity=0.254  Sum_probs=20.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +..|+|++|+|||+|+..++..+.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va   26 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMA   26 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHh
Confidence            457899999999999999987643

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.94  E-value=0.0064  Score=57.36  Aligned_cols=49  Identities=22%  Similarity=0.188  Sum_probs=36.5

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..|.++|..+-+...++.|.|++|+|||+|+.+++...... -..++|+.
T Consensus         6 ~~LD~~l~GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs   55 (226)
T PF06745_consen    6 PGLDELLGGGIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVS   55 (226)
T ss_dssp             TTHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEE
T ss_pred             hhHHHhhcCCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEE
Confidence            34566665555567789999999999999999998876555 56677776

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.93  E-value=0.034  Score=51.14  Aligned_cols=59  Identities=24%  Similarity=0.287  Sum_probs=36.0

Q ss_pred             HHHHHHHhcCCCeEEEEecCCChH---HHHHH---hcCcCCCCCCCEEEEeccchhhhhhcCCCeeE
Q 009306          282 LNFQSRRLTRKKVLIVFDDVDHPR---QIKIL---VGRLDLFASGSRIIITTRDRQVLANCGVDEVY  342 (538)
Q Consensus       282 ~~~l~~~l~~k~~LlVlDdv~~~~---~~~~l---~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~  342 (538)
                      ...+.+.+--+|-+.|||+.|+=-   .++..   ...+.  .+++-++|.|....++.....+.++
T Consensus       152 R~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr--~~~~~~liITHy~rll~~i~pD~vh  216 (251)
T COG0396         152 RNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALR--EEGRGVLIITHYQRLLDYIKPDKVH  216 (251)
T ss_pred             HHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHh--cCCCeEEEEecHHHHHhhcCCCEEE
Confidence            344555556688899999987532   22222   22222  4566777778888788777544443

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.93  E-value=0.022  Score=56.80  Aligned_cols=52  Identities=15%  Similarity=0.164  Sum_probs=36.5

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc------ceeeEEEEe
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR------HFSGSYFAR  246 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~------~f~~~~~~~  246 (538)
                      .-...|..+|..+-....++-|+|++|+|||+||..++-....      .-..++|++
T Consensus       107 tG~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyId  164 (342)
T PLN03186        107 TGSRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYID  164 (342)
T ss_pred             CCCHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEE
Confidence            3445666777655566788999999999999999988854221      112577776

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

Probab=95.93  E-value=0.034  Score=53.28  Aligned_cols=30  Identities=30%  Similarity=0.404  Sum_probs=25.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ....++|||++|.|||-+|+.++..+.-.|
T Consensus       165 ~Pkg~ll~GppGtGKTlla~~Vaa~mg~nf  194 (388)
T KOG0651|consen  165 PPKGLLLYGPPGTGKTLLARAVAATMGVNF  194 (388)
T ss_pred             CCceeEEeCCCCCchhHHHHHHHHhcCCce
Confidence            356799999999999999999999876554

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=95.92  E-value=0.034  Score=50.53  Aligned_cols=28  Identities=32%  Similarity=0.425  Sum_probs=24.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+++|+|++|+||||+|+.+...+..
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~~   44 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLES   44 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4568999999999999999999987653

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK14528 adenylate kinase; Provisional

Probab=95.92  E-value=0.05  Score=49.52  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=20.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+.|.|++|+||||+|+.++..+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998765

>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=95.92  E-value=0.027  Score=50.94  Aligned_cols=35  Identities=26%  Similarity=0.228  Sum_probs=25.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|.|+.|.|||||++.++..... ..+.+.+
T Consensus        25 ~G~~~~i~G~nGsGKSTLl~~l~G~~~~-~~G~i~~   59 (178)
T cd03229          25 AGEIVALLGPSGSGKSTLLRCIAGLEEP-DSGSILI   59 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCC-CceEEEE
Confidence            3457999999999999999999865432 3444444

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.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.91  E-value=0.0065  Score=55.39  Aligned_cols=26  Identities=31%  Similarity=0.220  Sum_probs=22.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.++++|.|++|+||||+|+.++..+
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            35689999999999999999999765

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.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=95.91  E-value=0.0068  Score=54.66  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=22.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +++.++|++|+||||+|+.+.....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5799999999999999999998754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=95.90  E-value=0.045  Score=51.31  Aligned_cols=26  Identities=27%  Similarity=0.388  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||++.++...
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (220)
T cd03263          27 KGEIFGLLGHNGAGKTTTLKMLTGEL   52 (220)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999998743

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=95.90  E-value=0.07  Score=48.96  Aligned_cols=26  Identities=27%  Similarity=0.294  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|.|+.|.|||||.+.++...
T Consensus        34 ~Ge~~~l~G~nGsGKStLl~~i~Gl~   59 (194)
T cd03213          34 PGELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999998765

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.90  E-value=0.012  Score=53.50  Aligned_cols=36  Identities=19%  Similarity=0.277  Sum_probs=30.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+++.|+|++|+|||||+..+.......|..++...
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            467999999999999999999999888886555543

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 ....

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.89  E-value=0.036  Score=49.23  Aligned_cols=23  Identities=35%  Similarity=0.668  Sum_probs=20.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|+|++|+||||+|+.+...+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~   23 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLG   23 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999998763

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.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.88  E-value=0.018  Score=63.19  Aligned_cols=98  Identities=17%  Similarity=0.118  Sum_probs=58.1

Q ss_pred             hhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCC-
Q 009306          196 PMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGN-  273 (538)
Q Consensus       196 ~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~-  273 (538)
                      -...|..+|. .+-+..+++-|+|++|+||||||..++......-..++|+.....    ... ..++    .++...+ 
T Consensus        44 Gi~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t----~~~-~~A~----~lGvDl~~  114 (790)
T PRK09519         44 GSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHA----LDP-DYAK----KLGVDTDS  114 (790)
T ss_pred             CcHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccc----hhH-HHHH----HcCCChhH
Confidence            3456677776 455667889999999999999999887765455566777762211    111 1222    2222110 


Q ss_pred             ----CCCchhhcHHHHHHHhc-CCCeEEEEecCC
Q 009306          274 ----VKNFLNTDLNFQSRRLT-RKKVLIVFDDVD  302 (538)
Q Consensus       274 ----~~~~~~~~~~~l~~~l~-~k~~LlVlDdv~  302 (538)
                          .....+.....+...+. ++.-|||+|.+.
T Consensus       115 llv~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        115 LLVSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCeEEEEcchh
Confidence                01233344444444443 466799999874

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=95.88  E-value=0.21  Score=53.15  Aligned_cols=48  Identities=31%  Similarity=0.466  Sum_probs=38.5

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++|....++.+.+.+..-......|.|+|.+|+||+.+|+.+++.-
T Consensus       212 ~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S  259 (526)
T TIGR02329       212 DDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLS  259 (526)
T ss_pred             hheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhc
Confidence            568999999998888775422334569999999999999999998753

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

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

Probab=95.88  E-value=0.23  Score=51.57  Aligned_cols=73  Identities=22%  Similarity=0.226  Sum_probs=47.2

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc-cceeeEEEEeehhhhhhcCChHHHHHHHHHHH
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS-RHFSGSYFARNVREAEETCRLGDLRQQLLSTL  268 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~-~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l  268 (538)
                      ..|...-+..|.+++. +-....++.|.|.+|+|||++|..++.... .+-..++|++.      .-....+...++...
T Consensus       174 ~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fSl------Em~~~~l~~Rl~~~~  246 (421)
T TIGR03600       174 LTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSL------EMSAEQLGERLLASK  246 (421)
T ss_pred             CcceeCCChhHHHHhc-CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC------CCCHHHHHHHHHHHH
Confidence            4555556666666665 444566899999999999999999997664 33334555441      234455566665544


Q ss_pred             h
Q 009306          269 L  269 (538)
Q Consensus       269 ~  269 (538)
                      .
T Consensus       247 ~  247 (421)
T TIGR03600       247 S  247 (421)
T ss_pred             c
Confidence            3

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.88  E-value=0.026  Score=55.54  Aligned_cols=89  Identities=18%  Similarity=0.185  Sum_probs=53.7

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhc-CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEET-CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~-~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ..+.|+|+.|+||||+++.++..+....  ...+-+.+..+.... ....        .+.  ..  .........++..
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v--------~~~--~~--~~~~~~~~~l~~a  200 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVV--------QLR--TS--DDAISMTRLLKAT  200 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEE--------EEE--ec--CCCCCHHHHHHHH
Confidence            3588999999999999999998875532  223333322221110 0000        000  00  1112455677788


Q ss_pred             hcCCCeEEEEecCCChHHHHHHhc
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILVG  312 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~~  312 (538)
                      |+..+=.||+.++.+.+.++.+..
T Consensus       201 LR~~pD~iivGEiR~~ea~~~l~a  224 (299)
T TIGR02782       201 LRLRPDRIIVGEVRGGEALDLLKA  224 (299)
T ss_pred             hcCCCCEEEEeccCCHHHHHHHHH
Confidence            888999999999988776665443

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.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.88  E-value=0.021  Score=57.75  Aligned_cols=52  Identities=23%  Similarity=0.314  Sum_probs=35.6

Q ss_pred             CCceeccchhHHHHHhhhc------------CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          188 EDLVGVRLPMKEIESLLRT------------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~------------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ..++|.+...+.+...+..            +....+-+.++|++|+|||+||+.++..+...|
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~f   75 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   75 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            4466776666666443331            011235689999999999999999999876544

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.

>PRK00625 shikimate kinase; Provisional

Probab=95.87  E-value=0.007  Score=54.32  Aligned_cols=23  Identities=26%  Similarity=0.418  Sum_probs=21.2

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |.|+|++|+||||+++.+++++.
T Consensus         3 I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          3 IFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            88999999999999999998764

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=95.86  E-value=0.05  Score=49.92  Aligned_cols=108  Identities=15%  Similarity=0.084  Sum_probs=55.8

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccc---e-ee-EEEEeehhhhhhc-CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRH---F-SG-SYFARNVREAEET-CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~---f-~~-~~~~~~~~~~~~~-~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      ..|.|++|+|||||.+.++.-+...   | +. ++-++.-++.... .+....  .+...+.-. +.....+-....++ 
T Consensus       140 tLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~--~~g~R~dVl-d~cpk~~gmmmaIr-  215 (308)
T COG3854         140 TLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQH--GRGRRMDVL-DPCPKAEGMMMAIR-  215 (308)
T ss_pred             eEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchh--hhhhhhhhc-ccchHHHHHHHHHH-
Confidence            7788999999999999999865433   3 22 2333211111110 000000  000000000 00011111222222 


Q ss_pred             HhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          288 RLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                        ...|=++|+|++-..++..++...+   ..|.+++.|....
T Consensus       216 --sm~PEViIvDEIGt~~d~~A~~ta~---~~GVkli~TaHG~  253 (308)
T COG3854         216 --SMSPEVIIVDEIGTEEDALAILTAL---HAGVKLITTAHGN  253 (308)
T ss_pred             --hcCCcEEEEeccccHHHHHHHHHHH---hcCcEEEEeeccc
Confidence              3467799999998777766666554   5688888776544

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=95.86  E-value=0.07  Score=53.08  Aligned_cols=23  Identities=22%  Similarity=0.378  Sum_probs=20.9

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++++|++|.||||+++.+...+.
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~   24 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLR   24 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHH
Confidence            67899999999999999998775

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 eukaryotic proteins with this activity.

>PRK06547 hypothetical protein; Provisional

Probab=95.85  E-value=0.0085  Score=53.74  Aligned_cols=27  Identities=37%  Similarity=0.460  Sum_probs=23.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....+|+|.|++|+||||+|+.++...
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            457789999999999999999999864

>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=95.85  E-value=0.027  Score=52.79  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=21.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +++|.|++|+||||||+.+...+.
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999998775

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

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

Probab=95.84  E-value=0.026  Score=57.69  Aligned_cols=27  Identities=22%  Similarity=0.262  Sum_probs=23.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.|+|++|+|||+||+.++..+...
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~~l~~p  143 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLARILNVP  143 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHHhcCCC
Confidence            468999999999999999999876433

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.82  E-value=0.012  Score=54.36  Aligned_cols=38  Identities=26%  Similarity=0.346  Sum_probs=29.4

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ....+++|+|++|+||||||+.+...+.......+++.
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~ld   59 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLD   59 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEEc
Confidence            34668999999999999999999987755433455553

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.81  E-value=0.0069  Score=56.04  Aligned_cols=22  Identities=32%  Similarity=0.009  Sum_probs=20.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .+++|+|+.|.||||+.+.++.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6799999999999999999984

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>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=95.81  E-value=0.043  Score=54.01  Aligned_cols=102  Identities=17%  Similarity=0.073  Sum_probs=54.7

Q ss_pred             HHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCC-CC
Q 009306          198 KEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGN-VK  275 (538)
Q Consensus       198 ~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~-~~  275 (538)
                      ..|...|. .+-+..+++-|+|+.|+||||||..+..........++|+..-    .... ...++.+.-.+....- .+
T Consensus        39 ~~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~~q~~g~~~a~ID~e----~~ld-~~~a~~lGvdl~rllv~~P  113 (322)
T PF00154_consen   39 PALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKQGGICAFIDAE----HALD-PEYAESLGVDLDRLLVVQP  113 (322)
T ss_dssp             HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEESS----S----HHHHHHTT--GGGEEEEE-
T ss_pred             cccchhhccCccccCceEEEeCCCCCchhhhHHHHHHhhhcccceeEEecCc----ccch-hhHHHhcCccccceEEecC
Confidence            34555565 3334577899999999999999999998766556677887621    1111 1222222222111100 01


Q ss_pred             CchhhcHHHHHHHhcC-CCeEEEEecCCCh
Q 009306          276 NFLNTDLNFQSRRLTR-KKVLIVFDDVDHP  304 (538)
Q Consensus       276 ~~~~~~~~~l~~~l~~-k~~LlVlDdv~~~  304 (538)
                      ...++....+...++. .--++|+|.|...
T Consensus       114 ~~~E~al~~~e~lirsg~~~lVVvDSv~al  143 (322)
T PF00154_consen  114 DTGEQALWIAEQLIRSGAVDLVVVDSVAAL  143 (322)
T ss_dssp             SSHHHHHHHHHHHHHTTSESEEEEE-CTT-
T ss_pred             CcHHHHHHHHHHHhhcccccEEEEecCccc
Confidence            2334444444444443 3458899988543

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 ....

>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=95.81  E-value=0.0063  Score=54.29  Aligned_cols=24  Identities=29%  Similarity=0.513  Sum_probs=20.7

Q ss_pred             EEEeccCCCchhHHHHHHHHhhcc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +.|+|.+|+|||||++.+++.++.
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            789999999999999999998753

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.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.78  E-value=0.0089  Score=54.08  Aligned_cols=26  Identities=38%  Similarity=0.515  Sum_probs=22.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +|+|.|.+|+||||||..+...+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~~~   26 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRVN   26 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            48999999999999999999887543

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=95.78  E-value=0.011  Score=52.71  Aligned_cols=46  Identities=28%  Similarity=0.360  Sum_probs=33.6

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +||.+..++++.+.+..-......|.|+|..|.||+.+|+.+.+.-
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            4678888888887776522333558899999999999999999853

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 ....

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=95.78  E-value=0.021  Score=56.75  Aligned_cols=132  Identities=15%  Similarity=0.117  Sum_probs=68.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee-------eEEEEe-e------hhhhhhcCChHHHHHHHHHHHhcC-----
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS-------GSYFAR-N------VREAEETCRLGDLRQQLLSTLLND-----  271 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~-------~~~~~~-~------~~~~~~~~~~~~l~~~l~~~l~~~-----  271 (538)
                      .-++.|+|.+|+||||+.+.+.........       +.+-+. +      .++.....+-..+++++.+..++.     
T Consensus       409 GdvvaVvGqSGaGKttllRmi~G~~~~~~ee~y~p~sg~v~vp~nt~~a~iPge~Ep~f~~~tilehl~s~tGD~~~Ave  488 (593)
T COG2401         409 GDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGKVEVPKNTVSALIPGEYEPEFGEVTILEHLRSKTGDLNAAVE  488 (593)
T ss_pred             CCeEEEEecCCCCcchHHHHHHHHhhcccccccCCCCCceeccccchhhccCcccccccCchhHHHHHhhccCchhHHHH
Confidence            346899999999999999998875433211       111110 0      001111112224455554443331     


Q ss_pred             --------CC-------CC-CchhhcHHHHHHHhcCCCeEEEEecCCCh---HHHHHHhcCcCCC--CCCCEEEEeccch
Q 009306          272 --------GN-------VK-NFLNTDLNFQSRRLTRKKVLIVFDDVDHP---RQIKILVGRLDLF--ASGSRIIITTRDR  330 (538)
Q Consensus       272 --------~~-------~~-~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~~~~l~~~l~~~--~~~~~iiiTtR~~  330 (538)
                              ..       .+ ..-+.-...+.+.+.+++-++++|.+...   .....++..+...  ..|..+++.|+.+
T Consensus       489 ILnraGlsDAvlyRr~f~ELStGQKeR~KLAkllaerpn~~~iDEF~AhLD~~TA~rVArkiselaRe~giTlivvThrp  568 (593)
T COG2401         489 ILNRAGLSDAVLYRRKFSELSTGQKERAKLAKLLAERPNVLLIDEFAAHLDELTAVRVARKISELAREAGITLIVVTHRP  568 (593)
T ss_pred             HHHhhccchhhhhhccHhhcCcchHHHHHHHHHHhcCCCcEEhhhhhhhcCHHHHHHHHHHHHHHHHHhCCeEEEEecCH
Confidence                    00       00 11122234556677888899999998432   1111111111111  2477788888888


Q ss_pred             hhhhhcCCCeeE
Q 009306          331 QVLANCGVDEVY  342 (538)
Q Consensus       331 ~~~~~~~~~~~~  342 (538)
                      ++...+..+..+
T Consensus       569 Ev~~AL~PD~li  580 (593)
T COG2401         569 EVGNALRPDTLI  580 (593)
T ss_pred             HHHhccCCceeE
Confidence            887777655443

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=95.78  E-value=0.37  Score=46.81  Aligned_cols=126  Identities=9%  Similarity=0.007  Sum_probs=69.3

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-------------eeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-------------FSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-------------f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      ++|...+..+ .-.....++|+.|+||+++|..++..+-..             ++...++.-.     .          
T Consensus         7 ~~L~~~i~~~-rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~-----~----------   70 (290)
T PRK05917          7 EALIQRVRDQ-KVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQ-----G----------   70 (290)
T ss_pred             HHHHHHHHcC-CcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecC-----C----------
Confidence            3445555432 235568899999999999999999865321             1111221100     0          


Q ss_pred             HHHHhcCCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc-hhhhhhc
Q 009306          265 LSTLLNDGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD-RQVLANC  336 (538)
Q Consensus       265 ~~~l~~~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~-~~~~~~~  336 (538)
                             ......+++.. .+.+.+     .++.=++|+|+++.  .+....++..+....++..+|++|.+ ..+++..
T Consensus        71 -------~~~~I~idqiR-~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI  142 (290)
T PRK05917         71 -------KGRLHSIETPR-AIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTI  142 (290)
T ss_pred             -------CCCcCcHHHHH-HHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHH
Confidence                   00001122211 122222     23445889999974  45677787777765667776666655 4444443


Q ss_pred             -CCCeeEEcCCC
Q 009306          337 -GVDEVYQMEEL  347 (538)
Q Consensus       337 -~~~~~~~l~~L  347 (538)
                       .....+.+.++
T Consensus       143 ~SRcq~~~~~~~  154 (290)
T PRK05917        143 RSRSLSIHIPME  154 (290)
T ss_pred             HhcceEEEccch
Confidence             23456677665

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=95.77  E-value=0.093  Score=55.42  Aligned_cols=48  Identities=23%  Similarity=0.322  Sum_probs=38.3

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++|+...+..+.+.+..-......+.|+|.+|+|||++|+.+....
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s  185 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHS  185 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcC
Confidence            468999988888887775433345568999999999999999988753

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.77  E-value=0.049  Score=59.37  Aligned_cols=26  Identities=23%  Similarity=0.437  Sum_probs=22.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|++|.|||||++.+...+
T Consensus       375 ~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        375 AGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44579999999999999999998765

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

Probab=95.77  E-value=0.015  Score=55.56  Aligned_cols=43  Identities=26%  Similarity=0.351  Sum_probs=33.2

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      .+|...+....++..+++|+|.||.|||||.-++..++..+-.
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~   80 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGH   80 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCc
Confidence            3445555555567789999999999999999999988766543

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.77  E-value=0.065  Score=49.52  Aligned_cols=27  Identities=22%  Similarity=0.202  Sum_probs=23.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|+.|+|||||++.++....
T Consensus        32 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          32 PGEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             CCcEEEEECCCCCCHHHHHHHhcccCC
Confidence            445799999999999999999887654

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.76  E-value=0.0085  Score=51.75  Aligned_cols=25  Identities=32%  Similarity=0.476  Sum_probs=22.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +|.|.|++|+||||+|+.+++.+.-
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl   26 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGL   26 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCC
Confidence            5889999999999999999987643

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.74  E-value=0.027  Score=60.10  Aligned_cols=52  Identities=17%  Similarity=0.176  Sum_probs=40.1

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .-+..|.++|..+-....++.|.|++|+|||+|+..++.........++|+.
T Consensus       257 tGi~~lD~~l~GG~~~g~~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yis  308 (509)
T PRK09302        257 SGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFA  308 (509)
T ss_pred             CCcHHHHHhhcCCCCCCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3455666777655556678999999999999999999987666666777776

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.74  E-value=0.03  Score=52.69  Aligned_cols=22  Identities=32%  Similarity=0.517  Sum_probs=20.5

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |.|.|++|+||||+|+.+++.+
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            8899999999999999998875

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.73  E-value=0.04  Score=50.43  Aligned_cols=27  Identities=30%  Similarity=0.159  Sum_probs=23.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+..|.|++|+|||+++..++..+..
T Consensus        32 g~l~~i~g~~g~GKT~~~~~l~~~~~~   58 (193)
T PF13481_consen   32 GELTLIAGPPGSGKTTLALQLAAALAT   58 (193)
T ss_dssp             TSEEEEEECSTSSHHHHHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            347899999999999999999987654

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=95.70  E-value=0.049  Score=51.69  Aligned_cols=26  Identities=27%  Similarity=0.346  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        27 ~G~i~~iiGpNG~GKSTLLk~l~g~l   52 (258)
T COG1120          27 KGEITGILGPNGSGKSTLLKCLAGLL   52 (258)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccC
Confidence            45689999999999999999998743

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.69  E-value=0.017  Score=53.37  Aligned_cols=24  Identities=25%  Similarity=-0.035  Sum_probs=21.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..++++|+|+.|.||||+.+.++.
T Consensus        28 ~~~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          28 SSRFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            347899999999999999998875

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=95.69  E-value=0.0072  Score=54.90  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +|.|.|++|+||||+|+.++.++
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999999999998875

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.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.66  E-value=0.038  Score=53.48  Aligned_cols=36  Identities=17%  Similarity=0.214  Sum_probs=29.5

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      .+..++.|.|.+|.|||||+..+...+.......+.
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~~~~~VI  137 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMRLKDSVPCAVI  137 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHhccCCCEEEE
Confidence            457889999999999999999999987766544444

>PRK10436 hypothetical protein; Provisional

Probab=95.66  E-value=0.038  Score=57.56  Aligned_cols=99  Identities=12%  Similarity=0.091  Sum_probs=57.3

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCC-
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK-  275 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~-  275 (538)
                      ++.+.+++..   ....+.|+|+.|+||||....+...+......++-+.+.-+    ..+..+     .+.    ... 
T Consensus       207 ~~~l~~~~~~---~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE----~~l~gi-----~Q~----~v~~  270 (462)
T PRK10436        207 LAQFRQALQQ---PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVE----IPLAGI-----NQT----QIHP  270 (462)
T ss_pred             HHHHHHHHHh---cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCcc----ccCCCc-----ceE----eeCC
Confidence            4445555542   34579999999999999888777765443222222321111    111000     000    001 


Q ss_pred             CchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHh
Q 009306          276 NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       276 ~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      ..-......++..|+..|=.|++.++.+.+..+...
T Consensus       271 ~~g~~f~~~lr~~LR~dPDvI~vGEIRD~eta~~al  306 (462)
T PRK10436        271 KAGLTFQRVLRALLRQDPDVIMVGEIRDGETAEIAI  306 (462)
T ss_pred             ccCcCHHHHHHHHhcCCCCEEEECCCCCHHHHHHHH
Confidence            111235667788888999999999998887766433

>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=95.65  E-value=0.016  Score=57.34  Aligned_cols=58  Identities=22%  Similarity=0.237  Sum_probs=40.1

Q ss_pred             CCCCceeccchhHHH---HHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEE
Q 009306          186 ENEDLVGVRLPMKEI---ESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSY  243 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l---~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~  243 (538)
                      ....+||.....+..   .++...+.-..+.+.|.|++|.|||+||..+++.+....+.+.
T Consensus        22 ~~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~   82 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVS   82 (398)
T ss_dssp             EETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEE
T ss_pred             ccccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeE
Confidence            346899998766544   4455554445688999999999999999999999987766443

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.

>PRK13947 shikimate kinase; Provisional

Probab=95.64  E-value=0.0095  Score=53.40  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.2

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .|.|+|++|+||||+|+.+++++.-
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~   27 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSF   27 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            3899999999999999999988743

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=95.64  E-value=0.059  Score=58.69  Aligned_cols=26  Identities=23%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|++|.|||||++.+...+
T Consensus       360 ~G~~v~IvG~sGsGKSTLl~lL~gl~  385 (588)
T PRK13657        360 PGQTVAIVGPTGAGKSTLINLLQRVF  385 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            34569999999999999999988643

>PF13245 AAA_19: Part of AAA domain

Probab=95.63  E-value=0.02  Score=43.60  Aligned_cols=25  Identities=28%  Similarity=0.262  Sum_probs=18.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+++.|.|++|.|||+++......+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3467789999999996555555443

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.63  E-value=0.0089  Score=51.47  Aligned_cols=25  Identities=20%  Similarity=0.474  Sum_probs=21.7

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ++|+|++|+|||||++.++..+...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~   26 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPN   26 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCcc
Confidence            7899999999999999999876444

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.

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

Probab=95.62  E-value=0.051  Score=57.52  Aligned_cols=53  Identities=25%  Similarity=0.327  Sum_probs=33.7

Q ss_pred             HHHHHHHhcCCCeEEEEecCCC---hHHHHHHhcCcCCCCCCCEEEEeccchhhhhhc
Q 009306          282 LNFQSRRLTRKKVLIVFDDVDH---PRQIKILVGRLDLFASGSRIIITTRDRQVLANC  336 (538)
Q Consensus       282 ~~~l~~~l~~k~~LlVlDdv~~---~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~  336 (538)
                      ...+.+.|-.+|=+++||+--+   .+.+..+-..+.. -+| .+||+|-++..+..+
T Consensus       161 Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~-~~g-tviiVSHDR~FLd~V  216 (530)
T COG0488         161 RVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKR-YPG-TVIVVSHDRYFLDNV  216 (530)
T ss_pred             HHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHh-CCC-cEEEEeCCHHHHHHH
Confidence            3455566778899999998643   2333333333322 234 788899999887765

>PRK06217 hypothetical protein; Validated

Probab=95.60  E-value=0.0099  Score=54.05  Aligned_cols=24  Identities=29%  Similarity=0.569  Sum_probs=21.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|+|.|++|+||||+|+++...+.
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~   26 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLD   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            389999999999999999998764

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.60  E-value=0.014  Score=63.01  Aligned_cols=59  Identities=15%  Similarity=0.244  Sum_probs=46.1

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEee
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARN  247 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~  247 (538)
                      ..-+.++|.+..++.|...+..+    +.+.|+|++|+||||+|+.++..+... +....|+.+
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~n   87 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPN   87 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeC
Confidence            44577899999888888877643    368999999999999999999876543 366677664

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=95.59  E-value=0.097  Score=45.22  Aligned_cols=47  Identities=13%  Similarity=0.081  Sum_probs=29.2

Q ss_pred             HHHHHHHHhcceEEEEeccCcccchhhHHHHHHHHHHHhhcCCeEEEEE
Q 009306           62 QSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVF  110 (538)
Q Consensus        62 ~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~~~~~~~~~~~v~pv~  110 (538)
                      .++.++|++++.+|.|++...-.+.+. .++...+.... .+.+++.|+
T Consensus         3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~~~~-~~k~~iivl   49 (141)
T cd01857           3 RQLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVKEVD-PRKKNILLL   49 (141)
T ss_pred             HHHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHHhcc-CCCcEEEEE
Confidence            567899999999999998765444442 24555444331 234455554

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.

>TIGR00959 ffh signal recognition particle protein

Probab=95.57  E-value=0.053  Score=55.85  Aligned_cols=27  Identities=26%  Similarity=0.322  Sum_probs=23.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++.++|++|+||||++..++..+.
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            357899999999999999999998765

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.

>PRK15115 response regulator GlrR; Provisional

Probab=95.56  E-value=0.24  Score=51.92  Aligned_cols=48  Identities=27%  Similarity=0.214  Sum_probs=34.3

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++|....+..+.+....-......+.|+|.+|+|||++|+.+...-
T Consensus       134 ~~lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s  181 (444)
T PRK15115        134 EAIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNAS  181 (444)
T ss_pred             hcccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhc
Confidence            357888777766665443322233458899999999999999888754

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=95.55  E-value=0.11  Score=47.76  Aligned_cols=21  Identities=38%  Similarity=0.357  Sum_probs=19.4

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +++|+|+.|.|||||++.++.
T Consensus        24 ~~~i~G~nGsGKStll~al~~   44 (197)
T cd03278          24 LTAIVGPNGSGKSNIIDAIRW   44 (197)
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            789999999999999999874

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.55  E-value=0.0087  Score=54.28  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=21.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +|+|.|.+|+||||||+.++..+
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999876

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=95.55  E-value=0.055  Score=55.76  Aligned_cols=29  Identities=28%  Similarity=0.407  Sum_probs=25.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...++.++|++|+||||++..++..++..
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~  127 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            36789999999999999999999877665

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.54  E-value=0.061  Score=57.78  Aligned_cols=26  Identities=23%  Similarity=0.296  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|+|||||++.+..-+
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g~~  385 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTGLL  385 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45579999999999999999998643

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>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=95.54  E-value=0.012  Score=53.55  Aligned_cols=33  Identities=21%  Similarity=0.076  Sum_probs=27.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.|.|++|+|||+|+.+++......-..++|+.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            678999999999999999887665556677765

A related protein is found in archaea.

>PRK13764 ATPase; Provisional

Probab=95.54  E-value=0.03  Score=59.80  Aligned_cols=85  Identities=15%  Similarity=0.147  Sum_probs=49.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      ..+.|+|++|+||||++++++..+..+...+..+.+..+......        ..++.   ....+...   .....|..
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~~~~--------i~q~~---~~~~~~~~---~~~~lLR~  323 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQVPPE--------ITQYS---KLEGSMEE---TADILLLV  323 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccCCCc--------ceEEe---eccccHHH---HHHHHHhh
Confidence            458999999999999999999877654333334432222111100        00000   00011111   12223567


Q ss_pred             CCeEEEEecCCChHHHHHH
Q 009306          292 KKVLIVFDDVDHPRQIKIL  310 (538)
Q Consensus       292 k~~LlVlDdv~~~~~~~~l  310 (538)
                      +|=.|++|++.+.+.++.+
T Consensus       324 rPD~IivGEiRd~Et~~~~  342 (602)
T PRK13764        324 RPDYTIYDEMRKTEDFKIF  342 (602)
T ss_pred             CCCEEEECCCCCHHHHHHH
Confidence            8899999999988887765

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.53  E-value=0.011  Score=53.56  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|+|++|+|||||++.++..+.
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3689999999999999999988754

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.

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=95.53  E-value=0.075  Score=49.55  Aligned_cols=26  Identities=31%  Similarity=0.348  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|.|+.|.|||||++.++...
T Consensus        23 ~Ge~~~i~G~nGsGKSTLl~~l~G~~   48 (213)
T TIGR01277        23 DGEIVAIMGPSGAGKSTLLNLIAGFI   48 (213)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999998753

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=95.53  E-value=0.012  Score=65.46  Aligned_cols=24  Identities=25%  Similarity=0.023  Sum_probs=21.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +.+++.|+|+.+.||||+.+.++-
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl  349 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGL  349 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHH
Confidence            457899999999999999998865

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.53  E-value=0.24  Score=50.44  Aligned_cols=29  Identities=38%  Similarity=0.474  Sum_probs=24.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ++-+.+.|++|.|||.|+++++.+....|
T Consensus       186 ~rglLLfGPpgtGKtmL~~aiAsE~~atf  214 (428)
T KOG0740|consen  186 VRGLLLFGPPGTGKTMLAKAIATESGATF  214 (428)
T ss_pred             cchhheecCCCCchHHHHHHHHhhhcceE
Confidence            45578999999999999999999865543

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.52  E-value=0.084  Score=49.31  Aligned_cols=24  Identities=38%  Similarity=0.367  Sum_probs=20.9

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|.|.|++|+||||+|+.++.++.
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            388999999999999999987653

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=95.50  E-value=0.036  Score=47.43  Aligned_cols=29  Identities=31%  Similarity=0.589  Sum_probs=25.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      .-++.|.|.+|.||||+++++.+++.-.|
T Consensus        12 k~~i~vmGvsGsGKSTigk~L~~~l~~~F   40 (191)
T KOG3354|consen   12 KYVIVVMGVSGSGKSTIGKALSEELGLKF   40 (191)
T ss_pred             ceeEEEEecCCCChhhHHHHHHHHhCCcc
Confidence            34789999999999999999999987554

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=95.49  E-value=0.058  Score=58.05  Aligned_cols=27  Identities=26%  Similarity=0.186  Sum_probs=22.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++..|+|.+|.||||++..+...+..
T Consensus       160 ~~~~vitGgpGTGKTt~v~~ll~~l~~  186 (586)
T TIGR01447       160 SNFSLITGGPGTGKTTTVARLLLALVK  186 (586)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            357999999999999999988876543

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.48  E-value=0.011  Score=51.37  Aligned_cols=24  Identities=33%  Similarity=0.473  Sum_probs=21.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|.|.|++|+||||+|+.++.++.
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~   24 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999998753

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.48  E-value=0.075  Score=57.40  Aligned_cols=27  Identities=26%  Similarity=0.210  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++..|+|.+|.||||+++.+...+..
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~  193 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQ  193 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            457999999999999999988876543

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=95.47  E-value=0.2  Score=46.39  Aligned_cols=25  Identities=40%  Similarity=0.497  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|.|||||++.++..
T Consensus        33 ~G~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          33 AGEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3457999999999999999999864

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.46  E-value=0.038  Score=56.83  Aligned_cols=102  Identities=14%  Similarity=0.033  Sum_probs=61.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ...++.++||.|+||||....+...+......++-+.+.-+.. -.++..           ....+..--.....++..|
T Consensus       257 p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~~-~~gI~Q-----------~qVN~k~gltfa~~LRa~L  324 (500)
T COG2804         257 PQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEYQ-LPGINQ-----------VQVNPKIGLTFARALRAIL  324 (500)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeeee-cCCcce-----------eecccccCCCHHHHHHHHh
Confidence            4568999999999999999998887766555444444221110 001100           0000011112345677788


Q ss_pred             cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEec
Q 009306          290 TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                      ++-|=+|.+.++.|.+..+....+.    -.++.++||
T Consensus       325 RqDPDvImVGEIRD~ETAeiavqAa----lTGHLVlST  358 (500)
T COG2804         325 RQDPDVIMVGEIRDLETAEIAVQAA----LTGHLVLST  358 (500)
T ss_pred             ccCCCeEEEeccCCHHHHHHHHHHH----hcCCeEeee
Confidence            8999999999998887766555431    234556555

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.46  E-value=0.035  Score=54.80  Aligned_cols=52  Identities=13%  Similarity=0.233  Sum_probs=43.7

Q ss_pred             CCCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          187 NEDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...|+|.+..+.++.+.+..    .....+++.+.||.|.|||||+..+.+-+...
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y  115 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEEY  115 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhheE
Confidence            35799999999999998875    23457899999999999999999988876554

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

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.46  E-value=0.011  Score=54.77  Aligned_cols=29  Identities=17%  Similarity=0.297  Sum_probs=24.0

Q ss_pred             cCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          206 TGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       206 ~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+....+.++|+|++|+|||||+..+...
T Consensus         8 ~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          8 NKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            34456788999999999999999998754

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.46  E-value=0.024  Score=53.36  Aligned_cols=48  Identities=17%  Similarity=0.179  Sum_probs=35.7

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|.++|..+-....++.|.|.+|+|||++|.+++.....+-..++|+.
T Consensus         4 ~LD~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s   51 (224)
T TIGR03880         4 GLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYIS   51 (224)
T ss_pred             hhHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            455566555456778999999999999999999887544445566665

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.46  E-value=0.0098  Score=54.82  Aligned_cols=23  Identities=43%  Similarity=0.648  Sum_probs=21.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +++|.|++|+|||||++.+...+
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999998876

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.

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=95.46  E-value=0.07  Score=49.36  Aligned_cols=20  Identities=45%  Similarity=0.395  Sum_probs=19.0

Q ss_pred             EEEEeccCCCchhHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~  232 (538)
                      +++|.|+.|.|||||..+++
T Consensus        24 ~~~i~G~NGsGKTTLl~ai~   43 (204)
T cd03240          24 LTLIVGQNGAGKTTIIEALK   43 (204)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            79999999999999999985

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=95.45  E-value=0.12  Score=48.47  Aligned_cols=25  Identities=36%  Similarity=0.460  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|.|||||++.++..
T Consensus        29 ~Ge~~~i~G~nGsGKSTLl~~l~G~   53 (221)
T cd03244          29 PGEKVGIVGRTGSGKSSLLLALFRL   53 (221)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcC
Confidence            3457999999999999999999864

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

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

Probab=95.45  E-value=0.03  Score=56.81  Aligned_cols=52  Identities=21%  Similarity=0.297  Sum_probs=36.9

Q ss_pred             CCceeccchhHHHHHhhhc---------C---CCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          188 EDLVGVRLPMKEIESLLRT---------G---STNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~---------~---~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ..++|.+...+.+...+..         +   ......+.++|++|+|||+||+.++..+...|
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~f   78 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   78 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChh
Confidence            4577777777777655532         0   01135689999999999999999998765443

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.44  E-value=0.016  Score=49.97  Aligned_cols=35  Identities=20%  Similarity=0.318  Sum_probs=26.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      +++.|+|+.|+|||||++.+.+.+..+ +...++..
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            478999999999999999999988754 44443443

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=95.43  E-value=0.13  Score=48.75  Aligned_cols=26  Identities=19%  Similarity=0.238  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||++.++...
T Consensus        28 ~Ge~~~l~G~nGsGKSTLl~~i~G~~   53 (238)
T cd03249          28 PGKTVALVGSSGCGKSTVVSLLERFY   53 (238)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            34579999999999999999998754

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=95.43  E-value=0.014  Score=54.76  Aligned_cols=24  Identities=29%  Similarity=-0.014  Sum_probs=21.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..+++.|+|+.|.||||+.+.+..
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~   52 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGV   52 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHH
Confidence            467899999999999999998774

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

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

Probab=95.43  E-value=0.058  Score=58.70  Aligned_cols=26  Identities=27%  Similarity=0.291  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|.|||||++.++..+
T Consensus       368 ~G~~~aIvG~sGsGKSTLl~ll~gl~  393 (582)
T PRK11176        368 AGKTVALVGRSGSGKSTIANLLTRFY  393 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            34569999999999999999998744

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.41  E-value=0.14  Score=46.73  Aligned_cols=49  Identities=16%  Similarity=0.100  Sum_probs=36.8

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|...|..+-+...++.|-|..|.|||.|.+.+++-.-..-..+.++.
T Consensus        15 delDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvs   63 (235)
T COG2874          15 DELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVS   63 (235)
T ss_pred             HHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHHHhCCceEEEEE
Confidence            3566666655566788999999999999999999987655544555554

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=95.41  E-value=0.13  Score=49.94  Aligned_cols=27  Identities=26%  Similarity=0.474  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....++|+|+.|.|||||++.++..+.
T Consensus        29 ~Ge~~~IvG~nGsGKSTLl~~L~gl~~   55 (275)
T cd03289          29 PGQRVGLLGRTGSGKSTLLSAFLRLLN   55 (275)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhhhcC
Confidence            345799999999999999999987653

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

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

Probab=95.41  E-value=0.015  Score=53.94  Aligned_cols=25  Identities=36%  Similarity=0.416  Sum_probs=21.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|+|++|+|||||++.++--
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl   56 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGL   56 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhcc
Confidence            3457999999999999999999863

>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=95.38  E-value=0.015  Score=56.39  Aligned_cols=27  Identities=19%  Similarity=0.297  Sum_probs=22.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+.+.++|++|+|||++++.+...+..
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~   59 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDS   59 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTT
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCc
Confidence            456899999999999999998876543

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=95.37  E-value=0.021  Score=56.28  Aligned_cols=48  Identities=29%  Similarity=0.340  Sum_probs=34.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      .+++.++|.||+||||+|.+.+-........+.-++    .++.+++.+.+.
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g~kvLlvS----tDPAhsL~d~f~   49 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVS----TDPAHSLGDVFD   49 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcCCcEEEEE----eCCCCchHhhhc
Confidence            468899999999999999998888777665555554    444455555443

>PRK15453 phosphoribulokinase; Provisional

Probab=95.37  E-value=0.02  Score=54.85  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=24.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+|+|+|.+|+||||+|+.+...+..
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~if~~   31 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKIFRR   31 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4578999999999999999999977654

>PRK08506 replicative DNA helicase; Provisional

Probab=95.35  E-value=0.17  Score=53.29  Aligned_cols=73  Identities=19%  Similarity=0.155  Sum_probs=47.2

Q ss_pred             ceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHh
Q 009306          190 LVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLL  269 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~  269 (538)
                      ..|-..-+..|..++ .+-....++.|.|.+|+|||++|..++.....+-..++|++      -.-....+...+++...
T Consensus       172 ~~Gi~TG~~~LD~~~-~G~~~G~LivIaarpg~GKT~fal~ia~~~~~~g~~V~~fS------lEMs~~ql~~Rlla~~s  244 (472)
T PRK08506        172 IIGLDTGFVELNKMT-KGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFS------LEMPAEQLMLRMLSAKT  244 (472)
T ss_pred             CCcccCChHHHHhhc-CCCCCCceEEEEcCCCCChHHHHHHHHHHHHhcCCcEEEEe------CcCCHHHHHHHHHHHhc
Confidence            445555566666654 34445668999999999999999999987654433455544      12345556666665443

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

Probab=95.34  E-value=0.026  Score=56.54  Aligned_cols=53  Identities=23%  Similarity=0.213  Sum_probs=40.8

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      ..++|++..+..+...+..+.    .+.+.|++|+|||+||+.++..+...|..+.+
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~~----~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~   76 (329)
T COG0714          24 KVVVGDEEVIELALLALLAGG----HVLLEGPPGVGKTLLARALARALGLPFVRIQC   76 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcCC----CEEEECCCCccHHHHHHHHHHHhCCCeEEEec
Confidence            448898888888777666443    38999999999999999999988755543333

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=95.33  E-value=0.032  Score=60.38  Aligned_cols=56  Identities=14%  Similarity=0.238  Sum_probs=42.5

Q ss_pred             CCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          187 NEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      .+.++|.+..++.+...+..+    +.+.++|++|+||||+|+.+++.+... |...+++.
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~----~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~   73 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQK----RNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYP   73 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcC----CCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEe
Confidence            367899998888888777643    247799999999999999999987654 33344444

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

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.33  E-value=0.025  Score=50.44  Aligned_cols=29  Identities=24%  Similarity=0.300  Sum_probs=25.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..++++|+|+.|+|||||++.+...+..+
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~~   33 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCAR   33 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhhc
Confidence            45689999999999999999999887653

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=95.32  E-value=0.015  Score=51.06  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=20.8

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |.|+|++|+||||+|+.++..+.
T Consensus         2 i~l~G~~GsGKstla~~la~~l~   24 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhC
Confidence            78999999999999999998763

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.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=95.32  E-value=0.053  Score=58.38  Aligned_cols=100  Identities=13%  Similarity=0.030  Sum_probs=56.5

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCC
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKN  276 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~  276 (538)
                      ++.+.+++..   ....|.|+|+.|+||||+...+...+...-...+-+.+.-+    ..+..+     .++.-.   ..
T Consensus       305 ~~~l~~~~~~---~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE----~~~~~~-----~q~~v~---~~  369 (564)
T TIGR02538       305 KALFLEAIHK---PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVE----INLPGI-----NQVNVN---PK  369 (564)
T ss_pred             HHHHHHHHHh---cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCce----ecCCCc-----eEEEec---cc
Confidence            4445555542   34579999999999999988877765332111222221111    111000     010000   01


Q ss_pred             chhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHh
Q 009306          277 FLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       277 ~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      .-......++..|+..|=.|++.++.+.+.....+
T Consensus       370 ~g~~~~~~l~~~LR~dPDvI~vGEiRd~eta~~a~  404 (564)
T TIGR02538       370 IGLTFAAALRSFLRQDPDIIMVGEIRDLETAEIAI  404 (564)
T ss_pred             cCCCHHHHHHHHhccCCCEEEeCCCCCHHHHHHHH
Confidence            11234566778888999999999999888766444

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

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

Probab=95.30  E-value=0.027  Score=60.39  Aligned_cols=50  Identities=20%  Similarity=0.283  Sum_probs=38.2

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +..+-|....+.|.+..........+|.|+|++|+||||+|+.++.++..
T Consensus       369 P~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L~~  418 (568)
T PRK05537        369 PEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKLME  418 (568)
T ss_pred             ChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHhhh
Confidence            44556666666666666554455668999999999999999999998764

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=95.30  E-value=0.2  Score=47.27  Aligned_cols=26  Identities=27%  Similarity=0.288  Sum_probs=22.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||.+.++...
T Consensus        28 ~G~~~~i~G~nGsGKSTLl~~l~G~~   53 (229)
T cd03254          28 PGETVAIVGPTGAGKTTLINLLMRFY   53 (229)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            34579999999999999999998754

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=95.29  E-value=0.041  Score=50.74  Aligned_cols=28  Identities=25%  Similarity=0.330  Sum_probs=21.8

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....++.|.|.+|.||||++..+...+.
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~   40 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFG   40 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT-
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhcc
Confidence            4567888899999999999999888763

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=95.29  E-value=0.2  Score=46.25  Aligned_cols=26  Identities=23%  Similarity=0.364  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||++.++...
T Consensus        30 ~G~~~~i~G~nG~GKSTLl~~i~G~~   55 (204)
T cd03250          30 KGELVAIVGPVGSGKSSLLSALLGEL   55 (204)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCcC
Confidence            45579999999999999999998754

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.29  E-value=0.02  Score=57.02  Aligned_cols=96  Identities=18%  Similarity=0.120  Sum_probs=53.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLT  290 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~  290 (538)
                      ...+.|+|+.|+||||+++++...+.... .++-+.+..+....... ... .+   ...........-.....++..|+
T Consensus       160 ~~nili~G~tgSGKTTll~aL~~~ip~~~-ri~tiEd~~El~l~~~~-n~~-~~---~~~~~~~~~~~~~~~~ll~~~LR  233 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFTNAALREIPAIE-RLITVEDAREIVLSNHP-NRV-HL---LASKGGQGRAKVTTQDLIEACLR  233 (332)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHhhCCCCC-eEEEecCCCccccccCC-CEE-EE---EecCCCCCcCcCcHHHHHHHHhc
Confidence            34599999999999999999998775542 22223222111100000 000 00   00000001111123556777788


Q ss_pred             CCCeEEEEecCCChHHHHHHhc
Q 009306          291 RKKVLIVFDDVDHPRQIKILVG  312 (538)
Q Consensus       291 ~k~~LlVlDdv~~~~~~~~l~~  312 (538)
                      ..|=.||++++.+.+.+..+..
T Consensus       234 ~~PD~IivGEiR~~ea~~~l~a  255 (332)
T PRK13900        234 LRPDRIIVGELRGAEAFSFLRA  255 (332)
T ss_pred             cCCCeEEEEecCCHHHHHHHHH
Confidence            8999999999988776655443

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=95.29  E-value=0.013  Score=51.25  Aligned_cols=20  Identities=35%  Similarity=0.526  Sum_probs=18.6

Q ss_pred             EEEEeccCCCchhHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~  232 (538)
                      .|+|+|.||+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            48999999999999999887

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=95.28  E-value=0.015  Score=53.67  Aligned_cols=21  Identities=29%  Similarity=0.093  Sum_probs=19.9

Q ss_pred             eEEEEeccCCCchhHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      ++++|+|+.|.|||||.+.+.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            689999999999999999988

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D

Probab=95.28  E-value=0.088  Score=49.82  Aligned_cols=26  Identities=27%  Similarity=0.192  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|.|+.|.|||||.+.++...
T Consensus        25 ~Ge~~~i~G~nGsGKSTLl~~l~g~~   50 (232)
T cd03300          25 EGEFFTLLGPSGCGKTTLLRLIAGFE   50 (232)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999998754

PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. 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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=95.28  E-value=0.032  Score=55.42  Aligned_cols=40  Identities=28%  Similarity=0.437  Sum_probs=29.7

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+.+.+....+...+|+|+|++|+|||||+..+...+...
T Consensus        44 ~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         44 ELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             HHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            3444333323456789999999999999999998877654

>PRK05439 pantothenate kinase; Provisional

Probab=95.28  E-value=0.019  Score=56.28  Aligned_cols=29  Identities=31%  Similarity=0.402  Sum_probs=24.8

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...-+|+|.|.+|+||||+|+.+...+..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~~  112 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLSR  112 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            45678999999999999999999886643

>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]

Probab=95.27  E-value=0.053  Score=55.55  Aligned_cols=124  Identities=21%  Similarity=0.184  Sum_probs=66.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceee-----EEEEeehhhhhh-----------------cCChHHHHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSG-----SYFARNVREAEE-----------------TCRLGDLRQQLLSTL  268 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~-----~~~~~~~~~~~~-----------------~~~~~~l~~~l~~~l  268 (538)
                      .+..+++|..|+|||||.+++++.....|+.     .+++........                 ...+..+...++..+
T Consensus       106 GrRYGLvGrNG~GKsTLLRaia~~~v~~f~veqE~~g~~t~~~~~~l~~D~~~~dfl~~e~~l~~~~~l~ei~~~~L~gl  185 (582)
T KOG0062|consen  106 GRRYGLVGRNGIGKSTLLRAIANGQVSGFHVEQEVRGDDTEALQSVLESDTERLDFLAEEKELLAGLTLEEIYDKILAGL  185 (582)
T ss_pred             ccccceeCCCCCcHHHHHHHHHhcCcCccCchhheeccchHHHhhhhhccHHHHHHHHhhhhhhccchHHHHHHHHHHhC
Confidence            4568999999999999999999844444432     222221111000                 001222233233333


Q ss_pred             hcCCCCC-------CchhhcHHHHHHHhcCCCeEEEEecCCChH---HHHHHhcCcCCCCCCCEEEEeccchhhhhhc
Q 009306          269 LNDGNVK-------NFLNTDLNFQSRRLTRKKVLIVFDDVDHPR---QIKILVGRLDLFASGSRIIITTRDRQVLANC  336 (538)
Q Consensus       269 ~~~~~~~-------~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~---~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~  336 (538)
                      +-..+..       ..--...-.+.+.+-.++=||.||+--+.-   .+..+...+.  ..+..+||.|-+...+...
T Consensus       186 GFt~emq~~pt~slSGGWrMrlaLARAlf~~pDlLLLDEPTNhLDv~av~WLe~yL~--t~~~T~liVSHDr~FLn~V  261 (582)
T KOG0062|consen  186 GFTPEMQLQPTKSLSGGWRMRLALARALFAKPDLLLLDEPTNHLDVVAVAWLENYLQ--TWKITSLIVSHDRNFLNTV  261 (582)
T ss_pred             CCCHHHHhccccccCcchhhHHHHHHHHhcCCCEEeecCCcccchhHHHHHHHHHHh--hCCceEEEEeccHHHHHHH
Confidence            3221111       111123345556667789999999875433   3333333333  2236678888887666543

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.27  E-value=0.023  Score=50.50  Aligned_cols=25  Identities=24%  Similarity=0.376  Sum_probs=22.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.||+|+|||||++.+..+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4579999999999999999999876

>PHA02244 ATPase-like protein

Probab=95.27  E-value=0.015  Score=57.85  Aligned_cols=47  Identities=17%  Similarity=0.208  Sum_probs=32.0

Q ss_pred             CCceeccchhHH----HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          188 EDLVGVRLPMKE----IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       188 ~~~vGR~~~l~~----l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..++|....+..    +..++..+    ..+.|+|++|+|||+||++++......
T Consensus        96 ~~~ig~sp~~~~~~~ri~r~l~~~----~PVLL~GppGtGKTtLA~aLA~~lg~p  146 (383)
T PHA02244         96 TTKIASNPTFHYETADIAKIVNAN----IPVFLKGGAGSGKNHIAEQIAEALDLD  146 (383)
T ss_pred             CcccCCCHHHHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            456666555543    33344322    238889999999999999999875433

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=95.26  E-value=0.018  Score=56.75  Aligned_cols=35  Identities=31%  Similarity=0.377  Sum_probs=27.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +++.+.|-||+||||+|.+++-....+...+..++
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G~rtLlvS   36 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRGKRTLLVS   36 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCCCCeeEee
Confidence            57899999999999999999987776654455554

...

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=95.24  E-value=0.038  Score=62.44  Aligned_cols=225  Identities=18%  Similarity=0.163  Sum_probs=108.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce----eeEEEEeeh--hhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF----SGSYFARNV--REAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQS  286 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f----~~~~~~~~~--~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~  286 (538)
                      -+.|+|.+|.||||+...++-......    +..+++..-  ........-..+..-+...+....    ..........
T Consensus       224 ~~~Ilg~pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~~~~q~~~~~~l~~~~~~~~----~~~~~~~~~~  299 (824)
T COG5635         224 KLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQG----IAKQLIEAHQ  299 (824)
T ss_pred             heeeecCCCCCceehHHHHHHHhccCcCCcccCceeeechhHHHhhhhHhhccHHHHHHHHHhccC----CcchhhHHHH
Confidence            589999999999999998887544332    223333311  111111000022222222222221    1222222224


Q ss_pred             HHhcCCCeEEEEecCCChHH------HHHHhcCcCCCCCCCEEEEeccchhhhhhcCCCeeEEcCCCCHHHHHHHHHh--
Q 009306          287 RRLTRKKVLIVFDDVDHPRQ------IKILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQMEELVHDDALRLFSR--  358 (538)
Q Consensus       287 ~~l~~k~~LlVlDdv~~~~~------~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~~~~~l~~L~~~ea~~Lf~~--  358 (538)
                      +.+...++++++|.+|....      +..+-..+++ -+..++|+|+|....-........+++..+.++...+....  
T Consensus       300 e~l~~g~~llLlDGlDe~~~~~~~~~~~~i~~f~~~-~~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i~~~~~~~~  378 (824)
T COG5635         300 ELLKTGKLLLLLDGLDELEPKNQRALIREINKFLQE-YPDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQINQFILYQW  378 (824)
T ss_pred             HHHhccchhhHhhccchhhhhhHHHHHHHHHHHhhh-ccCCeEEEEeccchhhhhhhhhhhccchhhhHHHHHHHHHHHH
Confidence            66788999999999976421      2222222222 34788999998775433333334555666655544433331  


Q ss_pred             ------hhcCCCCCC-CchH-H---HHHHHHHHhcCCcHHHHHHHHHhc------CCCHHHHHHHHHHhhcCCCCcHHHH
Q 009306          359 ------HAFGGDHPH-ESHT-E---LACKTIKYARGVPLALEVLGRYLY------GKRREVWENAKSKWETAPPKGIQDA  421 (538)
Q Consensus       359 ------~~~~~~~~~-~~~~-~---~~~~i~~~~~G~PLal~~~~~~L~------~~~~~~~~~~l~~l~~~~~~~v~~~  421 (538)
                            ..++..... ..+. .   -..+..+.....|+.|.+.+..-.      ....+-++..++.+-...+..-...
T Consensus       379 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ik~l~~~p~~L~l~c~~~~~~~~lP~~~~~ly~~~~~~~~~~~d~~~~~~  458 (824)
T COG5635         379 LDAFIEDWFGDSRLLAKKLLERLKLPENRRIKELALTPLLLALECLIWQAQGDLPESRAELYEQAVDALLGREDETRGIK  458 (824)
T ss_pred             HHHHHHhhhcccchhhHHHHHHhcchhhHHHHHhccCHHHHHHHHHhhhHHhhCCCCcHHHHHHHHHHHHhccchhhhhc
Confidence                  111111111 0000 0   112334444888999988875443      2345666666665443332111112


Q ss_pred             HHHhHhCCC-HHhHH-Hhhcccc
Q 009306          422 LKISYDGLD-DKEQN-IFLDIAC  442 (538)
Q Consensus       422 l~~s~~~L~-~~~k~-~l~~la~  442 (538)
                      ....|..+. +...+ ++..++.
T Consensus       459 ~~~~~~~~~~~~~~~~l~~~la~  481 (824)
T COG5635         459 WSKTYAKLTTDQQDKWLLQLLAA  481 (824)
T ss_pred             chhhhcccchHHHHHHHHHHHHH
Confidence            334444443 23333 5555543

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.21  E-value=0.059  Score=56.33  Aligned_cols=29  Identities=21%  Similarity=0.273  Sum_probs=24.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|++|+||||++..++..+...
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~  377 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQ  377 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            35789999999999999999998876544

>PRK13949 shikimate kinase; Provisional

Probab=95.21  E-value=0.017  Score=51.64  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=21.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|.|+|++|.||||+++.++..+.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELG   26 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            489999999999999999998764

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.18  E-value=0.078  Score=52.47  Aligned_cols=87  Identities=17%  Similarity=0.138  Sum_probs=50.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhc-CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEET-CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~-~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      .+.|+|..|+||||+++++...+....  ...+-+.+..+.... .....        +.     ....-.....++..|
T Consensus       146 nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El~~~~~n~v~--------l~-----~~~~~~~~~lv~~aL  212 (323)
T PRK13833        146 NIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCAAENAVA--------LH-----TSDTVDMARLLKSTM  212 (323)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCcccccCCCCEEE--------ec-----cCCCcCHHHHHHHHh
Confidence            488999999999999999998764221  122222211111000 00000        00     011123445667778


Q ss_pred             cCCCeEEEEecCCChHHHHHHhc
Q 009306          290 TRKKVLIVFDDVDHPRQIKILVG  312 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~~  312 (538)
                      +..|-.||+.++.+.+.+..+..
T Consensus       213 R~~PD~IivGEiRg~ea~~~l~a  235 (323)
T PRK13833        213 RLRPDRIIVGEVRDGAALTLLKA  235 (323)
T ss_pred             CCCCCEEEEeecCCHHHHHHHHH
Confidence            88999999999988776665443

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=95.17  E-value=0.13  Score=57.22  Aligned_cols=69  Identities=16%  Similarity=0.071  Sum_probs=42.8

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcC
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLND  271 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~  271 (538)
                      ....+|.+.+.    ..+++.|.|+.|+||||-.-+++.+..-...+.+-+.    ....-...++.+.+...++..
T Consensus        53 ~~~~~i~~ai~----~~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~t----QPRRlAArsvA~RvAeel~~~  121 (845)
T COG1643          53 AVRDEILKAIE----QNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCT----QPRRLAARSVAERVAEELGEK  121 (845)
T ss_pred             HHHHHHHHHHH----hCCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEec----CchHHHHHHHHHHHHHHhCCC
Confidence            35556666665    4568999999999999998888876432223334433    122223445666666666553

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

Probab=95.16  E-value=0.1  Score=52.43  Aligned_cols=26  Identities=23%  Similarity=0.325  Sum_probs=22.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++.++||.|+||||-...++.++.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~  228 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYV  228 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHH
Confidence            78999999999999977777777655

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.13  E-value=0.22  Score=45.43  Aligned_cols=42  Identities=19%  Similarity=0.242  Sum_probs=28.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..++|-...++.+.-    +-....+.++.||+|+||||+.+.+-.
T Consensus        14 ~~yYg~~~aL~~i~l----~i~~~~VTAlIGPSGcGKST~LR~lNR   55 (253)
T COG1117          14 NLYYGDKHALKDINL----DIPKNKVTALIGPSGCGKSTLLRCLNR   55 (253)
T ss_pred             eEEECchhhhccCce----eccCCceEEEECCCCcCHHHHHHHHHh
Confidence            345664444433322    224567899999999999999986543

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.13  E-value=0.42  Score=48.05  Aligned_cols=24  Identities=29%  Similarity=0.517  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -..|+|+||.|+|||||.+.+.-.
T Consensus       613 dSRiaIVGPNGVGKSTlLkLL~Gk  636 (807)
T KOG0066|consen  613 DSRIAIVGPNGVGKSTLLKLLIGK  636 (807)
T ss_pred             cceeEEECCCCccHHHHHHHHhcC
Confidence            345999999999999999988864

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=95.12  E-value=0.023  Score=49.49  Aligned_cols=33  Identities=27%  Similarity=0.276  Sum_probs=25.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      -.++|+||+|+|||||.+.++.-+...-....|
T Consensus        30 e~iaitGPSG~GKStllk~va~Lisp~~G~l~f   62 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLISPTSGTLLF   62 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhccCCCCceEEE
Confidence            359999999999999999999865544333333

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=95.12  E-value=0.11  Score=55.71  Aligned_cols=25  Identities=20%  Similarity=0.335  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|+|+.|+|||||++.+...
T Consensus       347 ~G~~~~ivG~sGsGKSTL~~ll~g~  371 (529)
T TIGR02857       347 PGERVALVGPSGAGKSTLLNLLLGF  371 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4457999999999999999999864

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.10  E-value=0.019  Score=48.89  Aligned_cols=24  Identities=29%  Similarity=0.386  Sum_probs=21.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +-|.|+|.||.|||||+.+++...
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~   31 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEKT   31 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHHh
Confidence            348999999999999999999754

>PRK14530 adenylate kinase; Provisional

Probab=95.10  E-value=0.019  Score=53.74  Aligned_cols=23  Identities=22%  Similarity=0.397  Sum_probs=21.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|+|.|++|+||||+|+.++..+
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998876

>PRK13948 shikimate kinase; Provisional

Probab=95.09  E-value=0.022  Score=51.56  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=24.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+.|.++|+.|+||||+++.++..+..
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~   36 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALML   36 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4567999999999999999999988643

>PLN02674 adenylate kinase

Probab=95.09  E-value=0.21  Score=47.33  Aligned_cols=24  Identities=29%  Similarity=0.275  Sum_probs=21.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+.|.|++|+||||+|+.++.++
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~   55 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEY   55 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc
Confidence            458899999999999999888765

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=95.08  E-value=0.02  Score=52.52  Aligned_cols=25  Identities=40%  Similarity=0.402  Sum_probs=22.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++.|.|++|+||||+|+.++.++
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4579999999999999999999874

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

Probab=95.07  E-value=0.032  Score=54.42  Aligned_cols=56  Identities=23%  Similarity=0.291  Sum_probs=42.8

Q ss_pred             CCCCCceeccchhHH---HHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          185 SENEDLVGVRLPMKE---IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~---l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      ...+.|||.....+.   +.++...+.-..+.|.|.|++|.|||+||..+++.+...-+
T Consensus        36 ~~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvP   94 (450)
T COG1224          36 FIGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVP   94 (450)
T ss_pred             EcCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCC
Confidence            345789998765543   34566655556778999999999999999999999876544

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=95.06  E-value=0.16  Score=50.08  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|.|||||.+.++..
T Consensus        27 ~Gei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        27 KGRIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHhCC
Confidence            4557999999999999999999864

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.06  E-value=0.075  Score=52.68  Aligned_cols=88  Identities=17%  Similarity=0.183  Sum_probs=50.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce--eeEEEEeehhhhhhc-CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF--SGSYFARNVREAEET-CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSR  287 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f--~~~~~~~~~~~~~~~-~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~  287 (538)
                      ...+.|+|..|+||||++++++..+....  ...+-+.+..+.... ....        ++.  .   ...-.....++.
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v--------~~~--~---~~~~~~~~ll~~  214 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYV--------QYH--T---SIDVNMTALLKT  214 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEE--------EEe--c---CCCCCHHHHHHH
Confidence            34589999999999999999997642211  222222221111000 0000        000  0   001124456677


Q ss_pred             HhcCCCeEEEEecCCChHHHHHHh
Q 009306          288 RLTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      .|+..|=.||+.++.+.+.+..+.
T Consensus       215 aLR~~PD~IivGEiR~~Ea~~~l~  238 (319)
T PRK13894        215 TLRMRPDRILVGEVRGPEALDLLM  238 (319)
T ss_pred             HhcCCCCEEEEeccCCHHHHHHHH
Confidence            788889999999998887666543

>PRK13946 shikimate kinase; Provisional

Probab=95.06  E-value=0.019  Score=52.21  Aligned_cols=26  Identities=19%  Similarity=0.330  Sum_probs=23.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.|.++|++|+||||+++.++.++.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg   35 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLG   35 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            34699999999999999999998873

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.03  E-value=0.017  Score=52.33  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=21.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++++|+|++|+|||||++.++...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            468999999999999999999854

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.

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=95.03  E-value=0.23  Score=52.28  Aligned_cols=49  Identities=24%  Similarity=0.283  Sum_probs=36.7

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++|....+.++...+..-......+.|.|.+|.||+++|+.+.....
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~  182 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSP  182 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCC
Confidence            4588888888777776654333344588999999999999998887543

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.01  E-value=0.02  Score=53.08  Aligned_cols=27  Identities=22%  Similarity=0.336  Sum_probs=23.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|+|++|+|||||++.++....
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            345799999999999999999998653

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=95.01  E-value=0.027  Score=52.98  Aligned_cols=36  Identities=31%  Similarity=0.285  Sum_probs=24.1

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.+.+...+..    ..+..|+|++|.|||+++..+...+
T Consensus         6 Q~~Ai~~~~~~----~~~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen    6 QREAIQSALSS----NGITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             HHHHHHHHCTS----SE-EEEE-STTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC----CCCEEEECCCCCChHHHHHHHHHHh
Confidence            44455555542    2268999999999998888777766

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.01  E-value=0.031  Score=59.02  Aligned_cols=49  Identities=16%  Similarity=0.114  Sum_probs=37.2

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..|.++|..+-...+++.|.|++|+|||+||.+++.+-..+ -+.++|+.
T Consensus         8 ~gLD~il~GGlp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs   57 (484)
T TIGR02655         8 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVT   57 (484)
T ss_pred             hhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            34556666666678899999999999999999998764333 45667766

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>smart00072 GuKc Guanylate kinase homologues

Probab=95.00  E-value=0.025  Score=51.43  Aligned_cols=30  Identities=23%  Similarity=0.426  Sum_probs=24.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      .+++.|+|++|+||+||+..+.......|.
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~~~~~~   31 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEIPDAFE   31 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcCCcceE
Confidence            357999999999999999999987654443

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.

>PRK14737 gmk guanylate kinase; Provisional

Probab=94.98  E-value=0.022  Score=51.82  Aligned_cols=26  Identities=27%  Similarity=0.287  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++.|+|++|+|||||++.+..+.
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45689999999999999999998764

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.98  E-value=0.08  Score=49.61  Aligned_cols=93  Identities=13%  Similarity=0.059  Sum_probs=61.0

Q ss_pred             CceEEEEeccCCCchh-HHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKT-TIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKT-tLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...++.|+|..|+||| |+|..+-++.+..+...+-+.+.-         ++..+--..+........+.+.....+++.
T Consensus       126 kRGLviiVGaTGSGKSTtmAaMi~yRN~~s~gHIiTIEDPI---------Efih~h~~CIvTQREvGvDTesw~~AlkNt  196 (375)
T COG5008         126 KRGLVIIVGATGSGKSTTMAAMIGYRNKNSTGHIITIEDPI---------EFIHKHKRCIVTQREVGVDTESWEVALKNT  196 (375)
T ss_pred             cCceEEEECCCCCCchhhHHHHhcccccCCCCceEEecChH---------HHHhcccceeEEeeeeccchHHHHHHHHHH
Confidence            3457899999999998 566666677777777666655322         221111112222223334555666778888


Q ss_pred             hcCCCeEEEEecCCChHHHHHHh
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILV  311 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~  311 (538)
                      ++..|-+|++-+|.+.+..+.-.
T Consensus       197 lRQapDvI~IGEvRsretMeyAi  219 (375)
T COG5008         197 LRQAPDVILIGEVRSRETMEYAI  219 (375)
T ss_pred             HhcCCCeEEEeecccHhHHHHHH
Confidence            99999999999998887766554

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=94.97  E-value=0.026  Score=50.56  Aligned_cols=36  Identities=17%  Similarity=0.365  Sum_probs=31.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...|.|-|++|+|||+|..+.+..++++|...+--.
T Consensus        13 ~~~i~v~Gp~GSGKTaLie~~~~~L~~~~~~aVI~~   48 (202)
T COG0378          13 MLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITG   48 (202)
T ss_pred             eEEEEecCCCCcCHHHHHHHHHHHHHhhCCeEEEec
Confidence            467999999999999999999999999888666554

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

Probab=94.97  E-value=0.024  Score=46.11  Aligned_cols=22  Identities=36%  Similarity=0.374  Sum_probs=19.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      ...++|.|++|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4679999999999999999876

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

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=94.97  E-value=0.11  Score=56.48  Aligned_cols=26  Identities=23%  Similarity=0.226  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|.|||||++.+...+
T Consensus       357 ~G~~v~IvG~sGsGKSTLl~lL~gl~  382 (571)
T TIGR02203       357 PGETVALVGRSGSGKSTLVNLIPRFY  382 (571)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            34569999999999999999987643

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=94.96  E-value=0.16  Score=48.68  Aligned_cols=171  Identities=13%  Similarity=0.208  Sum_probs=81.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHh-hccce-eeEEEEeehhhhhhcCChHHHHHHHHHHHhcC-------------------
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK-ISRHF-SGSYFARNVREAEETCRLGDLRQQLLSTLLND-------------------  271 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~-~~~~f-~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~-------------------  271 (538)
                      +..|+|+.|+|||+|.+.+..- +-+-- +.++|+.--.+.-........-.++...--..                   
T Consensus        89 I~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIpp~E~~aW~~Ql~EgNY~~~~~gTi~P~t~t~~P~Fv~  168 (369)
T PF02456_consen   89 IGVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIPPQEITAWETQLCEGNYDCGPDGTIVPQTGTFRPKFVE  168 (369)
T ss_pred             EEEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCCHHHHHHHHHHHHhcCCCCCCCCeecccccccccccee
Confidence            4557899999999999988763 22333 34555541111111111122222222210000                   


Q ss_pred             -------CCCCCchhhcHHHHHHHhcCCCeEEEEecCC----ChHHHHHHhcCcC-----CCC--CCCEEEEeccchhhh
Q 009306          272 -------GNVKNFLNTDLNFQSRRLTRKKVLIVFDDVD----HPRQIKILVGRLD-----LFA--SGSRIIITTRDRQVL  333 (538)
Q Consensus       272 -------~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~----~~~~~~~l~~~l~-----~~~--~~~~iiiTtR~~~~~  333 (538)
                             .+.+-++....+...+..+..++-||+|+.-    .-..+..|..+++     ++.  .|.-|+|.-.+-.-.
T Consensus       169 msy~e~t~~~NldI~~p~NiF~~Aa~~GPiaIImDECMe~Lg~~~~is~fFHAlPSKL~~rfp~CTgy~VfVVLHNmnPR  248 (369)
T PF02456_consen  169 MSYDEATSPENLDITNPNNIFAQAAKKGPIAIIMDECMEKLGSHKSISKFFHALPSKLHDRFPKCTGYYVFVVLHNMNPR  248 (369)
T ss_pred             ecHhhhCCccccCCCCchHHHHHHHhcCCEEEEhHHHHHHhcCCCChhHHHhcCcHHHhhhccCCceeEEEEEeccCCcc
Confidence                   0011223333455566677899999999862    1223444443332     122  244455543322111


Q ss_pred             hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          334 ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       334 ~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      ...+.    .+..|....-.-++        .+.-..-.+.+-|..++.|+|.+|.++-..+
T Consensus       249 ~d~gG----NI~~LKiqAK~HIi--------Sp~~~p~QlsRFin~yt~glp~~i~~LLKdi  298 (369)
T PF02456_consen  249 RDIGG----NIANLKIQAKCHII--------SPKMHPSQLSRFINNYTKGLPTAISLLLKDI  298 (369)
T ss_pred             cccCC----Cccchhhhceeeee--------cCCCCHHHHHHHHHHhccCCChhHHHHHHHH
Confidence            11100    11112111111111        1222335678888999999999997776544

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=94.93  E-value=0.12  Score=57.41  Aligned_cols=27  Identities=22%  Similarity=0.147  Sum_probs=23.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +++.|+|.+|.||||+++.+...+...
T Consensus       369 ~~~il~G~aGTGKTtll~~i~~~~~~~  395 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKAAREAWEAA  395 (744)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHHHhC
Confidence            578999999999999999998766554

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	538
3ozi_A	204	Crystal Structure Of The Tir Domain From The Flax D		6e-24
3jrn_A	176	Crystal Structure Of Tir Domain From Arabidopsis Th		6e-24

>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease Resistance Protein L6 Length = 204

Iteration: 1
 Score =  108 bits (271), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 62/159 (38%), Positives = 92/159 (57%), Gaps = 5/159 (3%)
Query: 1   MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDE 59
           ++ S++P  S   P ++Y+VFLSF G DTRE FT  LY +L R  + TF DDD L +G E
Sbjct: 21  ISDSTNPSGSF--PSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKE 78
Query: 60  ISQSLLDXXXXXXXXXXXXXXXXXXXRWCLDELLKILECKKEYA-QIVVPVFYRVDPSHV 118
           I  +LL                    +WCL EL +I+  ++E   +I++P+FY VDPS V
Sbjct: 79  IGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDV 138
Query: 119 RKQTGNFGDSFLKLEERFPDK-MQSWRNALTEAADLSGF 156
           R QTG +  +F K   +F  + +Q+W++AL +  DL G+
Sbjct: 139 RHQTGCYKKAFRKHANKFDGQTIQNWKDALKKVGDLKGW 177

>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana Length = 176

Iteration: 1
 Score =  108 bits (271), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 65/161 (40%), Positives = 86/161 (53%), Gaps = 4/161 (2%)
Query: 17  KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDXXXXXXXXX 75
           KYDVFLSF G DTR +F S LY  L R ++ TF DD +L  G   S  L           
Sbjct: 8   KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAV 67
Query: 76  XXXXXXXXXXRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEER 135
                      WCLDEL+ I++ +K+ +  V+P+FY V+P+HVR QTG   + F K   R
Sbjct: 68  VVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR 127
Query: 136 F-PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAI 175
             P+K+  WR ALT  A LSG        +S L+++I N I
Sbjct: 128 EDPEKVLKWRQALTNFAQLSG--DCSGDDDSKLVDKIANEI 166

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	538
3ozi_A	204	L6TR; plant TIR domain, plant protein; 2.30A {Linu	6e-92
3jrn_A	176	AT1G72930 protein; TIR domain arabidopsis thaliana	5e-90
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	3e-65
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	1e-39
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-37
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-31
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	5e-18
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	9e-15
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	2e-06
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	1e-05
2js7_A	160	Myeloid differentiation primary response protein M	1e-04
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	7e-04

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum} Length = 204

 Score =  278 bits (714), Expect = 6e-92
 Identities = 73/183 (39%), Positives = 111/183 (60%), Gaps = 5/183 (2%)

Query: 1   MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDE 59
           ++ S++P  S + P ++Y+VFLSF G DTRE FT  LY +L R  + TF DDD L +G E
Sbjct: 21  ISDSTNP--SGSFPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKE 78

Query: 60  ISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEY-AQIVVPVFYRVDPSHV 118
           I  +LL AI+ S I + I S  YA S+WCL EL +I+  ++E   +I++P+FY VDPS V
Sbjct: 79  IGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDV 138

Query: 119 RKQTGNFGDSFLKLEERF-PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILK 177
           R QTG +  +F K   +F    +Q+W++AL +  DL G+       + A+ +++   I  
Sbjct: 139 RHQTGCYKKAFRKHANKFDGQTIQNWKDALKKVGDLKGWHIGKNDKQGAIADKVSADIWS 198

Query: 178 RLD 180
            + 
Sbjct: 199 HIS 201

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana} Length = 176

 Score =  272 bits (699), Expect = 5e-90
 Identities = 76/182 (41%), Positives = 103/182 (56%), Gaps = 12/182 (6%)

Query: 3   SSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDD-LRRGDEIS 61
           SS            KYDVFLSF G DTR +F S LY  L R ++ TF DD  L  G   S
Sbjct: 2   SSHTAT--------KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFS 53

Query: 62  QSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQ 121
             L   IE S  ++++ SE+YA+S WCLDEL+ I++ +K+ +  V+P+FY V+P+HVR Q
Sbjct: 54  PELKSPIEVSRFAVVVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQ 113

Query: 122 TGNFGDSFLKLEERF-PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAILKRLD 180
           TG   + F K   R  P+K+  WR ALT  A LSG  S     +S L+++I N I  +  
Sbjct: 114 TGVLAEQFKKHASREDPEKVLKWRQALTNFAQLSGDCSG--DDDSKLVDKIANEISNKKT 171

Query: 181 DT 182
             
Sbjct: 172 IY 173

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222} Length = 154

 Score =  208 bits (531), Expect = 3e-65
 Identities = 30/150 (20%), Positives = 60/150 (40%), Gaps = 4/150 (2%)

Query: 1   MASSSHPYASLTNPEI-KYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGD 58
           M  ++ P  +        +D+F+S   ED +  F   L   L     E + DD  LR GD
Sbjct: 3   MKPTAGPTTNADLTSAPPHDIFISHAWED-KADFVEALAHTLRAAGAEVWYDDFSLRPGD 61

Query: 59  EISQSLLDAIEASSISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVDPSHV 118
            + +S+   + +S   I++ S  +    W   EL  + + +      ++P++++V    V
Sbjct: 62  SLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEV 121

Query: 119 RKQTGNFGDSFLKLEERF-PDKMQSWRNAL 147
              +    D           D++ +   A+
Sbjct: 122 ASFSPTMADKLAFNTSTKSVDEIVADLMAI 151

>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 =  150 bits (380), Expect = 1e-39
 Identities = 64/427 (14%), Positives = 136/427 (31%), Gaps = 53/427 (12%)

Query: 116 SHVRKQTGNFGDSFLKLEERFPDKMQSWRNALTEAADLSGFDSLVVSPESALIEEIVNAI 175
              R+Q    G       + F    QS      E       +   +     +  +    +
Sbjct: 59  RIYRRQASELGPLI----DFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQM 114

Query: 176 LKRLDDTFHSENEDLVGVRLPMKE--IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN 233
           L R     +   +    +R    +  I+ L      + + L + G  G GK+ IA    +
Sbjct: 115 LDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALS 174

Query: 234 K----ISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLN------ 283
           K    I  ++    + ++   A +     DL   +L  L ++ ++ NF + +        
Sbjct: 175 KSDQLIGINYDSIVWLKDSGTAPK--STFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLK 232

Query: 284 --FQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANC-GVDE 340
               +  + R   L VFDDV     I+             R ++TTRD ++        E
Sbjct: 233 RMICNALIDRPNTLFVFDDVVQEETIR------WAQELRLRCLVTTRDVEISNAASQTCE 286

Query: 341 VYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRR 400
             ++  L  D+       +        E   ++  KTI+ + G P  L +  +    K  
Sbjct: 287 FIEVTSLEIDECYDFLEAYGMPMPVG-EKEEDVLNKTIELSSGNPATLMMFFKSCEPKTF 345

Query: 401 EVWENAKSKWETAP-----------PKGIQDALKISYDGLDDKEQNIFLDIACFFIDED- 448
           E      +K E+              K +  AL+   + L D++++            D 
Sbjct: 346 EKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDI 405

Query: 449 ----------RDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIE---MHYLLRAMGR 495
                      D  +   +  +      ++ L  +  +       +    + +++    +
Sbjct: 406 PVKLWSCVIPVDICSNEEEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLK 465

Query: 496 EIVRQES 502
            +V  ++
Sbjct: 466 HVVDAQT 472

>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 =  146 bits (368), Expect = 4e-37
 Identities = 100/571 (17%), Positives = 179/571 (31%), Gaps = 138/571 (24%)

Query: 28  DTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSR 86
           D       + Y  +     + F+D+ D +   ++       +    I  II     A S 
Sbjct: 8   DFETGEHQYQYKDILSVFEDAFVDNFDCK---DVQDMPKSILSKEEIDHII-MSKDAVSG 63

Query: 87  WCLDELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFP----DKMQS 142
                L   L  K+E    +V  F  V+     +    F  S +K E+R P         
Sbjct: 64  --TLRLFWTLLSKQEE---MVQKF--VEEVL--RINYKFLMSPIKTEQRQPSMMTRMYIE 114

Query: 143 WRNALTEAADLSGFDSLVVS-PESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIE 201
            R+ L    D   F    VS  +     ++  A+L+                        
Sbjct: 115 QRDRLYN--DNQVFAKYNVSRLQ--PYLKLRQALLE------------------------ 146

Query: 202 SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN--KISRHFSGSYFARNVREAEETCRLGD 259
             LR        + I G+ G GKT +A  +    K+        F  N++       + +
Sbjct: 147 --LRPAK----NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 260 LRQQLLSTLLNDGN--VKNFLNTDLNFQS-----RRLTR----KKVLIVFDDVDHPRQIK 308
           + Q+LL  +  +      +  N  L   S     RRL +    +  L+V  +V + +   
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW- 259

Query: 309 ILVGRLDLFASGSRIIITTRDRQVLANCGVDEVYQ--MEE----LVHDDALRLFSRHAFG 362
                 + F    +I++TTR +QV             ++     L  D+   L  +    
Sbjct: 260 ------NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK-YLD 312

Query: 363 ---GDHPHESHTELACKTIKYARGVPLALEVLGRYLY-GKRREVWENAKSKWETAPPKGI 418
               D P E        T       P  L ++   +  G     W+N    W+      +
Sbjct: 313 CRPQDLPRE-----VLTTN------PRRLSIIAESIRDGLAT--WDN----WKHVNCDKL 355

Query: 419 QDALKISYDGLDDKE-QNIFLDIACFFIDEDRDTATKFL---------DDCEFFAT---- 464
              ++ S + L+  E + +F  ++ F         T  L          D          
Sbjct: 356 TTIIESSLNVLEPAEYRKMFDRLSVF--PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 465 -SAIEVLVDKHLITI---------SVLNKIEMHYLLRAMGREIVRQESTNDPGKR----- 509
            S +E    +  I+I          + N+  +H  +      I +   ++D         
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH-YNIPKTFDSDDLIPPYLDQY 472

Query: 510 --SRLWHH---KEVYKILSENRVSNNDFSFL 535
             S + HH    E  + ++  R+   DF FL
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFL 503

>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 =  127 bits (321), Expect = 2e-31
 Identities = 52/282 (18%), Positives = 99/282 (35%), Gaps = 38/282 (13%)

Query: 186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN---KISRHFSGS 242
                V  +  +  I+  L         + I G+ G GK+ +A         +   F G 
Sbjct: 122 RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGG 181

Query: 243 YFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR------KKVLI 296
               +V + +++  L  L+  L + L  D +    L  ++     RL         + L+
Sbjct: 182 VHWVSVGKQDKSGLLMKLQ-NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLL 240

Query: 297 VFDDV---DHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCG--VDEVYQMEELVHDD 351
           + DDV               L  F S  +I++TTRD+ V  +       V     L  + 
Sbjct: 241 ILDDVWDSWV----------LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEK 290

Query: 352 ALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRRE---VWENAKS 408
            L + S              E A   IK  +G PL + ++G  L           +  ++
Sbjct: 291 GLEILSLFVN---MKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQN 347

Query: 409 K-WETAPPK------GIQDALKISYDGLDDKEQNIFLDIACF 443
           K ++            + +A+ IS + L +  ++ + D++  
Sbjct: 348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSIL 389

>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 = 86.8 bits (215), Expect = 5e-18
 Identities = 60/325 (18%), Positives = 121/325 (37%), Gaps = 49/325 (15%)

Query: 214 LGIWGIGGIGKTTIAGAI---FNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN 270
           + I+G+ G GK+ +A       + +   FSG     ++ + +++  L  L Q L   L  
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKL-QNLCMRLDQ 208

Query: 271 DGNVKNFLNTDLNFQSRRLT------RKKVLIVFDDVDHPRQIKILVGRLDLFASGSRII 324
           + +    L  ++     RL         + L++ DDV  P         L  F +  +I+
Sbjct: 209 EESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWV-------LKAFDNQCQIL 261

Query: 325 ITTRDRQVLANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYAR 382
           +TTRD+ V  +       V     L  +  L + S      +   E     A   IK  +
Sbjct: 262 LTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFV---NMKKEDLPAEAHSIIKECK 318

Query: 383 GVPLALEVLG----------RYLYGKRREVWENAKSKWETAPPKGIQDALKISYDGLDDK 432
           G PL + ++G           Y   + +        K  +   + + +A+ IS + L + 
Sbjct: 319 GSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLRED 378

Query: 433 EQNIFLDIACFFIDED--RDTATKFLDDCEFFATSAIEVLVDKHLITIS--------VLN 482
            ++ + D++    D            D         ++  V+K L+  +         L+
Sbjct: 379 IKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLH 438

Query: 483 KIEMHYL-------LRAMGREIVRQ 500
            +++ +L       L+ + R++V Q
Sbjct: 439 DLQVDFLTEKNRSQLQDLHRKMVTQ 463

>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 = 70.5 bits (173), Expect = 9e-15
 Identities = 23/113 (20%), Positives = 41/113 (36%), Gaps = 9/113 (7%)

Query: 17  KYDVFLSFGGEDTRESFTSHLYSAL--SRETVETFIDD-DLRRGDEISQSLLDAIEASSI 73
            YDV +    ED        L S L  S  ++  F+   D   G  I   L  A+ +S  
Sbjct: 10  DYDVCVCHSEED--LVAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHC 67

Query: 74  SIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVD----PSHVRKQT 122
            +++ +  +    WC  ++L+ L          +P+   +     P  +R   
Sbjct: 68  RVLLITPGFLQDPWCKYQMLQALTEAPGAEGCTIPLLSGLSRAAYPPELRFMY 120

>2j67_A TOLL like receptor 10; TIR, IL-1, TLR10, membrane, innate immunity, immune response, leucine-rich repeat, glycoprotein, transmembrane; 2.20A {Homo sapiens} PDB: 1fyv_A Length = 178

 Score = 47.2 bits (112), Expect = 2e-06
 Identities = 20/107 (18%), Positives = 44/107 (41%), Gaps = 5/107 (4%)

Query: 15  EIKYDVFLSFGGEDTRESFTSHLYSALSRE--TVETFIDD-DLRRGDEISQSLLDAIEAS 71
            +++  F+S+   D      + L   L +E  ++   + +     G  IS++++  IE S
Sbjct: 33  NVRFHAFISYSEHD-SLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKS 91

Query: 72  SISIIIFSESYASSRWCLDELLKIL-ECKKEYAQIVVPVFYRVDPSH 117
             SI + S ++  + WC  E          E +  ++ +     P +
Sbjct: 92  YKSIFVLSPNFVQNEWCHYEFYFAHHNLFHENSDHIILILLEPIPFY 138

>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 = 44.7 bits (105), Expect = 1e-05
 Identities = 22/119 (18%), Positives = 38/119 (31%), Gaps = 14/119 (11%)

Query: 17  KYDVFLSFGGEDTR---------ESFTSHLYSAL--SRETVETFIDD-DLRRGDEISQSL 64
            YD +LS+   D           E F   +   +       + FI D DL       + +
Sbjct: 2   DYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDV 61

Query: 65  LDAIEASSISIIIFSESYA-SSRWCLDELLKIL-ECKKEYAQIVVPVFYRVDPSHVRKQ 121
              ++ S   II+ + +Y     W + EL   L          V+ +        +  Q
Sbjct: 62  ARCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELRGIMNYQ 120

>2js7_A Myeloid differentiation primary response protein MYD88; MYD88_human, TIR domain, TOLL like receptor adaptor domain, innate immune signaling; NMR {Homo sapiens} PDB: 2z5v_A Length = 160

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 18/115 (15%), Positives = 43/115 (37%), Gaps = 7/115 (6%)

Query: 11  LTNPEIKYDVFLSFGGEDTRESFTSHLYSAL--SRETVETFIDD-DLRRGDEISQSLLDA 67
           L +   ++D F+ +   D    F   +   L  +   ++  + D D+  G  +     + 
Sbjct: 10  LGHMPERFDAFICYCPSD--IQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASEL 67

Query: 68  IEASSI-SIIIFSESYASSRWCLDELLKIL-ECKKEYAQIVVPVFYRVDPSHVRK 120
           IE      +++ S+ Y  S+ C  +    L      + + ++P+ Y+        
Sbjct: 68  IEKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPS 122

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 384

 Score = 41.3 bits (96), Expect = 7e-04
 Identities = 39/224 (17%), Positives = 78/224 (34%), Gaps = 32/224 (14%)

Query: 197 MKEIESLLRT-----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREA 251
           +++    +R         +       G+ G GKT ++  IFN+I          ++V++A
Sbjct: 29  LRDAAIAIRYFVKNEVKFSNL---FLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQA 85

Query: 252 EETC-RLGDLRQQLLSTLLNDGNVKNFLNT------DLNFQSRRLTRKKVLIVFDDVDH- 303
              C  +G   Q +LS+L       +           ++         + +I  D+VD  
Sbjct: 86  YVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTL 145

Query: 304 ---PRQIKILVGRLDLFASGSRIIITTR-------DRQVLANCG---VDEVYQMEELVHD 350
                   +L   L   A+ S I+I+         + +VL++ G   + + Y  E+L   
Sbjct: 146 VKRRGGDIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLK-- 203

Query: 351 DALRLFSRHAFGGDHPHESHTELACKTIKYARGVP-LALEVLGR 393
             L  ++ +        +              G    A+ +L R
Sbjct: 204 FILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFR 247

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	538
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	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
3h16_A	154	TIR protein; bacteria TIR domain, signaling protei	99.96
3ub2_A	146	TOLL/interleukin-1 receptor domain-containing ADA	99.91
2js7_A	160	Myeloid differentiation primary response protein M	99.86
1fyx_A	149	TOLL-like receptor 2; beta-alpha-beta fold, signal	99.86
2j67_A	178	TOLL like receptor 10; TIR, IL-1, TLR10, membrane,	99.85
1t3g_A	159	X-linked interleukin-1 receptor accessory protein-	99.85
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.84
2fna_A	357	Conserved hypothetical protein; structural genomic	99.8
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.75
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.7
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.67
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.66
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.64
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.57
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.4
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.36
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.22
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.22
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.22
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.1
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.02
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.98
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.88
3bos_A	242	Putative DNA replication factor; P-loop containing	98.86
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.85
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.84
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.84
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.82
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.78
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.77
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.76
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.75
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.73
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.71
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.68
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.66
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.66
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.65
3pvs_A	447	Replication-associated recombination protein A; ma	98.65
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.64
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.64
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.61
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.6
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.59
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.59
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.48
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.48
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.46
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.41
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.35
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.34
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.34
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.33
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.31
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.27
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.25
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.25
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.22
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.21
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.15
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.14
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	98.13
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.1
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.1
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.1
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.09
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.09
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.08
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	98.05
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.0
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.0
3co5_A	143	Putative two-component system transcriptional RES	97.98
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.92
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.83
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.75
1eiw_A	111	Hypothetical protein MTH538; CHEY-like fold, flavo	97.74
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.74
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.72
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	97.72
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.7
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.68
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.66
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.57
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.36
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.36
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.3
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.24
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.22
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.19
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	97.18
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	97.06
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	97.02
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.0
2qgz_A	308	Helicase loader, putative primosome component; str	96.99
3io5_A	333	Recombination and repair protein; storage dimer, i	96.93
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.9
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.9
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.88
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	96.88
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.85
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.77
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.74
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.73
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.71
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.69
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.66
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.64
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.62
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.57
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.56
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.55
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.47
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.45
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.43
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.43
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.37
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.32
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	96.32
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.28
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.27
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.24
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.24
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.22
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.21
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.2
3hyn_A	189	Putative signal transduction protein; DUF1863 fami	96.18
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.11
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	96.11
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.11
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.03
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.03
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.03
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.0
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.99
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.92
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.92
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.9
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.88
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.88
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.88
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	95.87
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	95.83
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.82
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.78
1tue_A	212	Replication protein E1; helicase, replication, E1E	95.78
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.77
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.76
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.76
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.74
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.74
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	95.73
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.72
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.7
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.68
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.67
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.66
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.64
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.62
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.62
1via_A	175	Shikimate kinase; structural genomics, transferase	95.59
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.58
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.56
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.54
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.52
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.51
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.5
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	95.46
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.45
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.44
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.44
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.43
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.42
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.41
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.41
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.4
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.4
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.4
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.39
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.39
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	95.37
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.37
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.34
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.32
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.31
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.28
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.26
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.26
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.25
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.24
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.23
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.22
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.21
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.2
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	95.19
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.18
2xxa_A	433	Signal recognition particle protein; protein trans	95.18
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.18
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.17
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.13
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.09
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.09
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.03
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.02
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.0
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.99
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.99
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.98
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	94.98
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.97
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.97
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.96
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	94.93
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.91
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.89
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	94.88
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	94.88
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.88
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.87
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	94.87
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.85
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.84
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.84
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	94.83
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.79
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.79
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.77
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.76
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.72
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.72
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	94.71
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.69
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.68
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	94.66
3ice_A	422	Transcription termination factor RHO; transcriptio	94.65
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.65
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.64
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.59
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.58
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.56
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.55
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	94.54
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.53
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.51
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.47
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.47
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.42
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	94.41
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.4
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.39
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	94.38
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.38
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.36
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	94.34
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.34
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.26
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	94.26
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	94.25
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.24
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.21
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.2
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.17
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	94.17
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.16
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.16
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.15
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.13
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.1
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.08
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.03
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.0
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.0
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.96
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.94
2og2_A	359	Putative signal recognition particle receptor; nuc	93.93
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.85
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	93.84
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.81
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	93.81
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.78
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.77
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.75
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	93.71
1b0u_A	262	Histidine permease; ABC transporter, transport pro	93.66
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	93.66
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.64
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	93.57
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.56
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	93.55
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.51
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	93.47
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.46
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	93.45
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	93.42
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.37
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.37
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.35
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.34
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.33
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.31
1g6h_A	257	High-affinity branched-chain amino acid transport	93.3
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	93.26
1sgw_A	214	Putative ABC transporter; structural genomics, P p	93.26
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.25
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.25
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.24
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.23
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.22
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.2
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.19
3end_A	307	Light-independent protochlorophyllide reductase ir	93.18
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.17
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.17
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.17
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.16
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.13
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.13
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.12
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	93.06
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.03
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.02
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	92.91
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	92.89
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	92.87
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	92.87
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	92.82
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	92.75
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	92.7
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.69
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.51
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	92.5
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	92.48
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	92.44
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	92.39
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	92.38
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.35
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.33
3kta_A	182	Chromosome segregation protein SMC; structural mai	92.33
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	92.31
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.31
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.31
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	92.26
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.23
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.21
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	92.16
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	92.1
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	92.09
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	92.07
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.01
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	92.01
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	92.0
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	91.99
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	91.98
2ged_A	193	SR-beta, signal recognition particle receptor beta	91.91
2wji_A	165	Ferrous iron transport protein B homolog; membrane	91.9
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	91.86
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.84
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	91.81
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.79
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.76
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.76
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.69
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	91.68
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	91.67
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	91.66
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.6
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	91.5
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.5
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	91.5
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	91.37
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	91.37
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	91.33
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	91.33
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	91.31
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.26
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	91.23
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	91.18
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	91.17
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.05
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.05
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	91.03
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	90.97
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.86
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	90.83
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	90.79
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	90.77
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.76
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	90.73
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	90.69
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	90.68
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	90.61
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	90.59
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	90.58
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	90.58
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	90.56
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	90.54
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	90.53
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	90.53
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	90.52
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	90.52
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	90.43
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	90.42
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	90.41
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	90.41
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	90.4
1nrj_B	218	SR-beta, signal recognition particle receptor beta	90.39
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	90.35
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	90.35
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	90.33
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	90.31
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	90.3
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	90.26
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.26
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	90.24
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	90.21
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	90.17
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	90.14
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	90.1
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	90.09
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	90.09
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	90.07
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	90.06
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	90.01
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	90.01
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	89.98
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	89.98
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	89.97
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	89.92
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	89.91
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	89.91
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	89.83
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	89.79
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	89.77
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	89.77
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	89.73
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	89.72
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	89.68
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	89.65
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	89.61
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	89.6
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	89.55
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	89.5
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	89.48
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	89.46
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	89.46
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	89.44
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	89.42
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	89.41
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	89.4
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	89.4
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	89.39
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	89.37
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	89.34
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	89.32
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	89.3
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	89.29
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	89.27
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	89.25
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	89.24
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	89.23
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	89.23
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	89.23
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	89.21
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	89.2
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	89.17
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	89.14
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	89.14
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	89.1
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	89.06
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	89.02
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	89.0
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	88.95
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	88.93
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	88.89
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	88.89
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	88.87
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	88.85
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	88.84
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	88.83
2fh5_B	214	SR-beta, signal recognition particle receptor beta	88.82
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	88.75
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	88.73
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	88.71
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	88.7
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	88.67
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	88.65
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	88.61
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	88.59
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	88.54
3llu_A	196	RAS-related GTP-binding protein C; structural geno	88.54
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	88.53
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	88.49
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	88.47
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	88.45

>3ozi_A L6TR; plant TIR domain, plant protein; 2.30A {Linum usitatissimum}

Probab=100.00  E-value=5.5e-47  Score=338.28  Aligned_cols=181  Identities=40%  Similarity=0.693  Sum_probs=157.5

Q ss_pred             CCCCCCCCCCCCCCCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEec
Q 009306            1 MASSSHPYASLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFS   79 (538)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S   79 (538)
                      ||.++|+++|++.+.++|||||||+|+|+|..|+.||+++|+++||++|+|+ ++++|+.|.++|.+||++|+++|+|||
T Consensus        19 ~~~~~s~~~s~~~~~~~yDVFISfrg~D~r~~Fv~~L~~aL~~~GI~~f~D~~el~~G~~I~~~l~~aIe~Sri~IvV~S   98 (204)
T 3ozi_A           19 DAISDSTNPSGSFPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVPIIS   98 (204)
T ss_dssp             ---------------CCCCEEEEECHHHHTTTHHHHHHHHHHHTTCCEEEEETTTCCGGGTTTTHHHHHHHCSEEEEEEC
T ss_pred             cccccCCCCcCCCCCcCCeEEEeccccCCCHHHHHHHHHHHHHCCCcEEEeCCccCCCCchHHHHHHHHHhCcEeeEEEE
Confidence            4667777778888899999999999999998999999999999999999998 999999999999999999999999999


Q ss_pred             cCcccchhhHHHHHHHHHHHhh-cCCeEEEEEEeecCCcccccCCchHHHHHHHHhhCh-hhHHHHHHHhhhhccccCcc
Q 009306           80 ESYASSRWCLDELLKILECKKE-YAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERFP-DKMQSWRNALTEAADLSGFD  157 (538)
Q Consensus        80 ~~y~~s~~c~~El~~~~~~~~~-~~~~v~pv~~~v~~~~v~~~~~~~~~~~~~~~~~~~-~~~~~w~~al~~~~~~~g~~  157 (538)
                      ++|++|.||++||.+|++|.+. ++++|+||||+|+|++||+|+|+|+++|.+|++++. +++++|+.||+++++++||+
T Consensus        99 ~nYa~S~WCl~EL~~I~e~~~~~~~~~ViPIFY~VdPs~Vr~q~g~fg~af~~~~~~~~~~~v~~Wr~AL~~va~lsG~~  178 (204)
T 3ozi_A           99 SGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDGQTIQNWKDALKKVGDLKGWH  178 (204)
T ss_dssp             TTGGGCHHHHHHHHHHHHHHHHCTTSEECCEEESSCHHHHHHTCTTHHHHHHHHTTTSCHHHHHHHHHHHHHHHTSCBEE
T ss_pred             cccccCcHHHHHHHHHHHHHHhcCCeeeEEEEeecCHHHHHhccccHHHHHHHHHHhhCHHHHHHHHHHHHHHhccCcee
Confidence            9999999999999999999865 578999999999999999999999999999998875 45999999999999999999


Q ss_pred             cCCCChhhHHHHHHHHhhhccccc
Q 009306          158 SLVVSPESALIEEIVNAILKRLDD  181 (538)
Q Consensus       158 ~~~~~~e~~~i~~i~~~~~~~~~~  181 (538)
                      +.....+.+++++|+++++++++.
T Consensus       179 ~~~~~~e~~~i~~Iv~di~~kl~~  202 (204)
T 3ozi_A          179 IGKNDKQGAIADKVSADIWSHISK  202 (204)
T ss_dssp             ECTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhcc
Confidence            988776899999999999988753

>3jrn_A AT1G72930 protein; TIR domain arabidopsis thaliana, plant protein; 2.00A {Arabidopsis thaliana}

Probab=100.00  E-value=3.2e-45  Score=322.34  Aligned_cols=169  Identities=44%  Similarity=0.717  Sum_probs=142.1

Q ss_pred             CCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHH
Q 009306           14 PEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDEL   92 (538)
Q Consensus        14 ~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El   92 (538)
                      ..++|||||||+|+|+|++|++||+++|+++||++|+|+ ++++|+.|.++|.+||++|+++|+|||+||++|+||++||
T Consensus         5 ~~~~yDVFiSfrg~D~r~~Fv~~L~~~L~~~gi~~f~D~~~l~~G~~i~~~l~~aIe~Sri~IvV~S~ny~~S~WCl~EL   84 (176)
T 3jrn_A            5 TATKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVVVVSENYAASSWCLDEL   84 (176)
T ss_dssp             --CCEEEEEEECHHHHTTTHHHHHHHHHHHTTCCEECCCC--------------CCTTEEEEEEEECTTTTTCHHHHHHH
T ss_pred             CCCCCeEEEECcCcccChHHHHHHHHHHHHCCCEEEEEcccccCCCchHHHHHHHHHhCCEEEEEecCCcCCChhHHHHH
Confidence            568999999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCeEEEEEEeecCCcccccCCchHHHHHHHHhhC-hhhHHHHHHHhhhhccccCcccCCCChhhHHHHHH
Q 009306           93 LKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKLEERF-PDKMQSWRNALTEAADLSGFDSLVVSPESALIEEI  171 (538)
Q Consensus        93 ~~~~~~~~~~~~~v~pv~~~v~~~~v~~~~~~~~~~~~~~~~~~-~~~~~~w~~al~~~~~~~g~~~~~~~~e~~~i~~i  171 (538)
                      .+|++|.+.++++|+||||+|+|++||+|+|+|+++|.+|+.+. .+++++|+.||+++++++|+++. .+ |+++|++|
T Consensus        85 ~~i~~~~~~~~~~ViPIfy~V~ps~Vr~q~g~fg~af~~~~~~~~~~~~~~Wr~AL~~va~~~G~~~~-~~-e~~~i~~I  162 (176)
T 3jrn_A           85 VTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASREDPEKVLKWRQALTNFAQLSGDCSG-DD-DSKLVDKI  162 (176)
T ss_dssp             HHHHHHHHTTSCEEEEEECSSCHHHHHHTCTHHHHHHHHHHTTSCHHHHHHHHHHHHHHTTSCCEECC-SC-HHHHHHHH
T ss_pred             HHHHhhhccCCCEEEEEEecCCHHHhhhccCcHHHHHHHHHhccCHHHHHHHHHHHHHHhcccceecC-CC-HHHHHHHH
Confidence            99999998889999999999999999999999999999998873 35699999999999999999983 34 99999999


Q ss_pred             HHhhhccccccCC
Q 009306          172 VNAILKRLDDTFH  184 (538)
Q Consensus       172 ~~~~~~~~~~~~~  184 (538)
                      ++++.+.+.+++|
T Consensus       163 v~~v~~~l~~~~~  175 (176)
T 3jrn_A          163 ANEISNKKTIYAT  175 (176)
T ss_dssp             HHHHHTTCC----
T ss_pred             HHHHHHHhcCCCC
Confidence            9999999887654

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=3.9e-40  Score=351.47  Aligned_cols=300  Identities=16%  Similarity=0.140  Sum_probs=224.6

Q ss_pred             eeccchhHHHHHhhhcC-CCCceEEEEeccCCCchhHHHHHHHH----hhccceeeEEEEeehhhhhhcCChHHHHHHHH
Q 009306          191 VGVRLPMKEIESLLRTG-STNVYKLGIWGIGGIGKTTIAGAIFN----KISRHFSGSYFARNVREAEETCRLGDLRQQLL  265 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~-~~~~~~v~I~G~~GiGKTtLa~~~~~----~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~  265 (538)
                      +||+.++++|.++|..+ ....++|+|+||||+||||||+++|+    +++.+|++++|+. ++.... .++..+++.++
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~-vs~~~~-~~~~~~~~~il  208 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK-DSGTAP-KSTFDLFTDIL  208 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE-CCCCST-THHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEE-ECCCCC-CCHHHHHHHHH
Confidence            49999999999999754 34589999999999999999999996    6888999999995 332211 35778889999


Q ss_pred             HHHhcCCC--CC-----CchhhcHHHHHHHhcCC-CeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhhhcC
Q 009306          266 STLLNDGN--VK-----NFLNTDLNFQSRRLTRK-KVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLANCG  337 (538)
Q Consensus       266 ~~l~~~~~--~~-----~~~~~~~~~l~~~l~~k-~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~  337 (538)
                      .+++....  ..     .+...+...+++.+.++ ++||||||||+..++ .+..     .+|++||||||+..++..++
T Consensus       209 ~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~  282 (549)
T 2a5y_B          209 LMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAAS  282 (549)
T ss_dssp             HHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGCC
T ss_pred             HHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHcC
Confidence            98876532  11     22344578889999996 999999999998876 3332     27999999999999888765


Q ss_pred             -CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHH-hhcCCC
Q 009306          338 -VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSK-WETAPP  415 (538)
Q Consensus       338 -~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~-l~~~~~  415 (538)
                       ...+|+|++|+.+++++||.++++.... .+...+.+.+|+++|+|+||||+.+|+.|+.+.. .|...+.. +.....
T Consensus       283 ~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~-~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~w-~~~~~l~~~l~~~~~  360 (549)
T 2a5y_B          283 QTCEFIEVTSLEIDECYDFLEAYGMPMPV-GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTF-EKMAQLNNKLESRGL  360 (549)
T ss_dssp             SCEEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSH-HHHHHHHHHHHHHCS
T ss_pred             CCCeEEECCCCCHHHHHHHHHHHhcCCCC-chhHHHHHHHHHHHhCCChHHHHHHHHHhccchH-HHHHHhHHHhhcccH
Confidence             3468999999999999999999876532 3567788999999999999999999999987743 33333332 222123


Q ss_pred             CcHHHHHHHhHhCCC-----------HHhHHHhhccccccCCCCHHHHHHHHHhC--CCC-----------hHHHHHHHh
Q 009306          416 KGIQDALKISYDGLD-----------DKEQNIFLDIACFFIDEDRDTATKFLDDC--EFF-----------ATSAIEVLV  471 (538)
Q Consensus       416 ~~v~~~l~~s~~~L~-----------~~~k~~l~~la~f~~~~~~~~l~~l~~~~--~~~-----------~~~~l~~L~  471 (538)
                      ..+..++..||+.|+           +.++.+|.+||+||.+++.+  ..+|.+.  |+.           ...+++.|+
T Consensus       361 ~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~--i~~w~a~~~G~i~~~~~~~~~~~~~~~l~~L~  438 (549)
T 2a5y_B          361 VGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP--VKLWSCVIPVDICSNEEEQLDDEVADRLKRLS  438 (549)
T ss_dssp             STTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE--HHHHHHHSCC-------CCCTHHHHHHHHHTT
T ss_pred             HHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee--eeeeeeeccceeccCCCCCCHHHHHHHHHHHH
Confidence            344444455555554           44455555999999887766  5566665  332           223799999


Q ss_pred             hCCceeEecC---CcEEecHHHHHHHHHHHhhcC
Q 009306          472 DKHLITISVL---NKIEMHYLLRAMGREIVRQES  502 (538)
Q Consensus       472 ~~~Li~~~~~---~~~~~H~lv~~~~~~~~~~~~  502 (538)
                      ++|||+....   ++|.|||+||+||++++.+++
T Consensus       439 ~rsLl~~~~~~~~~~~~mHdlv~~~a~~~~~~~~  472 (549)
T 2a5y_B          439 KRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQT  472 (549)
T ss_dssp             TBSSCSEEECSSSCEEECCHHHHHHHHTTSCTHH
T ss_pred             HcCCeeEecCCCceEEEeChHHHHHHHHHHHHHH
Confidence            9999997543   469999999999998876653

>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=100.00  E-value=1.2e-36  Score=356.19  Aligned_cols=307  Identities=20%  Similarity=0.243  Sum_probs=244.2

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh---hccceeeEE-EEeehhhhhhcCCh
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK---ISRHFSGSY-FARNVREAEETCRL  257 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~---~~~~f~~~~-~~~~~~~~~~~~~~  257 (538)
                      ..|..+..||||+.++++|.++|....++.++++|+||||+||||||++++++   ...+|...+ |+. +.... ....
T Consensus       118 ~~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~-~~~~~-~~~~  195 (1249)
T 3sfz_A          118 GVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS-IGKQD-KSGL  195 (1249)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEE-CCSCC-HHHH
T ss_pred             CCCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEE-ECCcC-chHH
Confidence            34566788999999999999999766667899999999999999999999987   355576555 554 33211 1223


Q ss_pred             HHHHHHHHHHHhcCCC----CCCchhhcHHHHHHHhcCC--CeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          258 GDLRQQLLSTLLNDGN----VKNFLNTDLNFQSRRLTRK--KVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~----~~~~~~~~~~~l~~~l~~k--~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ...+..++..+.....    .....+.....++..+.++  ++||||||+|+..+++.+       ++|++||||||++.
T Consensus       196 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~  268 (1249)
T 3sfz_A          196 LMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKS  268 (1249)
T ss_dssp             HHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTT
T ss_pred             HHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHH
Confidence            3445556666654332    1245666777777777766  999999999998776543       67999999999998


Q ss_pred             hhhh-cCCCeeEEcCC-CCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 009306          332 VLAN-CGVDEVYQMEE-LVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSK  409 (538)
Q Consensus       332 ~~~~-~~~~~~~~l~~-L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~  409 (538)
                      ++.. ......+++++ |+.+|+++||...++..   .+...+.+.+|+++|+|+||||+++|++|+.++ ..|...+..
T Consensus       269 ~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~---~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~  344 (1249)
T 3sfz_A          269 VTDSVMGPKHVVPVESGLGREKGLEILSLFVNMK---KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQ  344 (1249)
T ss_dssp             TTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSC---STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHH
T ss_pred             HHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCC---hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHH
Confidence            8744 34557889996 99999999999988332   234456789999999999999999999998766 468888888


Q ss_pred             hhcCCC-----------CcHHHHHHHhHhCCCHHhHHHhhccccccCC--CCHHHHHHHHHhCCCChHHHHHHHhhCCce
Q 009306          410 WETAPP-----------KGIQDALKISYDGLDDKEQNIFLDIACFFID--EDRDTATKFLDDCEFFATSAIEVLVDKHLI  476 (538)
Q Consensus       410 l~~~~~-----------~~v~~~l~~s~~~L~~~~k~~l~~la~f~~~--~~~~~l~~l~~~~~~~~~~~l~~L~~~~Li  476 (538)
                      +.....           ..+..+|..||+.|++++|.||++||+||++  ++.+.+..+|..++......++.|+++|||
T Consensus       345 l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~~~~~~~~l~~L~~~sl~  424 (1249)
T 3sfz_A          345 LQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLL  424 (1249)
T ss_dssp             HHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSC
T ss_pred             HhhhhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCCHHHHHHHHHHHHhccce
Confidence            755432           3588999999999999999999999999986  578899999987777788899999999999


Q ss_pred             eEecCCc---EEecHHHHHHHHHHHhhc
Q 009306          477 TISVLNK---IEMHYLLRAMGREIVRQE  501 (538)
Q Consensus       477 ~~~~~~~---~~~H~lv~~~~~~~~~~~  501 (538)
                      +...++.   |+||+++|+|+++.+.++
T Consensus       425 ~~~~~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          425 FCNRNGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             EEEESSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             EEecCCCceEEEecHHHHHHHHhhhhHH
Confidence            9876665   999999999999987654

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=6.3e-36  Score=323.17  Aligned_cols=333  Identities=18%  Similarity=0.205  Sum_probs=246.4

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh---cccee-eEEEEeehhhhhhcCCh
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI---SRHFS-GSYFARNVREAEETCRL  257 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~---~~~f~-~~~~~~~~~~~~~~~~~  257 (538)
                      ..|..+..||||+.++++|.++|....++.++++|+||||+||||||.+++++.   ..+|+ .++|+.. ..... ..+
T Consensus       118 ~~P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~-~~~~~-~~~  195 (591)
T 1z6t_A          118 GVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSV-GKQDK-SGL  195 (591)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEE-ESCCH-HHH
T ss_pred             CCCCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEEC-CCCch-HHH
Confidence            345667889999999999999998655568899999999999999999999864   66785 5677653 22111 112


Q ss_pred             HHHHHHHHHHHhcCC----CCCCchhhcHHHHHHHhcC--CCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          258 GDLRQQLLSTLLNDG----NVKNFLNTDLNFQSRRLTR--KKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~----~~~~~~~~~~~~l~~~l~~--k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ...+..+...+....    ......+.....+...+.+  +++||||||+|+..+++.+       +++++||||||+..
T Consensus       196 ~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~  268 (591)
T 1z6t_A          196 LMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKS  268 (591)
T ss_dssp             HHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGG
T ss_pred             HHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcH
Confidence            222223333443211    1124455666777777765  7899999999997766532       57899999999998


Q ss_pred             hhhhcCCCeeEEc---CCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHH
Q 009306          332 VLANCGVDEVYQM---EELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKS  408 (538)
Q Consensus       332 ~~~~~~~~~~~~l---~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~  408 (538)
                      ++..+. ...+++   ++|+.+|+.+||...++..   .....+.+.+|+++|+|+||||+++|+.++.+. ..|...+.
T Consensus       269 ~~~~~~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~---~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-~~w~~~l~  343 (591)
T 1z6t_A          269 VTDSVM-GPKYVVPVESSLGKEKGLEILSLFVNMK---KADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLK  343 (591)
T ss_dssp             GGTTCC-SCEEEEECCSSCCHHHHHHHHHHHHTSC---GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-TCHHHHHH
T ss_pred             HHHhcC-CCceEeecCCCCCHHHHHHHHHHHhCCC---cccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-hhHHHHHH
Confidence            776543 334554   5899999999999988431   222345789999999999999999999997654 36888888


Q ss_pred             HhhcCC-----------CCcHHHHHHHhHhCCCHHhHHHhhccccccCC--CCHHHHHHHHHhCCCChHHHHHHHhhCCc
Q 009306          409 KWETAP-----------PKGIQDALKISYDGLDDKEQNIFLDIACFFID--EDRDTATKFLDDCEFFATSAIEVLVDKHL  475 (538)
Q Consensus       409 ~l~~~~-----------~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~~--~~~~~l~~l~~~~~~~~~~~l~~L~~~~L  475 (538)
                      .+....           ..++..++..||+.|++++|.||+++|||+.+  ++.+.+..+|..+.......++.|+++||
T Consensus       344 ~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~~~~~~~~l~~L~~~~L  423 (591)
T 1z6t_A          344 QLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSL  423 (591)
T ss_dssp             HHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTS
T ss_pred             HHHHhHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccCHHHHHHHHHHHHhCcC
Confidence            776432           13688999999999999999999999999875  67788888897665567788999999999


Q ss_pred             eeEecCC---cEEecHHHHHHHHHHHhhc-------------------CCCCCCCcccccCcchHHHHHccCCCc
Q 009306          476 ITISVLN---KIEMHYLLRAMGREIVRQE-------------------STNDPGKRSRLWHHKEVYKILSENRVS  528 (538)
Q Consensus       476 i~~~~~~---~~~~H~lv~~~~~~~~~~~-------------------~~~~~~~r~rl~~~~~i~~~l~~~~~~  528 (538)
                      |....++   +|.||+++++++++....+                   -...+..+.++|++..+++++..+..+
T Consensus       424 l~~~~~~~~~~~~~H~lv~~~~~~~~~~~~~~~h~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~~~a~~~~  498 (591)
T 1z6t_A          424 LFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHK  498 (591)
T ss_dssp             SEEEEETTEEEEECCHHHHHHHHHHTGGGHHHHHHHHHHHHTTTCCGGGCCTTSTTHHHHHHHHHHHHHHTTCHH
T ss_pred             eEEecCCCccEEEEcHHHHHHHHhhhhhHHHHHHHHHHHHHHhhcCCCCCCCCCCCEEeehhhHHHHHHhcCCHH
Confidence            9965433   6999999999999873210                   012344566677777777777766554

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=1.2e-35  Score=322.24  Aligned_cols=306  Identities=14%  Similarity=0.130  Sum_probs=227.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHH--hhccceee-EEEEeehhhhhhcCChHHHHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN--KISRHFSG-SYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~--~~~~~f~~-~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      +..|||+.++++|.++|... +..++++|+||||+||||||+++++  +++.+|+. ++|+. ++   .......++..+
T Consensus       128 k~~VGRe~eLeeL~elL~~~-d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVs-Vs---~~~d~~~IL~~L  202 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN-LK---NCNSPETVLEML  202 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHHC-CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEE-CC---CSSSHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhcc-CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEE-eC---CCCCHHHHHHHH
Confidence            45599999999999999753 3478999999999999999999997  46788987 66666 33   233445555555


Q ss_pred             HHHHhcCC---CC--------CCchhhcHHHHHHHh---cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          265 LSTLLNDG---NV--------KNFLNTDLNFQSRRL---TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       265 ~~~l~~~~---~~--------~~~~~~~~~~l~~~l---~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ...+....   ..        ....+.....+++.+   .++++||||||||+.++++.+.       +|++||||||+.
T Consensus       203 l~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~  275 (1221)
T 1vt4_I          203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFK  275 (1221)
T ss_dssp             HHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCS
T ss_pred             HHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccCh
Confidence            54332211   00        012334455566655   6799999999999998888752       689999999999


Q ss_pred             hhhhhcCCCeeEEcC------CCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCC--CHHH
Q 009306          331 QVLANCGVDEVYQME------ELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGK--RREV  402 (538)
Q Consensus       331 ~~~~~~~~~~~~~l~------~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~--~~~~  402 (538)
                      .++..+.....|+|+      +|+.+||++||..+. +..     ..++..+   .|+|+||||+++|+.|+.+  +...
T Consensus       276 ~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~-g~~-----~eeL~~e---ICgGLPLALkLaGs~Lr~k~~s~ee  346 (1221)
T 1vt4_I          276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL-DCR-----PQDLPRE---VLTTNPRRLSIIAESIRDGLATWDN  346 (1221)
T ss_dssp             HHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHH-CCC-----TTTHHHH---HCCCCHHHHHHHHHHHHHSCSSHHH
T ss_pred             HHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHc-CCC-----HHHHHHH---HhCCCHHHHHHHHHHHhCCCCCHHH
Confidence            887543322355666      999999999999985 221     1223333   4999999999999999876  6777


Q ss_pred             HHHHHHHhhcCCCCcHHHHHHHhHhCCCHHh-HHHhhccccccCC--CCHHHHHHHHHhCCC-ChHHHHHHHhhCCceeE
Q 009306          403 WENAKSKWETAPPKGIQDALKISYDGLDDKE-QNIFLDIACFFID--EDRDTATKFLDDCEF-FATSAIEVLVDKHLITI  478 (538)
Q Consensus       403 ~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~-k~~l~~la~f~~~--~~~~~l~~l~~~~~~-~~~~~l~~L~~~~Li~~  478 (538)
                      |...       ....+..+|+.||+.|++++ |.||++||+||.+  ++.+.+..+|.+++. .....++.|+++|||+.
T Consensus       347 W~~~-------~~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeGeedAe~~L~eLvdRSLLq~  419 (1221)
T 1vt4_I          347 WKHV-------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK  419 (1221)
T ss_dssp             HHHC-------SCHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSCSHHHHHHHHHHHTSSSSSB
T ss_pred             HhcC-------ChhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHhhCCEEE
Confidence            8653       34679999999999999999 9999999999986  466788999987642 46778999999999998


Q ss_pred             ec-CCcEEecHHHHHHHHHHHhhcCCCCCCCcccccCcchHHHHHccCC
Q 009306          479 SV-LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENR  526 (538)
Q Consensus       479 ~~-~~~~~~H~lv~~~~~~~~~~~~~~~~~~r~rl~~~~~i~~~l~~~~  526 (538)
                      .. .++|+||+++++++     +.....+..++|++++..+.+++.+..
T Consensus       420 d~~~~rYrMHDLllELr-----~~~~e~~alHrRLvd~Y~~~~vf~~~~  463 (1221)
T 1vt4_I          420 QPKESTISIPSIYLELK-----VKLENEYALHRSIVDHYNIPKTFDSDD  463 (1221)
T ss_dssp             CSSSSEEBCCCHHHHHH-----HHHSCCTTHHHHHHHHHHHHHHCCCSS
T ss_pred             eCCCCEEEehHHHHHHh-----cCCCcHHHHHHHHHHHHHhhCcCCCCC
Confidence            63 56899999998733     111234667778887777776665443

>3h16_A TIR protein; bacteria TIR domain, signaling protein; 2.50A {Paracoccus denitrificans PD1222}

Probab=99.96  E-value=8e-31  Score=230.52  Aligned_cols=120  Identities=22%  Similarity=0.381  Sum_probs=110.5

Q ss_pred             CCCCCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHH
Q 009306           12 TNPEIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLD   90 (538)
Q Consensus        12 ~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~   90 (538)
                      ..+.++|||||||+++| +..|+.+|+..|+++|+++|+|+ ++.+|+.|.++|.++|++|+++|+|+|++|++|.||+.
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            45679999999999999 55899999999999999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCeEEEEEEeecCCcccccCCchHHHHHHH
Q 009306           91 ELLKILECKKEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLKL  132 (538)
Q Consensus        91 El~~~~~~~~~~~~~v~pv~~~v~~~~v~~~~~~~~~~~~~~  132 (538)
                      |+..++++...++.+|+||||+++|++|++|.|.|+++|...
T Consensus        94 El~~~~~~~~~~~~~iiPV~~~v~p~~v~~~~~~~~~~~~~~  135 (154)
T 3h16_A           94 ELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFN  135 (154)
T ss_dssp             HHHHHTCCCTTSCCCEEEEEESCCTGGGTTTCCCCCSSCCEE
T ss_pred             HHHHHHHHHhcCCCEEEEEEecCCHHHHhhCCccHHHHHhhh
Confidence            999999987777789999999999999999999998776553

>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=99.91  E-value=4e-26  Score=197.26  Aligned_cols=107  Identities=19%  Similarity=0.327  Sum_probs=81.1

Q ss_pred             CCCCCCCcccEEEcCcccccccchHHHHHHHHhh--CCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccch
Q 009306           10 SLTNPEIKYDVFLSFGGEDTRESFTSHLYSALSR--ETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSR   86 (538)
Q Consensus        10 ~~~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~--~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~   86 (538)
                      +|....+.|||||||+++|  ..||.+|...|++  .|+++|+|+ |+.||+.|.++|.++|++|+++|+|+|++|++|.
T Consensus         3 ~~~r~~k~YDvFISy~~~D--~~~v~~L~~~Le~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~I~VlS~~y~~S~   80 (146)
T 3ub2_A            3 GSSRWSKDYDVCVCHSEED--LVAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHCRVLLITPGFLQDP   80 (146)
T ss_dssp             -CCTTSSSEEEEEECCGGG--HHHHHHHHHHHHC------------------CCCEEECCTTCCEEEEEEEECHHHHHCH
T ss_pred             CCCCCCCcceEEEeCChhh--HHHHHHHHHHHhCcCCCeEEEEECccccccccHHHHHHHHHHhCCEEEEEECcccccCH
Confidence            4466788999999999999  5689999999998  599999988 9999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHhhcCCeEEEEEEeecCCcc
Q 009306           87 WCLDELLKILECKKEYAQIVVPVFYRVDPSHV  118 (538)
Q Consensus        87 ~c~~El~~~~~~~~~~~~~v~pv~~~v~~~~v  118 (538)
                      ||+.|+..|+.+......+|||||++++++++
T Consensus        81 wc~~El~~al~~~~~~~~~vIpv~~~v~~~~l  112 (146)
T 3ub2_A           81 WCKYQMLQALTEAPGAEGCTIPLLSGLSRAAY  112 (146)
T ss_dssp             HHHHHHHHHHHTSSSSSSEEEEEECSCCGGGS
T ss_pred             HHHHHHHHHHHHHhhcCCcEEEEEcCCChhhC
Confidence            99999999999873334478899998876554

>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=99.86  E-value=6.2e-23  Score=180.32  Aligned_cols=101  Identities=17%  Similarity=0.295  Sum_probs=91.1

Q ss_pred             CCCCCcccEEEcCcccccccchHHHHHHHHhhC--CCeeEeeC-CCCCCCcchHHHHHHHH-hcceEEEEeccCcccchh
Q 009306           12 TNPEIKYDVFLSFGGEDTRESFTSHLYSALSRE--TVETFIDD-DLRRGDEISQSLLDAIE-ASSISIIIFSESYASSRW   87 (538)
Q Consensus        12 ~~~~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~--g~~~~~d~-~~~~g~~~~~~i~~~i~-~s~~~i~v~S~~y~~s~~   87 (538)
                      ....+.|||||||+++|  +.||.+|...|+++  |+++|+|+ |+.||+.|.++|.++|+ +|+++|+|+|++|++|.|
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 GHMPERFDAFICYCPSD--IQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKE   88 (160)
T ss_dssp             SCCTTCEEEEEECCGGG--HHHHHHHHHHHHTSSSCCCCEESCCSSSSSCSCCCCCGGGHHHHEEEEEEECCHHHHHSHH
T ss_pred             CCCCcceEEEEEccccc--HHHHHHHHHHHhcCCCceEEEEeCCCCCCCCcHHHHHHHHHHHhCCEEEEEECcchhcCHH
Confidence            34468999999999999  78999999999985  69999998 99999999999999999 799999999999999999


Q ss_pred             hHHHHHHHHHHH-hhcCCeEEEEEEeec
Q 009306           88 CLDELLKILECK-KEYAQIVVPVFYRVD  114 (538)
Q Consensus        88 c~~El~~~~~~~-~~~~~~v~pv~~~v~  114 (538)
                      |+.|+..|+.+. ...+.+||||+|+.-
T Consensus        89 c~~El~~a~~~~~~~~~~~vIpV~~~~~  116 (160)
T 2js7_A           89 CDFQTKFALSLSPGAHQKRLIPIKYKAM  116 (160)
T ss_dssp             HHHHHHHHHHHCTTHHHHTEEEEESSCC
T ss_pred             HHHHHHHHHHHHHccCCCEEEEEEEccc
Confidence            999999999876 444568999999843

>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=99.86  E-value=2.7e-23  Score=180.79  Aligned_cols=97  Identities=22%  Similarity=0.373  Sum_probs=89.0

Q ss_pred             CCCcccEEEcCcccccccchHHH-HHHHHhhC--CCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhH
Q 009306           14 PEIKYDVFLSFGGEDTRESFTSH-LYSALSRE--TVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCL   89 (538)
Q Consensus        14 ~~~~~dvFiSy~~~D~~~~~~~~-l~~~l~~~--g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~   89 (538)
                      ..+.|||||||+++|  ..||.+ |.+.|+++  |+++|+|+ |+.||+.+.++|.++|++|+++|+|+||+|++|.||+
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 RNIXYDAFVSYSERD--AYWVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWXK   79 (149)
T ss_dssp             CSCCEEEEEECCGGG--HHHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCccceEEEECCccc--HHHHHHHHHHHHhcCCCCeEEeeccccCCCchhHHHHHHHHHHHcCEEEEEeCcchhccchHH
Confidence            467899999999999  579997 99999986  99999998 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH-hhcCCeEEEEEEe
Q 009306           90 DELLKILECK-KEYAQIVVPVFYR  112 (538)
Q Consensus        90 ~El~~~~~~~-~~~~~~v~pv~~~  112 (538)
                      .|+..|+.+. +.++.+||||||+
T Consensus        80 ~El~~a~~~~~~~~~~~vIpv~~~  103 (149)
T 1fyx_A           80 YELDFSHFRLFDENNDAAILILLE  103 (149)
T ss_dssp             HHSCCSCCTTCGGGTTCCEEEESS
T ss_pred             HHHHHHHHHHHhcCCCEEEEEEec
Confidence            9999988543 5567789999987

>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=99.85  E-value=1.2e-22  Score=181.34  Aligned_cols=99  Identities=18%  Similarity=0.410  Sum_probs=86.5

Q ss_pred             CCCCCcccEEEcCcccccccchHHH-HHHHHhh--CCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchh
Q 009306           12 TNPEIKYDVFLSFGGEDTRESFTSH-LYSALSR--ETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRW   87 (538)
Q Consensus        12 ~~~~~~~dvFiSy~~~D~~~~~~~~-l~~~l~~--~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~   87 (538)
                      ....+.|||||||+++|  ..||.+ |.+.|++  .|+++|+|+ |+.||+.|.++|.++|++|+++|+|+||+|++|.|
T Consensus        30 ~~~~~~yDvFISys~~D--~~fv~~~L~~~LE~~~~g~~~~l~~rD~~~G~~i~~~i~~aI~~Sr~~IvVlS~~yl~S~w  107 (178)
T 2j67_A           30 LKRNVRFHAFISYSEHD--SLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKSYKSIFVLSPNFVQNEW  107 (178)
T ss_dssp             CCCSCCEEEEEECCGGG--HHHHHHTHHHHHTTCC-CCCEEEHHHHCCTTSCHHHHHHHHHHTEEEEEEEECHHHHHHTG
T ss_pred             cCCCccceEEEECCCCC--HHHHHHHHHHHHhcccCCeEEEEecccCCCCccHHHHHHHHHHhCCEEEEEecccccccch
Confidence            45678999999999999  689985 9999998  899999998 99999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHH-hhcCCeEEEEEEe
Q 009306           88 CLDELLKILECK-KEYAQIVVPVFYR  112 (538)
Q Consensus        88 c~~El~~~~~~~-~~~~~~v~pv~~~  112 (538)
                      |+.|+..|+.+. +.++.+||||||+
T Consensus       108 c~~El~~a~~~~~~~~~~~vIpV~~~  133 (178)
T 2j67_A          108 CHYEFYFAHHNLFHENSDHIILILLE  133 (178)
T ss_dssp             GGTHHHHTTCC-------CEEEEESS
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEEEec
Confidence            999999998654 4556789999987

>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR, IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo sapiens}

Probab=99.85  E-value=5.7e-22  Score=173.98  Aligned_cols=97  Identities=23%  Similarity=0.323  Sum_probs=87.3

Q ss_pred             CcccEEEcCccccc---------ccchHHHHHH-HHh-hCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcc
Q 009306           16 IKYDVFLSFGGEDT---------RESFTSHLYS-ALS-RETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYA   83 (538)
Q Consensus        16 ~~~dvFiSy~~~D~---------~~~~~~~l~~-~l~-~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~   83 (538)
                      +.|||||||+++|.         ++.||.+|.. .|+ +.|+++|+|+ |+.||+.+.++|.++|++|+++|+|+|++|+
T Consensus         1 k~yDaFISy~~~D~~wv~~~~~~~~~fv~~ll~~~LE~~~g~~l~~~~rD~~~G~~i~~~i~~~I~~Sr~~IvVlS~~y~   80 (159)
T 1t3g_A            1 KDYDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVARCVDQSKRLIIVMTPNYV   80 (159)
T ss_dssp             CCBSEEEECCCCC-------CCSHHHHHHTHHHHHHHHTSCCCEECHHHHCCCCTTHHHHHHHHHHTBSEEEEEECHHHH
T ss_pred             CCceEEEeCccccchhhhccchhhHHHHHHHHHHHHcCCCCeEEEEEcccccCccchHHHHHHHHHHcCEEEEEEccchh
Confidence            57999999999996         3568888676 699 7999999998 9999999999999999999999999999997


Q ss_pred             -cchhhHHHHHHHHHHH-hhcCCeEEEEEEe
Q 009306           84 -SSRWCLDELLKILECK-KEYAQIVVPVFYR  112 (538)
Q Consensus        84 -~s~~c~~El~~~~~~~-~~~~~~v~pv~~~  112 (538)
                       .|.||..|+..|+.+. ..++.+||||+++
T Consensus        81 ~~S~wc~~El~~a~~~~~~~~~~~vI~I~~~  111 (159)
T 1t3g_A           81 VRRGWSIFELETRLRNMLVTGEIKVILIECS  111 (159)
T ss_dssp             HTTTTHHHHHSHHHHHHHHTTSSEEEEEECS
T ss_pred             hcChHHHHHHHHHHHHHHhcCCCEEEEEEec
Confidence             9999999999999886 5667899999976

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.84  E-value=9.6e-20  Score=183.05  Aligned_cols=294  Identities=15%  Similarity=0.112  Sum_probs=182.6

Q ss_pred             ccccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhh---hcC
Q 009306          179 LDDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAE---ETC  255 (538)
Q Consensus       179 ~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~---~~~  255 (538)
                      +.+.++..+..|+||+.+++.|.+++..+    +++.|+|++|+|||||+++++++..     .+|+.. ....   ...
T Consensus         3 F~~~~~~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~~-----~~~~~~-~~~~~~~~~~   72 (350)
T 2qen_A            3 FDLRPKTRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNERP-----GILIDC-RELYAERGHI   72 (350)
T ss_dssp             SCCSCCCSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHSS-----EEEEEH-HHHHHTTTCB
T ss_pred             CCCCCCCChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHcC-----cEEEEe-ecccccccCC
Confidence            34455567788999999999999998753    6899999999999999999998752     455552 2221   011


Q ss_pred             ChHHHHHHHHHHHhc---------------CCCC---CCchhhcHHHHHHHhcC-CCeEEEEecCCChH---------HH
Q 009306          256 RLGDLRQQLLSTLLN---------------DGNV---KNFLNTDLNFQSRRLTR-KKVLIVFDDVDHPR---------QI  307 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~---------------~~~~---~~~~~~~~~~l~~~l~~-k~~LlVlDdv~~~~---------~~  307 (538)
                      ....+...+...+..               ....   ..........+.+.... ++++|||||++...         .+
T Consensus        73 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~  152 (350)
T 2qen_A           73 TREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELL  152 (350)
T ss_dssp             CHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHH
Confidence            334444444443321               0000   12333444445444432 48999999996532         22


Q ss_pred             HHHhcCcCCCCCCCEEEEeccchhhhhh----------c--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHH
Q 009306          308 KILVGRLDLFASGSRIIITTRDRQVLAN----------C--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELAC  375 (538)
Q Consensus       308 ~~l~~~l~~~~~~~~iiiTtR~~~~~~~----------~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~  375 (538)
                      ..+...... .++.++|+|++....+..          .  .....+.+.+|+.+|+.+++........  .....+.+.
T Consensus       153 ~~L~~~~~~-~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~--~~~~~~~~~  229 (350)
T 2qen_A          153 ALFAYAYDS-LPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVN--LDVPENEIE  229 (350)
T ss_dssp             HHHHHHHHH-CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTT--CCCCHHHHH
T ss_pred             HHHHHHHHh-cCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcC--CCCCHHHHH
Confidence            323222111 247889999887643221          1  1134789999999999999987541111  122356788


Q ss_pred             HHHHHhcCCcHHHHHHHHHhcC-CCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCC---CHHhHHHhhccccccCCCCHHH
Q 009306          376 KTIKYARGVPLALEVLGRYLYG-KRREVWENAKSKWETAPPKGIQDALKISYDGL---DDKEQNIFLDIACFFIDEDRDT  451 (538)
Q Consensus       376 ~i~~~~~G~PLal~~~~~~L~~-~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L---~~~~k~~l~~la~f~~~~~~~~  451 (538)
                      .+++.++|+|++++.++..+.. .+...+   ...+.    +.+...+...+..+   ++..+.++..+|+  ...+...
T Consensus       230 ~i~~~tgG~P~~l~~~~~~~~~~~~~~~~---~~~~~----~~~~~~~~~~l~~l~~~~~~~~~~l~~la~--g~~~~~~  300 (350)
T 2qen_A          230 EAVELLDGIPGWLVVFGVEYLRNGDFGRA---MKRTL----EVAKGLIMGELEELRRRSPRYVDILRAIAL--GYNRWSL  300 (350)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCCHHHH---HHHHH----HHHHHHHHHHHHHHHHHCHHHHHHHHHHHT--TCCSHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHhccccHhHH---HHHHH----HHHHHHHHHHHHHHHhCChhHHHHHHHHHh--CCCCHHH
Confidence            9999999999999999876532 222221   11110    11222233333444   7889999999998  3456677


Q ss_pred             HHHHHHhC--CC---ChHHHHHHHhhCCceeEecCCcEEe-cHHHHHHHH
Q 009306          452 ATKFLDDC--EF---FATSAIEVLVDKHLITISVLNKIEM-HYLLRAMGR  495 (538)
Q Consensus       452 l~~l~~~~--~~---~~~~~l~~L~~~~Li~~~~~~~~~~-H~lv~~~~~  495 (538)
                      +...+...  +.   ....+++.|.+.+||... ++.|.+ |++++.+.+
T Consensus       301 l~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~-~~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          301 IRDYLAVKGTKIPEPRLYALLENLKKMNWIVEE-DNTYKIADPVVATVLR  349 (350)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEE-TTEEEESSHHHHHHHT
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHhCCCEEec-CCEEEEecHHHHHHHc
Confidence            76665221  22   235689999999999987 566654 889988754

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.80  E-value=1.2e-18  Score=175.38  Aligned_cols=288  Identities=13%  Similarity=0.096  Sum_probs=171.9

Q ss_pred             cccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhh-hhcCChH
Q 009306          180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREA-EETCRLG  258 (538)
Q Consensus       180 ~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~-~~~~~~~  258 (538)
                      .+.++..++.|+||+.+++.|.+ +..     +++.|+|++|+|||+|+++++++....   .+|+...... .......
T Consensus         5 ~~~~~~~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~   75 (357)
T 2fna_A            5 DTSPKDNRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINELNLP---YIYLDLRKFEERNYISYK   75 (357)
T ss_dssp             CSSCCCSGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHHHTCC---EEEEEGGGGTTCSCCCHH
T ss_pred             CCCCCCCHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHhcCCC---EEEEEchhhccccCCCHH
Confidence            34445567889999999999999 763     589999999999999999999876532   4565522110 0001222


Q ss_pred             HHHHHHHHHHh-------------cC-C-----CC----------CCchhhcHHHHHHHhcCCCeEEEEecCCChH----
Q 009306          259 DLRQQLLSTLL-------------ND-G-----NV----------KNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----  305 (538)
Q Consensus       259 ~l~~~l~~~l~-------------~~-~-----~~----------~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----  305 (538)
                      .+...+...+.             .. .     ..          ..........+.+... ++++|||||++...    
T Consensus        76 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~  154 (357)
T 2fna_A           76 DFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRG  154 (357)
T ss_dssp             HHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTT
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCc
Confidence            33333322221             00 0     00          0122223333322211 48999999995422    


Q ss_pred             --HHHHHhcCcCCCCCCCEEEEeccchhhhhh----------c-C-CCeeEEcCCCCHHHHHHHHHhhhcC-CCCCCCch
Q 009306          306 --QIKILVGRLDLFASGSRIIITTRDRQVLAN----------C-G-VDEVYQMEELVHDDALRLFSRHAFG-GDHPHESH  370 (538)
Q Consensus       306 --~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~----------~-~-~~~~~~l~~L~~~ea~~Lf~~~~~~-~~~~~~~~  370 (538)
                        .+..+...... .++.++|+|++.......          . + ....+.+.+|+.+|+.+++...... +.... . 
T Consensus       155 ~~~~~~l~~~~~~-~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~-~-  231 (357)
T 2fna_A          155 VNLLPALAYAYDN-LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK-D-  231 (357)
T ss_dssp             CCCHHHHHHHHHH-CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC-C-
T ss_pred             hhHHHHHHHHHHc-CCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCC-c-
Confidence              12222111111 246789999987653221          1 1 1357899999999999999875411 11122 1 


Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHhcC-CCHHHHHHHHHHhhcCCCCcHHHHHHHhHh-------CCCHHhHHHhhcccc
Q 009306          371 TELACKTIKYARGVPLALEVLGRYLYG-KRREVWENAKSKWETAPPKGIQDALKISYD-------GLDDKEQNIFLDIAC  442 (538)
Q Consensus       371 ~~~~~~i~~~~~G~PLal~~~~~~L~~-~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~-------~L~~~~k~~l~~la~  442 (538)
                         ...+++.++|+|++++.++..+.. .+...|...   +.    +.+...+...+.       .|++..+.++..+|+
T Consensus       232 ---~~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~---~~----~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~la~  301 (357)
T 2fna_A          232 ---YEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQ---TL----EYAKKLILKEFENFLHGREIARKRYLNIMRTLSK  301 (357)
T ss_dssp             ---HHHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHH---HH----HHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHTT
T ss_pred             ---HHHHHHHhCCCHHHHHHHHHHHccccchHHHHHH---HH----HHHHHHHHHHHHHHhhccccccHHHHHHHHHHHc
Confidence               178999999999999999887632 233333211   10    011122222222       678899999999998


Q ss_pred             ccCCCCHHHHHHHHH-hCC-----CChHHHHHHHhhCCceeEecCCcEE-ecHHHHHHH
Q 009306          443 FFIDEDRDTATKFLD-DCE-----FFATSAIEVLVDKHLITISVLNKIE-MHYLLRAMG  494 (538)
Q Consensus       443 f~~~~~~~~l~~l~~-~~~-----~~~~~~l~~L~~~~Li~~~~~~~~~-~H~lv~~~~  494 (538)
                       . . +...+...+. ..+     .....+++.|.+.+||... ++.|. .|++++++.
T Consensus       302 -g-~-~~~~l~~~~~~~~g~~~~~~~~~~~L~~L~~~gli~~~-~~~y~f~~~~~~~~l  356 (357)
T 2fna_A          302 -C-G-KWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKE-GEKYCPSEPLISLAF  356 (357)
T ss_dssp             -C-B-CHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHTTSEEES-SSCEEESSHHHHHHT
T ss_pred             -C-C-CHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEec-CCEEEecCHHHHHhh
Confidence             3 3 6777665432 112     2345689999999999987 46666 589999874

>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=99.75  E-value=3.4e-17  Score=168.33  Aligned_cols=285  Identities=12%  Similarity=0.028  Sum_probs=172.5

Q ss_pred             CCCCCceeccchhHHHHHhh-hc--CC--CCceEEEE--eccCCCchhHHHHHHHHhhccce-----e-eEEEEeehhhh
Q 009306          185 SENEDLVGVRLPMKEIESLL-RT--GS--TNVYKLGI--WGIGGIGKTTIAGAIFNKISRHF-----S-GSYFARNVREA  251 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L-~~--~~--~~~~~v~I--~G~~GiGKTtLa~~~~~~~~~~f-----~-~~~~~~~~~~~  251 (538)
                      ..+..|+||+.+++.|.+.+ ..  .+  ...+.+.|  +|++|+|||||++.+++.....+     . ..+|+.+    
T Consensus        19 ~~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~----   94 (412)
T 1w5s_A           19 YIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNA----   94 (412)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEG----
T ss_pred             cCCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEEC----
Confidence            34578999999999999988 53  12  23456777  99999999999999998765531     2 2455542    


Q ss_pred             hhcCChHHHHHHHHHHHhcCCCC-CCchhhcHHHHHHHhc--CCCeEEEEecCCCh--------HHHHHHhcCcCCC---
Q 009306          252 EETCRLGDLRQQLLSTLLNDGNV-KNFLNTDLNFQSRRLT--RKKVLIVFDDVDHP--------RQIKILVGRLDLF---  317 (538)
Q Consensus       252 ~~~~~~~~l~~~l~~~l~~~~~~-~~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~--------~~~~~l~~~l~~~---  317 (538)
                      ........++..++..++..... ..........+.+.+.  +++++|||||++..        +.+..+...+...   
T Consensus        95 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~  174 (412)
T 1w5s_A           95 FNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSR  174 (412)
T ss_dssp             GGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCT
T ss_pred             CCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccC
Confidence            23345667788888877543221 1233444555555553  67999999999653        3333333222111   


Q ss_pred             C--CCCEEEEeccchhhhhhc---------CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhc----
Q 009306          318 A--SGSRIIITTRDRQVLANC---------GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYAR----  382 (538)
Q Consensus       318 ~--~~~~iiiTtR~~~~~~~~---------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~----  382 (538)
                      +  .+..+|+||+...+...+         .....+.+++|+.+++.++|..++...........+....+++.++    
T Consensus       175 ~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  254 (412)
T 1w5s_A          175 DGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKG  254 (412)
T ss_dssp             TSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGT
T ss_pred             CCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhcc
Confidence            2  344577788755432111         1123499999999999999976542111112234677889999999    


Q ss_pred             --CCcHHHHHHHHHhc------CC---CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhcccccc----CCC
Q 009306          383 --GVPLALEVLGRYLY------GK---RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFF----IDE  447 (538)
Q Consensus       383 --G~PLal~~~~~~L~------~~---~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~----~~~  447 (538)
                        |+|..+..+.....      +.   +...+...+.....      ...+...+..|++.++.+|..++++.    ..+
T Consensus       255 ~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~------~~~~~~~l~~l~~~~~~~l~aia~l~~~~~~~~  328 (412)
T 1w5s_A          255 GDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEA------ASIQTHELEALSIHELIILRLIAEATLGGMEWI  328 (412)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------------CCSSSSSCHHHHHHHHHHHHHHHTTCSSB
T ss_pred             CCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc------cchHHHHHHcCCHHHHHHHHHHHHHHhcCCCCc
Confidence              99976665554321      11   22333333322110      23345567889999999999998754    234


Q ss_pred             CHHHHHH----HH-HhCCC------ChHHHHHHHhhCCceeEe
Q 009306          448 DRDTATK----FL-DDCEF------FATSAIEVLVDKHLITIS  479 (538)
Q Consensus       448 ~~~~l~~----l~-~~~~~------~~~~~l~~L~~~~Li~~~  479 (538)
                      +...+..    +. ...+.      ....+++.|.+.|||...
T Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~  371 (412)
T 1w5s_A          329 NAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAK  371 (412)
T ss_dssp             CHHHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhCCCEEee
Confidence            4443322    22 22221      134679999999999864

>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=99.70  E-value=6.6e-16  Score=157.03  Aligned_cols=321  Identities=14%  Similarity=0.078  Sum_probs=186.9

Q ss_pred             CCCCCceeccchhHHHHHhhhcC--CCCceEEEEeccCCCchhHHHHHHHHhhccce---eeEEEEeehhhhhhcCChHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTG--STNVYKLGIWGIGGIGKTTIAGAIFNKISRHF---SGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f---~~~~~~~~~~~~~~~~~~~~  259 (538)
                      ..+..|+||+.+++.|.+++...  ....+.+.|+|++|+|||||++.++......+   ...+|+.+    ........
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~----~~~~~~~~   92 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINT----RQIDTPYR   92 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEH----HHHCSHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEEC----CCCCCHHH
Confidence            44588999999999999988742  33456799999999999999999999876543   23455542    22334455


Q ss_pred             HHHHHHHHHhcCCCCC-CchhhcHHHHHHHhc--CCCeEEEEecCCCh------HHHHHHhcCcCC-CCCCCEEEEeccc
Q 009306          260 LRQQLLSTLLNDGNVK-NFLNTDLNFQSRRLT--RKKVLIVFDDVDHP------RQIKILVGRLDL-FASGSRIIITTRD  329 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l~--~k~~LlVlDdv~~~------~~~~~l~~~l~~-~~~~~~iiiTtR~  329 (538)
                      +...++..++...... .........+.+.+.  +++.+||||+++..      ..+..+...+.. ...+..+|+||+.
T Consensus        93 ~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~  172 (386)
T 2qby_A           93 VLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITND  172 (386)
T ss_dssp             HHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESC
T ss_pred             HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECC
Confidence            5666655553321111 223444455555553  34899999999543      234444332211 1345667777776


Q ss_pred             hhhhhhcC-------CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhc---CCcHHHHHHHHHh-c--
Q 009306          330 RQVLANCG-------VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYAR---GVPLALEVLGRYL-Y--  396 (538)
Q Consensus       330 ~~~~~~~~-------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~---G~PLal~~~~~~L-~--  396 (538)
                      ......+.       ....+.+++++.++..+++...+...........+....+++.++   |+|..+..+.... .  
T Consensus       173 ~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a  252 (386)
T 2qby_A          173 VKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIA  252 (386)
T ss_dssp             GGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            54322211       125899999999999999988652111122344677788888888   9998444333322 1  


Q ss_pred             ---C---CCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccccC-C---CCHHHH----HHHHHh---C
Q 009306          397 ---G---KRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFI-D---EDRDTA----TKFLDD---C  459 (538)
Q Consensus       397 ---~---~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~-~---~~~~~l----~~l~~~---~  459 (538)
                         +   -+.+.+..++....       ...+...+..+++.++.+|..++.+.. +   ++...+    ..+...   .
T Consensus       253 ~~~~~~~i~~~~v~~a~~~~~-------~~~~~~~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g~~  325 (386)
T 2qby_A          253 ERMKDTKVKEEYVYMAKEEIE-------RDRVRDIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGVE  325 (386)
T ss_dssp             HHTTCSSCCHHHHHHHHHHHH-------HHHHHHHHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHHTCC
T ss_pred             HhcCCCccCHHHHHHHHHHHh-------hchHHHHHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhcCCC
Confidence               1   13444444444331       245677788999999999988885422 1   233222    222221   2


Q ss_pred             C---CChHHHHHHHhhCCceeEecCCcEEecHHHHHHHHHHHhhcCCCCCCCcccccCcchHHHHHcc-CCCcchhhh
Q 009306          460 E---FFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSE-NRVSNNDFS  533 (538)
Q Consensus       460 ~---~~~~~~l~~L~~~~Li~~~~~~~~~~H~lv~~~~~~~~~~~~~~~~~~r~rl~~~~~i~~~l~~-~~~~~~~~~  533 (538)
                      .   .....+++.|.+.|+|.....                 ...........+-.|++.+|.++|.+ ....++++|
T Consensus       326 ~~~~~~~~~~l~~L~~~gli~~~~~-----------------~~~~~g~y~~~~l~~~~~~v~~~l~~~~~~~~~~~~  386 (386)
T 2qby_A          326 AVTQRRVSDIINELDMVGILTAKVV-----------------NRGRYGKTKEIGLAVDKNIIVRSLIESDSRFADLWS  386 (386)
T ss_dssp             CCCHHHHHHHHHHHHHHTSEEEEEC-----------------CCTTSCCCEEEEESSCSHHHHHHHHHHC--------
T ss_pred             CCCHHHHHHHHHHHHhCCCEEEEee-----------------cCCCCCCeEEEEeCCCHHHHHHHHhcCChhhhhhcC
Confidence            2   123567999999999986521                 00000011234566888999999988 777776654

>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=99.67  E-value=9.2e-15  Score=148.66  Aligned_cols=278  Identities=15%  Similarity=0.082  Sum_probs=175.7

Q ss_pred             CCCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccc--------eeeEEEEeehhhhhhcC-
Q 009306          187 NEDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--------FSGSYFARNVREAEETC-  255 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--------f~~~~~~~~~~~~~~~~-  255 (538)
                      +..|+||+.+++.+..++..  .....+.+.|+|++|+|||+||+.+++.+...        ....+++.    ..... 
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~----~~~~~~   94 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN----CREVGG   94 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE----HHHHCS
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE----CccCCC
Confidence            47899999999999988764  23345689999999999999999999876443        22344554    22233 


Q ss_pred             ChHHHHHHHHHHHhcCCCCC--CchhhcHHHHHHHhcCCCeEEEEecCCChHH-------HHHHhcCcCCCCCCCEEEEe
Q 009306          256 RLGDLRQQLLSTLLNDGNVK--NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQ-------IKILVGRLDLFASGSRIIIT  326 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~--~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~-------~~~l~~~l~~~~~~~~iiiT  326 (538)
                      ....++..++..+.+.....  .........+.+.+..++.+|||||++....       +..+....    .+..+|+|
T Consensus        95 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~iI~~  170 (384)
T 2qby_B           95 TPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD----ANISVIMI  170 (384)
T ss_dssp             CHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS----SCEEEEEE
T ss_pred             CHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC----cceEEEEE
Confidence            56667777777774432221  3334556667777776666999999975432       33333222    67788888


Q ss_pred             ccchhhh----hhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhc---CCcH-HHHHHHHHh-
Q 009306          327 TRDRQVL----ANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYAR---GVPL-ALEVLGRYL-  395 (538)
Q Consensus       327 tR~~~~~----~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~---G~PL-al~~~~~~L-  395 (538)
                      |+.....    ..+  .....+.+++++.++..+++..++...........+....+++.++   |+|. ++..+-... 
T Consensus       171 t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~  250 (384)
T 2qby_B          171 SNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQ  250 (384)
T ss_dssp             CSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             ECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence            8865321    111  1123899999999999999998752111112233566778888888   9987 443333322 


Q ss_pred             -c----CCCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccccC-CCCHHHHHHHHHhCC---CC---h
Q 009306          396 -Y----GKRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFI-DEDRDTATKFLDDCE---FF---A  463 (538)
Q Consensus       396 -~----~~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~-~~~~~~l~~l~~~~~---~~---~  463 (538)
                       .    .-+.+.+...+....       ...+..+++.|++.++.++..++.... +-.......+...-+   ..   .
T Consensus       251 ~a~~~~~i~~~~v~~~~~~~~-------~~~~~~~~~~l~~~~~~~l~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  323 (384)
T 2qby_B          251 LASGGGIIRKEHVDKAIVDYE-------QERLIEAVKALPFHYKLALRSLIESEDVMSAHKMYTDLCNKFKQKPLSYRRF  323 (384)
T ss_dssp             HTTSSSCCCHHHHHHHHHHHH-------HHHHHHHHHSSCHHHHHHHHHHHTCCBHHHHHHHHHHHHHHTTCCCCCHHHH
T ss_pred             HhcCCCccCHHHHHHHHHHHh-------cchHHHHHHcCCHHHHHHHHHHHHhcccChHHHHHHHHHHHcCCCCCCHHHH
Confidence             1    124556666655442       245677789999999999888876111 100122333333222   21   3


Q ss_pred             HHHHHHHhhCCceeEe
Q 009306          464 TSAIEVLVDKHLITIS  479 (538)
Q Consensus       464 ~~~l~~L~~~~Li~~~  479 (538)
                      ...++.|.++|||...
T Consensus       324 ~~~l~~L~~~gli~~~  339 (384)
T 2qby_B          324 SDIISELDMFGIVKIR  339 (384)
T ss_dssp             HHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhCCCEEEE
Confidence            4578899999999964

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.66  E-value=6.8e-15  Score=149.86  Aligned_cols=305  Identities=13%  Similarity=0.048  Sum_probs=186.6

Q ss_pred             CCCCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccce-eeEEEEeehhhhhhcCChHHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-SGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      .++.++||+.+++.|..++..    ..+..+.+.|+|++|+|||||++.++....... ...+++.    .........+
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~----~~~~~~~~~~   90 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN----GFIYRNFTAI   90 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE----TTTCCSHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe----CccCCCHHHH
Confidence            447899999999999998865    222234799999999999999999998876542 2344554    2233445667


Q ss_pred             HHHHHHHHhcCCCCC-CchhhcHHHHHHHhc--CCCeEEEEecCCC--hHHHHHHhcCcCCCC----CCCEEEEeccchh
Q 009306          261 RQQLLSTLLNDGNVK-NFLNTDLNFQSRRLT--RKKVLIVFDDVDH--PRQIKILVGRLDLFA----SGSRIIITTRDRQ  331 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l~--~k~~LlVlDdv~~--~~~~~~l~~~l~~~~----~~~~iiiTtR~~~  331 (538)
                      ...++..++...... .........+.+.+.  +++.+||||+++.  ...+..+...+....    .+..+|++|+...
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            777777665432211 233444444444443  5688999999965  344555544443222    3667888877653


Q ss_pred             hhhhcC-------CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh---------cCCcHHHHHHHHHh
Q 009306          332 VLANCG-------VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA---------RGVPLALEVLGRYL  395 (538)
Q Consensus       332 ~~~~~~-------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~---------~G~PLal~~~~~~L  395 (538)
                      ....+.       ....+.+++++.++..+++...+...........+....+++.+         +|+|..+..+....
T Consensus       171 ~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a  250 (389)
T 1fnn_A          171 VLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRS  250 (389)
T ss_dssp             HHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHH
T ss_pred             HHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHH
Confidence            322221       12368999999999999998876221112234567888999999         79986555444332


Q ss_pred             c------CC---CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhcccccc---C--CCCHHHHHHHHHh---
Q 009306          396 Y------GK---RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFF---I--DEDRDTATKFLDD---  458 (538)
Q Consensus       396 ~------~~---~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~---~--~~~~~~l~~l~~~---  458 (538)
                      .      +.   +.+..........   ...    +...+..|+..++.+|..++.+.   .  .++...+......   
T Consensus       251 ~~~a~~~~~~~i~~~~v~~~~~~~~---~~~----~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~  323 (389)
T 1fnn_A          251 AYAAQQNGRKHIAPEDVRKSSKEVL---FGI----SEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCE  323 (389)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHS---CCC----CHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCcCHHHHHHHHHHHh---hhh----HHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHH
Confidence            1      11   2233333333221   222    23346778899999988888654   2  3444444433222   


Q ss_pred             ----CC---CChHHHHHHHhhCCceeEecC-------CcE-------EecHHHHHHHHHHHhhc
Q 009306          459 ----CE---FFATSAIEVLVDKHLITISVL-------NKI-------EMHYLLRAMGREIVRQE  501 (538)
Q Consensus       459 ----~~---~~~~~~l~~L~~~~Li~~~~~-------~~~-------~~H~lv~~~~~~~~~~~  501 (538)
                          ..   ......++.|.++|||.....       |++       ..|+++..+..+++.++
T Consensus       324 ~~~~~~~~~~~~~~~l~~L~~~gli~~~~~~~~~g~~g~~~~~~l~~~~~~v~~~~~~~~~~~~  387 (389)
T 1fnn_A          324 EYGERPRVHSQLWSYLNDLREKGIVETRQNKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKEE  387 (389)
T ss_dssp             HTTCCCCCHHHHHHHHHHHHHTTSSEEEEC---------CEEEECCSSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCCCCHHHHHHHHHHHHhCCCeEEeeeccCCCCCCceeEEEeCCCHHHHHHHHHHHHHHHh
Confidence                11   123457999999999997433       322       24677777777777654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.64  E-value=1.9e-14  Score=146.40  Aligned_cols=314  Identities=13%  Similarity=0.075  Sum_probs=189.5

Q ss_pred             CCCCceeccchhHHHHHhhhcC--CCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEeehhhhhhcCCh
Q 009306          186 ENEDLVGVRLPMKEIESLLRTG--STNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFARNVREAEETCRL  257 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~~~~~~~~~~~~  257 (538)
                      .++.|+||+.+++.+..++...  ....+.+.|+|++|+||||||+.+++.....      -...+++.    .......
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~----~~~~~~~   92 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN----ARHRETP   92 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE----TTTSCSH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE----CCcCCCH
Confidence            4478999999999999988542  3345679999999999999999999876443      12334444    2233455


Q ss_pred             HHHHHHHHHHHhcCCCCC-CchhhcHHHHHHHh--cCCCeEEEEecCCChH----HHHHH---hcCcCCC--CCCCEEEE
Q 009306          258 GDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRL--TRKKVLIVFDDVDHPR----QIKIL---VGRLDLF--ASGSRIII  325 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~----~~~~l---~~~l~~~--~~~~~iii  325 (538)
                      ..+...++..++...... .........+.+.+  .+++.+|||||++...    ..+.+   .......  ..+..+|+
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            667777777775432222 23444455555555  3458899999997643    22222   2222111  34567777


Q ss_pred             eccchhh--------hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhc---CCcHHH-HHHHH
Q 009306          326 TTRDRQV--------LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYAR---GVPLAL-EVLGR  393 (538)
Q Consensus       326 TtR~~~~--------~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~---G~PLal-~~~~~  393 (538)
                      ||+....        ...+ ....+.+++++.++..+++...+...........+....+++.++   |+|..+ ..+..
T Consensus       173 ~t~~~~~~~~l~~~l~~r~-~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~  251 (387)
T 2v1u_A          173 ITNSLGFVENLEPRVKSSL-GEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRV  251 (387)
T ss_dssp             ECSCSTTSSSSCHHHHTTT-TSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             EECCCchHhhhCHHHHhcC-CCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHH
Confidence            7766522        1111 125789999999999999988752111112233456778888888   999433 33322


Q ss_pred             Hh---c--C---CCHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccccCC---CCHHHHH----HHHHh
Q 009306          394 YL---Y--G---KRREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFFID---EDRDTAT----KFLDD  458 (538)
Q Consensus       394 ~L---~--~---~~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~~~---~~~~~l~----~l~~~  458 (538)
                      ..   .  +   -+.+.+...+....       ...+..++..|++.++.++..++....+   +....+.    .+...
T Consensus       252 a~~~a~~~~~~~i~~~~v~~a~~~~~-------~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (387)
T 2v1u_A          252 AGEIAERRREERVRREHVYSARAEIE-------RDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTST  324 (387)
T ss_dssp             HHHHHHHTTCSCBCHHHHHHHHHHHH-------HHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCcCHHHHHHHHHHHh-------hchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHh
Confidence            22   1  1   13455555554431       2356677899999999998888754322   2333222    22222


Q ss_pred             C---CC---ChHHHHHHHhhCCceeEec--CCcEEecHHHHHHHHHHHhhcCCCCCCCcccccCcchHHHHHccCCCcch
Q 009306          459 C---EF---FATSAIEVLVDKHLITISV--LNKIEMHYLLRAMGREIVRQESTNDPGKRSRLWHHKEVYKILSENRVSNN  530 (538)
Q Consensus       459 ~---~~---~~~~~l~~L~~~~Li~~~~--~~~~~~H~lv~~~~~~~~~~~~~~~~~~r~rl~~~~~i~~~l~~~~~~~~  530 (538)
                      .   ..   .....++.|...|++....  .|+.                   ....+.+.+|++.+|.++|.++....+
T Consensus       325 ~~~~~~~~~~~~~~l~~L~~~gli~~~~~~~g~~-------------------g~~~~~~l~~~~~~i~~~l~~~~~~~~  385 (387)
T 2v1u_A          325 LGLEHVTLRRVSGIISELDMLGIVKSRVVSRGRY-------------------GKTREVSLDADRLAVENALSEDPFVAR  385 (387)
T ss_dssp             TTCCCCCHHHHHHHHHHHHHTTSEEEEEEECGGG-------------------CEEEEEEECSCHHHHHHHHHHSTTGGG
T ss_pred             cCCCCCCHHHHHHHHHHHHhCCCeEEEeecCCCC-------------------CceeEEEecCCHHHHHHHHhccHhhhh
Confidence            1   11   2345788999999999642  1210                   011245577888888888887766544

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.57  E-value=1.2e-15  Score=170.98  Aligned_cols=101  Identities=19%  Similarity=0.329  Sum_probs=90.7

Q ss_pred             CCCCcccEEEcCcccccccchH-HHHHHHHhh-----CCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccc
Q 009306           13 NPEIKYDVFLSFGGEDTRESFT-SHLYSALSR-----ETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASS   85 (538)
Q Consensus        13 ~~~~~~dvFiSy~~~D~~~~~~-~~l~~~l~~-----~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s   85 (538)
                      ...+.|||||||+++|  +.|| .+|.+.|+.     .|+++|+++ |+.||+.+.++|.++|++|+++|+|+|++|+.|
T Consensus       666 ~~~~~yd~fisy~~~d--~~~v~~~l~~~Le~~~~~~~~~~~~~~~rd~~~G~~~~~~i~~~i~~sr~~i~vls~~~~~s  743 (844)
T 3j0a_A          666 PDMYKYDAYLCFSSKD--FTWVQNALLKHLDTQYSDQNRFNLCFEERDFVPGENRIANIQDAIWNSRKIVCLVSRHFLRD  743 (844)
T ss_dssp             SSCCCCSEEEECCSTT--HHHHHHTHHHHHHSTTTTTTCSCEECSSSSCCSSSCHHHHHHHHHHHSSEEEEEECTTHHHH
T ss_pred             ccceeccEEEEeeCCc--HHHHHHHHHHHHhhccccCCceEEEEEccccCCCchHHHHHHHHHHHhCeEEEEeccccccC
Confidence            4578999999999999  5677 779999985     689999999 999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHHH-hhcCCeEEEEEEeecC
Q 009306           86 RWCLDELLKILECK-KEYAQIVVPVFYRVDP  115 (538)
Q Consensus        86 ~~c~~El~~~~~~~-~~~~~~v~pv~~~v~~  115 (538)
                      .||..|+..|+.+. ++.+.+||||||+.-|
T Consensus       744 ~wc~~e~~~a~~~~~~~~~~~~i~i~~~~~~  774 (844)
T 3j0a_A          744 GWCLEAFSYAQGRCLSDLNSALIMVVVGSLS  774 (844)
T ss_dssp             TSTTHHHHHHHSCCCCSSCTTEEEEESSCCC
T ss_pred             hHHHHHHHHHHHHHHHhcCCcEEEEEeccCC
Confidence            99999999988766 5667789999988433

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.40  E-value=4.4e-12  Score=119.74  Aligned_cols=199  Identities=13%  Similarity=0.051  Sum_probs=119.3

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      .....++||+..++.|..++..+. ..+.+.|+|++|+||||||+.+++.....+.......        ..... ...+
T Consensus        20 ~~~~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~--------~~~~~-~~~~   89 (250)
T 1njg_A           20 QTFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPC--------GVCDN-CREI   89 (250)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCC--------SCSHH-HHHH
T ss_pred             ccHHHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCC--------cccHH-HHHH
Confidence            344679999999999999987543 2347899999999999999999987654321100000        00000 0000


Q ss_pred             HHHH----hcCCCCCCchhhcHHHHHHH-----hcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccchhhh
Q 009306          265 LSTL----LNDGNVKNFLNTDLNFQSRR-----LTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDRQVL  333 (538)
Q Consensus       265 ~~~l----~~~~~~~~~~~~~~~~l~~~-----l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~  333 (538)
                      ....    ................+.+.     ..+++.+|||||++.  ...+..+...+.....+..+|+||+.....
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~  169 (250)
T 1njg_A           90 EQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  169 (250)
T ss_dssp             HTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGS
T ss_pred             hccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhC
Confidence            0000    00000000000001111111     124678999999964  455666655554445677888888665321


Q ss_pred             -hh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          334 -AN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       334 -~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                       .. ......+++++++.++..+++...+....  .....+....+++.++|+|..+..+...+
T Consensus       170 ~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~--~~~~~~~~~~l~~~~~G~~~~~~~~~~~~  231 (250)
T 1njg_A          170 PVTILSRCLQFHLKALDVEQIRHQLEHILNEEH--IAHEPRALQLLARAAEGSLRDALSLTDQA  231 (250)
T ss_dssp             CHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTT--CCBCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence             11 12246899999999999999988763321  23346778899999999999888776544

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.36  E-value=3.2e-12  Score=119.03  Aligned_cols=187  Identities=11%  Similarity=0.079  Sum_probs=115.7

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eee-EEEEeehhhhhhcCChHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSG-SYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~-~~~~~~~~~~~~~~~~~~l~  261 (538)
                      |.....++||+..++.+..++..+.  .+.+.|+|++|+|||+||+.+++.+... +.. .+.+. .   ........+.
T Consensus        13 p~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~-~---~~~~~~~~~~   86 (226)
T 2chg_A           13 PRTLDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN-A---SDERGIDVVR   86 (226)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEE-T---TCTTCHHHHH
T ss_pred             CCCHHHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEec-c---ccccChHHHH
Confidence            3445679999999999999997542  2238999999999999999999876433 222 22222 1   1111222211


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchhhh-hh-cC
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQVL-AN-CG  337 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~~-~~-~~  337 (538)
                       ..+........              ....++.+|||||++..  ...+.+...+.....+..+|+||+..... .. ..
T Consensus        87 -~~~~~~~~~~~--------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~  151 (226)
T 2chg_A           87 -HKIKEFARTAP--------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQS  151 (226)
T ss_dssp             -HHHHHHHTSCC--------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHT
T ss_pred             -HHHHHHhcccC--------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHH
Confidence             11111111100              01256789999999653  34444544443335677888888765321 11 12


Q ss_pred             CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          338 VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       338 ~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      ....+++++++.++..+++...+....  .....+....+++.++|+|..+..+..
T Consensus       152 r~~~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~l~~~~~g~~r~l~~~l~  205 (226)
T 2chg_A          152 RCAVFRFKPVPKEAMKKRLLEICEKEG--VKITEDGLEALIYISGGDFRKAINALQ  205 (226)
T ss_dssp             TSEEEECCCCCHHHHHHHHHHHHHHHT--CCBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hCceeecCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            234889999999999999988763211  124466788899999999986554444

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.22  E-value=4.8e-11  Score=117.95  Aligned_cols=188  Identities=15%  Similarity=0.225  Sum_probs=114.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-ee-eEEEEeehhhhhhcCChHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FS-GSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~-~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      |.....++|++..++.|..++..+.  .+.+.|+|++|+|||++|+.+++.+... +. ..+.+.    ........ ..
T Consensus        17 p~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~----~~~~~~~~-~i   89 (323)
T 1sxj_B           17 PQVLSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN----ASDDRGID-VV   89 (323)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC----TTSCCSHH-HH
T ss_pred             CCCHHHHHCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEec----CccccChH-HH
Confidence            3344679999999999999987643  2238999999999999999999886432 22 122222    11111211 11


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchhh-hhh-c
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQV-LAN-C  336 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~-~~~-~  336 (538)
                      +.++..+....              ..+ .+++.+|||||++..  .....+...+....+++.+|++|+.... ... .
T Consensus        90 ~~~~~~~~~~~--------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~  155 (323)
T 1sxj_B           90 RNQIKHFAQKK--------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQ  155 (323)
T ss_dssp             HTHHHHHHHBC--------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHH
T ss_pred             HHHHHHHHhcc--------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHH
Confidence            22222211000              001 345789999999753  3344444433333456788887765422 111 1


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHHHHH
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVLGRY  394 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~~~~  394 (538)
                      .....+++.+++.++..+++...+...  ......+....+++.++|+|. ++..+...
T Consensus       156 sr~~~i~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~~~~G~~r~a~~~l~~~  212 (323)
T 1sxj_B          156 SQCAILRYSKLSDEDVLKRLLQIIKLE--DVKYTNDGLEAIIFTAEGDMRQAINNLQST  212 (323)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhceEEeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            234589999999999999998876221  112346778899999999995 44544433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.22  E-value=8e-11  Score=116.57  Aligned_cols=190  Identities=16%  Similarity=0.128  Sum_probs=116.3

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce-e-eEEEEeehhhhhhcCChHHH
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-S-GSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~-~~~~~~~~~~~~~~~~~~~l  260 (538)
                      .|.....++|++..++.|..++..+  ..+.+.|+|++|+|||++|+.+++.+.... . ..+.+. .........+...
T Consensus        20 ~p~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~   96 (327)
T 1iqp_A           20 RPQRLDDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELN-ASDERGINVIREK   96 (327)
T ss_dssp             CCCSTTTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE-TTCHHHHHTTHHH
T ss_pred             CCCCHHHhhCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEee-ccccCchHHHHHH
Confidence            3445577999999999999998764  233489999999999999999998764321 1 122222 1110000011111


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchhh-hhhc-
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQV-LANC-  336 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~~-~~~~-  336 (538)
                      ...+.    ....              ...+++.+||+||++..  .....+...+.....++++|+||..... ...+ 
T Consensus        97 ~~~~~----~~~~--------------~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~  158 (327)
T 1iqp_A           97 VKEFA----RTKP--------------IGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQ  158 (327)
T ss_dssp             HHHHH----HSCC--------------GGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHH
T ss_pred             HHHHH----hhCC--------------cCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHH
Confidence            11110    0000              01256789999999753  4455555444433567788888765422 1111 


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                      .....+.+.+++.++..+++...+...  ......+....+++.++|+|..+..+...+
T Consensus       159 sr~~~~~~~~l~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~~~~g~~r~~~~~l~~~  215 (327)
T 1iqp_A          159 SRCAIFRFRPLRDEDIAKRLRYIAENE--GLELTEEGLQAILYIAEGDMRRAINILQAA  215 (327)
T ss_dssp             HTEEEEECCCCCHHHHHHHHHHHHHTT--TCEECHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhCcEEEecCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            122478999999999999998876322  223456778899999999998665544433

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.22  E-value=6.1e-10  Score=110.15  Aligned_cols=257  Identities=17%  Similarity=0.131  Sum_probs=151.6

Q ss_pred             CCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      .....|+|++..++.+...+..   .......+.|+|++|+|||+||+.+++.....|   .++. .   ........+.
T Consensus         9 ~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~---~~~~-~---~~~~~~~~l~   81 (324)
T 1hqc_A            9 KTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNL---RVTS-G---PAIEKPGDLA   81 (324)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTCCE---EEEC-T---TTCCSHHHHH
T ss_pred             ccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCCCE---EEEe-c---cccCChHHHH
Confidence            3457899999999998887753   112335689999999999999999998764332   2332 1   1111111111


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCC------------------CCCC
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLF------------------ASGS  321 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~------------------~~~~  321 (538)
                          ..+..                 . ..++.+|+||+++..  .....+...+...                  .++.
T Consensus        82 ----~~l~~-----------------~-~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~  139 (324)
T 1hqc_A           82 ----AILAN-----------------S-LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF  139 (324)
T ss_dssp             ----HHHTT-----------------T-CCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCC
T ss_pred             ----HHHHH-----------------h-ccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCE
Confidence                11100                 0 135679999999754  2333332211110                  1245


Q ss_pred             EEEEeccchhhh-hhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCC
Q 009306          322 RIIITTRDRQVL-ANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGK  398 (538)
Q Consensus       322 ~iiiTtR~~~~~-~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~  398 (538)
                      .+|.+|...... ..+  .....+.+++++.++..+++...+....  .....+....++++++|+|..+..+...+...
T Consensus       140 ~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~--~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~  217 (324)
T 1hqc_A          140 TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLG--VRITEEAALEIGRRSRGTMRVAKRLFRRVRDF  217 (324)
T ss_dssp             EEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTT--CCCCHHHHHHHHHHSCSCHHHHHHHHHHHTTT
T ss_pred             EEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHccCCHHHHHHHHHHHHHH
Confidence            666666543221 111  1235789999999999999988763322  23456778899999999998887776655321


Q ss_pred             ---------CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccc--cCCCCHHHHHHHHHhCCCChHHHH
Q 009306          399 ---------RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACF--FIDEDRDTATKFLDDCEFFATSAI  467 (538)
Q Consensus       399 ---------~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f--~~~~~~~~l~~l~~~~~~~~~~~l  467 (538)
                               +.......+..+            ......+++.++.++..+...  .++++...+...++.+.......+
T Consensus       218 a~~~~~~~i~~~~~~~~~~~~------------~~~~~~l~~~e~~~i~~~~~~~~g~~~~~~~~a~~lgi~~~tl~~~l  285 (324)
T 1hqc_A          218 AQVAGEEVITRERALEALAAL------------GLDELGLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVH  285 (324)
T ss_dssp             STTTSCSCCCHHHHHHHHHHH------------TCCTTCCCHHHHHHHHHHHHHSCSSCCCHHHHHHHTTSCHHHHHHHT
T ss_pred             HHHhcCCCCCHHHHHHHHHHh------------cccccCCCHHHHHHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHH
Confidence                     122222222221            122345777777777766543  234667777777654433334444


Q ss_pred             HH-HhhCCceeEecCCcE
Q 009306          468 EV-LVDKHLITISVLNKI  484 (538)
Q Consensus       468 ~~-L~~~~Li~~~~~~~~  484 (538)
                      +. +++.++|.....|+.
T Consensus       286 ~~~~i~~~li~~~~~g~~  303 (324)
T 1hqc_A          286 EPYLIRQGLLKRTPRGRV  303 (324)
T ss_dssp             HHHHHHTTSEEEETTEEE
T ss_pred             hHHHHHhcchhcCCccce
Confidence            44 889999997755543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=99.10  E-value=1.3e-09  Score=107.39  Aligned_cols=188  Identities=11%  Similarity=0.072  Sum_probs=116.3

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eee-EEEEeehhhhhhcCChHH
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSG-SYFARNVREAEETCRLGD  259 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~-~~~~~~~~~~~~~~~~~~  259 (538)
                      ..|.....++|++..++.+..++..+.  .+.+.|+|++|+|||++|+.+++.+... +.. .+.+. .........+..
T Consensus        11 ~~p~~~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~   87 (319)
T 2chq_A           11 YRPRTLDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN-ASDERGIDVVRH   87 (319)
T ss_dssp             TSCSSGGGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEE-TTSTTCTTTSSH
T ss_pred             cCCCCHHHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEe-CccccChHHHHH
Confidence            344455779999999999999887542  2338999999999999999999876322 111 12222 111000011111


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-hhhh
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-VLAN  335 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~  335 (538)
                      ....+....                   .+ .+++.++||||++..  .....+...+.....+..+|++|.... +...
T Consensus        88 ~~~~~~~~~-------------------~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~  148 (319)
T 2chq_A           88 KIKEFARTA-------------------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEP  148 (319)
T ss_dssp             HHHHHHHSC-------------------CSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHH
T ss_pred             HHHHHHhcC-------------------CCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchH
Confidence            111111000                   01 246789999999753  445666666655556777887776543 2111


Q ss_pred             -cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          336 -CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       336 -~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                       ......+++.+++.++..+++...+...  ......+....+++.++|++..+.....
T Consensus       149 l~sr~~~i~~~~~~~~~~~~~l~~~~~~~--~~~i~~~~l~~l~~~~~G~~r~~~~~l~  205 (319)
T 2chq_A          149 IQSRCAVFRFKPVPKEAMKKRLLEICEKE--GVKITEDGLEALIYISGGDFRKAINALQ  205 (319)
T ss_dssp             HHTTCEEEECCCCCHHHHHHHHHHHHHTT--CCCBCHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             HHhhCeEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence             1233589999999999999998876322  2234567788899999999976544433

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.02  E-value=6.3e-09  Score=103.50  Aligned_cols=262  Identities=15%  Similarity=0.141  Sum_probs=152.9

Q ss_pred             CCCCCceeccchhHHHHHhhhcC---CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTG---STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~---~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      .....++|++..++.+..++...   ......+.|+|++|+|||+||+.+++.....|   +.+. ..   .......+.
T Consensus        26 ~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~---~~~~-~~---~~~~~~~~~   98 (338)
T 3pfi_A           26 SNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSANI---KTTA-AP---MIEKSGDLA   98 (338)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCE---EEEE-GG---GCCSHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCe---EEec-ch---hccchhHHH
Confidence            34578999999999999888642   23345689999999999999999998865443   2222 11   011111110


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCC------------------CCCC
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLF------------------ASGS  321 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~------------------~~~~  321 (538)
                       .+                    +..  ..++.+|+||+++..  .....+...+...                  .++.
T Consensus        99 -~~--------------------~~~--~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~  155 (338)
T 3pfi_A           99 -AI--------------------LTN--LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKF  155 (338)
T ss_dssp             -HH--------------------HHT--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCC
T ss_pred             -HH--------------------HHh--ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCe
Confidence             11                    100  245679999999743  3333332222110                  1235


Q ss_pred             EEEEeccchhhh-hhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhc--
Q 009306          322 RIIITTRDRQVL-ANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLY--  396 (538)
Q Consensus       322 ~iiiTtR~~~~~-~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~--  396 (538)
                      .+|.+|...... ..+  .....+.+++++.++..+++...+..  .......+....+++.+.|+|-.+..+...+.  
T Consensus       156 ~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~--~~~~~~~~~~~~l~~~~~G~~r~l~~~l~~~~~~  233 (338)
T 3pfi_A          156 TLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALK--LNKTCEEKAALEIAKRSRSTPRIALRLLKRVRDF  233 (338)
T ss_dssp             EEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHH--TTCEECHHHHHHHHHTTTTCHHHHHHHHHHHHHH
T ss_pred             EEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHh--cCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            566666543221 111  23468999999999999999887622  12234567788889999999966655444321  


Q ss_pred             ----CC---CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhcccccc-CCCCHHHHHHHHHhCCCChHHHHH
Q 009306          397 ----GK---RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACFF-IDEDRDTATKFLDDCEFFATSAIE  468 (538)
Q Consensus       397 ----~~---~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f~-~~~~~~~l~~l~~~~~~~~~~~l~  468 (538)
                          +.   +.......+..            +..+...++..++.++..++-.. ...+...+...++.+.......++
T Consensus       234 a~~~~~~~i~~~~~~~~~~~------------~~~~~~~l~~~e~~~l~~l~~~~~~~~~~~~~a~~lg~~~~tl~~~l~  301 (338)
T 3pfi_A          234 ADVNDEEIITEKRANEALNS------------LGVNELGFDAMDLRYLELLTAAKQKPIGLASIAAALSEDENTIEDVIE  301 (338)
T ss_dssp             HHHTTCSEECHHHHHHHHHH------------HTCCTTCCCHHHHHHHHHHHHSCSCCBCHHHHHHHTTCCHHHHHHTTH
T ss_pred             HHhhcCCccCHHHHHHHHHH------------hCCcccCCCHHHHHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHHh
Confidence                11   12222222221            12223345555566666665542 235677777777554444455666


Q ss_pred             -HHhhCCceeEecCCcEEecHHH
Q 009306          469 -VLVDKHLITISVLNKIEMHYLL  490 (538)
Q Consensus       469 -~L~~~~Li~~~~~~~~~~H~lv  490 (538)
                       .|++.++|.....|+.....-+
T Consensus       302 ~~l~~~gli~~~~~g~~~t~~~~  324 (338)
T 3pfi_A          302 PYLLANGYIERTAKGRIASAKSY  324 (338)
T ss_dssp             HHHHHTTSEEEETTEEEECHHHH
T ss_pred             HHHHHcCceecCCCcccccHHHH
Confidence             8999999998867766544433

>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=98.98  E-value=3e-09  Score=107.23  Aligned_cols=196  Identities=13%  Similarity=0.091  Sum_probs=114.5

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQL  264 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l  264 (538)
                      .....++|++..++.|...+..+. ..+.+.|+|++|+||||+|+.+++.+....... ...       ...... ...+
T Consensus        13 ~~~~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~-~~~-------~~~~~~-~~~~   82 (373)
T 1jr3_A           13 QTFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT-ATP-------CGVCDN-CREI   82 (373)
T ss_dssp             CSTTTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSC-SSC-------CSSSHH-HHHH
T ss_pred             CchhhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCC-CCC-------CcccHH-HHHH
Confidence            344679999999999999887543 234689999999999999999998764321100 000       000000 0000


Q ss_pred             HHH----Hhc-CCCCCCchhhcHHHHHHHh-----cCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccchh-
Q 009306          265 LST----LLN-DGNVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDRQ-  331 (538)
Q Consensus       265 ~~~----l~~-~~~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~~-  331 (538)
                      ...    +.. ........+. ...+.+.+     .+++.+|||||++.  ......+...+.....+..+|++|.... 
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~  161 (373)
T 1jr3_A           83 EQGRFVDLIEIDAASRTKVED-TRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQK  161 (373)
T ss_dssp             HTSCCSSCEEEETTCSCCSSC-HHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGG
T ss_pred             hccCCCceEEecccccCCHHH-HHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHh
Confidence            000    000 0000011111 12222222     24568999999964  3445556555544445667777765442 


Q ss_pred             hhhh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          332 VLAN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       332 ~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      +... ......+++.+++.++..+++...+...  ......+....+++.++|+|..+..+..
T Consensus       162 l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~--~~~~~~~a~~~l~~~~~G~~r~~~~~l~  222 (373)
T 1jr3_A          162 LPVTILSRCLQFHLKALDVEQIRHQLEHILNEE--HIAHEPRALQLLARAAEGSLRDALSLTD  222 (373)
T ss_dssp             SCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             CcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            2111 1234689999999999999998765221  1223466788899999999987766543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.88  E-value=8.8e-09  Score=100.27  Aligned_cols=168  Identities=10%  Similarity=0.068  Sum_probs=98.7

Q ss_pred             CCceeccchhHHHHHhhhc--CCCCceEEEEeccCCCchhHHHHHHHHhhccce-------eeEEEEeehhhhhhcCChH
Q 009306          188 EDLVGVRLPMKEIESLLRT--GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-------SGSYFARNVREAEETCRLG  258 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~--~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-------~~~~~~~~~~~~~~~~~~~  258 (538)
                      ..+.||+.|+++|...|..  ..+....+.|+|++|.|||++++.+++++....       -..+++.+.    ......
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~----~~~t~~   95 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDAL----ELAGMD   95 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETT----CCC--H
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEecc----ccCCHH
Confidence            3488999999999988765  234566789999999999999999999875321       123444422    234455


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHh---cCCCeEEEEecCCChH---HHHHHhcCcCCCCCCCEEEEeccchh-
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL---TRKKVLIVFDDVDHPR---QIKILVGRLDLFASGSRIIITTRDRQ-  331 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l---~~k~~LlVlDdv~~~~---~~~~l~~~l~~~~~~~~iiiTtR~~~-  331 (538)
                      .++..+..++.+..............+...+   .+++++++||+++...   .+-.+............||.++.... 
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            6677777777554221111122222222222   4567999999997642   22222211000011223333343221 


Q ss_pred             ---hh-----hhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          332 ---VL-----ANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       332 ---~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                         .+     ..+. ...+.+++++.+|..+++..++
T Consensus       176 ~~~~L~~~v~SR~~-~~~i~F~pYt~~el~~Il~~Rl  211 (318)
T 3te6_A          176 IREQINIMPSLKAH-FTEIKLNKVDKNELQQMIITRL  211 (318)
T ss_dssp             CHHHHHTCHHHHTT-EEEEECCCCCHHHHHHHHHHHH
T ss_pred             chhhcchhhhccCC-ceEEEeCCCCHHHHHHHHHHHH
Confidence               11     1221 2578999999999999998887

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.86  E-value=6.1e-09  Score=97.97  Aligned_cols=176  Identities=14%  Similarity=0.107  Sum_probs=102.5

Q ss_pred             CCCCceecc---chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          186 ENEDLVGVR---LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       186 ~~~~~vGR~---~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      ..++|+|+.   ..++.+..+...+  ..+.+.|+|++|+||||||+.+++........+.++.. .....  .+     
T Consensus        26 ~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~-~~~~~--~~-----   95 (242)
T 3bos_A           26 TFTSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPL-GIHAS--IS-----   95 (242)
T ss_dssp             STTTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEG-GGGGG--SC-----
T ss_pred             ChhhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEH-HHHHH--HH-----
Confidence            346788743   4455555555432  45679999999999999999999887654334455542 11100  00     


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH--H--HHHHhcCcCCC-CCC-CEEEEeccchh-----
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR--Q--IKILVGRLDLF-ASG-SRIIITTRDRQ-----  331 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--~--~~~l~~~l~~~-~~~-~~iiiTtR~~~-----  331 (538)
                                      ....    +.+ .++.+|||||++...  .  .+.+...+... ..+ .++|+||+...     
T Consensus        96 ----------------~~~~----~~~-~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~  154 (242)
T 3bos_A           96 ----------------TALL----EGL-EQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGF  154 (242)
T ss_dssp             ----------------GGGG----TTG-GGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTC
T ss_pred             ----------------HHHH----Hhc-cCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHH
Confidence                            0000    001 346799999996431  1  22222221100 122 24777776331     


Q ss_pred             ----hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHH
Q 009306          332 ----VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRY  394 (538)
Q Consensus       332 ----~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~  394 (538)
                          +...+.....+++++++.++..+++...+...  ......+....+++.++|++..+..+...
T Consensus       155 ~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~~~~g~~r~l~~~l~~  219 (242)
T 3bos_A          155 VLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMR--GLQLPEDVGRFLLNRMARDLRTLFDVLDR  219 (242)
T ss_dssp             CCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHT--TCCCCHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             hhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHccCCHHHHHHHHHH
Confidence                11111122689999999999999998876321  12344677889999999998776655443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.85  E-value=7.3e-09  Score=93.54  Aligned_cols=49  Identities=18%  Similarity=0.295  Sum_probs=41.4

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....++||+.+++.+.+.+..+  ..+.+.|+|++|+|||+||+.+++.+.
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             cccccccchHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            3467999999999999988753  345689999999999999999998764

>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=98.84  E-value=8.3e-08  Score=96.00  Aligned_cols=203  Identities=15%  Similarity=0.107  Sum_probs=115.5

Q ss_pred             hhHHHHHHHHhhhccccccCCCCCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHH
Q 009306          164 ESALIEEIVNAILKRLDDTFHSENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       164 e~~~i~~i~~~~~~~~~~~~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +...++.+...+....+   +..-..++|.+..++.|.+.+..          .....+.+.|+|++|+|||+||+.++.
T Consensus        63 ~~~~~~~i~~~i~~~~~---~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~  139 (357)
T 3d8b_A           63 EPKMIELIMNEIMDHGP---PVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIAS  139 (357)
T ss_dssp             CHHHHHHHHHHTBCCSC---CCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHH
T ss_pred             ChHHHHHHHhhcccCCC---CCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            45566666666654433   33446799999999999887642          112355799999999999999999998


Q ss_pred             hhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHH-HHHHHhcCCCeEEEEecCCCh--------
Q 009306          234 KISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLN-FQSRRLTRKKVLIVFDDVDHP--------  304 (538)
Q Consensus       234 ~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~-~l~~~l~~k~~LlVlDdv~~~--------  304 (538)
                      .....|   +.+. ....... ..                  ........ .+......++.+|+||+++..        
T Consensus       140 ~~~~~~---~~i~-~~~l~~~-~~------------------g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~  196 (357)
T 3d8b_A          140 QSGATF---FSIS-ASSLTSK-WV------------------GEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGE  196 (357)
T ss_dssp             HTTCEE---EEEE-GGGGCCS-ST------------------THHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC-----
T ss_pred             HcCCeE---EEEe-hHHhhcc-cc------------------chHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCc
Confidence            764322   2222 2111100 00                  00011111 111122356789999999532        


Q ss_pred             -----HHHHHHhcCcC----CCCCCCEEEEeccchhhh-hh--cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHH
Q 009306          305 -----RQIKILVGRLD----LFASGSRIIITTRDRQVL-AN--CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTE  372 (538)
Q Consensus       305 -----~~~~~l~~~l~----~~~~~~~iiiTtR~~~~~-~~--~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~  372 (538)
                           .....++..+.    ....+..||.||.....+ ..  -.....+.++..+.++..+++...+...  ......+
T Consensus       197 ~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~--~~~l~~~  274 (357)
T 3d8b_A          197 HESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKE--QCCLSEE  274 (357)
T ss_dssp             -CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTS--CBCCCHH
T ss_pred             chHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhc--CCCccHH
Confidence                 11223322221    112344556566543211 11  1334578899999999999988776222  1123356


Q ss_pred             HHHHHHHHhcC-CcHHHHHHHHH
Q 009306          373 LACKTIKYARG-VPLALEVLGRY  394 (538)
Q Consensus       373 ~~~~i~~~~~G-~PLal~~~~~~  394 (538)
                      ....+++.+.| .+..|..+...
T Consensus       275 ~l~~la~~t~G~s~~dl~~l~~~  297 (357)
T 3d8b_A          275 EIEQIVQQSDAFSGADMTQLCRE  297 (357)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHH
Confidence            77889999988 45566666553

>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=98.84  E-value=3.5e-08  Score=103.80  Aligned_cols=195  Identities=15%  Similarity=0.177  Sum_probs=107.0

Q ss_pred             CCCCCCCceeccchhHHHHHhhhcC---------------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEee
Q 009306          183 FHSENEDLVGVRLPMKEIESLLRTG---------------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARN  247 (538)
Q Consensus       183 ~~~~~~~~vGR~~~l~~l~~~L~~~---------------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~  247 (538)
                      .|.....++|++..++.|..++...               .+..+.+.|+|++|+|||++|+.+++...  +. .+.+. 
T Consensus        34 rP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~--~~-~i~in-  109 (516)
T 1sxj_A           34 APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG--YD-ILEQN-  109 (516)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT--CE-EEEEC-
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC--CC-EEEEe-
Confidence            3445578999999999999988641               01346899999999999999999999873  21 22222 


Q ss_pred             hhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-----HHHHHHhcCcCCCCCCCE
Q 009306          248 VREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-----RQIKILVGRLDLFASGSR  322 (538)
Q Consensus       248 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~  322 (538)
                      .   +.... ..+....+..................  ......++.+|+||+++..     ..+..+...+.  ..+..
T Consensus       110 ~---s~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~--~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~--~~~~~  181 (516)
T 1sxj_A          110 A---SDVRS-KTLLNAGVKNALDNMSVVGYFKHNEE--AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTP  181 (516)
T ss_dssp             T---TSCCC-HHHHHHTGGGGTTBCCSTTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSC
T ss_pred             C---CCcch-HHHHHHHHHHHhccccHHHHHhhhhh--hhhccCCCeEEEEECCCccchhhHHHHHHHHHHHH--hcCCC
Confidence            1   11111 12222222211111111111111000  0011357789999999643     11233332222  12344


Q ss_pred             EEEeccchh---hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH-HHHH
Q 009306          323 IIITTRDRQ---VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA-LEVL  391 (538)
Q Consensus       323 iiiTtR~~~---~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa-l~~~  391 (538)
                      ||+++.+..   +.........+.+++++.++..+++...+.....  ....+....+++.++|.+-. +..+
T Consensus       182 iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~--~i~~~~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          182 LILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKF--KLDPNVIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             EEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTC--CCCTTHHHHHHHHTTTCHHHHHHHH
T ss_pred             EEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHcCCcHHHHHHHH
Confidence            555554321   2222233467899999999999998776532111  12345578899999996644 4444

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.82  E-value=2.4e-08  Score=96.62  Aligned_cols=183  Identities=19%  Similarity=0.215  Sum_probs=104.3

Q ss_pred             CCCCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh
Q 009306          185 SENEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE  253 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~  253 (538)
                      ....+++|.+..+++|.+.+..           +....+.+.|+|++|+|||+||+.++......|   +.+. ......
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~---~~v~-~~~~~~   89 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATF---IRVV-GSELVK   89 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEE---EEEE-GGGGCC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCE---EEEe-hHHHHH
Confidence            3457799999999999887643           123445699999999999999999998865432   1222 111100


Q ss_pred             cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcC--
Q 009306          254 TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLD--  315 (538)
Q Consensus       254 ~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~--  315 (538)
                      . ....                 ........+.......+.+|+|||++..                ..+..++..+.  
T Consensus        90 ~-~~~~-----------------~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~  151 (285)
T 3h4m_A           90 K-FIGE-----------------GASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGF  151 (285)
T ss_dssp             C-STTH-----------------HHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTT
T ss_pred             h-ccch-----------------HHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCC
Confidence            0 0000                 0011111122223456789999999643                12222222221  


Q ss_pred             CCCCCCEEEEeccchhhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcC-CcHHHH
Q 009306          316 LFASGSRIIITTRDRQVLA-----NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARG-VPLALE  389 (538)
Q Consensus       316 ~~~~~~~iiiTtR~~~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G-~PLal~  389 (538)
                      ....+..||.||.....+.     .......+.++.++.++..+++...........   ......++..+.| .|-.|.
T Consensus       152 ~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~---~~~~~~l~~~~~g~~~~~i~  228 (285)
T 3h4m_A          152 DARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAE---DVNLEEIAKMTEGCVGAELK  228 (285)
T ss_dssp             CSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCT---TCCHHHHHHHCTTCCHHHHH
T ss_pred             CCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCC---cCCHHHHHHHcCCCCHHHHH
Confidence            1133566777776543321     112335789999999999999988873322211   1124567777777 454555


Q ss_pred             HHH
Q 009306          390 VLG  392 (538)
Q Consensus       390 ~~~  392 (538)
                      .+.
T Consensus       229 ~l~  231 (285)
T 3h4m_A          229 AIC  231 (285)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.78  E-value=3.4e-08  Score=98.67  Aligned_cols=196  Identities=9%  Similarity=0.061  Sum_probs=112.0

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc--eee-EEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--FSG-SYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--f~~-~~~~~~~~~~~~~~~~~~l  260 (538)
                      |.....++|++..++.|...+..+..  +.+.|+|++|+||||+|+.++..+...  +.. ...+. .   ........+
T Consensus        33 p~~~~~i~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~-~---~~~~~~~~~  106 (353)
T 1sxj_D           33 PKNLDEVTAQDHAVTVLKKTLKSANL--PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN-A---SDERGISIV  106 (353)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTTC--CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC-S---SSCCCHHHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHhcCCC--CEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEc-c---ccccchHHH
Confidence            44457899999999999999875432  238999999999999999999875421  211 12222 1   111122221


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-  336 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-  336 (538)
                       .............. ....   .....-..++-+|++|+++..  .....+...+.......++|++|.... +...+ 
T Consensus       107 -~~~~~~~~~~~~~~-~~~~---~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~  181 (353)
T 1sxj_D          107 -REKVKNFARLTVSK-PSKH---DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLA  181 (353)
T ss_dssp             -TTHHHHHHHSCCCC-CCTT---HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHH
T ss_pred             -HHHHHHHhhhcccc-cchh---hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhh
Confidence             22222211110000 0000   000111234569999999643  334444443333345567777764432 21111 


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHH
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLG  392 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~  392 (538)
                      .....+.+.+++.++..+.+...+...  ......+....+++.++|+|..+..+.
T Consensus       182 sR~~~i~~~~~~~~~~~~~l~~~~~~~--~~~i~~~~l~~l~~~~~G~~r~~~~~l  235 (353)
T 1sxj_D          182 SQCSKFRFKALDASNAIDRLRFISEQE--NVKCDDGVLERILDISAGDLRRGITLL  235 (353)
T ss_dssp             HHSEEEECCCCCHHHHHHHHHHHHHTT--TCCCCHHHHHHHHHHTSSCHHHHHHHH
T ss_pred             ccCceEEeCCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            112478999999999999998876322  223446788999999999997654443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.77  E-value=1.4e-07  Score=94.93  Aligned_cols=203  Identities=11%  Similarity=0.022  Sum_probs=108.5

Q ss_pred             CCCceeccchhHHHH---HhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          187 NEDLVGVRLPMKEIE---SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~---~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      .+.|+|++..++.+.   ..+..+....+.+.|+|++|+|||+||+.++..+....+.. .+.+..-............+
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~  121 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFT-AIAGSEIFSLEMSKTEALTQ  121 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEE-EEEGGGGSCSSSCHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcc-cccchhhhhcccchhHHHHH
Confidence            468999999877654   44444433346799999999999999999999876432211 12211111111122222222


Q ss_pred             HHHHHhcC--------------------C--------CC--CCchhhcHHHHHHHh-----cCC----CeEEEEecCCCh
Q 009306          264 LLSTLLND--------------------G--------NV--KNFLNTDLNFQSRRL-----TRK----KVLIVFDDVDHP  304 (538)
Q Consensus       264 l~~~l~~~--------------------~--------~~--~~~~~~~~~~l~~~l-----~~k----~~LlVlDdv~~~  304 (538)
                      .+....+.                    .        ..  ..........+....     .++    +.+|+||+++..
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~~l  201 (368)
T 3uk6_A          122 AFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHML  201 (368)
T ss_dssp             HHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGGGS
T ss_pred             HHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhcccc
Confidence            22221100                    0        00  000111111111111     122    469999999753


Q ss_pred             --HHHHHHhcCcCCCCCCCEEEEeccc------------h-hhhh-hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCC
Q 009306          305 --RQIKILVGRLDLFASGSRIIITTRD------------R-QVLA-NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHE  368 (538)
Q Consensus       305 --~~~~~l~~~l~~~~~~~~iiiTtR~------------~-~~~~-~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~  368 (538)
                        +....+...+...... .++++|..            . .+.. .......+.+++++.++..+++...+..  ....
T Consensus       202 ~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~--~~~~  278 (368)
T 3uk6_A          202 DIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEE--EDVE  278 (368)
T ss_dssp             BHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHH--TTCC
T ss_pred             ChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHH--cCCC
Confidence              4445555444432222 34444421            1 0101 1112245899999999999999987632  1233


Q ss_pred             chHHHHHHHHHHhc-CCcHHHHHHHH
Q 009306          369 SHTELACKTIKYAR-GVPLALEVLGR  393 (538)
Q Consensus       369 ~~~~~~~~i~~~~~-G~PLal~~~~~  393 (538)
                      ...+....+++.+. |.|..+..+..
T Consensus       279 ~~~~~l~~l~~~~~~G~~r~~~~ll~  304 (368)
T 3uk6_A          279 MSEDAYTVLTRIGLETSLRYAIQLIT  304 (368)
T ss_dssp             BCHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCCHHHHHHHHH
Confidence            45677889999998 88876655444

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.76  E-value=4.2e-08  Score=98.09  Aligned_cols=201  Identities=11%  Similarity=0.038  Sum_probs=108.6

Q ss_pred             cCCCCCCCceeccchhHHHHHhh-hcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEee-------------
Q 009306          182 TFHSENEDLVGVRLPMKEIESLL-RTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARN-------------  247 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L-~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~-------------  247 (538)
                      ..|.....++|++..++.+..++ ..+. ... +.|+|++|+||||+++.++..+.....+.+.+..             
T Consensus         8 yrP~~~~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~   85 (354)
T 1sxj_E            8 YRPKSLNALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLEL   85 (354)
T ss_dssp             TCCCSGGGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeeccccccccee
Confidence            34455578999999999999888 5432 233 8999999999999999999854222111111100             


Q ss_pred             ----------hhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcC
Q 009306          248 ----------VREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLD  315 (538)
Q Consensus       248 ----------~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~  315 (538)
                                ..............+.++..+..........     .+ ..+..++-++|||+++..  .....+...+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~-----~l-s~l~~~~~vlilDE~~~L~~~~~~~L~~~le  159 (354)
T 1sxj_E           86 NVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQD-----SK-DGLAHRYKCVIINEANSLTKDAQAALRRTME  159 (354)
T ss_dssp             CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHH
T ss_pred             eeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccc-----cc-cccCCCCeEEEEeCccccCHHHHHHHHHHHH
Confidence                      0000000000001122222221111000000     00 002346779999999753  33344444333


Q ss_pred             CCCCCCEEEEeccch-hhhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCch-HHHHHHHHHHhcCCcHHHHHHH
Q 009306          316 LFASGSRIIITTRDR-QVLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESH-TELACKTIKYARGVPLALEVLG  392 (538)
Q Consensus       316 ~~~~~~~iiiTtR~~-~~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~-~~~~~~i~~~~~G~PLal~~~~  392 (538)
                      ....+..+|++|.+. .+...+ .....+++++++.++..+++...+....  .... .+.+..+++.++|.+..+..+.
T Consensus       160 ~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          160 KYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNER--IQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             HSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHT--CEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcC--CCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            334567777777653 222221 2236899999999999999987762211  1223 4667889999999986554443

>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=98.75  E-value=1.3e-07  Score=93.20  Aligned_cols=185  Identities=13%  Similarity=0.088  Sum_probs=106.9

Q ss_pred             CCCCCceeccchhHHHHHhhh----------cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          185 SENEDLVGVRLPMKEIESLLR----------TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~----------~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ..-..++|.+..++.|.+.+.          ......+.+.|+|++|+|||+||+.+++.....|   +.+. ...... 
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~---~~v~-~~~l~~-   89 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTF---FSVS-SSDLVS-   89 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEE---EEEE-HHHHHT-
T ss_pred             CCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCE---EEEc-hHHHhh-
Confidence            344678999999999988762          1122245699999999999999999998864432   2222 111100 


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHH-HHHHHhcCCCeEEEEecCCChH-------------HHHHHhcCcC---CC
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLN-FQSRRLTRKKVLIVFDDVDHPR-------------QIKILVGRLD---LF  317 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~-~l~~~l~~k~~LlVlDdv~~~~-------------~~~~l~~~l~---~~  317 (538)
                                  ...      ........ ........++.+|+||+++...             ....++..+.   ..
T Consensus        90 ------------~~~------g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  151 (322)
T 3eie_A           90 ------------KWM------GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGND  151 (322)
T ss_dssp             ------------TTG------GGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTS
T ss_pred             ------------ccc------chHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhcccccc
Confidence                        000      00111111 1122224577899999997431             1233322221   12


Q ss_pred             CCCCEEEEeccchhhhhh---cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHHH
Q 009306          318 ASGSRIIITTRDRQVLAN---CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLGR  393 (538)
Q Consensus       318 ~~~~~iiiTtR~~~~~~~---~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~~  393 (538)
                      ..+..||.||.....+..   -.....+.++..+.++-.+++..++..  .+..........+++.+.|. +-.|..+..
T Consensus       152 ~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~--~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          152 SQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGD--TPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             CCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTT--CCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             CCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhcc--CCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            345556666655322110   024467889999999999999988732  22223455677888888874 555555544


Q ss_pred             H
Q 009306          394 Y  394 (538)
Q Consensus       394 ~  394 (538)
                      .
T Consensus       230 ~  230 (322)
T 3eie_A          230 D  230 (322)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.73  E-value=5.6e-08  Score=99.93  Aligned_cols=185  Identities=16%  Similarity=0.138  Sum_probs=106.5

Q ss_pred             CCCce-eccchh--HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee--eEEEEeehhhhhhcCChHHHH
Q 009306          187 NEDLV-GVRLPM--KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS--GSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       187 ~~~~v-GR~~~l--~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~--~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      .++|+ |....+  ..+......... ...+.|+|++|+||||||+.+++.+...++  ..+++. ..         .+.
T Consensus       104 fd~fv~g~~n~~a~~~~~~~a~~~~~-~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~-~~---------~~~  172 (440)
T 2z4s_A          104 FENFVVGPGNSFAYHAALEVAKHPGR-YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT-SE---------KFL  172 (440)
T ss_dssp             GGGCCCCTTTHHHHHHHHHHHHSTTS-SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEE-HH---------HHH
T ss_pred             hhhcCCCCchHHHHHHHHHHHhCCCC-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee-HH---------HHH
Confidence            34566 655443  233333333222 567999999999999999999998765542  234443 11         122


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----HHHHHHhcCcCC-CCCCCEEEEeccch------
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----RQIKILVGRLDL-FASGSRIIITTRDR------  330 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----~~~~~l~~~l~~-~~~~~~iiiTtR~~------  330 (538)
                      ..+...+...         ....+.+.+..++.+|+|||++..    ...+.+...+.. ...+..||+||.+.      
T Consensus       173 ~~~~~~~~~~---------~~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~  243 (440)
T 2z4s_A          173 NDLVDSMKEG---------KLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSE  243 (440)
T ss_dssp             HHHHHHHHTT---------CHHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSS
T ss_pred             HHHHHHHHcc---------cHHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHH
Confidence            2333333221         112233334436789999999532    222333322211 13567888888753      


Q ss_pred             ---hhhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          331 ---QVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       331 ---~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                         .+...+.....+.+++++.++..+++...+....  .....+....+++.++|++--+.-+..
T Consensus       244 l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~--~~i~~e~l~~la~~~~gn~R~l~~~L~  307 (440)
T 2z4s_A          244 FQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEH--GELPEEVLNFVAENVDDNLRRLRGAII  307 (440)
T ss_dssp             CCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHT--CCCCTTHHHHHHHHCCSCHHHHHHHHH
T ss_pred             HHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHHhcCCCHHHHHHHHH
Confidence               2222232335788999999999999988762111  122345577888999999876654433

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=98.71  E-value=3.8e-07  Score=87.58  Aligned_cols=169  Identities=13%  Similarity=0.097  Sum_probs=93.9

Q ss_pred             CCceeccchhHHHHH-------hhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHH
Q 009306          188 EDLVGVRLPMKEIES-------LLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~-------~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~  259 (538)
                      ..++|....++.+..       .+.. +....+.+.|+|++|+|||+||+.+++.....|   +.+.+.... .......
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~---~~i~~~~~~-~g~~~~~  108 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPF---IKICSPDKM-IGFSETA  108 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSE---EEEECGGGC-TTCCHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCE---EEEeCHHHh-cCCchHH
Confidence            567888877666655       2221 234567899999999999999999998754332   222211100 0000000


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh------------HHHHHHhcCcCC---CCCCCEEE
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP------------RQIKILVGRLDL---FASGSRII  324 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~------------~~~~~l~~~l~~---~~~~~~ii  324 (538)
                      .                 .......+......++.+|+|||++..            ..++.+...+..   .+....||
T Consensus       109 ~-----------------~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii  171 (272)
T 1d2n_A          109 K-----------------CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLII  171 (272)
T ss_dssp             H-----------------HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEE
T ss_pred             H-----------------HHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEE
Confidence            0                 011111122223356789999998643            223444333322   12234466


Q ss_pred             Eeccchhhhhhc----CCCeeEEcCCCCH-HHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC
Q 009306          325 ITTRDRQVLANC----GVDEVYQMEELVH-DDALRLFSRHAFGGDHPHESHTELACKTIKYARGV  384 (538)
Q Consensus       325 iTtR~~~~~~~~----~~~~~~~l~~L~~-~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~  384 (538)
                      .||.....+...    .....+.+++++. ++..+++....       ....+....+++.+.|.
T Consensus       172 ~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~~-------~~~~~~~~~l~~~~~g~  229 (272)
T 1d2n_A          172 GTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLG-------NFKDKERTTIAQQVKGK  229 (272)
T ss_dssp             EEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHHT-------CSCHHHHHHHHHHHTTS
T ss_pred             EecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHhcC-------CCCHHHHHHHHHHhcCC
Confidence            677766544431    1246789999988 66666665532       12356678888888883

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.68  E-value=2.2e-07  Score=91.61  Aligned_cols=180  Identities=14%  Similarity=0.136  Sum_probs=100.3

Q ss_pred             CCCce-eccch--hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          187 NEDLV-GVRLP--MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       187 ~~~~v-GR~~~--l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      .++|+ |....  ...+..++.........+.|+|++|+||||||+.+++.....-...+++. ..         .+...
T Consensus        10 f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~-~~---------~~~~~   79 (324)
T 1l8q_A           10 LENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS-AD---------DFAQA   79 (324)
T ss_dssp             SSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE-HH---------HHHHH
T ss_pred             cccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE-HH---------HHHHH
Confidence            35666 54433  33444444433323456999999999999999999997654322234443 11         11222


Q ss_pred             HHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----HHHHHhcCcCC-CCCCCEEEEeccch--------
Q 009306          264 LLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----QIKILVGRLDL-FASGSRIIITTRDR--------  330 (538)
Q Consensus       264 l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----~~~~l~~~l~~-~~~~~~iiiTtR~~--------  330 (538)
                      +...+...         ....+...+. ++.+|+|||++...    ..+.+...+.. ...+..+|+|+...        
T Consensus        80 ~~~~~~~~---------~~~~~~~~~~-~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~  149 (324)
T 1l8q_A           80 MVEHLKKG---------TINEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVS  149 (324)
T ss_dssp             HHHHHHHT---------CHHHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSC
T ss_pred             HHHHHHcC---------cHHHHHHHhc-CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhh
Confidence            22222111         1111222222 46799999995432    22222222110 13456788887543        


Q ss_pred             -hhhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          331 -QVLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       331 -~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                       .+...+.....+++++ +.++..+++...+...  ......+....+++.+ |++-.+..
T Consensus       150 ~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~--~~~l~~~~l~~l~~~~-g~~r~l~~  206 (324)
T 1l8q_A          150 DRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEF--NLELRKEVIDYLLENT-KNVREIEG  206 (324)
T ss_dssp             HHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHT--TCCCCHHHHHHHHHHC-SSHHHHHH
T ss_pred             hHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhc--CCCCCHHHHHHHHHhC-CCHHHHHH
Confidence             1122222335789999 9999999998877321  2234467788899999 88754433

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.66  E-value=9.3e-07  Score=86.97  Aligned_cols=181  Identities=12%  Similarity=0.059  Sum_probs=103.2

Q ss_pred             CCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhh-ccceeeEEEEeehhhhhhcC
Q 009306          187 NEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKI-SRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~-~~~f~~~~~~~~~~~~~~~~  255 (538)
                      -.+++|.+..++.|.+.+..          .....+.+.|+|++|+|||+||+.++... ...|   +.+. ......  
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~---~~i~-~~~l~~--   84 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTF---FSIS-SSDLVS--   84 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEE---EEEE-CCSSCC--
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCCcE---EEEE-hHHHHh--
Confidence            35678888888777765521          11234679999999999999999999986 2222   1222 110000  


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHH-HHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCC---CC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQS-RRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDL---FA  318 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~-~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~---~~  318 (538)
                                      ... .........+. .....++.+|+||+++..             .....++..+..   ..
T Consensus        85 ----------------~~~-g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~  147 (322)
T 1xwi_A           85 ----------------KWL-GESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDN  147 (322)
T ss_dssp             ----------------SSC-CSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCC
T ss_pred             ----------------hhh-hHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccC
Confidence                            000 01111111121 222457889999999754             112233322221   12


Q ss_pred             CCCEEEEeccchh-----hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHH
Q 009306          319 SGSRIIITTRDRQ-----VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLG  392 (538)
Q Consensus       319 ~~~~iiiTtR~~~-----~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~  392 (538)
                      .+..||.||....     +..  .....+.++..+.++-.+++..+...  .+..........+++.+.|. +-.|..+.
T Consensus       148 ~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~--~~~~l~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          148 DGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGT--TQNSLTEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             TTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTT--CCBCCCHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3445555564332     122  34567889999999999999887722  22222356678889999887 44566555


Q ss_pred             HH
Q 009306          393 RY  394 (538)
Q Consensus       393 ~~  394 (538)
                      ..
T Consensus       224 ~~  225 (322)
T 1xwi_A          224 RD  225 (322)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.66  E-value=2.8e-07  Score=89.72  Aligned_cols=183  Identities=16%  Similarity=0.115  Sum_probs=103.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhcC----------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTG----------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE  253 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~----------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~  253 (538)
                      +..-..++|.+..++.|.+.+...          ....+.+.|+|++|+|||+||+.++......|   +.+. ......
T Consensus        17 ~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~~---~~i~-~~~l~~   92 (297)
T 3b9p_A           17 KVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSATF---LNIS-AASLTS   92 (297)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCEE---EEEE-STTTSS
T ss_pred             CCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCe---EEee-HHHHhh
Confidence            334478999999999998876320          11245789999999999999999998764332   1222 111100


Q ss_pred             cCChHHHHHHHHHHHhcCCCCCCchhhcHH-HHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcC---C
Q 009306          254 TCRLGDLRQQLLSTLLNDGNVKNFLNTDLN-FQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLD---L  316 (538)
Q Consensus       254 ~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~-~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~---~  316 (538)
                      ..                   ......... .+......++.+|+||+++..             .....++..+.   .
T Consensus        93 ~~-------------------~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~  153 (297)
T 3b9p_A           93 KY-------------------VGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPG  153 (297)
T ss_dssp             SS-------------------CSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC-
T ss_pred             cc-------------------cchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccc
Confidence            00                   000111111 111222457789999999543             11122222111   1


Q ss_pred             C--CCCCEEEEeccchh-----hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HH
Q 009306          317 F--ASGSRIIITTRDRQ-----VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-AL  388 (538)
Q Consensus       317 ~--~~~~~iiiTtR~~~-----~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al  388 (538)
                      .  +.+..||.||....     +..  .....+.++..+.++...++...+...  ...........+++.+.|++- .|
T Consensus       154 ~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~--~~~~~~~~~~~la~~~~g~~~~~l  229 (297)
T 3b9p_A          154 NPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQ--GSPLDTEALRRLAKITDGYSGSDL  229 (297)
T ss_dssp             -----CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGG--SCCSCHHHHHHHHHHTTTCCHHHH
T ss_pred             cCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHHHcCCCCHHHH
Confidence            1  12345666665432     222  234677888889988888887766221  122335667889999999875 56


Q ss_pred             HHHHH
Q 009306          389 EVLGR  393 (538)
Q Consensus       389 ~~~~~  393 (538)
                      ..+..
T Consensus       230 ~~l~~  234 (297)
T 3b9p_A          230 TALAK  234 (297)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55544

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=98.65  E-value=1e-06  Score=87.91  Aligned_cols=181  Identities=13%  Similarity=0.100  Sum_probs=104.1

Q ss_pred             CCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      .-.+++|.+..++.|.+.+..          .....+.+.|+|++|+|||+||+.++......|   +.+. ....    
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~---~~v~-~~~l----  120 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTF---FSVS-SSDL----  120 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEE---EEEE-HHHH----
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCE---EEee-HHHH----
Confidence            346789999999988876621          112234589999999999999999999874332   1222 1111    


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHH-HHHhcCCCeEEEEecCCChH-------------HHHHHhcCcC---CCC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQ-SRRLTRKKVLIVFDDVDHPR-------------QIKILVGRLD---LFA  318 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l-~~~l~~k~~LlVlDdv~~~~-------------~~~~l~~~l~---~~~  318 (538)
                               .....      .........+ ......++.+|+||+++...             ....++..+.   ...
T Consensus       121 ---------~~~~~------g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~  185 (355)
T 2qp9_X          121 ---------VSKWM------GESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDS  185 (355)
T ss_dssp             ---------HSCC---------CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---
T ss_pred             ---------hhhhc------chHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccC
Confidence                     00000      0011111111 12224578999999997431             1233332221   112


Q ss_pred             CCCEEEEeccchh-----hhhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHH
Q 009306          319 SGSRIIITTRDRQ-----VLANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLG  392 (538)
Q Consensus       319 ~~~~iiiTtR~~~-----~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~  392 (538)
                      .+..||.||....     +..  .....+.++..+.++-.+++..++...  +..........+++.+.|. +-.|..+.
T Consensus       186 ~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~--~~~~~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          186 QGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDT--PSVLTKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTS--CBCCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhC--CCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3455565665432     222  345678899999999999998887322  2222355678889999884 54565554


Q ss_pred             H
Q 009306          393 R  393 (538)
Q Consensus       393 ~  393 (538)
                      .
T Consensus       262 ~  262 (355)
T 2qp9_X          262 K  262 (355)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.65  E-value=1.9e-07  Score=95.86  Aligned_cols=180  Identities=15%  Similarity=0.194  Sum_probs=107.2

Q ss_pred             CCCCCceeccchh---HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPM---KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l---~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      .....++|.+..+   ..|...+..+  ..+.+.|+|++|+||||||+.+++.....|..   +..     ...+...+ 
T Consensus        23 ~~l~~ivGq~~~~~~~~~L~~~i~~~--~~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~---l~a-----~~~~~~~i-   91 (447)
T 3pvs_A           23 ENLAQYIGQQHLLAAGKPLPRAIEAG--HLHSMILWGPPGTGKTTLAEVIARYANADVER---ISA-----VTSGVKEI-   91 (447)
T ss_dssp             CSTTTCCSCHHHHSTTSHHHHHHHHT--CCCEEEEECSTTSSHHHHHHHHHHHTTCEEEE---EET-----TTCCHHHH-
T ss_pred             CCHHHhCCcHHHHhchHHHHHHHHcC--CCcEEEEECCCCCcHHHHHHHHHHHhCCCeEE---EEe-----ccCCHHHH-
Confidence            3457799999888   6777777654  34679999999999999999999987554321   111     11122221 


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEE-eccchh--hh-hh
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIII-TTRDRQ--VL-AN  335 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iii-TtR~~~--~~-~~  335 (538)
                      +.++...                .......++.+|+||+++..  .+.+.++..+..  ....+|. ||.+..  +. ..
T Consensus        92 r~~~~~a----------------~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL  153 (447)
T 3pvs_A           92 REAIERA----------------RQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSAL  153 (447)
T ss_dssp             HHHHHHH----------------HHHHHTTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHH
T ss_pred             HHHHHHH----------------HHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHH
Confidence            1111110                00111357789999999754  233334433331  2344444 444432  11 11


Q ss_pred             cCCCeeEEcCCCCHHHHHHHHHhhhcCCC-----CCCCchHHHHHHHHHHhcCCcHHHHHHHH
Q 009306          336 CGVDEVYQMEELVHDDALRLFSRHAFGGD-----HPHESHTELACKTIKYARGVPLALEVLGR  393 (538)
Q Consensus       336 ~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~-----~~~~~~~~~~~~i~~~~~G~PLal~~~~~  393 (538)
                      .....++.+++++.++..+++...+....     .......+....+++.++|++..+..+..
T Consensus       154 ~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~Le  216 (447)
T 3pvs_A          154 LSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLE  216 (447)
T ss_dssp             HTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHHH
T ss_pred             hCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            12345889999999999999988763311     22235577888999999999876554443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.64  E-value=5.3e-07  Score=91.30  Aligned_cols=187  Identities=13%  Similarity=0.085  Sum_probs=103.7

Q ss_pred             CCCCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE  253 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~  253 (538)
                      +..-..++|.+..++.|...+..          .....+.+.|+|++|+|||+||+.++.+....|   +.+. ......
T Consensus       111 ~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~~~---~~v~-~~~l~~  186 (389)
T 3vfd_A          111 AVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATF---FNIS-AASLTS  186 (389)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTCEE---EEEC-SCCC--
T ss_pred             CCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcCcE---EEee-HHHhhc
Confidence            33457899999999999887621          011245799999999999999999998754332   2222 111000


Q ss_pred             cCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCc----CC
Q 009306          254 TCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRL----DL  316 (538)
Q Consensus       254 ~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l----~~  316 (538)
                           ..        .+     .........+.......+.+|+||+++..             .....++..+    ..
T Consensus       187 -----~~--------~g-----~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  248 (389)
T 3vfd_A          187 -----KY--------VG-----EGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSA  248 (389)
T ss_dssp             -----------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC--
T ss_pred             -----cc--------cc-----hHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhccccc
Confidence                 00        00     00011111111222346689999999643             1112222111    11


Q ss_pred             CCCCCEEEEeccchhhh-hh--cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHHH
Q 009306          317 FASGSRIIITTRDRQVL-AN--CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVLG  392 (538)
Q Consensus       317 ~~~~~~iiiTtR~~~~~-~~--~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~~  392 (538)
                      ......||.||.....+ ..  ......+.++..+.++..+++...+..  .......+....+++.+.|..- .|..+.
T Consensus       249 ~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~--~~~~l~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          249 GDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCK--QGSPLTQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             ---CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTT--SCCCSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHh--cCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            12334555566543221 11  123457889999999999999887732  2223345677889999988654 665554


Q ss_pred             HH
Q 009306          393 RY  394 (538)
Q Consensus       393 ~~  394 (538)
                      ..
T Consensus       327 ~~  328 (389)
T 3vfd_A          327 KD  328 (389)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=98.64  E-value=5.6e-07  Score=85.68  Aligned_cols=184  Identities=15%  Similarity=0.142  Sum_probs=99.8

Q ss_pred             CCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          187 NEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      -.+++|.+..++.|.+++..          +....+.+.|+|++|+|||++|+.+++.....|   +.+. .........
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~---~~~~-~~~~~~~~~   80 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPF---LAMA-GAEFVEVIG   80 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCE---EEEE-TTTTSSSST
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCE---EEec-hHHHHhhcc
Confidence            35688888888777665431          112345689999999999999999998765432   2222 111100000


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-----------------HHHHHHhcCcCCC--
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-----------------RQIKILVGRLDLF--  317 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-----------------~~~~~l~~~l~~~--  317 (538)
                                        ..........+.......+.+|+|||++..                 ..+..++..+...  
T Consensus        81 ------------------~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~  142 (262)
T 2qz4_A           81 ------------------GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGT  142 (262)
T ss_dssp             ------------------THHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCT
T ss_pred             ------------------ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCC
Confidence                              000011111222223356789999999754                 1122333222211  


Q ss_pred             CCCCEEEEeccchhhhh-hc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHHH
Q 009306          318 ASGSRIIITTRDRQVLA-NC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEVL  391 (538)
Q Consensus       318 ~~~~~iiiTtR~~~~~~-~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~~  391 (538)
                      ..+..+|.||.....+. .+    .....+.++..+.++-.+++...+.... ...........+++.+.|++- .|..+
T Consensus       143 ~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~-~~~~~~~~~~~l~~~~~g~~~~~l~~l  221 (262)
T 2qz4_A          143 TDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLK-LTQSSTFYSQRLAELTPGFSGADIANI  221 (262)
T ss_dssp             TCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTT-CCBTHHHHHHHHHHTCTTCCHHHHHHH
T ss_pred             CCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCC-CCcchhhHHHHHHHHCCCCCHHHHHHH
Confidence            23455666665443221 11    2346788999999999999988762221 121222234678888888754 55544


Q ss_pred             HH
Q 009306          392 GR  393 (538)
Q Consensus       392 ~~  393 (538)
                      ..
T Consensus       222 ~~  223 (262)
T 2qz4_A          222 CN  223 (262)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=98.61  E-value=2.9e-06  Score=83.95  Aligned_cols=259  Identities=15%  Similarity=0.157  Sum_probs=139.3

Q ss_pred             CCCCceeccchhHHHHHhhhcC---CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRTG---STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~---~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      .-..++|.+..++.+...+..+   ......++|+|++|+||||||+.++..+...+.   ...  ...  ......+ .
T Consensus        23 ~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~---~~s--g~~--~~~~~~l-~   94 (334)
T 1in4_A           23 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIH---VTS--GPV--LVKQGDM-A   94 (334)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEE---EEE--TTT--CCSHHHH-H
T ss_pred             cHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEE---EEe--chH--hcCHHHH-H
Confidence            3466889888888887766532   223356899999999999999999998754322   111  000  0000010 0


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCC--------C----------CCCE
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLF--------A----------SGSR  322 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~--------~----------~~~~  322 (538)
                      .                     +...+ .++.++++|+++..  ...+.+...+...        +          +...
T Consensus        95 ~---------------------~~~~~-~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~  152 (334)
T 1in4_A           95 A---------------------ILTSL-ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFT  152 (334)
T ss_dssp             H---------------------HHHHC-CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCE
T ss_pred             H---------------------HHHHc-cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeE
Confidence            0                     01111 23457788988542  2223332211100        0          1122


Q ss_pred             EE-Eeccchhhhhhc--CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhc---
Q 009306          323 II-ITTRDRQVLANC--GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLY---  396 (538)
Q Consensus       323 ii-iTtR~~~~~~~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~---  396 (538)
                      ++ .|++...+....  .......+++++.++..+++.+.+..  .......+.+..+++.+.|.|-.+..+...+.   
T Consensus       153 li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~--~~~~~~~~~~~~ia~~~~G~~R~a~~ll~~~~~~a  230 (334)
T 1in4_A          153 LVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASL--MDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDML  230 (334)
T ss_dssp             EEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHH--TTCCBCHHHHHHHHHTSTTCHHHHHHHHHHHHHHH
T ss_pred             EEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHH--cCCCcCHHHHHHHHHhcCCChHHHHHHHHHHHHHH
Confidence            22 233332221111  12346789999999999999887621  12235567789999999999975544433221   


Q ss_pred             ---CC---CHHHHHHHHHHhhcCCCCcHHHHHHHhHhCCCHHhHHHhhccccc--cCCCCHHHHHHHHHhCCCChHHHHH
Q 009306          397 ---GK---RREVWENAKSKWETAPPKGIQDALKISYDGLDDKEQNIFLDIACF--FIDEDRDTATKFLDDCEFFATSAIE  468 (538)
Q Consensus       397 ---~~---~~~~~~~~l~~l~~~~~~~v~~~l~~s~~~L~~~~k~~l~~la~f--~~~~~~~~l~~l~~~~~~~~~~~l~  468 (538)
                         +.   +.+..+.++..+.            ..-..++...+.++..++-.  ..+...+.+....+.+....+...+
T Consensus       231 ~~~~~~~It~~~v~~al~~~~------------~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~t~~~~~~  298 (334)
T 1in4_A          231 TVVKADRINTDIVLKTMEVLN------------IDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYE  298 (334)
T ss_dssp             HHHTCSSBCHHHHHHHHHHHT------------CCTTCCCHHHHHHHHHHHHHSTTCCBCHHHHHHHHTSCHHHHHHHTH
T ss_pred             HHcCCCCcCHHHHHHHHHHhC------------CCcCCCCHHHHHHHHHHHHHhCCCcchHHHHHHHhCCCcchHHHHHH
Confidence               11   1222222222211            11134566666666554433  2345666776666443222233333


Q ss_pred             -HHhhCCceeEecCCcEEecH
Q 009306          469 -VLVDKHLITISVLNKIEMHY  488 (538)
Q Consensus       469 -~L~~~~Li~~~~~~~~~~H~  488 (538)
                       .|.+.|+|+....|++-...
T Consensus       299 ~~l~~~g~i~~~~~gr~~~~~  319 (334)
T 1in4_A          299 PYLLQAGFLARTPRGRIVTEK  319 (334)
T ss_dssp             HHHHHTTSEEEETTEEEECHH
T ss_pred             HHHHHcCCeecccccHHhhHH
Confidence             79999999998888765443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.60  E-value=1.5e-07  Score=92.85  Aligned_cols=175  Identities=15%  Similarity=0.184  Sum_probs=103.7

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      |...+.++|++..++.|..++..+. ...++.++|++|+|||++|+.+++.+...   .+.+. ..    ..... ..+.
T Consensus        22 P~~~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~l~~~---~~~i~-~~----~~~~~-~i~~   91 (324)
T 3u61_B           22 PSTIDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHDVNAD---MMFVN-GS----DCKID-FVRG   91 (324)
T ss_dssp             CCSTTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHHTTEE---EEEEE-TT----TCCHH-HHHT
T ss_pred             CCCHHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHHhCCC---EEEEc-cc----ccCHH-HHHH
Confidence            3445789999999999999998542 34568888999999999999999887422   22332 11    11221 2222


Q ss_pred             HHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH---HHHHHhcCcCCCCCCCEEEEeccchhh-----hhh
Q 009306          264 LLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR---QIKILVGRLDLFASGSRIIITTRDRQV-----LAN  335 (538)
Q Consensus       264 l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~---~~~~l~~~l~~~~~~~~iiiTtR~~~~-----~~~  335 (538)
                      .+........               ..+++.+|+|||++...   ....+...+.....+.++|+||....-     ...
T Consensus        92 ~~~~~~~~~~---------------~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR  156 (324)
T 3u61_B           92 PLTNFASAAS---------------FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSR  156 (324)
T ss_dssp             HHHHHHHBCC---------------CSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHH
T ss_pred             HHHHHHhhcc---------------cCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhh
Confidence            2221111100               12367899999998653   444444433322356788888765431     222


Q ss_pred             cCCCeeEEcCCCCHHHHHHHH-------HhhhcCCCCCCCchH-HHHHHHHHHhcCCcHHH
Q 009306          336 CGVDEVYQMEELVHDDALRLF-------SRHAFGGDHPHESHT-ELACKTIKYARGVPLAL  388 (538)
Q Consensus       336 ~~~~~~~~l~~L~~~ea~~Lf-------~~~~~~~~~~~~~~~-~~~~~i~~~~~G~PLal  388 (538)
                         ...+++++++.++-.+++       ...+...  ...... +....+++.++|++..+
T Consensus       157 ---~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~--~~~~~~~~~~~~l~~~~~gd~R~a  212 (324)
T 3u61_B          157 ---CRVITFGQPTDEDKIEMMKQMIRRLTEICKHE--GIAIADMKVVAALVKKNFPDFRKT  212 (324)
T ss_dssp             ---SEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH--TCCBSCHHHHHHHHHHTCSCTTHH
T ss_pred             ---CcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHc--CCCCCcHHHHHHHHHhCCCCHHHH
Confidence               257899999988843332       2222111  112223 67788888898887643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.59  E-value=3.3e-07  Score=89.66  Aligned_cols=167  Identities=12%  Similarity=0.111  Sum_probs=94.1

Q ss_pred             CceeccchhHHHHHhhhc-------------CCCCceEEEEeccCCCchhHHHHHHHHhhcccee----eEEEEeehhhh
Q 009306          189 DLVGVRLPMKEIESLLRT-------------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS----GSYFARNVREA  251 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-------------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~----~~~~~~~~~~~  251 (538)
                      .++|.+..++.|.+++..             .......+.|+|++|+|||+||+.+++.+.....    ..+.+. ....
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~-~~~l  110 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVT-RDDL  110 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEEC-GGGT
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEc-HHHh
Confidence            478888888877765431             1233456999999999999999999987643211    122222 1110


Q ss_pred             hhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCC-----------ChHHHHHHhcCcCCCCCC
Q 009306          252 EETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVD-----------HPRQIKILVGRLDLFASG  320 (538)
Q Consensus       252 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~-----------~~~~~~~l~~~l~~~~~~  320 (538)
                      ..                 . ............+..   .++.+|+||+++           +......+...+.....+
T Consensus       111 ~~-----------------~-~~g~~~~~~~~~~~~---~~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~  169 (309)
T 3syl_A          111 VG-----------------Q-YIGHTAPKTKEVLKR---AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDD  169 (309)
T ss_dssp             CC-----------------S-STTCHHHHHHHHHHH---HTTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTT
T ss_pred             hh-----------------h-cccccHHHHHHHHHh---cCCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCC
Confidence            00                 0 000000111111111   145699999997           334455555544443456


Q ss_pred             CEEEEeccchhh----------hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh
Q 009306          321 SRIIITTRDRQV----------LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA  381 (538)
Q Consensus       321 ~~iiiTtR~~~~----------~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~  381 (538)
                      ..+|.||.....          ...  ....+.+++++.++..+++...+...  ......+....+++.+
T Consensus       170 ~~~i~~~~~~~~~~~~~~~~~l~~R--~~~~i~~~~~~~~~~~~il~~~l~~~--~~~~~~~~~~~l~~~~  236 (309)
T 3syl_A          170 LVVILAGYADRMENFFQSNPGFRSR--IAHHIEFPDYSDEELFEIAGHMLDDQ--NYQMTPEAETALRAYI  236 (309)
T ss_dssp             CEEEEEECHHHHHHHHHHSTTHHHH--EEEEEEECCCCHHHHHHHHHHHHHHT--TCEECHHHHHHHHHHH
T ss_pred             EEEEEeCChHHHHHHHhhCHHHHHh--CCeEEEcCCcCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHH
Confidence            777777754321          111  23678999999999999998876221  1223344455555543

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=98.59  E-value=1.3e-06  Score=89.91  Aligned_cols=186  Identities=14%  Similarity=0.149  Sum_probs=107.0

Q ss_pred             CCCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          185 SENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ..-.+++|.+..++.|.+.+..          .....+.+.|+|++|+|||+||+.++......   .++..+..     
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~---~~~~v~~~-----  202 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNS---TFFSISSS-----  202 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCSS---EEEEECCC-----
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCCC---CEEEEeHH-----
Confidence            3446799999999888876521          11234679999999999999999999986211   11211111     


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCC---C
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLF---A  318 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~---~  318 (538)
                       .   +.    ....+.  ....+..   .+......++.+|+||+++..             .....++..+...   .
T Consensus       203 -~---l~----~~~~g~--~~~~~~~---~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~  269 (444)
T 2zan_A          203 -D---LV----SKWLGE--SEKLVKN---LFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDN  269 (444)
T ss_dssp             -------------------CCCTHHH---HHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCC
T ss_pred             -H---HH----hhhcch--HHHHHHH---HHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCC
Confidence             0   10    010010  0111111   122222457889999999754             2244455544332   3


Q ss_pred             CCCEEEEeccchhhhh-h--cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHHH
Q 009306          319 SGSRIIITTRDRQVLA-N--CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLGR  393 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~~-~--~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~~  393 (538)
                      .+..||.||.....+. .  -.....+.++..+.++-.+++..++..  .+..........+++.+.|. +-.|..+..
T Consensus       270 ~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~--~~~~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          270 DGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGS--TQNSLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             SSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTT--SCEECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            4556666665442211 1  134467889999999999999887722  22222355677888999884 445555544

>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=98.48  E-value=5.9e-06  Score=80.41  Aligned_cols=176  Identities=17%  Similarity=0.178  Sum_probs=100.0

Q ss_pred             CCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          187 NEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      -.+++|.+..+++|.+.+..           +....+.+.|+|++|+|||+||+.++......|   +.+. .       
T Consensus        14 ~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~---i~v~-~-------   82 (301)
T 3cf0_A           14 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANF---ISIK-G-------   82 (301)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEE---EEEC-H-------
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCE---EEEE-h-------
Confidence            35688999888888876542           223456799999999999999999998865322   2222 1       


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----------------HHHHHhcCcCC--C
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----------------QIKILVGRLDL--F  317 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----------------~~~~l~~~l~~--~  317 (538)
                        ..+.    ....+..     .......+.......+.+|+||+++...                ....++..+..  .
T Consensus        83 --~~l~----~~~~g~~-----~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~  151 (301)
T 3cf0_A           83 --PELL----TMWFGES-----EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  151 (301)
T ss_dssp             --HHHH----HHHHTTC-----TTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCT
T ss_pred             --HHHH----hhhcCch-----HHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccC
Confidence              1111    1111111     1111222223334578999999997431                12333322211  1


Q ss_pred             CCCCEEEEeccchhhhh-h-c---CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          318 ASGSRIIITTRDRQVLA-N-C---GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       318 ~~~~~iiiTtR~~~~~~-~-~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      ..+..||.||.....+. . .   .....+.++..+.++-.+++.............   ....++..+.|+|-+
T Consensus       152 ~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~---~~~~la~~~~g~sg~  223 (301)
T 3cf0_A          152 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV---DLEFLAKMTNGFSGA  223 (301)
T ss_dssp             TSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSC---CHHHHHHTCSSCCHH
T ss_pred             CCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccc---hHHHHHHHcCCCCHH
Confidence            23456676775543221 1 1   244678999999999999988776322211111   134556667777644

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.48  E-value=6.5e-07  Score=80.13  Aligned_cols=50  Identities=20%  Similarity=0.280  Sum_probs=41.6

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ....++||+.+++.+.+.+...  ..+.+.|+|++|+|||+||+.+++.+..
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~--~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSRR--TKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSS--SSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             ccchhhcchHHHHHHHHHHhCC--CCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            3467999999999999988753  3456799999999999999999987643

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.46  E-value=3.7e-06  Score=83.16  Aligned_cols=178  Identities=12%  Similarity=0.104  Sum_probs=99.8

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHH-------
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLST-------  267 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~-------  267 (538)
                      ...+.+...+..+ .-.+.+.++|++|+|||++|+.++..+....... ...       ...... ...+...       
T Consensus         9 ~~~~~l~~~i~~~-~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~-~~~-------c~~c~~-c~~~~~~~~~d~~~   78 (334)
T 1a5t_A            9 PDFEKLVASYQAG-RGHHALLIQALPGMGDDALIYALSRYLLCQQPQG-HKS-------CGHCRG-CQLMQAGTHPDYYT   78 (334)
T ss_dssp             HHHHHHHHHHHTT-CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT-TBC-------CSCSHH-HHHHHHTCCTTEEE
T ss_pred             HHHHHHHHHHHcC-CcceeEEEECCCCchHHHHHHHHHHHHhCCCCCC-CCC-------CCCCHH-HHHHhcCCCCCEEE
Confidence            3445566655533 2345689999999999999999998764322100 000       000000 0000000       


Q ss_pred             HhcCC-CCCCchhhcHHHHHHHh-----cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-C
Q 009306          268 LLNDG-NVKNFLNTDLNFQSRRL-----TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-G  337 (538)
Q Consensus       268 l~~~~-~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-~  337 (538)
                      +.... ......++... +.+.+     .+++-++|||+++..  .....++..+....++..+|++|.+.. +.+.+ .
T Consensus        79 ~~~~~~~~~~~i~~ir~-l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~S  157 (334)
T 1a5t_A           79 LAPEKGKNTLGVDAVRE-VTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRS  157 (334)
T ss_dssp             ECCCTTCSSBCHHHHHH-HHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHT
T ss_pred             EeccccCCCCCHHHHHH-HHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhh
Confidence            00000 00011111111 22222     245679999999753  445666666655455677777766542 32222 2


Q ss_pred             CCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHH
Q 009306          338 VDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEV  390 (538)
Q Consensus       338 ~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~  390 (538)
                      ....+++++++.++..+.+....       ....+.+..+++.++|.|..+..
T Consensus       158 Rc~~~~~~~~~~~~~~~~L~~~~-------~~~~~~~~~l~~~s~G~~r~a~~  203 (334)
T 1a5t_A          158 RCRLHYLAPPPEQYAVTWLSREV-------TMSQDALLAALRLSAGSPGAALA  203 (334)
T ss_dssp             TSEEEECCCCCHHHHHHHHHHHC-------CCCHHHHHHHHHHTTTCHHHHHH
T ss_pred             cceeeeCCCCCHHHHHHHHHHhc-------CCCHHHHHHHHHHcCCCHHHHHH
Confidence            34689999999999999998775       22356678899999999965543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.41  E-value=1.3e-06  Score=86.85  Aligned_cols=183  Identities=13%  Similarity=0.182  Sum_probs=104.8

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQ  262 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~  262 (538)
                      |..-..++|.+..++.|...+..+.  .+.+.++|++|+||||+|+.++..+... +...+.-.+   .....+...+ +
T Consensus        21 p~~~~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~---~~~~~~~~~i-r   94 (340)
T 1sxj_C           21 PETLDEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN---ASDDRGIDVV-R   94 (340)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC---TTSCCSHHHH-H
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEc---CcccccHHHH-H
Confidence            3344668899988998888887542  2238999999999999999999875432 111111111   1111112111 1


Q ss_pred             HHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-CC
Q 009306          263 QLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-GV  338 (538)
Q Consensus       263 ~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-~~  338 (538)
                      .....+.....              ...+.+-++|+|+++..  .....+...+.......++|++|.... +.+.+ ..
T Consensus        95 ~~i~~~~~~~~--------------~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR  160 (340)
T 1sxj_C           95 NQIKDFASTRQ--------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQ  160 (340)
T ss_dssp             THHHHHHHBCC--------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTT
T ss_pred             HHHHHHHhhcc--------------cCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhh
Confidence            11111110000              01134678999999643  334444443333345666776665432 21111 22


Q ss_pred             CeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHH
Q 009306          339 DEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLAL  388 (538)
Q Consensus       339 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal  388 (538)
                      ...+.+.+++.++..+.+...+-..  ......+....+++.++|.+--+
T Consensus       161 ~~~~~~~~l~~~~~~~~l~~~~~~~--~~~i~~~~~~~i~~~s~G~~r~~  208 (340)
T 1sxj_C          161 CTRFRFQPLPQEAIERRIANVLVHE--KLKLSPNAEKALIELSNGDMRRV  208 (340)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHTT--TCCBCHHHHHHHHHHHTTCHHHH
T ss_pred             ceeEeccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCCHHHH
Confidence            3578999999999999888765221  12344667788999999988643

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=98.35  E-value=3.1e-06  Score=87.76  Aligned_cols=180  Identities=16%  Similarity=0.142  Sum_probs=101.1

Q ss_pred             CCceeccchhHHHHHhhhcC-----------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRTG-----------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~-----------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      ..++|.+..+++|.+++...           ....+.+.|+|++|+|||+||+.+++.....|   +.+. ....... .
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~f---v~vn-~~~l~~~-~  278 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFF---FLIN-GPEIMSK-L  278 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEE---EEEE-HHHHHTS-C
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCE---EEEE-chHhhhh-h
Confidence            56899999999998876531           23445699999999999999999998764322   2222 2211110 0


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCC--CCCCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDL--FASGS  321 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~--~~~~~  321 (538)
                      ...                 ........+.....+++.+|+||+++..             .....++..+..  ...+.
T Consensus       279 ~g~-----------------~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v  341 (489)
T 3hu3_A          279 AGE-----------------SESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  341 (489)
T ss_dssp             TTH-----------------HHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCE
T ss_pred             cch-----------------hHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCce
Confidence            000                 0111122222333567889999999421             112223222221  12345


Q ss_pred             EEEEeccchhh-----hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC-cHHHHHHH
Q 009306          322 RIIITTRDRQV-----LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV-PLALEVLG  392 (538)
Q Consensus       322 ~iiiTtR~~~~-----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~-PLal~~~~  392 (538)
                      .||.||.....     .........+.++..+.++-.+++..++.......   ......+++.+.|+ +-.|..+.
T Consensus       342 ~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~---~~~l~~la~~t~g~s~~dL~~L~  415 (489)
T 3hu3_A          342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLAD---DVDLEQVANETHGHVGADLAALC  415 (489)
T ss_dssp             EEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCT---TCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             EEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcc---hhhHHHHHHHccCCcHHHHHHHH
Confidence            56666654422     11123446789999999999999988863221111   11235566777765 44454443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.34  E-value=5.6e-06  Score=85.71  Aligned_cols=149  Identities=13%  Similarity=0.129  Sum_probs=83.2

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~  258 (538)
                      ...+.++||+.+++.+...|...  ...-+.|+|++|+|||+||+.++..+....      ...++..+..         
T Consensus       177 ~~ld~iiGr~~~i~~l~~~l~r~--~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~---------  245 (468)
T 3pxg_A          177 DSLDPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG---------  245 (468)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC------------
T ss_pred             CCCCCccCcHHHHHHHHHHHhcc--CCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCC---------
Confidence            34467999999999999998753  233478999999999999999999864321      1112221111         


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhh----
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLA----  334 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~----  334 (538)
                             ....+     .........+...-..++.+|++|  ...+....+...+.  ....++|.+|.......    
T Consensus       246 -------~~~~g-----~~e~~~~~~~~~~~~~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~  309 (468)
T 3pxg_A          246 -------TKYRG-----EFEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEK  309 (468)
T ss_dssp             -------------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTT
T ss_pred             -------ccccc-----hHHHHHHHHHHHHHhcCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhc
Confidence                   00000     000111122222223567899999  22222333444443  23456666665443111    


Q ss_pred             --h-cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          335 --N-CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       335 --~-~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                        . ......+.+++++.++..+++....
T Consensus       310 ~~al~~Rf~~i~v~~p~~e~~~~iL~~~~  338 (468)
T 3pxg_A          310 DAALERRFQPIQVDQPSVDESIQILQGLR  338 (468)
T ss_dssp             CSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             CHHHHHhCccceeCCCCHHHHHHHHHHHH
Confidence              0 0122468999999999999998765

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.34  E-value=9.8e-06  Score=80.86  Aligned_cols=171  Identities=18%  Similarity=0.215  Sum_probs=99.3

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc-C
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET-C  255 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~-~  255 (538)
                      .++.|.+..+++|.+.+.-           +-...+-+.++||+|+|||.||++++.+....|-   .+. ..+.... .
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 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFI---RVS-GAELVQKYI  223 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEE---EEE-GGGGSCSST
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCce---EEE-hHHhhcccc
Confidence            5678899888888775421           2333566999999999999999999998765532   222 1111100 0


Q ss_pred             C-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC-
Q 009306          256 R-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF-  317 (538)
Q Consensus       256 ~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~-  317 (538)
                      + ....++.+                    ....-...|++|+||++|..                ..+..++..+..+ 
T Consensus       224 Gese~~vr~l--------------------F~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  283 (405)
T 4b4t_J          224 GEGSRMVREL--------------------FVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFE  283 (405)
T ss_dssp             THHHHHHHHH--------------------HHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTT
T ss_pred             chHHHHHHHH--------------------HHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccC
Confidence            0 01111111                    11222467999999999742                1133333333322 


Q ss_pred             -CCCCEEEEeccchhh-----hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 -ASGSRIIITTRDRQV-----LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 -~~~~~iiiTtR~~~~-----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                       ..+..||.||.....     ...-+.+..+.++..+.++-.++|..+.-+-......   ....+++.+.|.-
T Consensus       284 ~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dv---dl~~lA~~t~G~S  354 (405)
T 4b4t_J          284 TSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGI---NLRKVAEKMNGCS  354 (405)
T ss_dssp             CCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSC---CHHHHHHHCCSCC
T ss_pred             CCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccC---CHHHHHHHCCCCC
Confidence             234455666654422     2222456789999999999999998776322211111   1456778887764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.33  E-value=1.8e-06  Score=96.30  Aligned_cols=177  Identities=11%  Similarity=0.100  Sum_probs=91.2

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~  258 (538)
                      ...+.++||+.+++.+...|....  .+.+.|+|++|+|||+||+.++..+....      ...++..+......     
T Consensus       167 ~~ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~-----  239 (854)
T 1qvr_A          167 GKLDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA-----  239 (854)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC----------
T ss_pred             CCCcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc-----
Confidence            344679999999999999887532  33478999999999999999999864311      12222221111000     


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-c-CCCeEEEEecCCChH----------HHHHHhcCcCCCCCCCEEEEe
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-T-RKKVLIVFDDVDHPR----------QIKILVGRLDLFASGSRIIIT  326 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~-~k~~LlVlDdv~~~~----------~~~~l~~~l~~~~~~~~iiiT  326 (538)
                                 +.. ...........+...+ . +++.+|+||+++...          ....+...+.  ..+..+|.+
T Consensus       240 -----------g~~-~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~--~~~i~~I~a  305 (854)
T 1qvr_A          240 -----------GAK-YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGA  305 (854)
T ss_dssp             ------------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHH--TTCCCEEEE
T ss_pred             -----------cCc-cchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHh--CCCeEEEEe
Confidence                       000 0011111122222222 2 367899999997542          1111222221  234456655


Q ss_pred             ccchhh-----hhhc-CCCeeEEcCCCCHHHHHHHHHhhhcC--CCCCCCchHHHHHHHHHHhc
Q 009306          327 TRDRQV-----LANC-GVDEVYQMEELVHDDALRLFSRHAFG--GDHPHESHTELACKTIKYAR  382 (538)
Q Consensus       327 tR~~~~-----~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~~~~~~i~~~~~  382 (538)
                      |.....     ...+ .....+.+++++.++..+++....-.  .........+....+++.+.
T Consensus       306 t~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~  369 (854)
T 1qvr_A          306 TTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSH  369 (854)
T ss_dssp             ECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHH
T ss_pred             cCchHHhhhccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHh
Confidence            543322     1111 12245889999999999998754310  01112233455555666553

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.31  E-value=6.1e-07  Score=77.22  Aligned_cols=47  Identities=19%  Similarity=0.178  Sum_probs=36.2

Q ss_pred             CceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          189 DLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .++|+...++++.+.+..-......|.|+|++|+|||++|+.+++..
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            57899999999988775422233348999999999999999999864

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.27  E-value=9.8e-06  Score=76.85  Aligned_cols=181  Identities=18%  Similarity=0.139  Sum_probs=94.8

Q ss_pred             CCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      .-.+++|.+..++++.+++..          +....+-+.|+|++|+||||||+.++......|   +.+. ....... 
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~---~~i~-~~~~~~~-   84 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPF---FTIS-GSDFVEM-   84 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCE---EEEC-SCSSTTS-
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCE---EEEe-HHHHHHH-
Confidence            446788998888777665421          111234589999999999999999998764332   2222 1110000 


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC--
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF--  317 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~--  317 (538)
                                       ............+.......+.++++|+++..                ..+..++..+...  
T Consensus        85 -----------------~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  147 (257)
T 1lv7_A           85 -----------------FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG  147 (257)
T ss_dssp             -----------------CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS
T ss_pred             -----------------hhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCccc
Confidence                             00011111112222223456789999998421                1223333222111  


Q ss_pred             CCCCEEEEeccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcC-CcHHHHHH
Q 009306          318 ASGSRIIITTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARG-VPLALEVL  391 (538)
Q Consensus       318 ~~~~~iiiTtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G-~PLal~~~  391 (538)
                      ..+..||.||.....+ ..+    .....+.++..+.++-.+++..+........+.   ....++..+.| ++--|..+
T Consensus       148 ~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~---~~~~la~~~~G~~~~dl~~l  224 (257)
T 1lv7_A          148 NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI---DAAIIARGTPGFSGADLANL  224 (257)
T ss_dssp             SSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC---CHHHHHHTCTTCCHHHHHHH
T ss_pred             CCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccc---cHHHHHHHcCCCCHHHHHHH
Confidence            2344566666544321 111    234678888889888888887765221111111   13445666777 66555443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.25  E-value=2.6e-05  Score=78.86  Aligned_cols=171  Identities=17%  Similarity=0.197  Sum_probs=98.2

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh-cC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE-TC  255 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~-~~  255 (538)
                      .++.|.+..+++|.+.+.-           +-...+-|.++|++|+|||.||++++.+....|-   .+. ...... ..
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 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFI---RVI-GSELVQKYV  284 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEE---EEE-GGGGCCCSS
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeE---EEE-hHHhhcccC
Confidence            4688999888888775421           3344667999999999999999999998765432   222 111110 00


Q ss_pred             C-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC-
Q 009306          256 R-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF-  317 (538)
Q Consensus       256 ~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~-  317 (538)
                      + ....++                    ......-...|++|++|+++..                ..+..++..+..+ 
T Consensus       285 Gesek~ir--------------------~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~  344 (467)
T 4b4t_H          285 GEGARMVR--------------------ELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFD  344 (467)
T ss_dssp             SHHHHHHH--------------------HHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSC
T ss_pred             CHHHHHHH--------------------HHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccC
Confidence            0 011111                    1112223467999999999742                0122222222222 


Q ss_pred             -CCCCEEEEeccchhh-----hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 -ASGSRIIITTRDRQV-----LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 -~~~~~iiiTtR~~~~-----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                       ..+..||.||.....     ...-+.+..++++..+.++-.++|..+..+-......   ....+++.+.|.-
T Consensus       345 ~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dv---dl~~LA~~T~GfS  415 (467)
T 4b4t_H          345 PRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGI---RWELISRLCPNST  415 (467)
T ss_dssp             CTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSC---CHHHHHHHCCSCC
T ss_pred             CCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCC---CHHHHHHHCCCCC
Confidence             234445666654422     2222456789999999999999998776322111111   1456777887764

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=98.25  E-value=3.4e-06  Score=82.32  Aligned_cols=50  Identities=20%  Similarity=0.288  Sum_probs=37.8

Q ss_pred             CCceeccchhHHHHHhhhc------------CCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRT------------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~------------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +.++|++..++.+...+..            .......+.|+|++|+|||++|+.+++.+..
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   76 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   76 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4578888888888776643            0112345889999999999999999987743

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.22  E-value=1.8e-05  Score=80.27  Aligned_cols=172  Identities=19%  Similarity=0.259  Sum_probs=99.2

Q ss_pred             CCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh-c
Q 009306          187 NEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE-T  254 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~-~  254 (538)
                      -.++.|.+..+++|.+.+.-           +....+-+.++||+|+|||.||++++......|-   .+. ...... .
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            35678999988888775432           2334567999999999999999999998765432   222 111110 0


Q ss_pred             CC-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC
Q 009306          255 CR-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF  317 (538)
Q Consensus       255 ~~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~  317 (538)
                      .+ .....+                    ......-...|++|++|++|..                ..+..++..+..+
T Consensus       256 ~Gese~~ir--------------------~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~  315 (437)
T 4b4t_L          256 IGESARIIR--------------------EMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGF  315 (437)
T ss_dssp             SSHHHHHHH--------------------HHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSS
T ss_pred             chHHHHHHH--------------------HHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcc
Confidence            00 011111                    1111222468999999999732                1123333333222


Q ss_pred             --CCCCEEEEeccchhhhhh-c----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 --ASGSRIIITTRDRQVLAN-C----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 --~~~~~iiiTtR~~~~~~~-~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                        ..+..||.||.....+.. +    ..+..+.++..+.++-.++|..+..+-....+.   ....+++.+.|+-
T Consensus       316 ~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~---dl~~lA~~t~G~s  387 (437)
T 4b4t_L          316 DNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEF---DFEAAVKMSDGFN  387 (437)
T ss_dssp             SCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCC---CHHHHHHTCCSCC
T ss_pred             cCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCccc---CHHHHHHhCCCCC
Confidence              235567777765533221 1    234678899999999889888776332211111   1456777777764

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.21  E-value=5.9e-06  Score=83.66  Aligned_cols=172  Identities=16%  Similarity=0.176  Sum_probs=97.8

Q ss_pred             CCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh-c
Q 009306          187 NEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE-T  254 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~-~  254 (538)
                      -.++.|.+...++|.+.+..           +....+-+.++||+|+|||.||++++.+....|    +......... .
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f----~~v~~s~l~~~~  255 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATF----LKLAAPQLVQMY  255 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEE----EEEEGGGGCSSC
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCE----EEEehhhhhhcc
Confidence            36788999988888765321           233466799999999999999999999876543    2221111110 0


Q ss_pred             CC-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC
Q 009306          255 CR-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF  317 (538)
Q Consensus       255 ~~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~  317 (538)
                      .+ .....+.++                    ...-...|++|++|++|..                ..+..++..+..+
T Consensus       256 vGese~~ir~lF--------------------~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~  315 (434)
T 4b4t_M          256 IGEGAKLVRDAF--------------------ALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGF  315 (434)
T ss_dssp             SSHHHHHHHHHH--------------------HHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTS
T ss_pred             cchHHHHHHHHH--------------------HHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhcc
Confidence            00 011111111                    1112357899999998632                0123344444433


Q ss_pred             C--CCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 A--SGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 ~--~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .  .+..||.||.....+..     -..+..+.++..+.++-.++|..+.-+-......   ....+++.+.|+-
T Consensus       316 ~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dv---dl~~lA~~t~G~s  387 (434)
T 4b4t_M          316 SSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDI---NWQELARSTDEFN  387 (434)
T ss_dssp             CSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCC---CHHHHHHHCSSCC
T ss_pred             CCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcC---CHHHHHHhCCCCC
Confidence            2  34456667755433221     1244678899999998888887765221111111   1456777777753

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.15  E-value=7.2e-06  Score=73.17  Aligned_cols=49  Identities=20%  Similarity=0.198  Sum_probs=33.1

Q ss_pred             CCcee----ccchhHHHHHhhhcC-CCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVG----VRLPMKEIESLLRTG-STNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vG----R~~~l~~l~~~L~~~-~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|++    +...++.+.+++..- ......++|+|++|+|||||++.++..+.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           10 DTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             SSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            44554    334444444444331 12346799999999999999999999875

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.14  E-value=2.6e-05  Score=78.13  Aligned_cols=172  Identities=18%  Similarity=0.197  Sum_probs=97.3

Q ss_pred             CCCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh-c
Q 009306          187 NEDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE-T  254 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~-~  254 (538)
                      -.++-|.+...++|.+.+..           +....+-+.++||+|+|||.||++++.+....|-   .+. ..+... .
T Consensus       181 ~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi---~v~-~s~l~sk~  256 (437)
T 4b4t_I          181 YSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFL---RIV-GSELIQKY  256 (437)
T ss_dssp             GGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEE---EEE-SGGGCCSS
T ss_pred             ceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEE---EEE-HHHhhhcc
Confidence            35678899888888775421           2234567999999999999999999998765432   121 111110 0


Q ss_pred             CC-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC
Q 009306          255 CR-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF  317 (538)
Q Consensus       255 ~~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~  317 (538)
                      .+ .....+.+                    ....-...|++|++|++|..                ..+..++..+..+
T Consensus       257 vGesek~ir~l--------------------F~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~  316 (437)
T 4b4t_I          257 LGDGPRLCRQI--------------------FKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGF  316 (437)
T ss_dssp             SSHHHHHHHHH--------------------HHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHC
T ss_pred             CchHHHHHHHH--------------------HHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCc
Confidence            00 01111111                    11122467899999998632                1122333222211


Q ss_pred             --CCCCEEEEeccchhhhhh-c----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 --ASGSRIIITTRDRQVLAN-C----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 --~~~~~iiiTtR~~~~~~~-~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                        ..+..||.||.....+.. +    ..+..+.++..+.++-.++|..+.-+-....+.   ....+++.+.|+-
T Consensus       317 ~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dv---dl~~LA~~T~GfS  388 (437)
T 4b4t_I          317 DDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDV---NLETLVTTKDDLS  388 (437)
T ss_dssp             CCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCC---CHHHHHHHCCSCC
T ss_pred             CCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcC---CHHHHHHhCCCCC
Confidence              234456666655443321 1    234568899999999999998776322211111   1456777777763

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=98.13  E-value=1.1e-05  Score=78.39  Aligned_cols=146  Identities=11%  Similarity=0.093  Sum_probs=88.6

Q ss_pred             eccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc---cceeeEEEEeehhhhhhcCChHHHHHHHHHHH
Q 009306          192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS---RHFSGSYFARNVREAEETCRLGDLRQQLLSTL  268 (538)
Q Consensus       192 GR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~---~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l  268 (538)
                      |-+..++.|...+..+.  .+.+.++|++|+||||+|..+++...   ..++....+...   .....+.. .+.+....
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~---~~~~~id~-ir~li~~~   74 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE---GENIGIDD-IRTIKDFL   74 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS---SSCBCHHH-HHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCC---cCCCCHHH-HHHHHHHH
Confidence            44566777888777543  67899999999999999999987521   112223333210   00112222 22233322


Q ss_pred             hcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hhhhhcCCCeeEEcC
Q 009306          269 LNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QVLANCGVDEVYQME  345 (538)
Q Consensus       269 ~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~~~~~~~~l~  345 (538)
                      ...+                ..+++-++|+|+++.  ......++..+....+.+.+|++|.+. .+.+.+... .++++
T Consensus        75 ~~~p----------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~  137 (305)
T 2gno_A           75 NYSP----------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVV  137 (305)
T ss_dssp             TSCC----------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEE
T ss_pred             hhcc----------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCC
Confidence            2110                013456899999974  345566666665545677777666443 444555445 89999


Q ss_pred             CCCHHHHHHHHHhhh
Q 009306          346 ELVHDDALRLFSRHA  360 (538)
Q Consensus       346 ~L~~~ea~~Lf~~~~  360 (538)
                      +++.++..+.+....
T Consensus       138 ~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          138 VNVPKEFRDLVKEKI  152 (305)
T ss_dssp             CCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999999998876

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=98.10  E-value=2.3e-06  Score=81.78  Aligned_cols=153  Identities=14%  Similarity=0.187  Sum_probs=84.5

Q ss_pred             CCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      ....++|.+..++.|.+.+..          +....+.+.|+|++|+|||+||+.++......|-   .+. ...     
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~---~v~-~~~-----   79 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFF---SMG-GSS-----   79 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCC---CCC-SCT-----
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEE---Eec-hHH-----
Confidence            346799999998888876541          1112334889999999999999999987644321   111 000     


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChHH-----------------HHHHhcCcCCCC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQ-----------------IKILVGRLDLFA  318 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~-----------------~~~l~~~l~~~~  318 (538)
                       +..       ...+.  ..........   .....++.+|+|||++....                 +..++..+....
T Consensus        80 -~~~-------~~~~~--~~~~~~~~~~---~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~  146 (268)
T 2r62_A           80 -FIE-------MFVGL--GASRVRDLFE---TAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFG  146 (268)
T ss_dssp             -TTT-------SCSSS--CSSSSSTTHH---HHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSS
T ss_pred             -HHH-------hhcch--HHHHHHHHHH---HHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcc
Confidence             000       00000  0011222222   22235678999999964311                 222333322211


Q ss_pred             ---CCCEEEEeccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          319 ---SGSRIIITTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       319 ---~~~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                         ....||.||.....+     ........+.++.++.++-.+++....
T Consensus       147 ~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~  196 (268)
T 2r62_A          147 SENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHI  196 (268)
T ss_dssp             CSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHT
T ss_pred             cCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHH
Confidence               224566666544321     111233567888899999888887765

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.10  E-value=1.8e-05  Score=80.13  Aligned_cols=171  Identities=18%  Similarity=0.187  Sum_probs=92.1

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh-cC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE-TC  255 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~-~~  255 (538)
                      .++.|.+...++|.+.+..           +-...+-+.++||+|+|||+||+++++.....|-   .+. ..+... ..
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~---~v~-~~~l~~~~~  247 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFI---RVN-GSEFVHKYL  247 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEE---EEE-GGGTCCSSC
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeE---EEe-cchhhcccc
Confidence            5788999888888775431           3344667999999999999999999998765432   222 111100 00


Q ss_pred             C-hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC-
Q 009306          256 R-LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF-  317 (538)
Q Consensus       256 ~-~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~-  317 (538)
                      + ....++.+                    ....-...|++|++|+++..                ..+..++..+..+ 
T Consensus       248 Ge~e~~ir~l--------------------F~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~  307 (428)
T 4b4t_K          248 GEGPRMVRDV--------------------FRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFD  307 (428)
T ss_dssp             SHHHHHHHHH--------------------HHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSC
T ss_pred             chhHHHHHHH--------------------HHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCC
Confidence            0 01111111                    11222467899999998521                1123333322211 


Q ss_pred             -CCCCEEEEeccchhh-----hhhcCCCeeEEcCCC-CHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 -ASGSRIIITTRDRQV-----LANCGVDEVYQMEEL-VHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 -~~~~~iiiTtR~~~~-----~~~~~~~~~~~l~~L-~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                       ..+..||.||.....     ....+.+..++++.+ +.++-.++|..+.-+-....+.   ....+++.+.|.-
T Consensus       308 ~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~---dl~~lA~~t~G~s  379 (428)
T 4b4t_K          308 QSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEA---DLDSLIIRNDSLS  379 (428)
T ss_dssp             SSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTC---CHHHHHHHTTTCC
T ss_pred             CCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCccc---CHHHHHHHCCCCC
Confidence             234556667754422     111123456788765 4555556666555221111111   1456777777764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.10  E-value=3.1e-05  Score=85.34  Aligned_cols=149  Identities=13%  Similarity=0.125  Sum_probs=84.2

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhhhhcCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREAEETCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~~~~~~~~  258 (538)
                      ...+.++||+.+++.+...|...  ...-+.|+|++|+|||++|+.++..+....      ...++..+.          
T Consensus       177 ~~ld~iiG~~~~i~~l~~~l~~~--~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~----------  244 (758)
T 3pxi_A          177 DSLDPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM----------  244 (758)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC------------
T ss_pred             CCCCCccCchHHHHHHHHHHhCC--CCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc----------
Confidence            34467999999999999998753  233478999999999999999999863321      112221111          


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhhh----
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVLA----  334 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~----  334 (538)
                            .....+     .........+......++.+|+||  ...+....+...+.  ....++|.+|.......    
T Consensus       245 ------g~~~~G-----~~e~~l~~~~~~~~~~~~~iLfiD--~~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~  309 (758)
T 3pxi_A          245 ------GTKYRG-----EFEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEK  309 (758)
T ss_dssp             -------------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTT
T ss_pred             ------cccccc-----hHHHHHHHHHHHHHhcCCEEEEEc--CchhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhc
Confidence                  000000     001111222223334678899999  22333334444443  33466666665443111    


Q ss_pred             --hc-CCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          335 --NC-GVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       335 --~~-~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                        .+ .....+.++.++.++..+++....
T Consensus       310 d~al~rRf~~i~v~~p~~~~~~~il~~~~  338 (758)
T 3pxi_A          310 DAALERRFQPIQVDQPSVDESIQILQGLR  338 (758)
T ss_dssp             CSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             cHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence              00 112578999999999999998655

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=98.09  E-value=6.4e-05  Score=77.29  Aligned_cols=174  Identities=15%  Similarity=0.180  Sum_probs=97.0

Q ss_pred             CCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          187 NEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      ..+++|.+..++++.++...          +..-.+-+.|+|++|+|||+||+.++.+....|   +.+. ..+..... 
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f---~~is-~~~~~~~~-   89 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPF---FHIS-GSDFVELF-   89 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCE---EEEE-GGGTTTCC-
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCe---eeCC-HHHHHHHH-
Confidence            35688988887777665432          111234588999999999999999998764432   1222 11111100 


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCC--C
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLF--A  318 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~--~  318 (538)
                      ..                 .........+.......+.+|+||+++..                ..+..++..+..+  .
T Consensus        90 ~g-----------------~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~  152 (476)
T 2ce7_A           90 VG-----------------VGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSK  152 (476)
T ss_dssp             TT-----------------HHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGG
T ss_pred             hc-----------------ccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCC
Confidence            00                 00111122233334567899999999542                1233333322211  2


Q ss_pred             CCCEEEEeccchhhhh-h-c---CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          319 SGSRIIITTRDRQVLA-N-C---GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~~-~-~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .+..||.||.....+. . .   .....+.++..+.++-.+++..+........+.   ....+++.+.|+.
T Consensus       153 ~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v---~l~~la~~t~G~s  221 (476)
T 2ce7_A          153 EGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDV---NLEIIAKRTPGFV  221 (476)
T ss_dssp             GTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC---CHHHHHHTCTTCC
T ss_pred             CCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchh---hHHHHHHhcCCCc
Confidence            3556666666553322 1 1   244588899999888888887766322111111   1345778888887

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.09  E-value=2.3e-05  Score=76.39  Aligned_cols=50  Identities=18%  Similarity=0.333  Sum_probs=38.5

Q ss_pred             CCceeccchhHHHHHhhhcC------C-CCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTG------S-TNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~------~-~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..++|.+..++.+...+...      . .....+.|+|++|+|||++|+.++.....
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~   73 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFD   73 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHS
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcC
Confidence            45789988888887776542      1 11357999999999999999999987644

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.08  E-value=3.2e-05  Score=85.30  Aligned_cols=155  Identities=12%  Similarity=0.156  Sum_probs=89.4

Q ss_pred             CCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEeehhhhhhcCChH
Q 009306          185 SENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFARNVREAEETCRLG  258 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~~~~~~~~~~~~~  258 (538)
                      ...+.++||+.+++.+.+.|...  ....+.|+|++|+|||++|+.++..+...      ....++..+.....      
T Consensus       183 ~~~d~~iGr~~~i~~l~~~l~~~--~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~------  254 (758)
T 1r6b_X          183 GGIDPLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLL------  254 (758)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---------
T ss_pred             CCCCCccCCHHHHHHHHHHHhcc--CCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHh------
Confidence            34467999999999999988753  33457899999999999999999876321      12223322111100      


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------HH-HHHHhcCcCCCCCCCEEEEe
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------RQ-IKILVGRLDLFASGSRIIIT  326 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------~~-~~~l~~~l~~~~~~~~iiiT  326 (538)
                                .+. ......+.....+.+.+ ..++.+|+||+++..          .. ...+...+.  ....++|.+
T Consensus       255 ----------~~~-~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~--~~~~~~I~a  321 (758)
T 1r6b_X          255 ----------AGT-KYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGS  321 (758)
T ss_dssp             ----------CCC-CCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEE
T ss_pred             ----------ccc-cccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHh--CCCeEEEEE
Confidence                      000 00112222222222333 335789999999754          12 223333332  235566666


Q ss_pred             ccchhhhhhc-------CCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          327 TRDRQVLANC-------GVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       327 tR~~~~~~~~-------~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      |.........       .....+.++.++.++..+++....
T Consensus       322 t~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          322 TTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             ECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             eCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence            6544321111       112368899999999998887654

>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=98.05  E-value=2.3e-05  Score=74.58  Aligned_cols=49  Identities=22%  Similarity=0.182  Sum_probs=35.2

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +.++|.+..+..+.+.+..-......+.|+|++|+|||+||+.+++...
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            5689999998888776654112234588999999999999999998754

>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=98.00  E-value=0.00018  Score=74.24  Aligned_cols=95  Identities=8%  Similarity=-0.035  Sum_probs=57.7

Q ss_pred             eEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEec---------cc----h-hhhh-hcCCCeeEEcCCCCHHHHHHHH
Q 009306          294 VLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITT---------RD----R-QVLA-NCGVDEVYQMEELVHDDALRLF  356 (538)
Q Consensus       294 ~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTt---------R~----~-~~~~-~~~~~~~~~l~~L~~~ea~~Lf  356 (538)
                      -+++||+++.  .+....+...+...... .+|+.|         .+    . .+.+ .......+.+++++.++..+++
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~~~~~~~~~~~e~~~iL  375 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQII  375 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHTTEEEEECCCCCHHHHHHHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccccCChhHHhhcceeeCCCCCHHHHHHHH
Confidence            3899999964  45667777666543444 344333         11    1 1111 1112345799999999999999


Q ss_pred             HhhhcCCCCCCCchHHHHHHHHHHh-cCCcHHHHHH
Q 009306          357 SRHAFGGDHPHESHTELACKTIKYA-RGVPLALEVL  391 (538)
Q Consensus       357 ~~~~~~~~~~~~~~~~~~~~i~~~~-~G~PLal~~~  391 (538)
                      ..++-.  .......+....+++.+ .|.|.....+
T Consensus       376 ~~~~~~--~~~~~~~~~~~~i~~~a~~g~~r~a~~l  409 (456)
T 2c9o_A          376 KIRAQT--EGINISEEALNHLGEIGTKTTLRYSVQL  409 (456)
T ss_dssp             HHHHHH--HTCCBCHHHHHHHHHHHHHSCHHHHHHT
T ss_pred             HHHHHH--hCCCCCHHHHHHHHHHccCCCHHHHHHH
Confidence            877621  11224466778888888 8888644433

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.00  E-value=1.4e-05  Score=77.81  Aligned_cols=48  Identities=19%  Similarity=0.228  Sum_probs=38.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.++|+...+.++.+.+..-......+.|+|++|+|||++|+.+++..
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            458999999999888776522233458899999999999999999864

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.98  E-value=2.9e-06  Score=72.77  Aligned_cols=49  Identities=14%  Similarity=0.128  Sum_probs=34.7

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      -.++|++..++++.+.+..-......+.|+|++|+|||++|+.+++...
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~~   52 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGT   52 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTTS
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCC
Confidence            4578999999988887654112223488999999999999998887643

>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=97.92  E-value=5.2e-05  Score=82.56  Aligned_cols=173  Identities=16%  Similarity=0.169  Sum_probs=98.6

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .++.|.+..+++|.+++.-           +....+-|.++|++|+|||+||++++.+....|   +.+. ..+....  
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~---~~v~-~~~l~sk--  277 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFF---FLIN-GPEIMSK--  277 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEE---EEEE-HHHHHSS--
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeE---EEEE-hHHhhcc--
Confidence            4678999999888876531           123356799999999999999999999875442   2222 2111100  


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------HHHHHHhcCcCCC--CCCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------RQIKILVGRLDLF--ASGS  321 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~~~~~l~~~l~~~--~~~~  321 (538)
                                      ....................|.+|+||++|..             ..+..++..+...  ..+.
T Consensus       278 ----------------~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V  341 (806)
T 3cf2_A          278 ----------------LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  341 (806)
T ss_dssp             ----------------CTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCE
T ss_pred             ----------------cchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCE
Confidence                            00011111112222333567999999999642             1123333222211  2234


Q ss_pred             EEEEeccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          322 RIIITTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       322 ~iiiTtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .||.||.....+ +.+    .....++++..+.++-.++|..+..+.....+   .....+++.+.|+.
T Consensus       342 ~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~d---vdl~~lA~~T~Gfs  407 (806)
T 3cf2_A          342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADD---VDLEQVANETHGHV  407 (806)
T ss_dssp             EEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTT---CCHHHHHHHCCSCC
T ss_pred             EEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcc---cCHHHHHHhcCCCC
Confidence            455555544222 111    34568999999999999999877632211111   12456788887774

>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=97.83  E-value=0.00043  Score=65.19  Aligned_cols=174  Identities=16%  Similarity=0.161  Sum_probs=88.1

Q ss_pred             CCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcC
Q 009306          186 ENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETC  255 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~  255 (538)
                      ..++++|.+....++..+...          +..-.+-+.|+|++|+|||||++.++.....   ..+.+. ....... 
T Consensus        14 ~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~---~~i~~~-~~~~~~~-   88 (254)
T 1ixz_A           14 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV---PFITAS-GSDFVEM-   88 (254)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTC---CEEEEE-HHHHHHS-
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCC---CEEEee-HHHHHHH-
Confidence            335678887766666554321          0011223899999999999999999987652   223332 1111000 


Q ss_pred             ChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------------HHHHHHhcCcCCCC
Q 009306          256 RLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------------RQIKILVGRLDLFA  318 (538)
Q Consensus       256 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~~  318 (538)
                      ...                  ........+.+.. ...+.++++||++..                ..+..+...+....
T Consensus        89 ~~~------------------~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~  150 (254)
T 1ixz_A           89 FVG------------------VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFE  150 (254)
T ss_dssp             CTT------------------HHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCC
T ss_pred             Hhh------------------HHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCC
Confidence            000                  0011111222222 235689999998422                11223332222111


Q ss_pred             -CC-CEEEEeccchhhhh-----hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          319 -SG-SRIIITTRDRQVLA-----NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       319 -~~-~~iiiTtR~~~~~~-----~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                       .. ..++.+|.....+.     .......+.++..+.++-.+++..+.-+.....+   .....+++.+.|+-
T Consensus       151 ~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~---~~~~~la~~~~G~~  221 (254)
T 1ixz_A          151 KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPGFV  221 (254)
T ss_dssp             TTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTT---CCHHHHHHTCTTCC
T ss_pred             CCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcc---cCHHHHHHHcCCCC
Confidence             22 23444555544322     1134567899999999888888776522111111   11345666676654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.80  E-value=3.8e-05  Score=84.62  Aligned_cols=148  Identities=15%  Similarity=0.174  Sum_probs=83.3

Q ss_pred             CCceeccchhHHHHHhhhcCC-------CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGS-------TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~-------~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..++|.+..++.+...+....       .....+.++|++|+|||++|+.+++.........+.+. ..+........  
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~-~s~~~~~~~~~--  567 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRID-MSEYMEKHSTS--  567 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEE-GGGGCSSCCCC--
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEe-chhcccccccc--
Confidence            568999998888877665311       11236999999999999999999987633222233333 22221111110  


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCC-----------CCCCCEEEEec
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDL-----------FASGSRIIITT  327 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~-----------~~~~~~iiiTt  327 (538)
                                       .......++   .....+|+||+++..  +....++..+..           ...+.+||+||
T Consensus       568 -----------------~~~l~~~~~---~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~tt  627 (758)
T 3pxi_A          568 -----------------GGQLTEKVR---RKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTS  627 (758)
T ss_dssp             --------------------CHHHHH---HCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEE
T ss_pred             -----------------cchhhHHHH---hCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeC
Confidence                             111112221   134459999999643  333333322211           12356788888


Q ss_pred             cch-----------------hhhhhcCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          328 RDR-----------------QVLANCGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       328 R~~-----------------~~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ...                 .+..  ....++.+++++.++..+++....
T Consensus       628 n~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          628 NVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             SSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHH
T ss_pred             CCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHH
Confidence            621                 1111  234688999999999998887655

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.75  E-value=5.9e-05  Score=68.49  Aligned_cols=60  Identities=20%  Similarity=0.170  Sum_probs=39.7

Q ss_pred             CCCceeccc----hhHHHHHhhhcCCCC--ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          187 NEDLVGVRL----PMKEIESLLRTGSTN--VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       187 ~~~~vGR~~----~l~~l~~~L~~~~~~--~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .++|++...    .++.+..++......  .+.+.|+|++|+|||+||+.++.........++++.
T Consensus        24 f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           24 LSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             TTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            356666543    334445555433221  267999999999999999999998765544455554

>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=97.74  E-value=3.2e-05  Score=62.19  Aligned_cols=72  Identities=10%  Similarity=0.059  Sum_probs=52.8

Q ss_pred             CCcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeCCCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhHHHHHH
Q 009306           15 EIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCLDELLK   94 (538)
Q Consensus        15 ~~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~   94 (538)
                      ..+|.+||||+.+| .   ...|...|...|+..- |              ..|+.|+++|++.++....|+||..|+..
T Consensus         2 ~~~~~lFISh~~~d-~---~~~L~~~l~~~~f~~~-~--------------~~I~~~~~vIvL~G~~t~~s~wv~~EI~~   62 (111)
T 1eiw_A            2 TAEIRLYITEGEVE-D---YRVFLERLEQSGLEWR-P--------------ATPEDADAVIVLAGLWGTRRDEILGAVDL   62 (111)
T ss_dssp             CCCEEEEECCCCSH-H---HHHHHHHHHHHCSCEE-E--------------CCSSSCSEEEEEGGGTTTSHHHHHHHHHH
T ss_pred             CceEEEEEecccHh-H---HHHHHHHHhCCCCeee-c--------------CccccCCEEEEEeCCCcCCChHHHHHHHH
Confidence            35799999999998 2   4445555545555332 2              66889999999999999999999999986


Q ss_pred             HHHHHhhcCCeEEEE
Q 009306           95 ILECKKEYAQIVVPV  109 (538)
Q Consensus        95 ~~~~~~~~~~~v~pv  109 (538)
                      |.+    .+.+++-|
T Consensus        63 A~~----~gkpIigV   73 (111)
T 1eiw_A           63 ARK----SSKPIITV   73 (111)
T ss_dssp             HTT----TTCCEEEE
T ss_pred             HHH----cCCCEEEE
Confidence            664    34445544

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.74  E-value=0.00096  Score=63.77  Aligned_cols=175  Identities=15%  Similarity=0.158  Sum_probs=90.6

Q ss_pred             CCCCCceeccchhHHHHHhhhc----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          185 SENEDLVGVRLPMKEIESLLRT----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ...++++|.+....++..+...          +..-.+-+.|+|++|+|||||++.++.....   ..+.+. .......
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~---~~i~~~-~~~~~~~  112 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV---PFITAS-GSDFVEM  112 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTC---CEEEEE-HHHHHHS
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCC---CEEEec-HHHHHHH
Confidence            3446788888777776654321          0011223899999999999999999987652   223332 1111000


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------------HHHHHHhcCcCCC
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------------RQIKILVGRLDLF  317 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~  317 (538)
                       ...                  ........+.+.. ...+.++++||++..                ..+..+...+...
T Consensus       113 -~~~------------------~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg  173 (278)
T 1iy2_A          113 -FVG------------------VGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGF  173 (278)
T ss_dssp             -TTT------------------HHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTC
T ss_pred             -Hhh------------------HHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCC
Confidence             000                  0001111122222 245789999998421                1122333333221


Q ss_pred             C-CC-CEEEEeccchhhh-----hhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          318 A-SG-SRIIITTRDRQVL-----ANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       318 ~-~~-~~iiiTtR~~~~~-----~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      . .. ..++.+|.....+     ........+.++..+.++-.+++..+.-......+   .....++..+.|+.
T Consensus       174 ~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~---~~~~~la~~~~G~~  245 (278)
T 1iy2_A          174 EKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPGFV  245 (278)
T ss_dssp             CTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTT---CCHHHHHHTCTTCC
T ss_pred             CCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcc---cCHHHHHHHcCCCC
Confidence            1 12 2334455444332     11234568899999999888888876522111111   12345667777765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.72  E-value=0.00021  Score=69.04  Aligned_cols=29  Identities=34%  Similarity=0.568  Sum_probs=24.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.+.|+|++|+|||+||+.+++.....
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~~~   63 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMGIN   63 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            35578999999999999999999987443

>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=97.72  E-value=0.00023  Score=71.40  Aligned_cols=26  Identities=23%  Similarity=0.313  Sum_probs=22.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+.|+|++|+|||++|+.+++.+..
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~l~~   98 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKHLDI   98 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCC
Confidence            45899999999999999999988743

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.70  E-value=3.1e-05  Score=66.68  Aligned_cols=37  Identities=16%  Similarity=0.239  Sum_probs=27.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ....++|+|++|+|||||++.++..........+++.
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            3457999999999999999999987654322245554

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.66  E-value=0.0014  Score=67.69  Aligned_cols=172  Identities=15%  Similarity=0.159  Sum_probs=93.2

Q ss_pred             CCCCCceeccchhHHHHHhhhc--C--------CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhc
Q 009306          185 SENEDLVGVRLPMKEIESLLRT--G--------STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEET  254 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~--~--------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~  254 (538)
                      ....+++|.+..+.++.++...  .        ..-.+-+.|+|++|+|||+||+.++......   .+.+. .......
T Consensus        28 ~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~---~i~i~-g~~~~~~  103 (499)
T 2dhr_A           28 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVP---FITAS-GSDFVEM  103 (499)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCC---EEEEE-GGGGTSS
T ss_pred             CCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCC---EEEEe-hhHHHHh
Confidence            3446788988877777665421  1        1112348999999999999999999876522   22333 1111100


Q ss_pred             CChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh----cCCCeEEEEecCCCh----------------HHHHHHhcCc
Q 009306          255 CRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL----TRKKVLIVFDDVDHP----------------RQIKILVGRL  314 (538)
Q Consensus       255 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l----~~k~~LlVlDdv~~~----------------~~~~~l~~~l  314 (538)
                       ....                     ....+...+    ...+.++++|+++..                ..+..++..+
T Consensus       104 -~~g~---------------------~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~L  161 (499)
T 2dhr_A          104 -FVGV---------------------GAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEM  161 (499)
T ss_dssp             -CTTH---------------------HHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHG
T ss_pred             -hhhh---------------------HHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHh
Confidence             0000                     011111111    124689999999531                1223333333


Q ss_pred             CCC--CCCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          315 DLF--ASGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       315 ~~~--~~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      ..+  .....++.+|.....+..     ......+.++..+.++-.+++..++-+.....+   .....++..+.|+.
T Consensus       162 dg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~d---v~l~~lA~~t~G~~  236 (499)
T 2dhr_A          162 DGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPGFV  236 (499)
T ss_dssp             GGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCS---STTHHHHTTSCSCC
T ss_pred             cccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChH---HHHHHHHHhcCCCC
Confidence            221  223445556655544321     124468899999999999988877522111111   11445677777776

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.57  E-value=0.0019  Score=61.56  Aligned_cols=124  Identities=19%  Similarity=0.222  Sum_probs=68.2

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh-cCC
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRK  292 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k  292 (538)
                      ++|+|++|+|||||++.++......   .+.+.. .+... ......                  ......+.+.. ...
T Consensus        47 vlL~Gp~GtGKTtLakala~~~~~~---~i~i~g-~~l~~-~~~~~~------------------~~~i~~vf~~a~~~~  103 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANESGLN---FISVKG-PELLN-MYVGES------------------ERAVRQVFQRAKNSA  103 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHHTTCE---EEEEET-TTTCS-STTHHH------------------HHHHHHHHHHHHHTC
T ss_pred             EEEECCCCCcHHHHHHHHHHHcCCC---EEEEEc-HHHHh-hhhhHH------------------HHHHHHHHHHHHhcC
Confidence            9999999999999999999876432   233331 11100 000110                  01111122221 346


Q ss_pred             CeEEEEecCCCh-------------HHHHHHhcCcCCC--CCCCEEEEeccchhhhhh-----cCCCeeEEcCCCCHHHH
Q 009306          293 KVLIVFDDVDHP-------------RQIKILVGRLDLF--ASGSRIIITTRDRQVLAN-----CGVDEVYQMEELVHDDA  352 (538)
Q Consensus       293 ~~LlVlDdv~~~-------------~~~~~l~~~l~~~--~~~~~iiiTtR~~~~~~~-----~~~~~~~~l~~L~~~ea  352 (538)
                      +.++++|+++..             .....+...+...  ....-++.+|.....+..     ...+..+.++..+.++-
T Consensus       104 p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r  183 (274)
T 2x8a_A          104 PCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADR  183 (274)
T ss_dssp             SEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHH
T ss_pred             CCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHH
Confidence            789999999642             1122222222211  122335555655544321     14567888999999999


Q ss_pred             HHHHHhhh
Q 009306          353 LRLFSRHA  360 (538)
Q Consensus       353 ~~Lf~~~~  360 (538)
                      .+++....
T Consensus       184 ~~il~~~~  191 (274)
T 2x8a_A          184 LAILKTIT  191 (274)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHH
Confidence            99998765

>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=97.36  E-value=0.00035  Score=76.92  Aligned_cols=49  Identities=16%  Similarity=0.260  Sum_probs=37.8

Q ss_pred             CCceeccchhHHHHHhhhc---C----CCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRT---G----STNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~---~----~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++|.+..++.+...+..   +    ......+.++|++|+|||++|+.+++...
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~  513 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc
Confidence            4688999888888776643   1    11234689999999999999999998873

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.36  E-value=0.00073  Score=71.07  Aligned_cols=51  Identities=27%  Similarity=0.336  Sum_probs=35.8

Q ss_pred             CceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          189 DLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +++|.+...+.+.+.+.-    .......++|+|++|+||||||+.++......|
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~  136 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRKF  136 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCEE
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCCe
Confidence            367777766666543321    112355799999999999999999998875443

>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=97.30  E-value=0.0007  Score=61.99  Aligned_cols=45  Identities=22%  Similarity=0.107  Sum_probs=31.7

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|..++..+-....++.|.|++|+|||||+..++.   ..-..++|+.
T Consensus         8 ~LD~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i~   52 (220)
T 2cvh_A            8 SLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGL---LSGKKVAYVD   52 (220)
T ss_dssp             HHHHHTTSSBCTTSEEEEECSTTSSHHHHHHHHHH---HHCSEEEEEE
T ss_pred             HHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHH---HcCCcEEEEE
Confidence            44555543334556899999999999999999988   2233556655

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.24  E-value=0.00047  Score=63.74  Aligned_cols=49  Identities=18%  Similarity=0.251  Sum_probs=32.4

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|..++..+-....+++|.|++|+|||||++.++......-..+.|+.
T Consensus        10 ~~Ld~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           10 LDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             HHHHGGGTTSEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             hHHHHHhcCCCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3444444322234467999999999999999999976544333455544

>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=97.22  E-value=0.0018  Score=72.25  Aligned_cols=50  Identities=18%  Similarity=0.336  Sum_probs=38.3

Q ss_pred             CCceeccchhHHHHHhhhcC-------CCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTG-------STNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~-------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..++|.+..++.+...+...       ......+.|+|++|+|||++|+.+++....
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            35799999888887766431       112357999999999999999999987643

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.19  E-value=0.0011  Score=65.46  Aligned_cols=99  Identities=19%  Similarity=0.087  Sum_probs=57.9

Q ss_pred             chhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCC
Q 009306          195 LPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGN  273 (538)
Q Consensus       195 ~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~  273 (538)
                      .-...|...|. .+-....++.|.|++|+|||||+..++......-..++|+..    ....... ..    ..++....
T Consensus        44 TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~----E~s~~~~-ra----~rlgv~~~  114 (356)
T 3hr8_A           44 TGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDA----EHALDPV-YA----KNLGVDLK  114 (356)
T ss_dssp             CSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES----SCCCCHH-HH----HHHTCCGG
T ss_pred             CCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEec----ccccchH-HH----HHcCCchh
Confidence            34456777776 444556789999999999999999999876544445667652    1111111 22    22222111


Q ss_pred             -----CCCchhhcHHHHHHHhc-CCCeEEEEecCC
Q 009306          274 -----VKNFLNTDLNFQSRRLT-RKKVLIVFDDVD  302 (538)
Q Consensus       274 -----~~~~~~~~~~~l~~~l~-~k~~LlVlDdv~  302 (538)
                           ...+.++....+...+. .+.-++|+|.+.
T Consensus       115 ~l~i~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~  149 (356)
T 3hr8_A          115 SLLISQPDHGEQALEIVDELVRSGVVDLIVVDSVA  149 (356)
T ss_dssp             GCEEECCSSHHHHHHHHHHHHHTSCCSEEEEECTT
T ss_pred             hhhhhhccCHHHHHHHHHHHhhhcCCCeEEehHhh
Confidence                 01334444444444443 456789999874

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=97.18  E-value=0.0017  Score=67.21  Aligned_cols=46  Identities=17%  Similarity=0.130  Sum_probs=38.0

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +.++|++..++.+...+..+.    .+.|+|++|+|||+||+.++.....
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraLa~~l~~   67 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFAFQN   67 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHGGGGBSS
T ss_pred             hhhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHHHHHHhh
Confidence            468999999988887776432    4899999999999999999987643

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=97.06  E-value=0.0072  Score=59.53  Aligned_cols=165  Identities=9%  Similarity=-0.032  Sum_probs=102.1

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCc
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNF  277 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~  277 (538)
                      ++...+. + .-.++..++|+.|.||++.+..+...+.. .|.....+. ..   ....+..+...+..           
T Consensus         8 ~l~~~l~-~-~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~---~~~~~~~l~~~~~~-----------   70 (343)
T 1jr3_D            8 QLRAQLN-E-GLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFS-ID---PNTDWNAIFSLCQA-----------   70 (343)
T ss_dssp             THHHHHH-H-CCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEE-CC---TTCCHHHHHHHHHH-----------
T ss_pred             HHHHHHh-c-CCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEE-ec---CCCCHHHHHHHhcC-----------
Confidence            3444454 2 34568999999999999999999886542 232211111 11   11333333322211           


Q ss_pred             hhhcHHHHHHHhcCCCeEEEEecCCC---hHHHHHHhcCcCCCCCCCEEEEeccc-------hhhhhhc-CCCeeEEcCC
Q 009306          278 LNTDLNFQSRRLTRKKVLIVFDDVDH---PRQIKILVGRLDLFASGSRIIITTRD-------RQVLANC-GVDEVYQMEE  346 (538)
Q Consensus       278 ~~~~~~~l~~~l~~k~~LlVlDdv~~---~~~~~~l~~~l~~~~~~~~iiiTtR~-------~~~~~~~-~~~~~~~l~~  346 (538)
                               .-+.+.+-++|+|+++.   ....+.+...+....+++.+|+++..       ..+...+ .....++..+
T Consensus        71 ---------~plf~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~  141 (343)
T 1jr3_D           71 ---------MSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQT  141 (343)
T ss_dssp             ---------HHHCCSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECC
T ss_pred             ---------cCCccCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeC
Confidence                     11234566889999865   34566666665554567777766543       2344443 3346899999


Q ss_pred             CCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHH
Q 009306          347 LVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVL  391 (538)
Q Consensus       347 L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~  391 (538)
                      ++..+..+.+...+-  ........+.+..+++.++|.+..+...
T Consensus       142 l~~~~l~~~l~~~~~--~~g~~i~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          142 PEQAQLPRWVAARAK--QLNLELDDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             CCTTHHHHHHHHHHH--HTTCEECHHHHHHHHHSSTTCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH--HcCCCCCHHHHHHHHHHhchHHHHHHHH
Confidence            999999988888762  2223455778889999999998776543

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=97.02  E-value=0.0048  Score=60.02  Aligned_cols=54  Identities=19%  Similarity=0.107  Sum_probs=38.2

Q ss_pred             eccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       192 GR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      |-..-+..|..++ .+-....++.|.|.+|+||||||..++.....+...++|+.
T Consensus        50 ~i~TG~~~LD~~l-gGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           50 GVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             SBCCSCHHHHHHH-SSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CccCChHHHHhhc-CCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            3444455566666 44455678999999999999999999987654435566655

>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=97.00  E-value=0.0012  Score=58.76  Aligned_cols=117  Identities=15%  Similarity=0.047  Sum_probs=60.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHH---hc-CCCCC-------Cchhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTL---LN-DGNVK-------NFLNTD  281 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l---~~-~~~~~-------~~~~~~  281 (538)
                      .|.|++..|.||||.|..++-+...+-..+.++...... ...+...+++.+.-.+   +. -....       ......
T Consensus        30 ~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~-~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~  108 (196)
T 1g5t_A           30 IIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGT-WPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAV  108 (196)
T ss_dssp             CEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCS-SCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCC-CCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHH
Confidence            466777777999999999998877665556666422210 1112223333321000   00 00000       111223


Q ss_pred             HHHHHHHhcCC-CeEEEEecCCC-----hHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          282 LNFQSRRLTRK-KVLIVFDDVDH-----PRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       282 ~~~l~~~l~~k-~~LlVlDdv~~-----~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      ....++.+... -=|||||++..     .-..+.++..+........||+|+|..
T Consensus       109 l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          109 WQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            34444555444 45999999832     111222222222335678899999986

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.99  E-value=0.002  Score=62.48  Aligned_cols=51  Identities=18%  Similarity=0.255  Sum_probs=34.7

Q ss_pred             hhHHHHHhhhcCCC-CceEEEEeccCCCchhHHHHHHHHhhc-cceeeEEEEe
Q 009306          196 PMKEIESLLRTGST-NVYKLGIWGIGGIGKTTIAGAIFNKIS-RHFSGSYFAR  246 (538)
Q Consensus       196 ~l~~l~~~L~~~~~-~~~~v~I~G~~GiGKTtLa~~~~~~~~-~~f~~~~~~~  246 (538)
                      .++.+.+++..... ....+.|+|++|+|||+||..+++... .....+.++.
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            44445556654221 246789999999999999999999876 5444455554

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.93  E-value=0.0026  Score=61.03  Aligned_cols=49  Identities=14%  Similarity=0.049  Sum_probs=35.3

Q ss_pred             hHHHHHhhh----cCCCCceEEEEeccCCCchhHHHHHHHHhhccc--eeeEEEEe
Q 009306          197 MKEIESLLR----TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH--FSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~----~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~--f~~~~~~~  246 (538)
                      ...|...|.    .+-... ++.|.|++|+|||||+.+++......  -..++|++
T Consensus        11 i~~LD~~LGg~~~GGl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           11 IPMMNIALSGEITGGMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             CHHHHHHHHSSTTCCBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             CHHHHHHhCCCCCCCCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            345666666    443444 78999999999999999998876554  34567766

>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=96.90  E-value=0.0007  Score=65.23  Aligned_cols=25  Identities=24%  Similarity=0.193  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..+++.|+|++|+|||+||.+++..
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            3456889999999999999999886

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.90  E-value=0.0011  Score=72.35  Aligned_cols=171  Identities=19%  Similarity=0.234  Sum_probs=78.9

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      ..+.|.+...++|.+.+.-           +....+-+.++|++|+|||.||++++.+....|    +....        
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f----~~v~~--------  544 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANF----ISIKG--------  544 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEE----EECCH--------
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCce----EEecc--------
Confidence            4566777777777665432           112244588999999999999999999865432    21111        


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH-hcCCCeEEEEecCCCh----------------HHHHHHhcCcCCCCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR-LTRKKVLIVFDDVDHP----------------RQIKILVGRLDLFAS  319 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~~~  319 (538)
                       .    .+++...+     .. +..+..+.+. -...|++|+||++|..                ..+..|+..+.....
T Consensus       545 -~----~l~s~~vG-----es-e~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~  613 (806)
T 3cf2_A          545 -P----ELLTMWFG-----ES-EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST  613 (806)
T ss_dssp             -H----HHHTTTCS-----SC-HHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCS
T ss_pred             -c----hhhccccc-----hH-HHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCC
Confidence             1    11111111     11 2222222222 2457999999999632                113344433332222


Q ss_pred             --CCEEEEeccchhh-----hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCC
Q 009306          320 --GSRIIITTRDRQV-----LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGV  384 (538)
Q Consensus       320 --~~~iiiTtR~~~~-----~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~  384 (538)
                        +.-||-||.....     +..-+.+..+.++..+.++-.++|..+.-+.....+  . ....+++.+.|+
T Consensus       614 ~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~--~-dl~~la~~t~g~  682 (806)
T 3cf2_A          614 KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKD--V-DLEFLAKMTNGF  682 (806)
T ss_dssp             SSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------
T ss_pred             CCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCC--C-CHHHHHHhCCCC
Confidence              2233334433322     221234667888888888888888776622111111  1 134556666654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.88  E-value=0.0011  Score=60.93  Aligned_cols=110  Identities=15%  Similarity=0.002  Sum_probs=57.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC-C-CchhhcHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV-K-NFLNTDLNFQSR  287 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~-~-~~~~~~~~~l~~  287 (538)
                      ...++.|+|+.|+||||++..++.+...+...+..+....+.  . +..    ++.+.++..... . ....+....+.+
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~--r-~~~----~i~srlG~~~~~~~~~~~~~i~~~i~~   83 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDT--R-SIR----NIQSRTGTSLPSVEVESAPEILNYIMS   83 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCG--G-GCS----SCCCCCCCSSCCEEESSTHHHHHHHHS
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCc--h-HHH----HHHHhcCCCccccccCCHHHHHHHHHH
Confidence            356899999999999999999998876554444444311111  0 100    111222111000 0 122233333333


Q ss_pred             HhcC-CCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccc
Q 009306          288 RLTR-KKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       288 ~l~~-k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                      .+.. +.-+||+|.+..  .++++.+....   ..+..||+|.+.
T Consensus        84 ~~~~~~~dvViIDEaQ~l~~~~ve~l~~L~---~~gi~Vil~Gl~  125 (223)
T 2b8t_A           84 NSFNDETKVIGIDEVQFFDDRICEVANILA---ENGFVVIISGLD  125 (223)
T ss_dssp             TTSCTTCCEEEECSGGGSCTHHHHHHHHHH---HTTCEEEEECCS
T ss_pred             HhhCCCCCEEEEecCccCcHHHHHHHHHHH---hCCCeEEEEecc
Confidence            3322 345999999842  34444443211   137889999884

>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=96.88  E-value=0.022  Score=50.18  Aligned_cols=24  Identities=38%  Similarity=0.572  Sum_probs=21.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++|+|+.|+|||||++.++..+.
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            488999999999999999998654

>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=96.77  E-value=0.0017  Score=64.18  Aligned_cols=111  Identities=14%  Similarity=0.087  Sum_probs=63.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeE-EEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGS-YFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~-~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ..+++|+|+.|+|||||.+.+...+....... +.+.+..+.......         ..................+...|
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~---------~~v~q~~~~~~~~~~~~~La~aL  193 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKK---------CLVNQREVHRDTLGFSEALRSAL  193 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSS---------SEEEEEEBTTTBSCHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccc---------cceeeeeeccccCCHHHHHHHHh
Confidence            34899999999999999999988765442222 332211110000000         00000000011123345778888


Q ss_pred             cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhh
Q 009306          290 TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVL  333 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~  333 (538)
                      ...|=+|++|+.-+.+.++.+....   ..|..||+|+-.....
T Consensus       194 ~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          194 REDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             TSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHH
T ss_pred             hhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHH
Confidence            8999999999998877666544332   2366688887765443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.74  E-value=0.003  Score=61.81  Aligned_cols=55  Identities=13%  Similarity=0.080  Sum_probs=37.7

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|-..-+..|..++. +-....++.|.|.+|+||||||..++......-..+.|++
T Consensus        27 ~gi~TG~~~LD~~~g-Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS   81 (338)
T 4a1f_A           27 TGIPTGFVQLDNYTS-GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS   81 (338)
T ss_dssp             CSBCCSCHHHHHHHC-SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CcccCCChHHHHHhc-CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            344444555665553 3345568999999999999999999987655434455554

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.73  E-value=0.0007  Score=66.52  Aligned_cols=48  Identities=19%  Similarity=0.316  Sum_probs=39.7

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +.++|++..++.+...+..+.    .+.|+|++|+|||+||+.+++.....|
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~la~~~~~~~   74 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTLAKTMDLDF   74 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHHHHHTTCCE
T ss_pred             cceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            578999999988888776532    489999999999999999998775443

>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=96.71  E-value=0.0037  Score=61.95  Aligned_cols=55  Identities=24%  Similarity=0.144  Sum_probs=39.4

Q ss_pred             eccchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          192 GVRLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       192 GR~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +...-...|..+|. .+-....++.|.|++|+||||||..++......-..++|+.
T Consensus        54 ~i~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~  109 (366)
T 1xp8_A           54 VVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID  109 (366)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eecCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEE
Confidence            33444556666665 34345668999999999999999999887654444677776

>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=96.69  E-value=0.0051  Score=60.65  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=35.8

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc------ceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR------HFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~------~f~~~~~~~  246 (538)
                      ...|..+|..+-....++.|+|++|+||||||..++.....      .-..++|+.
T Consensus       108 ~~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~  163 (343)
T 1v5w_A          108 SQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID  163 (343)
T ss_dssp             CHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             ChhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            34556666544456778999999999999999999986422      224566766

>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=0.0036  Score=61.74  Aligned_cols=53  Identities=19%  Similarity=0.106  Sum_probs=38.4

Q ss_pred             cchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          194 RLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       194 ~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..-...|..+|. .+-....++.|.|++|+||||||..++......-..++|+.
T Consensus        43 ~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~   96 (349)
T 2zr9_A           43 PTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFID   96 (349)
T ss_dssp             CCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             ccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            334456666665 44445678999999999999999999977654444567766

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.64  E-value=0.0032  Score=58.47  Aligned_cols=49  Identities=20%  Similarity=0.206  Sum_probs=34.0

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc------ceeeEEEEe
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR------HFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~------~f~~~~~~~  246 (538)
                      ..|..+|..+-....++.|.|++|+|||||+..++.....      .-..++|+.
T Consensus        11 ~~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~   65 (243)
T 1n0w_A           11 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYID   65 (243)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE
T ss_pred             hHHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEE
Confidence            4455556443344568999999999999999999985322      124566665

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.62  E-value=0.0059  Score=58.92  Aligned_cols=36  Identities=22%  Similarity=0.315  Sum_probs=28.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+||||++..++..++..-..+.++
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv  138 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA  138 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEE
Confidence            457899999999999999999998776543334443

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.57  E-value=0.0035  Score=61.29  Aligned_cols=50  Identities=16%  Similarity=0.211  Sum_probs=35.0

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~  246 (538)
                      ...|..+|..+-....++.|+|++|+||||||..++......      -..++|+.
T Consensus        93 ~~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~  148 (324)
T 2z43_A           93 SQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYID  148 (324)
T ss_dssp             CHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE
T ss_pred             chhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            345555664433456689999999999999999999864322      23566765

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=96.56  E-value=0.0053  Score=60.65  Aligned_cols=55  Identities=18%  Similarity=0.155  Sum_probs=39.5

Q ss_pred             eccchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          192 GVRLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       192 GR~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +-..-...|..+|. .+-...+++.|.|++|+||||||..++......-..++|+.
T Consensus        43 ~i~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid   98 (356)
T 1u94_A           43 TISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   98 (356)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cccCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            33344556666665 44445678999999999999999999987655444677776

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.55  E-value=0.0027  Score=59.97  Aligned_cols=111  Identities=12%  Similarity=0.064  Sum_probs=60.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRL  289 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l  289 (538)
                      ...+++|+|+.|+|||||++.+...+...+.+.+++....-.........        +................+.+.+
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g~~i~~~~~~~~~--------~v~q~~~gl~~~~l~~~la~aL   95 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKS--------IVNQREVGEDTKSFADALRAAL   95 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSS--------EEEEEEBTTTBSCHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcCCcceeecCCcce--------eeeHHHhCCCHHHHHHHHHHHH
Confidence            45689999999999999999998866543334444331100000000000        0000000001122345566666


Q ss_pred             cCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchh
Q 009306          290 TRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQ  331 (538)
Q Consensus       290 ~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~  331 (538)
                      ...|-+|++|+..+.+....++...   ..|.-|++|+-+..
T Consensus        96 ~~~p~illlDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~  134 (261)
T 2eyu_A           96 REDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNT  134 (261)
T ss_dssp             HHCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSS
T ss_pred             hhCCCEEEeCCCCCHHHHHHHHHHH---ccCCEEEEEeCcch
Confidence            6678899999997665554443322   24666777776554

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.47  E-value=0.0031  Score=56.96  Aligned_cols=44  Identities=23%  Similarity=0.291  Sum_probs=32.1

Q ss_pred             ccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          193 VRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       193 R~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |+..++.|.+.+.. ......+++|+|++|+||||+++.+...+.
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            44455666555543 223467899999999999999999988664

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.45  E-value=0.024  Score=57.90  Aligned_cols=72  Identities=19%  Similarity=0.105  Sum_probs=45.6

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHHHHHHHHh
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQQLLSTLL  269 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~  269 (538)
                      .|-..-+..|..++ .+-....++.|.|.+|+||||||..++...... -..++|++.      ......+...++....
T Consensus       181 ~~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~sl------E~~~~~l~~R~~~~~~  253 (444)
T 2q6t_A          181 AGVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSL------EMPAAQLTLRMMCSEA  253 (444)
T ss_dssp             --CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES------SSCHHHHHHHHHHHHT
T ss_pred             CcccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEC------CCCHHHHHHHHHHHHc
Confidence            34444455666666 444556789999999999999999999876543 334566542      2334456666554433

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.43  E-value=0.0096  Score=53.91  Aligned_cols=88  Identities=18%  Similarity=0.168  Sum_probs=47.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEee---hhhhh-hcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARN---VREAE-ETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~---~~~~~-~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      +|.|.|++|+||+|.|+.++.++.     ...++.   +++.. ....+....+..... +.    ....+-....+.+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g-----~~~istGdllR~~i~~~t~lg~~~~~~~~~-G~----lvpd~iv~~lv~~~   71 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG-----FVHISTGDILREAVQKGTPLGKKAKEYMER-GE----LVPDDLIIALIEEV   71 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC-----CEEEEHHHHHHHHHHHTCHHHHHHHHHHHH-TC----CCCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC-----CeEEcHHHHHHHHHHhcChhhhhHHHHHhc-CC----cCCHHHHHHHHHHh
Confidence            478899999999999999988652     223331   11111 111122222222221 11    12233445666677


Q ss_pred             hcCCCeEEEEecC-CChHHHHHHh
Q 009306          289 LTRKKVLIVFDDV-DHPRQIKILV  311 (538)
Q Consensus       289 l~~k~~LlVlDdv-~~~~~~~~l~  311 (538)
                      +..... +|||.+ .+..|.+.|.
T Consensus        72 l~~~~~-~ilDGfPRt~~Qa~~l~   94 (206)
T 3sr0_A           72 FPKHGN-VIFDGFPRTVKQAEALD   94 (206)
T ss_dssp             CCSSSC-EEEESCCCSHHHHHHHH
T ss_pred             hccCCc-eEecCCchhHHHHHHHH
Confidence            765544 689998 4556665553

>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=96.43  E-value=0.0017  Score=57.29  Aligned_cols=26  Identities=15%  Similarity=0.171  Sum_probs=23.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+|.|+|++|+||||+|+.++.++..
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            46899999999999999999988653

>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=96.32  E-value=0.0025  Score=63.40  Aligned_cols=47  Identities=17%  Similarity=0.192  Sum_probs=34.3

Q ss_pred             ceeccchhHHHHHhhh-------------cCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          190 LVGVRLPMKEIESLLR-------------TGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~-------------~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|.+..++.+...+.             ........+.|+|++|+|||++|+.++....
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            5777777777766552             1111234589999999999999999998874

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=96.32  E-value=0.049  Score=55.49  Aligned_cols=54  Identities=19%  Similarity=0.108  Sum_probs=38.0

Q ss_pred             eccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       192 GR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      |-..-+..|..++. +-....++.|.|.+|+||||||..++.....+-..+.|++
T Consensus       179 gi~TG~~~LD~~lg-Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          179 GVPSGFTELDRMTY-GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             SBCCSCHHHHHHHS-SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             CcCCCcHHHHhhcC-CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            44444555666663 4445678999999999999999999987655434455554

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.28  E-value=0.017  Score=52.65  Aligned_cols=27  Identities=22%  Similarity=0.241  Sum_probs=24.1

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...++|.|.|++|+||||.|+.++.++
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            467899999999999999999998875

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.27  E-value=0.0031  Score=57.26  Aligned_cols=28  Identities=21%  Similarity=0.343  Sum_probs=24.4

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....+++|.|++|+|||||++.++..+.
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3567899999999999999999988765

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.24  E-value=0.0076  Score=58.78  Aligned_cols=38  Identities=26%  Similarity=0.252  Sum_probs=29.6

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|..+|..+-....++.|+|++|+|||+||..++..
T Consensus        84 ~~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           84 SSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             CHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             ChhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            44556666544445678999999999999999999875

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=96.24  E-value=0.022  Score=52.78  Aligned_cols=27  Identities=19%  Similarity=0.358  Sum_probs=22.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|+|+.|+|||||++.++.-+.
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   56 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEMD   56 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCSE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            345799999999999999999887543

>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=96.22  E-value=0.0019  Score=57.42  Aligned_cols=29  Identities=28%  Similarity=0.454  Sum_probs=24.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      |.|+|+||+|+|||||++.+..+....|.
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            46899999999999999999887665554

>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=96.21  E-value=0.0027  Score=55.46  Aligned_cols=24  Identities=17%  Similarity=0.116  Sum_probs=21.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|+|.|++|+||||+++.++.++.
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            689999999999999999998764

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.20  E-value=0.014  Score=52.56  Aligned_cols=26  Identities=31%  Similarity=0.479  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|++|+|||||++.++..+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            34679999999999999999998876

>3hyn_A Putative signal transduction protein; DUF1863 family protein, nucleotide-binding protein, structur genomics; HET: MSE; 1.20A {Eubacterium rectale atcc 33656}

Probab=96.18  E-value=0.025  Score=48.77  Aligned_cols=106  Identities=19%  Similarity=0.198  Sum_probs=72.0

Q ss_pred             CcccEEEcC--------------cccccccchHHHHHHHHhhCCCeeEeeC-CCC-------C-CCcchHHHHHHHHhcc
Q 009306           16 IKYDVFLSF--------------GGEDTRESFTSHLYSALSRETVETFIDD-DLR-------R-GDEISQSLLDAIEASS   72 (538)
Q Consensus        16 ~~~dvFiSy--------------~~~D~~~~~~~~l~~~l~~~g~~~~~d~-~~~-------~-g~~~~~~i~~~i~~s~   72 (538)
                      ++--+||+|              +.+|  ....+.|...-....+-.|.|. +..       . -+.|...+.+.|..|+
T Consensus         4 yrn~~YvaF~~~~~~~~~~~~~~a~~D--i~yy~lL~aWk~n~n~F~F~D~Hd~~y~vrDsS~~e~tIKrrLReRI~~Sk   81 (189)
T 3hyn_A            4 YQNANYSAFYVSEPFSESNLGANSTHD--FVYYNMLRMWKGEDNSFPFNDAHDKTYNVRDGSDWEKTLKPRLHTRLDNSK   81 (189)
T ss_dssp             CCCEEEEECCCCSSCCTTSTTGGGSTT--HHHHHHHHHHHHHCTTSSCCBTTTTCCCTTSCCCTTTTHHHHHHHHHHTEE
T ss_pred             cccCcEEEEeccCcccccccCCCccch--HHHHHHHHHHHcCCCceeecchhhccccccccccHHHHHHHHHHHHHHhcC
Confidence            345678888              5556  5567777776666555455564 442       2 3458899999999999


Q ss_pred             eEEEEeccCcccchhhHHHHHHHHHHHhhcCCeEEEEEEeec-CCcccccCCchH
Q 009306           73 ISIIIFSESYASSRWCLDELLKILECKKEYAQIVVPVFYRVD-PSHVRKQTGNFG  126 (538)
Q Consensus        73 ~~i~v~S~~y~~s~~c~~El~~~~~~~~~~~~~v~pv~~~v~-~~~v~~~~~~~~  126 (538)
                      .+|+++|++...|.|..+|+..++.   ..+.+||-|..+-+ .+++.+..|.+.
T Consensus        82 ~vIllIs~~T~~s~~v~wEIe~Ai~---~~~~PII~Vy~~~~~~~~i~~~~g~~~  133 (189)
T 3hyn_A           82 NIILFLSSITANSRALREEMNYGIG---TKGLPVIVIYPDYDKKSDIVDSNGNFK  133 (189)
T ss_dssp             EEEEECCTTCCCCHHHHHHHHHHTT---TTCCCEEEEETTCCSGGGTBCTTSCBC
T ss_pred             cEEEEEecCccccchhHHHHHHHHH---hcCCcEEEEECCccccchhhhccccch
Confidence            9999999999999999999998872   23455666553311 224554445543

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.11  E-value=0.041  Score=50.66  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=22.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+++|.|+.|+|||||.+.++.-+.
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            45799999999999999999887543

>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=96.11  E-value=0.025  Score=58.77  Aligned_cols=63  Identities=10%  Similarity=-0.060  Sum_probs=41.1

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHHHHHHHH
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQQLLSTL  268 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l  268 (538)
                      .|..++. +-....++.|.|.+|+||||||.+++...... -..+.|++.      ......+...++...
T Consensus       231 ~LD~~lg-Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~------E~s~~~l~~r~~~~~  294 (503)
T 1q57_A          231 GINDKTL-GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML------EESVEETAEDLIGLH  294 (503)
T ss_dssp             THHHHHC-CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES------SSCHHHHHHHHHHHH
T ss_pred             hhhHhhc-ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec------cCCHHHHHHHHHHHH
Confidence            3444442 44456789999999999999999999887654 345666652      223445555554443

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=96.11  E-value=0.038  Score=53.02  Aligned_cols=36  Identities=25%  Similarity=0.250  Sum_probs=28.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++++|++|+||||++..++..+...-..+.++.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            568999999999999999999987765433444443

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.03  E-value=0.011  Score=58.93  Aligned_cols=109  Identities=13%  Similarity=0.066  Sum_probs=60.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEE-EEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSY-FARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRR  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~-~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~  288 (538)
                      ...+++|+|+.|+|||||++.+...+.....+.+ ++.+..+.......        ..+.. .............++..
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e~~~e~~~~~~~--------~~v~Q-~~~g~~~~~~~~~l~~~  205 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKK--------SIVNQ-REVGEDTKSFADALRAA  205 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEESSCCSCCCCSS--------SEEEE-EEBTTTBSCSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEecccHhhhhccCc--------eEEEe-eecCCCHHHHHHHHHHH
Confidence            4567999999999999999999987654323333 33211000000000        00000 00000112335567777


Q ss_pred             hcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      +...+-+|++|++.+.+.+...+...   ..|..++.|+-..
T Consensus       206 L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~  244 (372)
T 2ewv_A          206 LREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTN  244 (372)
T ss_dssp             TTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCC
T ss_pred             hhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcc
Confidence            77788899999997766555443332   3455666666554

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.03  E-value=0.044  Score=51.59  Aligned_cols=25  Identities=40%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||.+.++.-.
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            4479999999999999999998755

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.03  E-value=0.0037  Score=55.47  Aligned_cols=26  Identities=19%  Similarity=0.367  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.|.|+|++|+||||+|+.++.++.
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            34689999999999999999998763

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.00  E-value=0.004  Score=56.11  Aligned_cols=26  Identities=31%  Similarity=0.432  Sum_probs=23.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|+|+|++|+||||+++.++..+.
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            45799999999999999999998763

>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=95.99  E-value=0.0054  Score=55.28  Aligned_cols=27  Identities=26%  Similarity=0.342  Sum_probs=24.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|++|+|||||++.++..+.
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            456899999999999999999998875

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.92  E-value=0.03  Score=57.34  Aligned_cols=54  Identities=15%  Similarity=0.173  Sum_probs=36.6

Q ss_pred             eccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          192 GVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       192 GR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      |-..-+..|..++ .+-....++.|.|.+|+|||||+..++...... ...++|+.
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            3333444555555 333456689999999999999999999876543 23455654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.92  E-value=0.0042  Score=55.00  Aligned_cols=26  Identities=23%  Similarity=0.411  Sum_probs=22.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++++|+|++|+|||||++.+.....
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            45799999999999999999988654

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.90  E-value=0.0074  Score=57.84  Aligned_cols=30  Identities=20%  Similarity=0.195  Sum_probs=25.4

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .....+|+|.|++|+||||||+.+...+..
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            345678999999999999999999887654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.88  E-value=0.0047  Score=57.45  Aligned_cols=48  Identities=15%  Similarity=0.147  Sum_probs=33.4

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|.++|..+-....++.|.|++|+|||||+..++......-..++|+.
T Consensus        11 ~LD~~l~gGl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           11 GVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             THHHHTTTSEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             hHHHHcCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            344445433334568999999999999999998876554444566655

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.88  E-value=0.006  Score=54.28  Aligned_cols=26  Identities=23%  Similarity=0.299  Sum_probs=23.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+|+|.|++|+||||+++.++.++..
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            36899999999999999999988754

>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=95.88  E-value=0.0046  Score=54.01  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=19.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+|+|.|++|+||||+|+.+ ..+
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            36899999999999999999 443

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=95.87  E-value=0.0039  Score=54.55  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=22.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|+|++|+||||+++.++..+.
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            3599999999999999999998754

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=95.83  E-value=0.014  Score=54.80  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=21.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||.+.++.-+
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4479999999999999999988754

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=95.82  E-value=0.0042  Score=61.24  Aligned_cols=49  Identities=16%  Similarity=0.111  Sum_probs=34.9

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....++|.+..++.+...+...  ....+.|+|++|+|||+||+.+++...
T Consensus        22 ~f~~i~G~~~~~~~l~~~~~~~--~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           22 PFSAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CchhccChHHHHHHHHHHhhCC--CCceEEEECCCCccHHHHHHHHHHhCc
Confidence            3456899988665544333221  122389999999999999999998764

>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=95.78  E-value=0.0054  Score=54.65  Aligned_cols=25  Identities=40%  Similarity=0.325  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|++|+|||||++.++..
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3567999999999999999999875

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=95.78  E-value=0.0073  Score=54.09  Aligned_cols=41  Identities=17%  Similarity=0.203  Sum_probs=30.7

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      -+..+..++.. .+..+.+.|+|++|+||||+|..+++.+..
T Consensus        44 f~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~~l~g   84 (212)
T 1tue_A           44 FLGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIHFIQG   84 (212)
T ss_dssp             HHHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            35566666653 233446999999999999999999987643

>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=95.76  E-value=0.0072  Score=53.81  Aligned_cols=25  Identities=24%  Similarity=0.232  Sum_probs=22.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+|.|.|++|+||||+++.++..+
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            4679999999999999999998876

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.76  E-value=0.0053  Score=54.01  Aligned_cols=22  Identities=27%  Similarity=0.238  Sum_probs=20.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .+|.|.|++|+||||+|+.++.
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            4689999999999999999987

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=95.74  E-value=0.0062  Score=56.80  Aligned_cols=26  Identities=19%  Similarity=0.049  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....|+|.|++|+||||+|+.+++++
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999998765

>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=95.74  E-value=0.0097  Score=54.60  Aligned_cols=38  Identities=26%  Similarity=0.344  Sum_probs=28.2

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..|..+|..+-....+++|.|++|+|||||++.++...
T Consensus        12 ~~LD~~l~ggi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           12 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             HHHHHHTTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             hhHHhHhcCCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34444554333456789999999999999999998743

>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=95.73  E-value=0.0048  Score=54.49  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.|.|+|++|+||||+++.++..+.
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            35689999999999999999998753

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.72  E-value=0.006  Score=53.16  Aligned_cols=26  Identities=23%  Similarity=0.324  Sum_probs=22.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.|+|.|++|+||||+++.++.++.
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            46799999999999999999998764

>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=95.70  E-value=0.023  Score=54.54  Aligned_cols=37  Identities=19%  Similarity=0.170  Sum_probs=27.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~  246 (538)
                      ...+++|+|++|+||||++..++..+.. ....+.++.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            3568999999999999999999987763 333344443

>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=95.68  E-value=0.0057  Score=55.55  Aligned_cols=28  Identities=25%  Similarity=0.383  Sum_probs=24.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+++|+|++|+|||||++.++..+..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            3568999999999999999999987653

>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=95.67  E-value=0.013  Score=59.33  Aligned_cols=36  Identities=22%  Similarity=0.200  Sum_probs=28.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...++.++|++|+||||++..++..++..-..+..+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv  131 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLV  131 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            367899999999999999999998776553334443

>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=95.66  E-value=0.016  Score=58.05  Aligned_cols=39  Identities=18%  Similarity=0.227  Sum_probs=29.3

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -+..|..+|..+-....++.|.|++|+|||||+..++-.
T Consensus       163 G~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~  201 (400)
T 3lda_A          163 GSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT  201 (400)
T ss_dssp             SCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHH
Confidence            345566666544445678999999999999999987643

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=95.64  E-value=0.0084  Score=52.57  Aligned_cols=25  Identities=20%  Similarity=0.417  Sum_probs=22.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|+|++|+||||+++.++..+
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            4679999999999999999998765

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.62  E-value=0.0071  Score=56.78  Aligned_cols=25  Identities=28%  Similarity=0.198  Sum_probs=22.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|.|++|+||||||+.++.++.
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            4689999999999999999998754

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.62  E-value=0.0095  Score=52.85  Aligned_cols=29  Identities=28%  Similarity=0.358  Sum_probs=24.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|.|++|+||||+++.++..+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~~   40 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQKE   40 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            35679999999999999999999877543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.59  E-value=0.0067  Score=53.26  Aligned_cols=24  Identities=29%  Similarity=0.472  Sum_probs=21.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|+|.|++|+||||+|+.++.++.
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            489999999999999999998764

>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=95.58  E-value=0.0064  Score=54.05  Aligned_cols=26  Identities=19%  Similarity=0.386  Sum_probs=23.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+|+|.|++|+||||+++.++.++..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~   29 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRK   29 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            46999999999999999999987653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.56  E-value=0.014  Score=55.86  Aligned_cols=27  Identities=30%  Similarity=0.404  Sum_probs=23.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++.|.|++|+||||+|+.+..++.
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~~   58 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEETQ   58 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999988753

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.54  E-value=0.0058  Score=55.09  Aligned_cols=24  Identities=25%  Similarity=0.441  Sum_probs=21.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+|+|+|++|+||||+|+.++..+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            469999999999999999998876

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.52  E-value=0.0083  Score=53.57  Aligned_cols=26  Identities=27%  Similarity=0.210  Sum_probs=22.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|+|.|++|+||||+|+.++..+.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999988753

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.51  E-value=0.017  Score=56.21  Aligned_cols=36  Identities=22%  Similarity=0.190  Sum_probs=28.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+||||++..++..+...-..+.++
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVlli  139 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIA  139 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            467899999999999999999998776543334444

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=95.50  E-value=0.006  Score=54.01  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|+|+|++|+||||+|+.++.++.
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC
Confidence            489999999999999999998754

>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=95.46  E-value=0.099  Score=49.89  Aligned_cols=26  Identities=27%  Similarity=0.359  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            44579999999999999999988654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.45  E-value=0.0066  Score=53.59  Aligned_cols=26  Identities=27%  Similarity=0.309  Sum_probs=18.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|.|.|++|+||||+|+.++..+.
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            34799999999999999999988754

>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=95.44  E-value=0.03  Score=57.44  Aligned_cols=27  Identities=26%  Similarity=0.300  Sum_probs=23.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      .+.|.|++|.|||+++..++..+....
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~   73 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTG   73 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcC
Confidence            799999999999999999998765543

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.44  E-value=0.0086  Score=53.81  Aligned_cols=25  Identities=40%  Similarity=0.648  Sum_probs=22.2

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .|+|.|+.|+||||+++.++..+..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~   26 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGY   26 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCC
Confidence            5899999999999999999987653

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.43  E-value=0.0099  Score=52.60  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=22.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...|+|.|++|+||||+++.++..+
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            3579999999999999999998765

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=95.42  E-value=0.0089  Score=56.04  Aligned_cols=27  Identities=19%  Similarity=0.413  Sum_probs=23.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+|+|+|++|+||||+|+.+...+.
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            456899999999999999999988654

>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=95.41  E-value=0.056  Score=54.64  Aligned_cols=36  Identities=22%  Similarity=0.127  Sum_probs=28.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...++.++|++|+||||++..++..++.+...+..+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv  134 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVV  134 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            467999999999999999999998776653333333

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.41  E-value=0.0068  Score=54.80  Aligned_cols=26  Identities=23%  Similarity=0.470  Sum_probs=23.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++++|+|++|+|||||++.+...+.
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            45799999999999999999998764

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=95.40  E-value=0.0073  Score=52.73  Aligned_cols=24  Identities=21%  Similarity=0.329  Sum_probs=21.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|+|+|++|+||||+|+.++..+.
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999998753

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.40  E-value=0.014  Score=69.33  Aligned_cols=97  Identities=20%  Similarity=0.097  Sum_probs=56.7

Q ss_pred             hHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCC--
Q 009306          197 MKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGN--  273 (538)
Q Consensus       197 l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~--  273 (538)
                      ...|..+|. .+-...+.+.|+|++|+|||+||.+++.....+-..+.|+.    .........     ...++...+  
T Consensus      1412 ~~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~----~e~~~~~l~-----a~~~G~dl~~l 1482 (2050)
T 3cmu_A         1412 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID----AEHALDPIY-----ARKLGVDIDNL 1482 (2050)
T ss_dssp             CHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC----TTSCCCHHH-----HHHTTCCTTTC
T ss_pred             CHHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEE----cccccCHHH-----HHHcCCCchhc
Confidence            344666665 33345678999999999999999999987665555667765    221112222     222221100  


Q ss_pred             ---CCCchhhcHHHHHHHh-cCCCeEEEEecCC
Q 009306          274 ---VKNFLNTDLNFQSRRL-TRKKVLIVFDDVD  302 (538)
Q Consensus       274 ---~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~  302 (538)
                         .....++....+.... ..++-+||+|.++
T Consensus      1483 ~v~~~~~~E~~l~~~~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1483 LCSQPDTGEQALEICDALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             eeecCChHHHHHHHHHHHHhcCCCCEEEEcChh
Confidence               0112233444444333 3578899999984

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.40  E-value=0.0085  Score=53.96  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=22.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||++.++...
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            3579999999999999999998764

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.39  E-value=0.011  Score=53.16  Aligned_cols=26  Identities=23%  Similarity=0.244  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|+|.|++|+||||+++.++..+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            45689999999999999999998765

>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=95.39  E-value=0.0097  Score=53.30  Aligned_cols=28  Identities=21%  Similarity=0.431  Sum_probs=23.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..++++|+|++|+|||||++.+......
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~~   45 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNPE   45 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCCc
Confidence            4567999999999999999999987543

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=95.37  E-value=0.0094  Score=52.87  Aligned_cols=24  Identities=33%  Similarity=0.361  Sum_probs=21.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|+|++|+||||+++.++..
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            457999999999999999999887

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.37  E-value=0.01  Score=52.82  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=21.7

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+|+|.|++|+||||+|+.++..+
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999998765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.34  E-value=0.0094  Score=53.33  Aligned_cols=25  Identities=28%  Similarity=0.218  Sum_probs=22.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+|+|.|++|+||||+|+.++.++.
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            5799999999999999999998764

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.32  E-value=0.015  Score=52.48  Aligned_cols=27  Identities=26%  Similarity=0.299  Sum_probs=23.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..|+|.|++|+||||+|+.++..+...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            579999999999999999999877553

>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=95.31  E-value=0.012  Score=51.16  Aligned_cols=29  Identities=21%  Similarity=0.177  Sum_probs=24.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..++++|.|++|+|||||+..+...+...
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            35689999999999999999999887654

>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=95.28  E-value=0.025  Score=55.24  Aligned_cols=104  Identities=13%  Similarity=-0.014  Sum_probs=57.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      ..++|+|+.|+|||||++.++..+... .+.+.+.+..+.... ...       ..+.-..   ..-......+...+..
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~-~g~i~i~~~~e~~~~-~~~-------~~i~~~~---ggg~~~r~~la~aL~~  239 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKE-ERIISIEDTEEIVFK-HHK-------NYTQLFF---GGNITSADCLKSCLRM  239 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTT-SCEEEEESSCCCCCS-SCS-------SEEEEEC---BTTBCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCC-CcEEEECCeeccccc-cch-------hEEEEEe---CCChhHHHHHHHHhhh
Confidence            359999999999999999998765443 445555432111000 000       0000000   0112334556667778


Q ss_pred             CCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          292 KKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       292 k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      .|-+|++|+..+.+.++.+... .  ..+.-+|+|+...
T Consensus       240 ~p~ilildE~~~~e~~~~l~~~-~--~g~~tvi~t~H~~  275 (330)
T 2pt7_A          240 RPDRIILGELRSSEAYDFYNVL-C--SGHKGTLTTLHAG  275 (330)
T ss_dssp             CCSEEEECCCCSTHHHHHHHHH-H--TTCCCEEEEEECS
T ss_pred             CCCEEEEcCCChHHHHHHHHHH-h--cCCCEEEEEEccc
Confidence            8889999999775555444322 1  1122356666544

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.26  E-value=0.012  Score=57.63  Aligned_cols=30  Identities=27%  Similarity=0.326  Sum_probs=24.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ....+.|+|++|+||||+++.++..+...|
T Consensus        23 ~~~~i~l~G~~G~GKTTl~~~la~~l~~~f   52 (359)
T 2ga8_A           23 YRVCVILVGSPGSGKSTIAEELCQIINEKY   52 (359)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHHH
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            456699999999999999999998765443

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.26  E-value=0.011  Score=53.54  Aligned_cols=27  Identities=33%  Similarity=0.463  Sum_probs=23.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|+|+.|+|||||++.++..+.
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999988654

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.25  E-value=0.011  Score=51.27  Aligned_cols=24  Identities=17%  Similarity=0.328  Sum_probs=21.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|+|+|++|+||||+|+.+...+.
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            489999999999999999998754

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=95.24  E-value=0.012  Score=52.34  Aligned_cols=26  Identities=23%  Similarity=0.203  Sum_probs=22.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|+|.|++|+||||+|+.++..+.
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            45799999999999999999988653

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=95.22  E-value=0.014  Score=52.54  Aligned_cols=26  Identities=27%  Similarity=0.309  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|+|+|++|+||||+|+.++..+.
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            44799999999999999999988763

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.21  E-value=0.01  Score=54.48  Aligned_cols=24  Identities=29%  Similarity=0.351  Sum_probs=21.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+|+|+|++|+||||+++.+...+
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            469999999999999999998765

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.20  E-value=0.011  Score=52.62  Aligned_cols=23  Identities=26%  Similarity=0.287  Sum_probs=20.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+++|.|++|+|||||++.++..
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            46899999999999999999863

>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=95.19  E-value=0.068  Score=53.26  Aligned_cols=34  Identities=24%  Similarity=0.384  Sum_probs=25.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|.|+.|+|||||.+.++.-..  ..+.+++
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaGl~~--~~G~I~i   79 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLRLLN--TEGEIQI   79 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTCSE--EEEEEEE
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCCC--CCeEEEE
Confidence            345799999999999999999986433  3344444

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.18  E-value=0.011  Score=53.29  Aligned_cols=25  Identities=28%  Similarity=0.395  Sum_probs=22.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|+|++|+||||+++.+....
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            4579999999999999999998876

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.18  E-value=0.17  Score=51.15  Aligned_cols=37  Identities=19%  Similarity=0.152  Sum_probs=29.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..++|.++|.+|+||||++..++..++.. ...+..+.
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd  136 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVS  136 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEe
Confidence            46789999999999999999999887765 33444443

>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=95.18  E-value=0.014  Score=52.83  Aligned_cols=28  Identities=14%  Similarity=0.179  Sum_probs=24.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+|+|.|++|+||||+++.++..+...
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            4579999999999999999999876543

>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=95.17  E-value=0.012  Score=53.81  Aligned_cols=26  Identities=23%  Similarity=0.311  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|+|.|++|+||||+|+.++..+.
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            34689999999999999999998764

>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=95.13  E-value=0.013  Score=51.56  Aligned_cols=27  Identities=26%  Similarity=0.331  Sum_probs=23.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|+|+.|+||||+++.+...+.
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~   30 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLV   30 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            346799999999999999999998764

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.09  E-value=0.013  Score=52.55  Aligned_cols=25  Identities=32%  Similarity=0.351  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+|+|+|+.|+||||+++.++..
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHC
Confidence            4668999999999999999999875

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.09  E-value=0.013  Score=53.06  Aligned_cols=26  Identities=31%  Similarity=0.566  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|+|++|+||||+++.+...+
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            45689999999999999999988754

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.03  E-value=0.012  Score=52.25  Aligned_cols=24  Identities=33%  Similarity=0.512  Sum_probs=21.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|+|.|+.|+||||+++.+...+.
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            589999999999999999998764

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.02  E-value=0.013  Score=53.12  Aligned_cols=27  Identities=15%  Similarity=0.123  Sum_probs=23.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+|+|.|++|+||||+++.+...+..
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            457999999999999999999987654

>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=95.00  E-value=0.023  Score=55.42  Aligned_cols=29  Identities=31%  Similarity=0.451  Sum_probs=25.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|+.|+||||+++.++..++..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~  156 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNH  156 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            46789999999999999999999876544

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.99  E-value=0.015  Score=62.02  Aligned_cols=49  Identities=14%  Similarity=0.236  Sum_probs=40.2

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ....++|.+..++.+...+..+    ..+.|+|++|+||||||+.++..+...
T Consensus        39 ~l~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~l~~~   87 (604)
T 3k1j_A           39 LIDQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAELLPTE   87 (604)
T ss_dssp             HHHHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHTSCCS
T ss_pred             ccceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhccCCcc
Confidence            3457899998888888887754    369999999999999999999876544

>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=94.99  E-value=0.013  Score=53.05  Aligned_cols=25  Identities=24%  Similarity=0.408  Sum_probs=22.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +|+|.|+.|+||||+++.+...+..
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            6899999999999999999987653

>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=94.98  E-value=0.012  Score=52.92  Aligned_cols=21  Identities=33%  Similarity=0.517  Sum_probs=19.8

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .|+|+|+.|+||||+++.++.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH
Confidence            589999999999999999987

>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=94.98  E-value=0.014  Score=54.94  Aligned_cols=26  Identities=23%  Similarity=0.445  Sum_probs=22.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|.|.|++|+||||+|+.++..+.
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            45799999999999999999998754

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.97  E-value=0.011  Score=55.10  Aligned_cols=48  Identities=23%  Similarity=0.205  Sum_probs=32.3

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc-cceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS-RHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~-~~f~~~~~~~  246 (538)
                      .|.++|..+-....++.|.|.+|+|||+||.+++.... .....++|+.
T Consensus        18 ~LD~~l~GGl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           18 GFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             TTGGGTTTSEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             HHHHhhcCCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            34445544434566899999999999999999876533 3333455544

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.97  E-value=0.017  Score=55.93  Aligned_cols=47  Identities=21%  Similarity=0.267  Sum_probs=32.6

Q ss_pred             ceeccchhHHHHHhhhcC--CCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          190 LVGVRLPMKEIESLLRTG--STNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       190 ~vGR~~~l~~l~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|-...+..+...+...  .....+++|.|++|+|||||++.+...+.
T Consensus        69 ~~~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           69 YVTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hhcchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            345555555555433332  33466899999999999999999887654

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.96  E-value=0.012  Score=51.49  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=19.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      ...+++|.|++|+|||||++.++
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHS
T ss_pred             CCEEEEEECCCCCCHHHHHHHHc
Confidence            35679999999999999999643

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=94.93  E-value=0.014  Score=53.17  Aligned_cols=23  Identities=35%  Similarity=0.505  Sum_probs=20.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|+|+|++|+||||+|+.++.++
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            37899999999999999998765

>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=94.91  E-value=0.015  Score=53.17  Aligned_cols=27  Identities=15%  Similarity=0.165  Sum_probs=23.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|++|+|||||.+.+.....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            356899999999999999999998765

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=94.89  E-value=0.069  Score=49.22  Aligned_cols=22  Identities=32%  Similarity=0.252  Sum_probs=17.7

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +.+.|.|+.|+||||+...+.-
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~   98 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFIL   98 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCcHHhHHHHHh
Confidence            4689999999999987665543

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=94.88  E-value=0.017  Score=54.04  Aligned_cols=26  Identities=23%  Similarity=0.336  Sum_probs=23.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|+|.|+.|+||||+++.++.++.
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhcC
Confidence            45799999999999999999998764

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=94.88  E-value=0.014  Score=53.47  Aligned_cols=25  Identities=32%  Similarity=0.226  Sum_probs=22.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..|.|.|++|+||||+++.++.++.
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999998764

>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=94.88  E-value=0.014  Score=54.40  Aligned_cols=26  Identities=27%  Similarity=0.364  Sum_probs=22.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+++|.|++|+|||||++.++.++.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999997653

>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=94.87  E-value=0.014  Score=52.71  Aligned_cols=22  Identities=45%  Similarity=0.564  Sum_probs=20.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .+++|+|+.|+||||+++.++.
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            3689999999999999999976

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=94.87  E-value=0.015  Score=53.37  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=22.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...|+|.|++|+||||+|+.++.++
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            3579999999999999999999875

>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=94.85  E-value=0.021  Score=55.05  Aligned_cols=29  Identities=21%  Similarity=0.219  Sum_probs=24.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|++|+|||||++.++..+...
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~  129 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNL  129 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            45689999999999999999999876544

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=94.84  E-value=0.015  Score=51.93  Aligned_cols=26  Identities=31%  Similarity=0.436  Sum_probs=22.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|+|+|+.|+||||+++.+...+
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            35689999999999999999998763

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=94.84  E-value=0.021  Score=57.76  Aligned_cols=51  Identities=22%  Similarity=0.310  Sum_probs=34.0

Q ss_pred             CceeccchhHHHHHhhhc------------CCCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          189 DLVGVRLPMKEIESLLRT------------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~------------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      .++|.+...+.|...+..            .....+-+.++|++|+|||++|+.++..+...|
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~   78 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   78 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCc
Confidence            456666666655444311            001234589999999999999999998875443

>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=94.83  E-value=0.015  Score=52.94  Aligned_cols=23  Identities=35%  Similarity=0.476  Sum_probs=20.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|+|+|++|+||||+|+.++.++
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            37899999999999999998765

>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=94.79  E-value=0.028  Score=55.36  Aligned_cols=38  Identities=26%  Similarity=0.344  Sum_probs=29.7

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..|..+|..+-....++.|+|++|+|||||+..++...
T Consensus       118 ~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          118 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             HHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34555555444567789999999999999999999875

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.79  E-value=0.012  Score=52.88  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=21.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +.++|+|++|+|||||++.+...+.
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCc
Confidence            4689999999999999999987654

>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=94.77  E-value=0.038  Score=56.11  Aligned_cols=27  Identities=30%  Similarity=0.708  Sum_probs=23.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      .++|+|++|+|||||+..+......++
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~~~~  179 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIAQEH  179 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCccHHHHHHHhhhhhcc
Confidence            589999999999999999998766544

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.76  E-value=0.017  Score=54.16  Aligned_cols=27  Identities=26%  Similarity=0.256  Sum_probs=23.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++.|+|++|+||||+|+.+...+.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            356799999999999999999998764

>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=94.72  E-value=0.022  Score=55.11  Aligned_cols=38  Identities=24%  Similarity=0.280  Sum_probs=30.6

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++.++|+|+|-||+||||.+..++..+......+.-+.
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~GkkVllID   83 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSILGKRVLQIG   83 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            36789999999999999999999988776655555554

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.72  E-value=0.019  Score=53.43  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||++.++..+
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            45689999999999999999998754

>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=94.71  E-value=0.017  Score=51.97  Aligned_cols=25  Identities=28%  Similarity=0.207  Sum_probs=22.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...|+|.|+.|+||||+++.+...+
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

>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=94.69  E-value=0.036  Score=56.65  Aligned_cols=35  Identities=23%  Similarity=0.439  Sum_probs=27.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+|||||++.++..+... .+.+++
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~-~G~V~l  326 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQ-GKSVML  326 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhc-CCeEEE
Confidence            46789999999999999999999876543 233444

>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=94.68  E-value=0.016  Score=52.38  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=23.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|+.|+|||||++.+...+.
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            345799999999999999999987653

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=94.66  E-value=0.017  Score=52.66  Aligned_cols=24  Identities=29%  Similarity=0.235  Sum_probs=21.7

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..|+|.|++|+||||+|+.++.++
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            468999999999999999999876

>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=94.65  E-value=0.013  Score=57.66  Aligned_cols=29  Identities=21%  Similarity=0.048  Sum_probs=24.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.++|+|++|+|||||++.++..+.+.
T Consensus       173 rGQr~~IvG~sG~GKTtLl~~Iar~i~~~  201 (422)
T 3ice_A          173 RGQRGLIVAPPKAGKTMLLQNIAQSIAYN  201 (422)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEecCCCCChhHHHHHHHHHHhhc
Confidence            34569999999999999999998876543

>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=94.65  E-value=0.029  Score=52.56  Aligned_cols=38  Identities=21%  Similarity=0.197  Sum_probs=29.1

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+..+|....+....+.|+|++|.|||.+|..+++..
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            34566666442345579999999999999999999864

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.64  E-value=0.036  Score=54.79  Aligned_cols=40  Identities=28%  Similarity=0.363  Sum_probs=29.4

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+...+........+|+|+|.+|+|||||+..++..+...
T Consensus        67 ~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~~~  106 (355)
T 3p32_A           67 QLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIER  106 (355)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             HHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            3333343333467789999999999999999998876543

>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=94.59  E-value=0.022  Score=49.12  Aligned_cols=27  Identities=26%  Similarity=0.319  Sum_probs=23.6

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....+++|.|+.|.|||||++.++..+
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            345689999999999999999999866

>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=94.58  E-value=0.022  Score=51.61  Aligned_cols=27  Identities=19%  Similarity=0.283  Sum_probs=23.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|++|+||||+++.+...+.
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            356899999999999999999998765

>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=94.56  E-value=0.021  Score=52.58  Aligned_cols=26  Identities=15%  Similarity=0.362  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+++|.|++|+||||+++.++..+.
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            34799999999999999999988763

>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=94.55  E-value=0.02  Score=55.44  Aligned_cols=28  Identities=21%  Similarity=0.353  Sum_probs=24.3

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....+++|.|+.|+|||||++.++..+.
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            3567899999999999999999988654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=94.54  E-value=0.017  Score=53.96  Aligned_cols=25  Identities=24%  Similarity=0.375  Sum_probs=22.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..|+|+|++|+||||+++.++..+.
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            3599999999999999999998764

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=94.53  E-value=0.022  Score=51.29  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=21.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|+|+|+.|+||||+++.++..+.
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            799999999999999999988754

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.51  E-value=0.015  Score=53.06  Aligned_cols=25  Identities=36%  Similarity=0.675  Sum_probs=22.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|+|++|+|||||++.++...
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            4569999999999999999998765

>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=94.47  E-value=0.031  Score=53.60  Aligned_cols=38  Identities=13%  Similarity=0.011  Sum_probs=28.4

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhcccee-eEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS-GSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~-~~~~~~  246 (538)
                      ....+++|.|++|+|||||++.++........ .+.|+.
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            34568999999999999999999987654422 344543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.47  E-value=0.096  Score=62.35  Aligned_cols=105  Identities=17%  Similarity=0.101  Sum_probs=63.3

Q ss_pred             CceeccchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHH
Q 009306          189 DLVGVRLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLST  267 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~  267 (538)
                      ...+...-...|..+|. .+-....++.|+|++|+||||||.+++......-..++|++.-    .....  +.   ...
T Consensus       360 ~~~~I~TG~~~LD~lLG~GGl~~G~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis~E----~s~~~--~~---a~~  430 (2050)
T 3cmu_A          360 DVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE----HALDP--IY---ARK  430 (2050)
T ss_dssp             SCCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTT----SCCCH--HH---HHH
T ss_pred             CCceeeCCCHHHHHHhccCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEcC----CCHHH--HH---HHH
Confidence            34455556667777776 4445567899999999999999999998776554566776621    11111  11   222


Q ss_pred             HhcCCC-----CCCchhhcHHHHHHHh-cCCCeEEEEecCC
Q 009306          268 LLNDGN-----VKNFLNTDLNFQSRRL-TRKKVLIVFDDVD  302 (538)
Q Consensus       268 l~~~~~-----~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~  302 (538)
                      ++...+     ...+.++....+.... ....-+||+|.+.
T Consensus       431 lGvd~~~L~I~~~~~~e~il~~~~~lv~~~~~~lIVIDSL~  471 (2050)
T 3cmu_A          431 LGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVA  471 (2050)
T ss_dssp             TTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             cCCCHHHeEEeCCCCHHHHHHHHHHHHHhcCCcEEEECCHH
Confidence            322111     1133444444444333 3567799999873

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.42  E-value=0.016  Score=55.44  Aligned_cols=27  Identities=15%  Similarity=0.198  Sum_probs=20.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+|+|+|+.|+||||+|+.+...+.
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            345799999999999999999988654

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=94.41  E-value=0.029  Score=54.00  Aligned_cols=29  Identities=28%  Similarity=0.392  Sum_probs=24.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|+.|+||||+++.++..+...
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~  127 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNE  127 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            45689999999999999999999876543

>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=94.40  E-value=0.037  Score=64.95  Aligned_cols=102  Identities=17%  Similarity=0.089  Sum_probs=60.3

Q ss_pred             eccchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhc
Q 009306          192 GVRLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN  270 (538)
Q Consensus       192 GR~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~  270 (538)
                      +...-...|..+|. .+-...+++.|+|++|+||||||.+++......-..++|++.-    .....  +.   ...++.
T Consensus       363 ~isTGi~~LD~lLg~GGl~~G~lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis~E----~s~~~--~~---a~~lGv  433 (1706)
T 3cmw_A          363 TISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE----HALDP--IY---ARKLGV  433 (1706)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTT----SCCCH--HH---HHHTTC
T ss_pred             eeccCcHHHHHHhccCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEcc----CchHH--HH---HHHcCC
Confidence            44444566777775 4444567899999999999999999998766555567777621    11111  11   222221


Q ss_pred             CCC-----CCCchhhcHHHHHHHh-cCCCeEEEEecCC
Q 009306          271 DGN-----VKNFLNTDLNFQSRRL-TRKKVLIVFDDVD  302 (538)
Q Consensus       271 ~~~-----~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~  302 (538)
                      ..+     ...+.++....+.... ..+.-+||+|.+.
T Consensus       434 d~~~L~i~~~~~~e~~l~~l~~lv~~~~~~lVVIDSL~  471 (1706)
T 3cmw_A          434 DIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVA  471 (1706)
T ss_dssp             CGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCST
T ss_pred             CHHHeEEcCCCCHHHHHHHHHHHHHhcCCCEEEECCHH
Confidence            110     0123344444444333 3567799999984

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.39  E-value=0.023  Score=55.35  Aligned_cols=25  Identities=24%  Similarity=0.319  Sum_probs=22.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+|+|.|++|+||||||..++..+.
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            5799999999999999999998764

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=94.38  E-value=0.035  Score=58.04  Aligned_cols=25  Identities=36%  Similarity=0.562  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++..
T Consensus        24 ~Gei~gLiGpNGaGKSTLlkiL~Gl   48 (538)
T 3ozx_A           24 NNTILGVLGKNGVGKTTVLKILAGE   48 (538)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            4568999999999999999998864

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=94.38  E-value=0.12  Score=54.46  Aligned_cols=33  Identities=18%  Similarity=-0.012  Sum_probs=25.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEE
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSY  243 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~  243 (538)
                      .+++.|+|++|.||||++..+...+......+.
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl  236 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVG  236 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEE
Confidence            357899999999999999999887654433333

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.36  E-value=0.024  Score=55.02  Aligned_cols=26  Identities=19%  Similarity=0.252  Sum_probs=23.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++|+|.|+.|+|||||+..++.++.
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            45899999999999999999998764

>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=94.34  E-value=0.038  Score=64.77  Aligned_cols=102  Identities=19%  Similarity=0.132  Sum_probs=58.6

Q ss_pred             eccchhHHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhc
Q 009306          192 GVRLPMKEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN  270 (538)
Q Consensus       192 GR~~~l~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~  270 (538)
                      +-..-..+|..+|. .+-....++.|.|++|+||||||.+++......-..+.|++.    ...  ...+.   ...++.
T Consensus       712 ~i~TG~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~----Ees--~~ql~---A~~lGv  782 (1706)
T 3cmw_A          712 TISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA----EHA--LDPIY---ARKLGV  782 (1706)
T ss_dssp             EECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECT----TSC--CCHHH---HHHTTC
T ss_pred             ccccCcHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEec----cch--HHHHH---HHHcCC
Confidence            33444556666665 333456689999999999999999999876654445666651    111  11111   222221


Q ss_pred             CCC-----CCCchhhcHHHHHHHh-cCCCeEEEEecCC
Q 009306          271 DGN-----VKNFLNTDLNFQSRRL-TRKKVLIVFDDVD  302 (538)
Q Consensus       271 ~~~-----~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~  302 (538)
                      ...     ...+.++....+++.. ..++-+||+|.+.
T Consensus       783 d~~~L~i~~~~~leei~~~l~~lv~~~~~~lVVIDsLq  820 (1706)
T 3cmw_A          783 DIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVA  820 (1706)
T ss_dssp             CGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCST
T ss_pred             ChhheEEecCCcHHHHHHHHHHHHHccCCCEEEEechh
Confidence            100     0123444444444333 3567899999984

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.34  E-value=0.025  Score=54.72  Aligned_cols=25  Identities=24%  Similarity=0.274  Sum_probs=22.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++++|+|++|+||||||..++.++.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5799999999999999999998753

>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=94.26  E-value=0.027  Score=54.06  Aligned_cols=26  Identities=19%  Similarity=0.267  Sum_probs=22.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++++|.|++|+||||||..++.++.
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhCc
Confidence            35789999999999999999998753

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=94.26  E-value=0.024  Score=51.89  Aligned_cols=23  Identities=30%  Similarity=0.429  Sum_probs=21.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|+|.|++|+||||+|+.++..+
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            48899999999999999998876

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=94.25  E-value=0.029  Score=51.76  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=22.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..|+|.|++|+||||+|+.++.++.
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4699999999999999999998764

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.24  E-value=0.044  Score=49.08  Aligned_cols=34  Identities=21%  Similarity=0.230  Sum_probs=27.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|+|-|.-|+||||.++.+++.+......+++..
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            4788899999999999999998876654455544

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=94.21  E-value=0.025  Score=51.37  Aligned_cols=23  Identities=30%  Similarity=0.300  Sum_probs=20.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|+|.|++|+||||+|+.++..+
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            37899999999999999998875

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.20  E-value=0.018  Score=53.04  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=16.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHH-Hhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIF-NKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~-~~~  235 (538)
                      ..+++|+|+.|+|||||++.++ ...
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            4579999999999999999998 654

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.17  E-value=0.044  Score=52.95  Aligned_cols=27  Identities=30%  Similarity=0.338  Sum_probs=23.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|+.|+|||||++.+...+.
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            457899999999999999999988654

>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=94.17  E-value=0.05  Score=50.02  Aligned_cols=28  Identities=21%  Similarity=0.380  Sum_probs=24.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+|+|.|++|+||||+++.++..+..
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            4567999999999999999999998765

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=94.16  E-value=0.028  Score=53.50  Aligned_cols=24  Identities=42%  Similarity=0.750  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...+|+|+|++|+||||+|+.+..
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            456899999999999999999983

>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=94.16  E-value=0.026  Score=50.28  Aligned_cols=26  Identities=23%  Similarity=0.215  Sum_probs=22.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.+.|+|++|+||||||.+++.+..
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~   59 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH   59 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC
Confidence            35689999999999999999998743

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=94.15  E-value=0.03  Score=50.95  Aligned_cols=23  Identities=35%  Similarity=0.446  Sum_probs=20.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..+|+|+|+.|+||||+++.+..
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            35799999999999999999876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.13  E-value=0.2  Score=51.56  Aligned_cols=37  Identities=19%  Similarity=0.128  Sum_probs=26.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++|+|+|.+|+||||++..++..+...-..+..+.
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd  136 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLIC  136 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEe
Confidence            4678999999999999999999987665433333333

>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=94.10  E-value=0.033  Score=51.49  Aligned_cols=26  Identities=27%  Similarity=0.153  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            34579999999999999999888643

>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=94.08  E-value=0.038  Score=48.42  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=23.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++++|+|++|+|||||+..+...+..
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            567999999999999999999987643

>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=94.03  E-value=0.035  Score=53.11  Aligned_cols=26  Identities=19%  Similarity=0.110  Sum_probs=23.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++++|.|+.|+||||||..++.++
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhC
Confidence            35689999999999999999999875

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.00  E-value=0.04  Score=51.06  Aligned_cols=24  Identities=21%  Similarity=0.187  Sum_probs=21.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+++|.|+.|+|||||.+.++.-.
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            689999999999999999998754

>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=94.00  E-value=0.067  Score=48.54  Aligned_cols=28  Identities=18%  Similarity=0.211  Sum_probs=24.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+|+|.|+.|+||||+++.+...+...
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~   33 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRER   33 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            4579999999999999999999987654

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.96  E-value=0.025  Score=50.36  Aligned_cols=24  Identities=25%  Similarity=0.309  Sum_probs=21.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +++|+|+.|+|||||++.++..+.
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            589999999999999999988653

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.94  E-value=0.042  Score=48.65  Aligned_cols=25  Identities=24%  Similarity=-0.086  Sum_probs=21.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++.|+|+.|+||||++..++.+..
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~   28 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYK   28 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4688999999999999988877654

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=93.93  E-value=0.041  Score=54.22  Aligned_cols=29  Identities=28%  Similarity=0.392  Sum_probs=24.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|+.|+||||+++.++..+...
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~  184 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNE  184 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhcccc
Confidence            45789999999999999999999876543

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=93.85  E-value=0.035  Score=57.34  Aligned_cols=28  Identities=4%  Similarity=0.099  Sum_probs=24.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+|.|+|++|+||||+|+.++.++..
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            3468999999999999999999998764

>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=93.84  E-value=0.097  Score=53.04  Aligned_cols=54  Identities=30%  Similarity=0.466  Sum_probs=34.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccce-eeEEEEeehhhhhhcCChHHHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHF-SGSYFARNVREAEETCRLGDLRQQLLST  267 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~~~~~~~~~~~~~~~~~~~l~~~l~~~  267 (538)
                      .+.++|.|.+|+|||+|+..+++.+.... +.++|.- +.+  ......++.+.+...
T Consensus       153 GQr~~Ifgg~G~GKT~L~~~i~~~~~~~~~~v~V~~~-iGE--R~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          153 GGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG-VGE--RTREGNDLYHEMIES  207 (482)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHTTTTCSSEEEEEE-ESC--CHHHHHHHHHHHHHH
T ss_pred             CCeeeeecCCCCChHHHHHHHHHhhHhhCCCEEEEEE-CCC--cchHHHHHHHHhhhc
Confidence            34589999999999999999998764432 3344432 222  123345555555543

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.81  E-value=0.02  Score=50.06  Aligned_cols=27  Identities=26%  Similarity=0.350  Sum_probs=23.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ++++|+|++|+|||||++.+...+...
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~   29 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER   29 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            468999999999999999998876543

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=93.81  E-value=0.037  Score=50.70  Aligned_cols=25  Identities=24%  Similarity=0.074  Sum_probs=21.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||.+.++.-.
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4579999999999999999988643

>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=93.78  E-value=0.047  Score=54.21  Aligned_cols=29  Identities=24%  Similarity=0.112  Sum_probs=24.4

Q ss_pred             CCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          207 GSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       207 ~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +-+....++|+|++|+|||||++.++...
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            33456689999999999999999999754

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=93.77  E-value=0.1  Score=55.24  Aligned_cols=25  Identities=36%  Similarity=0.384  Sum_probs=22.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||++.++...
T Consensus       382 Gei~~i~G~NGsGKSTLlk~l~Gl~  406 (607)
T 3bk7_A          382 GEVIGIVGPNGIGKTTFVKMLAGVE  406 (607)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4579999999999999999998754

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.75  E-value=0.03  Score=50.66  Aligned_cols=23  Identities=30%  Similarity=0.091  Sum_probs=20.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+++|.|+.|+|||||++.++.-
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            46999999999999999998865

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=93.71  E-value=0.06  Score=49.00  Aligned_cols=33  Identities=18%  Similarity=0.003  Sum_probs=25.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      .|.+.|.||+||||++..++.........+.++
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~   40 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAG   40 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEE
Confidence            478899999999999999998876654334443

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=93.66  E-value=0.044  Score=51.59  Aligned_cols=26  Identities=27%  Similarity=0.174  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44579999999999999999988643

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=93.66  E-value=0.23  Score=52.46  Aligned_cols=26  Identities=27%  Similarity=0.281  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|.|||||++.++.-+
T Consensus       368 ~G~~~~ivG~sGsGKSTll~~l~g~~  393 (582)
T 3b5x_A          368 QGKTVALVGRSGSGKSTIANLFTRFY  393 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999988643

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.64  E-value=0.068  Score=48.68  Aligned_cols=29  Identities=21%  Similarity=0.373  Sum_probs=24.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ....++|+|.+|+|||||+..++......
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~~~~~   65 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDNLKDK   65 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHHHTTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            46778999999999999999999875433

>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=93.57  E-value=0.038  Score=53.06  Aligned_cols=23  Identities=30%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+|.|.|++|+||||+|+.+..+
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            47899999999999999999875

>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=93.56  E-value=0.047  Score=51.37  Aligned_cols=26  Identities=19%  Similarity=0.095  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||++.++.-+
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            44579999999999999999988643

>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=93.55  E-value=0.11  Score=46.35  Aligned_cols=35  Identities=26%  Similarity=0.166  Sum_probs=26.8

Q ss_pred             eEEEEe-ccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIW-GIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~-G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|+|+ +-||+||||+|..++..+......+..+.
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~g~~vlliD   37 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRSGYNIAVVD   37 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEE
Confidence            467777 67999999999999998776544455554

>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=93.51  E-value=0.044  Score=51.89  Aligned_cols=25  Identities=24%  Similarity=0.255  Sum_probs=21.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||++.++.-+
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999988643

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=93.47  E-value=0.049  Score=50.27  Aligned_cols=26  Identities=27%  Similarity=0.363  Sum_probs=22.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|+|+|+.|+||||+++.++..+
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            45679999999999999999998765

>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=93.46  E-value=0.044  Score=51.11  Aligned_cols=28  Identities=25%  Similarity=0.247  Sum_probs=23.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+++|.|+.|+|||||.+.++.-+...
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~Gl~~p~   53 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAGMTSGK   53 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCCE
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            4479999999999999999988765443

>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=93.45  E-value=0.039  Score=55.81  Aligned_cols=26  Identities=23%  Similarity=0.187  Sum_probs=23.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|.|+|++|+||||+|+.++.++
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            46789999999999999999988765

>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=93.42  E-value=0.13  Score=52.40  Aligned_cols=52  Identities=31%  Similarity=0.415  Sum_probs=33.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDLRQQLLS  266 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l~~~l~~  266 (538)
                      +.++|.|.+|+|||+|+..+++.+... -+.++|.- +.+  ......++.+.+..
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~~a~~~~~v~V~~~-iGE--R~rEv~e~~~~~~~  218 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGG-VGE--RTREGNDLYMEMKE  218 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHHTTTTCSSCEEEEE-ESC--CSHHHHHHHHHHHH
T ss_pred             CeEEeecCCCCCchHHHHHHHHHHHhhCCCEEEEEE-ccc--CcHHHHHHHHhhhc
Confidence            348999999999999999999986543 34455543 222  12234555555554

>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=93.37  E-value=0.06  Score=51.58  Aligned_cols=36  Identities=19%  Similarity=0.108  Sum_probs=27.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+||||++..++..++..-..+.++
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~  132 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            356889999999999999999998776543334443

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.37  E-value=0.053  Score=50.93  Aligned_cols=27  Identities=26%  Similarity=0.319  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++|.|+.|+|||||++.++.-+.
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            345799999999999999999987543

>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=93.35  E-value=0.077  Score=48.93  Aligned_cols=36  Identities=19%  Similarity=0.261  Sum_probs=27.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..+|+|.|+.|+||||+++.++..+... +..+....
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            4579999999999999999999987654 33244443

>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=93.34  E-value=0.058  Score=51.18  Aligned_cols=27  Identities=22%  Similarity=0.217  Sum_probs=23.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++.|.|++|+|||||+..++..+.
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            455799999999999999999987554

>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=93.33  E-value=0.076  Score=49.67  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=23.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++.+.|.||+||||++..++..+.
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            456788999999999999999998766

>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=93.31  E-value=0.041  Score=51.11  Aligned_cols=25  Identities=24%  Similarity=0.145  Sum_probs=21.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++.-
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567999999999999999998864

>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=93.30  E-value=0.05  Score=51.00  Aligned_cols=26  Identities=27%  Similarity=0.216  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999988643

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=93.26  E-value=0.079  Score=51.52  Aligned_cols=36  Identities=31%  Similarity=0.262  Sum_probs=28.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++...|-||+||||+|..++..+......+..++
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   49 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALWMARSGKKTLVIS   49 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHHHHHCCCcEEEEe
Confidence            466777899999999999999998876644555554

>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=93.26  E-value=0.044  Score=49.79  Aligned_cols=25  Identities=32%  Similarity=0.392  Sum_probs=21.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||.+.++.-.
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3469999999999999999988644

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.25  E-value=0.056  Score=51.13  Aligned_cols=26  Identities=27%  Similarity=0.263  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||++.++.-+
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999988643

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.25  E-value=0.073  Score=48.76  Aligned_cols=28  Identities=25%  Similarity=0.265  Sum_probs=21.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...|+|.|+.|+||||+++.+++.+...
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            4579999999999999999999987654

>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=93.24  E-value=0.053  Score=50.27  Aligned_cols=24  Identities=33%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..+++|.|+.|+|||||.+.++.-
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            457999999999999999998864

>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=93.23  E-value=0.066  Score=51.39  Aligned_cols=27  Identities=15%  Similarity=0.260  Sum_probs=23.3

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +...+++|+|++|.|||||++.+..-+
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            345679999999999999999998765

>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=93.22  E-value=0.047  Score=51.55  Aligned_cols=25  Identities=24%  Similarity=0.330  Sum_probs=21.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||++.++.-
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3457999999999999999999875

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.20  E-value=0.076  Score=48.17  Aligned_cols=29  Identities=24%  Similarity=0.357  Sum_probs=24.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.++|+|.+|+|||||+..+.......
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~~~~~   57 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIERIGNE   57 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHHHTTT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            46789999999999999999999875444

>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=93.19  E-value=0.058  Score=50.49  Aligned_cols=26  Identities=35%  Similarity=0.353  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-.
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999988643

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=93.17  E-value=0.18  Score=45.48  Aligned_cols=108  Identities=14%  Similarity=0.058  Sum_probs=52.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCC--CchhhcHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVK--NFLNTDLNFQSR  287 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~--~~~~~~~~~l~~  287 (538)
                      ...+..++|+-|.||||.+...+.+...+...++.+.....  ...+-..    +.+.++......  ....+    +.+
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d--~R~ge~~----i~s~~g~~~~a~~~~~~~~----~~~   96 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCID--NRYSEED----VVSHNGLKVKAVPVSASKD----IFK   96 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC-----------------------CCEEECSSGGG----GGG
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccC--CcchHHH----HHhhcCCeeEEeecCCHHH----HHH
Confidence            35688999999999999999998877655444444431111  1111112    222222111100  11111    112


Q ss_pred             HhcCCCeEEEEecCC--ChHHHHHHhcCcCCCCCCCEEEEeccch
Q 009306          288 RLTRKKVLIVFDDVD--HPRQIKILVGRLDLFASGSRIIITTRDR  330 (538)
Q Consensus       288 ~l~~k~~LlVlDdv~--~~~~~~~l~~~l~~~~~~~~iiiTtR~~  330 (538)
                      .+.++--+|+||++.  +.++++.+....   ..+..||+|.++.
T Consensus        97 ~~~~~~dvViIDEaQF~~~~~V~~l~~l~---~~~~~Vi~~Gl~~  138 (214)
T 2j9r_A           97 HITEEMDVIAIDEVQFFDGDIVEVVQVLA---NRGYRVIVAGLDQ  138 (214)
T ss_dssp             GCCSSCCEEEECCGGGSCTTHHHHHHHHH---HTTCEEEEEECSB
T ss_pred             HHhcCCCEEEEECcccCCHHHHHHHHHHh---hCCCEEEEEeccc
Confidence            222233499999983  334454433211   2377899998853

>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=93.17  E-value=0.045  Score=51.11  Aligned_cols=24  Identities=21%  Similarity=0.273  Sum_probs=21.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999874

>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=93.17  E-value=0.055  Score=50.40  Aligned_cols=25  Identities=32%  Similarity=0.336  Sum_probs=21.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+++|.|+.|+|||||++.++.-+
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4579999999999999999987643

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.16  E-value=0.082  Score=48.28  Aligned_cols=28  Identities=29%  Similarity=0.310  Sum_probs=24.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+|+|.|+.|+||||+++.+.+.+..
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4568999999999999999999998765

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.13  E-value=0.095  Score=47.52  Aligned_cols=35  Identities=26%  Similarity=0.390  Sum_probs=26.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      .+|+|.|+.|+||||+++.++..+... +..+.+..
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            478999999999999999999987654 32344433

>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=93.13  E-value=0.052  Score=53.96  Aligned_cols=25  Identities=24%  Similarity=0.368  Sum_probs=22.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|+|.|++|+||||||..++..+.
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            5789999999999999999998764

>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=93.12  E-value=0.048  Score=51.44  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=21.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||++.++.-
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            3457999999999999999998864

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=93.06  E-value=0.075  Score=49.99  Aligned_cols=35  Identities=23%  Similarity=0.348  Sum_probs=27.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|+|.|-||+||||+|..++..+......+..++
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~G~~VlliD   36 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVG   36 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHCCCcEEEEc
Confidence            46778899999999999999998876544455554

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.03  E-value=0.058  Score=51.21  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        46 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           46 KGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34579999999999999999988644

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=93.02  E-value=0.046  Score=55.37  Aligned_cols=36  Identities=25%  Similarity=0.203  Sum_probs=28.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .++|+|+|++|+||||++..++..+......+.++.
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            467999999999999999999987765533444443

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=92.91  E-value=0.05  Score=56.89  Aligned_cols=29  Identities=24%  Similarity=0.416  Sum_probs=24.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+++|+|++|+|||||++.++..+...
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L~~~  396 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARLMEM  396 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHHHTT
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhhccc
Confidence            34679999999999999999999887543

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=92.89  E-value=0.063  Score=49.71  Aligned_cols=26  Identities=23%  Similarity=0.257  Sum_probs=23.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...|+|.|..|+||||+++.++..+.
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

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=92.87  E-value=0.068  Score=50.37  Aligned_cols=26  Identities=27%  Similarity=0.199  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34579999999999999999988643

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=92.87  E-value=0.067  Score=46.35  Aligned_cols=24  Identities=25%  Similarity=0.356  Sum_probs=21.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+-+.|.|++|+||||||.++..+
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            345899999999999999999885

>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=92.82  E-value=0.13  Score=50.55  Aligned_cols=39  Identities=21%  Similarity=0.172  Sum_probs=29.5

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+...++.+.|-||+||||+|..++..++..-..+..++
T Consensus        23 ~~~~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   61 (349)
T 3ug7_A           23 KDGTKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVS   61 (349)
T ss_dssp             SCSCEEEEEECSSSTTHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             cCCCEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEe
Confidence            345667777899999999999999998776644455554

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=92.75  E-value=0.5  Score=50.14  Aligned_cols=26  Identities=27%  Similarity=0.199  Sum_probs=21.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+.+.|+|++|.||||++..+...+.
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l~  189 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAALI  189 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            35799999999999999988876554

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=92.70  E-value=0.12  Score=50.60  Aligned_cols=29  Identities=34%  Similarity=0.440  Sum_probs=24.5

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ....+++|+|.+|.|||||+..++..+..
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~~~   82 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLLIR   82 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            45678999999999999999999876543

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.69  E-value=0.13  Score=50.36  Aligned_cols=28  Identities=29%  Similarity=0.520  Sum_probs=23.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....+++|.|++|+|||||.+.+...+.
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~   80 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLT   80 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            3567899999999999999999987554

>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=92.51  E-value=0.068  Score=47.40  Aligned_cols=25  Identities=20%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .-.++|.|++|+|||||.+.+....
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            3468999999999999999998753

>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=92.50  E-value=0.77  Score=43.42  Aligned_cols=39  Identities=10%  Similarity=0.092  Sum_probs=25.4

Q ss_pred             CCCc--chHHHHHHHHhcceEEEEeccCcccchhhHHHHHHH
Q 009306           56 RGDE--ISQSLLDAIEASSISIIIFSESYASSRWCLDELLKI   95 (538)
Q Consensus        56 ~g~~--~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~   95 (538)
                      ||..  ...++...+++++++|.|+.-.--.+..| .++...
T Consensus         7 PGhm~ka~~~~~~~l~~aDvVl~VvDAr~p~~~~~-~~l~~~   47 (282)
T 1puj_A            7 PGHMAKARREVTEKLKLIDIVYELVDARIPMSSRN-PMIEDI   47 (282)
T ss_dssp             --CTTHHHHHHHHHGGGCSEEEEEEETTSTTTTSC-HHHHHH
T ss_pred             chHHHHHHHHHHHHHhhCCEEEEEEeCCCCCccCC-HHHHHH
Confidence            5533  45788899999999999998755444444 244443

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=92.48  E-value=0.081  Score=47.53  Aligned_cols=25  Identities=16%  Similarity=0.089  Sum_probs=23.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+|+|.|+.|+||||+++.++.++.
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg   31 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYN   31 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999999875

>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=92.44  E-value=0.067  Score=52.58  Aligned_cols=25  Identities=32%  Similarity=0.231  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl   53 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGF   53 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcC
Confidence            3457999999999999999999874

>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=92.39  E-value=0.094  Score=49.96  Aligned_cols=35  Identities=23%  Similarity=0.372  Sum_probs=27.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|+|.|-||+||||+|..++..+...-..+..++
T Consensus         3 kvIavs~KGGvGKTT~a~nLA~~La~~G~rVlliD   37 (289)
T 2afh_E            3 RQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVG   37 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEeCCCcCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            56888999999999999999998765533444444

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=92.38  E-value=0.068  Score=48.54  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +++|+|+.|+||||+++.+...+
T Consensus         5 ~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            58999999999999999998865

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.35  E-value=0.071  Score=48.80  Aligned_cols=23  Identities=39%  Similarity=0.434  Sum_probs=20.9

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .++|.|++|+||||+|+.++..+
T Consensus        10 ~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A           10 RLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceeeECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999998875

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.33  E-value=0.096  Score=54.79  Aligned_cols=27  Identities=22%  Similarity=0.270  Sum_probs=23.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..+|.|+|++|+||||+|+.+...+..
T Consensus       372 ~~~I~l~G~~GsGKSTia~~La~~L~~  398 (546)
T 2gks_A          372 GFCVWLTGLPCAGKSTIAEILATMLQA  398 (546)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             ceEEEccCCCCCCHHHHHHHHHHHhhh
Confidence            567999999999999999999987654

>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=92.33  E-value=0.071  Score=46.80  Aligned_cols=23  Identities=35%  Similarity=0.452  Sum_probs=20.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.+|+|+.|+|||||+.+++.-+
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l   50 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVL   50 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHH
Confidence            78999999999999999988654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=92.31  E-value=0.043  Score=58.18  Aligned_cols=49  Identities=16%  Similarity=0.080  Sum_probs=34.9

Q ss_pred             CCCceeccchhHHHHHhhhcCCC---------CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          187 NEDLVGVRLPMKEIESLLRTGST---------NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       187 ~~~~vGR~~~l~~l~~~L~~~~~---------~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+.++|.+...+.+...|..+..         ...-+.|+|++|+|||+||+.++...
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            36788998876666555543310         00148999999999999999888765

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=92.31  E-value=0.1  Score=54.96  Aligned_cols=28  Identities=21%  Similarity=0.264  Sum_probs=24.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+|.|+|++|+||||+|+.+..++..
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~L~~  422 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVTLNQ  422 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHHhcc
Confidence            3568999999999999999999988653

>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=92.31  E-value=0.068  Score=51.39  Aligned_cols=25  Identities=32%  Similarity=0.405  Sum_probs=21.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|+|+.|+|||||++.++.-
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl  103 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRF  103 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcC
Confidence            3457999999999999999988764

>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=92.26  E-value=0.07  Score=47.59  Aligned_cols=23  Identities=22%  Similarity=0.491  Sum_probs=20.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -.++|.|++|+|||||.+.+...
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            45899999999999999999874

>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=92.23  E-value=0.059  Score=49.56  Aligned_cols=25  Identities=28%  Similarity=0.183  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+||||+++.++..
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            4578999999999999999988765

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.21  E-value=0.71  Score=46.46  Aligned_cols=25  Identities=24%  Similarity=0.198  Sum_probs=21.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHH
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...++..|.|++|.||||+..+.+.
T Consensus       159 ~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          159 SSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccccEEEEEcCCCCCHHHHHHHHhc
Confidence            4578999999999999999988764

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=92.16  E-value=0.12  Score=50.70  Aligned_cols=38  Identities=18%  Similarity=0.266  Sum_probs=30.1

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc--cceeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS--RHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~--~~f~~~~~~~  246 (538)
                      ...+++.+.|-||+||||+|..++..+.  .....+..+.
T Consensus        16 ~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~g~~vllid   55 (348)
T 3io3_A           16 DSLKWIFVGGKGGVGKTTTSSSVAVQLALAQPNEQFLLIS   55 (348)
T ss_dssp             TTCSEEEEECSTTSSHHHHHHHHHHHHHHHCTTSCEEEEE
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            3457889999999999999999999887  5544555554

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=92.10  E-value=0.11  Score=54.05  Aligned_cols=29  Identities=17%  Similarity=0.157  Sum_probs=24.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ...+|.++|++|.||||+|+.++..+.-.
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~~~   62 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLNWI   62 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            35679999999999999999999876433

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=92.09  E-value=0.076  Score=50.16  Aligned_cols=23  Identities=26%  Similarity=0.603  Sum_probs=20.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .++|.|+.|+|||||.+.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48899999999999999999753

>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=92.07  E-value=0.14  Score=50.01  Aligned_cols=37  Identities=19%  Similarity=0.269  Sum_probs=30.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++.+.|-||+||||+|..++..+......+..++
T Consensus        15 ~~~i~~~sgkGGvGKTt~a~~lA~~la~~g~~vllid   51 (334)
T 3iqw_A           15 SLRWIFVGGKGGVGKTTTSCSLAIQLAKVRRSVLLLS   51 (334)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHHHTTSSSCEEEEE
T ss_pred             CeEEEEEeCCCCccHHHHHHHHHHHHHhCCCcEEEEE
Confidence            4567888999999999999999998877655566555

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.01  E-value=0.096  Score=44.45  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +-++|.|.+|+|||||...+...
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            35899999999999999999874

>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=92.01  E-value=0.12  Score=51.92  Aligned_cols=36  Identities=19%  Similarity=0.108  Sum_probs=27.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ...+++|+|++|+||||++..++..+...-..+..+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllv  132 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            356889999999999999999998776553333333

>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=92.00  E-value=0.1  Score=48.25  Aligned_cols=33  Identities=30%  Similarity=0.611  Sum_probs=26.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      |+|.|-||+||||+|..++..+......+..++
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~g~~VlliD   35 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASDYDKIYAVD   35 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTTCSCEEEEE
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            566999999999999999998877654455554

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=91.99  E-value=0.15  Score=47.88  Aligned_cols=23  Identities=30%  Similarity=0.397  Sum_probs=19.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++|+|.+|+|||||...+...
T Consensus       100 ~~v~~vG~~~vGKSslin~l~~~  122 (262)
T 3cnl_A          100 ARVLIVGVPNTGKSTIINKLKGK  122 (262)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             hheEEeCCCCCCHHHHHHHHhcc
Confidence            35899999999999999988854

>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=91.98  E-value=0.083  Score=51.23  Aligned_cols=26  Identities=31%  Similarity=0.317  Sum_probs=22.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++++|+|+.|.|||||.+.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            46789999999999999999998653

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=91.91  E-value=0.12  Score=45.46  Aligned_cols=24  Identities=21%  Similarity=0.148  Sum_probs=21.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|.|.+|+|||||...+...
T Consensus        48 ~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           48 QPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999998875

>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=91.90  E-value=0.094  Score=45.09  Aligned_cols=23  Identities=30%  Similarity=0.573  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++|.|.+|+|||||...+...
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            45899999999999999999863

>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=91.86  E-value=0.067  Score=47.02  Aligned_cols=20  Identities=40%  Similarity=0.498  Sum_probs=18.7

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...++.
T Consensus         5 v~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            5 LMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEESCTTSSHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999876

>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=91.84  E-value=0.12  Score=50.73  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl   52 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGI   52 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCC
Confidence            3457999999999999999999864

>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=91.81  E-value=0.13  Score=50.66  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.+..-
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~GL   77 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNLL   77 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhcC
Confidence            3457999999999999999988864

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.79  E-value=0.13  Score=50.73  Aligned_cols=25  Identities=24%  Similarity=0.262  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl   52 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGI   52 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcC
Confidence            3457999999999999999999864

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.76  E-value=0.12  Score=50.73  Aligned_cols=25  Identities=36%  Similarity=0.383  Sum_probs=21.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3457999999999999999999864

>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=91.76  E-value=0.13  Score=50.96  Aligned_cols=26  Identities=23%  Similarity=0.123  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++--.
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            34579999999999999999998643

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=91.69  E-value=0.15  Score=51.29  Aligned_cols=85  Identities=12%  Similarity=-0.006  Sum_probs=47.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCch-hhcHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFL-NTDLNFQSRR  288 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~-~~~~~~l~~~  288 (538)
                      ...+++|+|+.|+|||||.+.+...+...-..+++..+.-+.. ....           . ........ -.....++..
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~ed~ie~~-~~~~-----------~-q~~v~~~~g~~f~~~lr~~  232 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFD-IDGI-----------G-QTQVNPRVDMTFARGLRAI  232 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSC-CSSS-----------E-EEECBGGGTBCHHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEecccchhc-cCCc-----------c-eEEEccccCcCHHHHHHHH
Confidence            4557999999999999999999987654422333333110000 0000           0 00000011 1223455666


Q ss_pred             hcCCCeEEEEecCCChHHH
Q 009306          289 LTRKKVLIVFDDVDHPRQI  307 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~  307 (538)
                      +...+-++++.++.+....
T Consensus       233 Lrq~pd~i~vgEiRd~et~  251 (418)
T 1p9r_A          233 LRQDPDVVMVGEIRDLETA  251 (418)
T ss_dssp             GGGCCSEEEESCCCSHHHH
T ss_pred             hccCCCeEEEcCcCCHHHH
Confidence            7777888889998775544

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=91.68  E-value=0.13  Score=53.78  Aligned_cols=48  Identities=13%  Similarity=0.123  Sum_probs=32.4

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+..+|..+-....+++|.|++|+|||||++.++......-..++++.
T Consensus       269 ~ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~  316 (525)
T 1tf7_A          269 RLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA  316 (525)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEE
Confidence            344555433334568999999999999999999986554322334443

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=91.67  E-value=0.21  Score=55.47  Aligned_cols=23  Identities=22%  Similarity=-0.119  Sum_probs=20.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      ...+++|+|+.|.||||+.+.++
T Consensus       661 ~g~i~~ItGpNGsGKSTlLr~ia  683 (934)
T 3thx_A          661 KQMFHIITGPNMGGKSTYIRQTG  683 (934)
T ss_dssp             TBCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            45789999999999999999884

>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=91.66  E-value=0.15  Score=45.79  Aligned_cols=29  Identities=21%  Similarity=0.472  Sum_probs=24.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      +.|+|-|.-|+||||+++.+++.+...++
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~~~~~   31 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLVKDYD   31 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHCCCC
Confidence            46889999999999999999998865444

>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=91.60  E-value=0.073  Score=53.46  Aligned_cols=25  Identities=20%  Similarity=0.355  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|.|++|+|||||.+.++..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhCC
Confidence            4558999999999999999999873

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=91.50  E-value=0.89  Score=41.71  Aligned_cols=40  Identities=28%  Similarity=0.151  Sum_probs=28.3

Q ss_pred             eeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          191 VGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       191 vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .=|..+.+.+..++..    . -+.|+|+.|.|||.+|..++...
T Consensus        93 ~l~~~Q~~ai~~~~~~----~-~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           93 SLRDYQEKALERWLVD----K-RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CCCHHHHHHHHHHTTT----S-EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHHHHhC----C-CEEEEeCCCCCHHHHHHHHHHHc
Confidence            3445555556655542    1 27889999999999999888765

>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=91.50  E-value=0.14  Score=50.59  Aligned_cols=25  Identities=32%  Similarity=0.227  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            3457999999999999999999863

>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=91.50  E-value=0.098  Score=44.45  Aligned_cols=22  Identities=32%  Similarity=0.643  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|++.|.+|+|||||+..+...
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            3889999999999999999864

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=91.37  E-value=0.18  Score=46.45  Aligned_cols=37  Identities=19%  Similarity=0.121  Sum_probs=27.8

Q ss_pred             CceEEEEec-cCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          210 NVYKLGIWG-IGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G-~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ..++|+|++ -||+||||+|..++..+... -..+..++
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~la~~~g~~VlliD   41 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFALSQEPDIHVLAVD   41 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHHHTTSTTCCEEEEE
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHHHHhCcCCCEEEEE
Confidence            346777774 68999999999999988776 44455554

>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=91.37  E-value=0.062  Score=50.49  Aligned_cols=27  Identities=22%  Similarity=0.225  Sum_probs=23.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ....|+|.|..|+||||+++.++..+.
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            456899999999999999998887763

>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=91.33  E-value=0.11  Score=51.48  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=23.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...++|+|++|+|||||++.++..+..
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~  196 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNT  196 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTC
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            467999999999999999999876543

>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=91.33  E-value=0.12  Score=50.67  Aligned_cols=26  Identities=27%  Similarity=0.116  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++--.
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            34579999999999999999998643

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=91.31  E-value=0.14  Score=46.83  Aligned_cols=26  Identities=12%  Similarity=0.090  Sum_probs=23.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+|+|.|+.|+||||+|+.++.++.
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~lg   39 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEELG   39 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999998764

>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=91.26  E-value=0.14  Score=50.60  Aligned_cols=24  Identities=29%  Similarity=0.173  Sum_probs=21.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..+++|.|+.|+|||||.+.++--
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCcHHHHHHHHHHcC
Confidence            457999999999999999999864

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=91.23  E-value=0.17  Score=49.79  Aligned_cols=28  Identities=21%  Similarity=0.381  Sum_probs=23.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...+++|+|++|+|||||...+......
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~~  100 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLTE  100 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhhh
Confidence            4678999999999999999999875543

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=91.18  E-value=0.1  Score=45.79  Aligned_cols=23  Identities=30%  Similarity=0.573  Sum_probs=20.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..|+|.|.+|+|||||...+...
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999874

>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=91.17  E-value=0.14  Score=43.77  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            34889999999999999999874

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=91.05  E-value=0.14  Score=54.13  Aligned_cols=27  Identities=26%  Similarity=0.331  Sum_probs=24.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+|.|+|++|+||||+|+.+..++.
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~   77 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLV   77 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            456899999999999999999998874

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.05  E-value=0.12  Score=51.11  Aligned_cols=34  Identities=24%  Similarity=0.227  Sum_probs=26.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++|+|+.|+|||||++.++..+... .+.+.+.
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~~~~-~g~I~ie  209 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEIPFD-QRLITIE  209 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTSCTT-SCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCCCC-ceEEEEC
Confidence            369999999999999999999865442 3445554

>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=91.03  E-value=0.11  Score=51.10  Aligned_cols=25  Identities=40%  Similarity=0.480  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3457999999999999999999864

>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=90.97  E-value=0.16  Score=48.86  Aligned_cols=33  Identities=21%  Similarity=0.321  Sum_probs=25.2

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +++|.+.+.     ..+++|.|++|+|||||.+.+. ..
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            445555543     2468999999999999999998 54

>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=90.86  E-value=0.12  Score=44.59  Aligned_cols=23  Identities=35%  Similarity=0.616  Sum_probs=20.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            34899999999999999998763

>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=90.83  E-value=0.13  Score=43.91  Aligned_cols=22  Identities=27%  Similarity=0.514  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999999864

>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=90.79  E-value=0.13  Score=43.81  Aligned_cols=22  Identities=27%  Similarity=0.569  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998864

>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=90.77  E-value=0.096  Score=46.27  Aligned_cols=25  Identities=16%  Similarity=0.477  Sum_probs=21.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....|+|.|.+|+|||||...+...
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            4556899999999999999999864

>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=90.76  E-value=0.13  Score=45.28  Aligned_cols=22  Identities=32%  Similarity=0.643  Sum_probs=19.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||+..+...
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4889999999999999999864

>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=90.73  E-value=0.19  Score=43.95  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....|+|.|.+|+|||||...+...
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            3456899999999999999988764

>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=90.69  E-value=0.12  Score=44.84  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..|+|.|.+|+|||||...+...
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            35889999999999999999864

>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=90.68  E-value=0.13  Score=44.01  Aligned_cols=23  Identities=26%  Similarity=0.471  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            34889999999999999999864

>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=90.61  E-value=0.21  Score=49.59  Aligned_cols=38  Identities=16%  Similarity=0.170  Sum_probs=29.3

Q ss_pred             CCceEEEEec-cCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWG-IGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G-~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++|+|+| -||+||||+|..++..+......+..++
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            3567888875 8999999999999998776644555555

>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=90.59  E-value=0.14  Score=43.84  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
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            3789999999999999999864

>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=90.58  E-value=0.19  Score=51.67  Aligned_cols=28  Identities=18%  Similarity=0.128  Sum_probs=23.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+|.++|++|+||||+++.++..+...
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~~~   66 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLNFI   66 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            4578999999999999999999876533

>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=90.58  E-value=0.14  Score=43.72  Aligned_cols=22  Identities=32%  Similarity=0.605  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3889999999999999999863

>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=90.56  E-value=0.14  Score=43.53  Aligned_cols=21  Identities=29%  Similarity=0.257  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999999764

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=90.54  E-value=0.41  Score=55.70  Aligned_cols=23  Identities=26%  Similarity=0.367  Sum_probs=20.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...++|+|+.|+|||||++.+..
T Consensus      1105 Ge~vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1105 GQTLALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             TCEEEEECSTTSSTTSHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            44699999999999999998876

>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=90.53  E-value=0.13  Score=44.02  Aligned_cols=21  Identities=38%  Similarity=0.605  Sum_probs=18.8

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      -|+|.|.+|+|||||...+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            488999999999999999864

>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=90.53  E-value=0.14  Score=43.83  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.9

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4889999999999999999874

>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=90.52  E-value=0.14  Score=44.91  Aligned_cols=23  Identities=22%  Similarity=0.248  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34889999999999999999874

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=90.52  E-value=0.13  Score=44.10  Aligned_cols=22  Identities=23%  Similarity=0.687  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4889999999999999999863

>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=90.43  E-value=0.14  Score=44.36  Aligned_cols=24  Identities=33%  Similarity=0.520  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            445899999999999999998864

>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=90.42  E-value=0.14  Score=43.77  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4889999999999999999863

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=90.41  E-value=0.24  Score=48.47  Aligned_cols=29  Identities=34%  Similarity=0.534  Sum_probs=24.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ....++|.|+.|+|||||.+.++......
T Consensus        70 ~Gq~~gIiG~nGaGKTTLl~~I~g~~~~~   98 (347)
T 2obl_A           70 IGQRIGIFAGSGVGKSTLLGMICNGASAD   98 (347)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHSCCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            34579999999999999999999876543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=90.41  E-value=0.15  Score=44.02  Aligned_cols=25  Identities=32%  Similarity=0.234  Sum_probs=21.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....|+|.|.+|+|||||...+...
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            3456899999999999999999863

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=90.40  E-value=0.18  Score=45.70  Aligned_cols=27  Identities=26%  Similarity=0.316  Sum_probs=24.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ...|.|.|+.|+||||+++.+.+.+..
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            457999999999999999999998765

>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=90.39  E-value=0.16  Score=45.76  Aligned_cols=26  Identities=19%  Similarity=0.096  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....|+|.|++|+|||||...+....
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34568999999999999999998753

>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=90.35  E-value=0.15  Score=44.13  Aligned_cols=23  Identities=26%  Similarity=0.612  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999864

>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=90.35  E-value=0.14  Score=44.87  Aligned_cols=22  Identities=27%  Similarity=0.372  Sum_probs=19.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999988764

>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=90.33  E-value=0.17  Score=42.90  Aligned_cols=24  Identities=29%  Similarity=0.293  Sum_probs=20.7

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+.+|+|+.|.|||||..+++.-+
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999887643

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=90.31  E-value=0.26  Score=47.98  Aligned_cols=37  Identities=24%  Similarity=0.299  Sum_probs=28.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++.+.|-||+||||+|..++..+......+..++
T Consensus        18 ~~~i~v~sgkGGvGKTTva~~LA~~lA~~G~rVllvD   54 (329)
T 2woo_A           18 SLKWIFVGGKGGVGKTTTSCSLAIQMSKVRSSVLLIS   54 (329)
T ss_dssp             TCCEEEEECSSSSSHHHHHHHHHHHHHTSSSCEEEEE
T ss_pred             CCEEEEEeCCCCCcHHHHHHHHHHHHHHCCCeEEEEE
Confidence            3456777899999999999999998877644555554

>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=90.30  E-value=0.13  Score=43.85  Aligned_cols=20  Identities=25%  Similarity=0.416  Sum_probs=18.3

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         5 i~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            5 VLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            78999999999999998864

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=90.26  E-value=0.31  Score=46.67  Aligned_cols=38  Identities=24%  Similarity=0.185  Sum_probs=29.6

Q ss_pred             CCceEEEEecc-CCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGI-GGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~-~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++|.|+|. ||+||||+|..++..+......+..++
T Consensus       102 ~~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID  140 (299)
T 3cio_A          102 TENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFID  140 (299)
T ss_dssp             CSCCEEEEEESSSSSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCChHHHHHHHHHHHHhCCCcEEEEE
Confidence            34678999985 899999999999998776544555554

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.26  E-value=0.5  Score=58.28  Aligned_cols=158  Identities=9%  Similarity=0.053  Sum_probs=0.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcC
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTR  291 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~  291 (538)
                      +.+.++|++|+|||++|+.+......  .....+.    .+.......+++.+-..+..........-....      .+
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~~~--~~~~~in----fsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~------~g 1335 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNSSL--YDVVGIN----FSKDTTTEHILSALHRHTNYVTTSKGLTLLPKS------DI 1335 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSCSS--CEEEEEE----CCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBS------SS
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcCCC--CceEEEE----eecCCCHHHHHHHHHHHhhhccccCCccccCCC------CC


Q ss_pred             CCeEEEEecCCCh-----------HHHHHHhcCcCCCCCCCEEEEeccchhhhhhcCCC----------------eeEEc
Q 009306          292 KKVLIVFDDVDHP-----------RQIKILVGRLDLFASGSRIIITTRDRQVLANCGVD----------------EVYQM  344 (538)
Q Consensus       292 k~~LlVlDdv~~~-----------~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~~~~----------------~~~~l  344 (538)
                      +++++.+||++-+           +.+..++..-.+......-.++-.+-.+...++..                .++.+
T Consensus      1336 k~~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf~vi~i 1415 (2695)
T 4akg_A         1336 KNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYL 1415 (2695)
T ss_dssp             SCEEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTEEEEEC
T ss_pred             ceEEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhheeeEEEe


Q ss_pred             CCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh
Q 009306          345 EELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA  381 (538)
Q Consensus       345 ~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~  381 (538)
                      +..+.++-..+|.......-...+.....+..++..+
T Consensus      1416 ~~P~~~~l~~I~~~il~~~l~~~~~v~~~~~~lv~at 1452 (2695)
T 4akg_A         1416 GYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARAS 1452 (2695)
T ss_dssp             CCCTTTHHHHHHHHHHHHHTTSSGGGGGGHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHH

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=90.24  E-value=0.15  Score=44.03  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=20.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            34889999999999999998863

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=90.21  E-value=0.15  Score=48.69  Aligned_cols=48  Identities=15%  Similarity=0.214  Sum_probs=31.4

Q ss_pred             hhHHHHHhhhcCCCCceEEEEec---cCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWG---IGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G---~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+.++.+.+..   ..++++|++   -||+||||+|..++..+......+..++
T Consensus        22 ~~~~~~r~~~~---~~~~i~v~~~s~KGGvGKTT~a~nLA~~la~~G~rVlliD   72 (298)
T 2oze_A           22 ILEELRRILSN---KNEAIVILNNYFKGGVGKSKLSTMFAYLTDKLNLKVLMID   72 (298)
T ss_dssp             HHHHHHHHHHH---HCSCEEEEECCSSSSSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHhcC---CCcEEEEEeccCCCCchHHHHHHHHHHHHHhCCCeEEEEe
Confidence            34455555543   234566665   8999999999999987765543444444

>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=90.17  E-value=0.16  Score=44.73  Aligned_cols=27  Identities=33%  Similarity=0.463  Sum_probs=21.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      --|+|.|.+|+|||||.+.+.......
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~~~~   41 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKVPEG   41 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhcccc
Confidence            348899999999999997776654433

>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=90.14  E-value=0.16  Score=43.44  Aligned_cols=22  Identities=23%  Similarity=0.386  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4889999999999999999863

>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=90.10  E-value=0.27  Score=49.57  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=21.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .++|.|.+|+|||+|+..+++....
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~~~  177 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQATV  177 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBC
T ss_pred             EEEEeCCCCcChHHHHHHHHHHHHh
Confidence            4789999999999999999887554

>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=90.09  E-value=0.35  Score=49.36  Aligned_cols=24  Identities=38%  Similarity=0.277  Sum_probs=19.2

Q ss_pred             eEEEEeccCCCchhHHHH-HHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAG-AIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~-~~~~~~  235 (538)
                      +.++|.|.+|+|||+||. .+++..
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~  200 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQK  200 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTT
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhh
Confidence            348999999999999965 666654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=90.09  E-value=0.22  Score=53.34  Aligned_cols=37  Identities=24%  Similarity=0.099  Sum_probs=24.7

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+.+.+...|..    ..+..|+||||.|||+.+.++...+
T Consensus       193 ~Q~~AV~~al~~----~~~~lI~GPPGTGKT~ti~~~I~~l  229 (646)
T 4b3f_X          193 SQKEAVLFALSQ----KELAIIHGPPGTGKTTTVVEIILQA  229 (646)
T ss_dssp             HHHHHHHHHHHC----SSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC----CCceEEECCCCCCHHHHHHHHHHHH
Confidence            345556666642    2368899999999997655555443

>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=90.07  E-value=0.22  Score=43.02  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...-|+|.|.+|+|||||...+...
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            3446899999999999999999874

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=90.06  E-value=0.32  Score=45.80  Aligned_cols=38  Identities=21%  Similarity=0.163  Sum_probs=29.5

Q ss_pred             CCceEEEEecc-CCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGI-GGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~-~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++|.|+|. ||.||||+|..++..+......+..++
T Consensus        80 ~~~kvI~vts~kgG~GKTt~a~nLA~~lA~~G~rVLLID  118 (271)
T 3bfv_A           80 SAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVD  118 (271)
T ss_dssp             CCCCEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCeEEEEe
Confidence            34678999875 899999999999998876555566655

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=90.01  E-value=0.49  Score=43.05  Aligned_cols=105  Identities=12%  Similarity=0.019  Sum_probs=51.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC--CCchhhcHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV--KNFLNTDLNFQSRR  288 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~--~~~~~~~~~~l~~~  288 (538)
                      ..+..++|.-|.||||-+...+.+...+...++.+.-..  +...+ ..+...+    +.....  .....+....    
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~--D~Ryg-~~i~sr~----G~~~~a~~i~~~~di~~~----   87 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAK--DTRYS-SSFCTHD----RNTMEALPACLLRDVAQE----   87 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETT--CCCC----------------CEEEEESSGGGGHHH----
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecC--Cccch-HHHHhhc----CCeeEEEecCCHHHHHHH----
Confidence            467899999999999888888777655443344433111  11222 3333222    211110  0112222222    


Q ss_pred             hcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccc
Q 009306          289 LTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       289 l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                      . +.--+|+||++.-...+..+...+.  ..|..||+|.++
T Consensus        88 ~-~~~dvViIDEaQF~~~v~el~~~l~--~~gi~VI~~GL~  125 (234)
T 2orv_A           88 A-LGVAVIGIDEGQFFPDIVEFCEAMA--NAGKTVIVAALD  125 (234)
T ss_dssp             H-TTCSEEEESSGGGCTTHHHHHHHHH--HTTCEEEEECCS
T ss_pred             h-ccCCEEEEEchhhhhhHHHHHHHHH--hCCCEEEEEecc
Confidence            2 3334999999821111333333322  257789999887

>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=90.01  E-value=0.16  Score=44.86  Aligned_cols=22  Identities=36%  Similarity=0.460  Sum_probs=19.9

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .|+|.|.+|+|||||...+...
T Consensus        25 ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999873

>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=89.98  E-value=0.16  Score=43.45  Aligned_cols=23  Identities=35%  Similarity=0.427  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .-|+|.|.+|+|||||...+...
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            45899999999999999999763

>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=89.98  E-value=0.16  Score=44.64  Aligned_cols=22  Identities=32%  Similarity=0.545  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            4889999999999999998864

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=89.97  E-value=0.42  Score=48.66  Aligned_cols=25  Identities=40%  Similarity=0.247  Sum_probs=19.5

Q ss_pred             ceEEEEeccCCCchhHHHH-HHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAG-AIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~-~~~~~~  235 (538)
                      .+.++|.|.+|+|||+||. .+++..
T Consensus       162 GQR~~Ifg~~g~GKT~Lal~~I~~~~  187 (502)
T 2qe7_A          162 GQRELIIGDRQTGKTTIAIDTIINQK  187 (502)
T ss_dssp             TCBCEEEECSSSCHHHHHHHHHHGGG
T ss_pred             CCEEEEECCCCCCchHHHHHHHHHhh
Confidence            3448999999999999965 666554

>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=89.92  E-value=0.17  Score=43.77  Aligned_cols=24  Identities=29%  Similarity=0.443  Sum_probs=20.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
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            345899999999999999999874

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=89.91  E-value=0.2  Score=44.02  Aligned_cols=24  Identities=25%  Similarity=0.526  Sum_probs=21.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|.|.+|+|||||...+...
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            446899999999999999999875

>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=89.91  E-value=0.14  Score=44.38  Aligned_cols=22  Identities=23%  Similarity=0.477  Sum_probs=19.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999999874

>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=89.83  E-value=0.19  Score=44.85  Aligned_cols=23  Identities=26%  Similarity=0.286  Sum_probs=20.0

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            35889999999999999988863

>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=89.79  E-value=0.16  Score=44.16  Aligned_cols=24  Identities=42%  Similarity=0.747  Sum_probs=20.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||...+...
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            345899999999999999999864

>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=89.77  E-value=0.16  Score=44.41  Aligned_cols=22  Identities=23%  Similarity=0.294  Sum_probs=19.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
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            3789999999999999998864

>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=89.77  E-value=0.17  Score=44.35  Aligned_cols=24  Identities=25%  Similarity=0.321  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||...+...
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            345899999999999999999863

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=89.73  E-value=0.15  Score=44.68  Aligned_cols=21  Identities=24%  Similarity=0.246  Sum_probs=19.3

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +.|+|.+|+|||++|.+++..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            689999999999999999865

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=89.72  E-value=0.36  Score=47.42  Aligned_cols=36  Identities=22%  Similarity=0.203  Sum_probs=28.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc--cceeeEEEEe
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS--RHFSGSYFAR  246 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~--~~f~~~~~~~  246 (538)
                      ..++...|-||+||||+|..++..+.  .....+..++
T Consensus        18 ~~i~v~sgKGGvGKTTvaanLA~~lA~~~~G~rVLLvD   55 (354)
T 2woj_A           18 HKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLIS   55 (354)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHHCTTSCEEEEE
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            45667779999999999999999887  6555555555

>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=89.68  E-value=0.18  Score=43.59  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=19.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4889999999999999999863

>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=89.65  E-value=0.18  Score=44.05  Aligned_cols=24  Identities=25%  Similarity=0.504  Sum_probs=20.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||...+...
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            345889999999999999999864

>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=89.61  E-value=0.18  Score=44.45  Aligned_cols=24  Identities=29%  Similarity=0.547  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||...+...
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            345899999999999999999874

>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=89.60  E-value=0.12  Score=46.36  Aligned_cols=25  Identities=16%  Similarity=0.259  Sum_probs=20.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|.|.+|+|||||.+.+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3456999999999999999987653

>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=89.55  E-value=0.18  Score=43.98  Aligned_cols=22  Identities=27%  Similarity=0.545  Sum_probs=19.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999999864

>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=89.50  E-value=0.18  Score=44.69  Aligned_cols=22  Identities=32%  Similarity=0.611  Sum_probs=19.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      --|+|.|.+|+|||||...+..
T Consensus         7 ~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            7 YRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3489999999999999999885

>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=89.48  E-value=0.25  Score=44.75  Aligned_cols=33  Identities=15%  Similarity=0.013  Sum_probs=24.6

Q ss_pred             eEEEEec-cCCCchhHHHHHHHHhhccceeeEEE
Q 009306          212 YKLGIWG-IGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       212 ~~v~I~G-~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      +++.|+| -||+||||++..++..++.....+..
T Consensus         2 k~I~v~s~kgGvGKTt~a~nLa~~la~~G~rVll   35 (224)
T 1byi_A            2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAG   35 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEE
Confidence            4677877 48999999999999887655333333

>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=89.46  E-value=0.19  Score=43.78  Aligned_cols=22  Identities=27%  Similarity=0.309  Sum_probs=19.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4889999999999999998863

>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=89.46  E-value=0.27  Score=43.81  Aligned_cols=26  Identities=19%  Similarity=0.166  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+|+|+|++|+||+|.|..+.+.+
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            45689999999999999999887755

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=89.44  E-value=0.26  Score=52.17  Aligned_cols=37  Identities=24%  Similarity=0.217  Sum_probs=29.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++.+.|.||+||||+|..++..+......+..++
T Consensus         7 ~~~i~~~sgkGGvGKTT~a~~lA~~lA~~G~rVLlvd   43 (589)
T 1ihu_A            7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS   43 (589)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEEeCCCcCHHHHHHHHHHHHHHHCCCcEEEEE
Confidence            4567889999999999999999988776644455554

>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=89.42  E-value=0.19  Score=43.74  Aligned_cols=23  Identities=26%  Similarity=0.460  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .-|+|.|.+|+|||||...+...
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            35889999999999999999863

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=89.41  E-value=0.3  Score=49.45  Aligned_cols=36  Identities=14%  Similarity=0.184  Sum_probs=27.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ....++|.|++|+|||||++.++...... .+.+.+.
T Consensus       156 ~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~-~G~i~~~  191 (438)
T 2dpy_A          156 RGQRMGLFAGSGVGKSVLLGMMARYTRAD-VIVVGLI  191 (438)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHSCCS-EEEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcccCCC-eEEEEEe
Confidence            45579999999999999999999876443 3344443

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=89.40  E-value=0.31  Score=45.84  Aligned_cols=26  Identities=27%  Similarity=0.572  Sum_probs=21.9

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .....|++.|.+|+|||||...++..
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            34556899999999999999999864

>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=89.40  E-value=0.19  Score=43.52  Aligned_cols=23  Identities=26%  Similarity=0.323  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35889999999999999999864

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=89.39  E-value=0.29  Score=45.78  Aligned_cols=25  Identities=24%  Similarity=0.567  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....|+|.|.+|+|||||...+...
T Consensus        35 ~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           35 NSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4456899999999999999999874

>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=89.37  E-value=0.19  Score=43.56  Aligned_cols=22  Identities=27%  Similarity=0.259  Sum_probs=19.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        10 ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D           10 KCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999988864

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=89.34  E-value=0.23  Score=51.73  Aligned_cols=37  Identities=22%  Similarity=0.143  Sum_probs=26.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHH-HhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIF-NKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~-~~~~~~f~~~~~~~  246 (538)
                      ...+++|.|++|+|||||++.++ .-+...-.+.+++.
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~   75 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   75 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            45679999999999999999963 33322224566665

>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=89.32  E-value=0.19  Score=44.42  Aligned_cols=23  Identities=35%  Similarity=0.670  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            34889999999999999999874

>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=89.30  E-value=0.19  Score=43.57  Aligned_cols=23  Identities=22%  Similarity=0.420  Sum_probs=20.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..-|+|.|.+|+|||||...+..
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~   28 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVE   28 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEEECcCCCCHHHHHHHHHc
Confidence            34589999999999999999985

>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=89.29  E-value=0.17  Score=48.62  Aligned_cols=20  Identities=35%  Similarity=0.647  Sum_probs=18.2

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|++|+|||||.+.++.
T Consensus        21 I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            69999999999999999764

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=89.27  E-value=0.53  Score=54.76  Aligned_cols=26  Identities=23%  Similarity=0.341  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|+|||||++.+...+
T Consensus       443 ~G~~vaivG~sGsGKSTll~ll~~~~  468 (1321)
T 4f4c_A          443 AGQTVALVGSSGCGKSTIISLLLRYY  468 (1321)
T ss_dssp             TTCEEEEEECSSSCHHHHHHHHTTSS
T ss_pred             CCcEEEEEecCCCcHHHHHHHhcccc
Confidence            34579999999999999999888643

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=89.25  E-value=0.71  Score=53.53  Aligned_cols=26  Identities=19%  Similarity=0.216  Sum_probs=21.9

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|+|||||++.+...+
T Consensus       415 ~G~~~~ivG~sGsGKSTl~~ll~g~~  440 (1284)
T 3g5u_A          415 SGQTVALVGNSGCGKSTTVQLMQRLY  440 (1284)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHTTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34579999999999999999887643

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=89.24  E-value=1.3  Score=48.37  Aligned_cols=34  Identities=24%  Similarity=0.143  Sum_probs=24.1

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHH
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +.+.+...+..    ...+.|+|+.|.||||++..+..
T Consensus        98 q~~~i~~~l~~----~~~vii~gpTGSGKTtllp~ll~  131 (773)
T 2xau_A           98 QRDEFLKLYQN----NQIMVFVGETGSGKTTQIPQFVL  131 (773)
T ss_dssp             GHHHHHHHHHH----CSEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhC----CCeEEEECCCCCCHHHHHHHHHH
Confidence            44555555653    23689999999999997766654

>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=89.23  E-value=0.2  Score=43.36  Aligned_cols=23  Identities=26%  Similarity=0.407  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999998864

>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=89.23  E-value=0.2  Score=44.04  Aligned_cols=22  Identities=32%  Similarity=0.308  Sum_probs=20.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4899999999999999999874

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=89.23  E-value=0.22  Score=43.10  Aligned_cols=24  Identities=29%  Similarity=0.505  Sum_probs=20.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..--|+|.|.+|+|||||...+..
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCS
T ss_pred             cceEEEEECCCCCCHHHHHHHHhc
Confidence            344589999999999999998875

>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=89.21  E-value=0.17  Score=45.04  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=19.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .-|+|.|.+|+|||||...+..
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3488999999999999998875

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=89.20  E-value=0.2  Score=44.29  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         8 ~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            8 YKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            34889999999999999999875

>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=89.17  E-value=0.15  Score=45.26  Aligned_cols=22  Identities=36%  Similarity=0.696  Sum_probs=19.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      .--|+|.|.+|+|||||...+.
T Consensus        23 ~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           23 IFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHTC
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
Confidence            3458999999999999999885

>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=89.14  E-value=0.2  Score=44.15  Aligned_cols=23  Identities=26%  Similarity=0.481  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            34899999999999999999864

>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=89.14  E-value=0.2  Score=44.76  Aligned_cols=24  Identities=25%  Similarity=0.502  Sum_probs=20.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||...+...
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            345899999999999999998864

>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=89.10  E-value=0.2  Score=44.88  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=20.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .--|+|.|.+|+|||||+..+...
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            345899999999999999999874

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=89.06  E-value=0.23  Score=44.74  Aligned_cols=23  Identities=39%  Similarity=0.547  Sum_probs=20.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .-.|+|+|.-|+||||+++.+..
T Consensus         9 ~~~iglTGgigsGKStv~~~l~~   31 (210)
T 4i1u_A            9 MYAIGLTGGIGSGKTTVADLFAA   31 (210)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHH
Confidence            34699999999999999998765

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=89.02  E-value=0.18  Score=51.46  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||++.++.-.
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            34569999999999999999998754

>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=89.00  E-value=0.21  Score=44.49  Aligned_cols=24  Identities=38%  Similarity=0.570  Sum_probs=20.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            8 LLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            445899999999999999999874

>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=88.95  E-value=0.21  Score=44.37  Aligned_cols=24  Identities=25%  Similarity=0.466  Sum_probs=20.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
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            345899999999999999998863

>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=88.93  E-value=0.21  Score=43.79  Aligned_cols=22  Identities=32%  Similarity=0.377  Sum_probs=19.8

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999863

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=88.89  E-value=0.27  Score=47.10  Aligned_cols=34  Identities=24%  Similarity=0.440  Sum_probs=25.1

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++++...+.     ..+++|.|++|+|||||.+.+....
T Consensus       160 v~~lf~~l~-----geiv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          160 IEELKEYLK-----GKISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             HHHHHHHHS-----SSEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             HHHHHHHhc-----CCeEEEECCCCCcHHHHHHHhcccc
Confidence            444555443     2368999999999999999887643

>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=88.89  E-value=0.22  Score=43.74  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=20.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999864

>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=88.87  E-value=0.35  Score=45.26  Aligned_cols=36  Identities=22%  Similarity=0.158  Sum_probs=27.2

Q ss_pred             CceEEEEe-ccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIW-GIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~-G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..++|+|+ |-||+||||+|..++..+. ....+..++
T Consensus        26 ~~~vI~v~s~kGGvGKTT~a~~LA~~la-~g~~VlliD   62 (267)
T 3k9g_A           26 KPKIITIASIKGGVGKSTSAIILATLLS-KNNKVLLID   62 (267)
T ss_dssp             CCEEEEECCSSSSSCHHHHHHHHHHHHT-TTSCEEEEE
T ss_pred             CCeEEEEEeCCCCchHHHHHHHHHHHHH-CCCCEEEEE
Confidence            45677775 6799999999999999888 544444444

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=88.85  E-value=0.21  Score=44.34  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=20.9

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
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            345899999999999999999874

>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=88.84  E-value=0.22  Score=43.83  Aligned_cols=22  Identities=32%  Similarity=0.370  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||||...+...
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4889999999999999999863

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=88.83  E-value=0.21  Score=48.95  Aligned_cols=25  Identities=20%  Similarity=0.282  Sum_probs=21.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|.|++|+|||||.+.+.....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            3689999999999999998886543

>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=88.82  E-value=0.22  Score=44.76  Aligned_cols=24  Identities=17%  Similarity=0.135  Sum_probs=20.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|.|.+|+|||||...+...
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            345899999999999999999864

>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=88.75  E-value=0.22  Score=43.86  Aligned_cols=23  Identities=30%  Similarity=0.371  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            34889999999999999999874

>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=88.73  E-value=0.2  Score=50.33  Aligned_cols=21  Identities=33%  Similarity=0.591  Sum_probs=19.4

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ++|+|++|+|||||.+.++..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            899999999999999998863

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=88.71  E-value=0.53  Score=44.68  Aligned_cols=38  Identities=18%  Similarity=0.127  Sum_probs=29.4

Q ss_pred             CCceEEEEec-cCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWG-IGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G-~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...++|.|+| -||+||||+|..++..+......+..++
T Consensus        90 ~~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID  128 (286)
T 3la6_A           90 AQNNVLMMTGVSPSIGMTFVCANLAAVISQTNKRVLLID  128 (286)
T ss_dssp             TTCCEEEEEESSSSSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            3467788886 5899999999999998877655566655

>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=88.70  E-value=0.23  Score=43.60  Aligned_cols=23  Identities=22%  Similarity=0.349  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .-|+|.|.+|+|||||...+...
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45899999999999999999863

>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=88.67  E-value=0.21  Score=44.37  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45899999999999999999864

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=88.65  E-value=0.33  Score=51.77  Aligned_cols=47  Identities=21%  Similarity=0.248  Sum_probs=30.2

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .+.+.+...+.     .++..|+|++|.|||+++..+...+...-...+.+.
T Consensus       184 ~Q~~av~~~l~-----~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~  230 (624)
T 2gk6_A          184 SQVYAVKTVLQ-----RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVC  230 (624)
T ss_dssp             HHHHHHHHHHT-----CSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEE
T ss_pred             HHHHHHHHHhc-----CCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEE
Confidence            34444555553     236889999999999988888776543223344444

>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=88.61  E-value=0.23  Score=43.84  Aligned_cols=22  Identities=27%  Similarity=0.764  Sum_probs=19.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      --|+|.|.+|+|||||...+..
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHc
Confidence            3589999999999999999986

>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=88.59  E-value=0.57  Score=46.79  Aligned_cols=28  Identities=21%  Similarity=0.275  Sum_probs=23.4

Q ss_pred             CCceEEEEe-ccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIW-GIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~-G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...++|+|+ |-||+||||+|..++..+.
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            346777777 7899999999999998876

>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=88.54  E-value=0.23  Score=44.01  Aligned_cols=24  Identities=21%  Similarity=0.401  Sum_probs=20.7

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..-|+|.|.+|+|||||...+...
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            345899999999999999999864

>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=88.54  E-value=0.21  Score=44.28  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=19.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+..+
T Consensus        21 ~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           21 PRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhc
Confidence            34899999999999999877664

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=88.53  E-value=0.22  Score=44.93  Aligned_cols=22  Identities=32%  Similarity=0.611  Sum_probs=19.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      --|+|.|.+|+|||||...+..
T Consensus        38 ~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           38 YRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3489999999999999999874

>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=88.49  E-value=0.21  Score=43.48  Aligned_cols=23  Identities=35%  Similarity=0.277  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      --|+|.|.+|+|||||...+...
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            34899999999999999999864

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=88.47  E-value=1.7  Score=40.41  Aligned_cols=50  Identities=8%  Similarity=-0.128  Sum_probs=37.8

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +..|.++|..+-....++.|.|.+|.|||+|+.++...-..+-+.++++.
T Consensus         7 i~~LD~~l~GGl~~gs~~li~g~p~~~~~~l~~qfl~~g~~~Ge~~~~~~   56 (260)
T 3bs4_A            7 IEELDREIGKIKKHSLILIHEEDASSRGKDILFYILSRKLKSDNLVGMFS   56 (260)
T ss_dssp             SHHHHHHHCCBCTTCEEEEEECSGGGCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             cHHHHHHhCCCCCCCcEEEEEeCCCccHHHHHHHHHHHHHHCCCcEEEEE
Confidence            44567777766667888999988888999999999886555555566654

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=88.45  E-value=0.23  Score=50.82  Aligned_cols=25  Identities=20%  Similarity=0.260  Sum_probs=22.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|.|+.|+|||||.+.++.-..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~Gl~~   54 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVTALI   54 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEECCCCCcHHHHHHHHhcCCC
Confidence            6899999999999999999887543

---

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	538
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	2e-39
d1fyva_	161	c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (H	3e-17
d1fyxa_	149	c.23.2.1 (A:) Toll-like receptor 2, TLR2 {Human (H	7e-16

>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 =  142 bits (359), Expect = 2e-39
 Identities = 44/242 (18%), Positives = 75/242 (30%), Gaps = 18/242 (7%)

Query: 200 IESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK---ISRHFSGSYFARNVREAEETCR 256
           I+ L      + + L + G  G GK+ IA    +K   +      S              
Sbjct: 33  IKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST 92

Query: 257 LGDLRQQLLSTLLNDGNVKNFLNTDL-------NFQSRRLTRKKVLIVFDDVDHPRQIKI 309
                  LL     D  +       +          +  + R   L VFDDV     I+ 
Sbjct: 93  FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIR- 151

Query: 310 LVGRLDLFASGSRIIITTRDRQVLANCGVD-EVYQMEELVHDDALRLFSRHAFGGDHPHE 368
                       R ++TTRD ++        E  ++  L  D+       +        +
Sbjct: 152 -----WAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEK 206

Query: 369 SHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWETAPPKGIQDALKISYDG 428
              ++  KTI+ + G P  L +  +    K  E      +K E+    G++     SY  
Sbjct: 207 -EEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKS 265

Query: 429 LD 430
           L 
Sbjct: 266 LA 267

>d1fyva_ c.23.2.1 (A:) Toll-like receptor 1, TLR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 161

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Toll/Interleukin receptor TIR domain
family: Toll/Interleukin receptor TIR domain
domain: Toll-like receptor 1, TLR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.7 bits (188), Expect = 3e-17
 Identities = 23/119 (19%), Positives = 51/119 (42%), Gaps = 3/119 (2%)

Query: 15  EIKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSI 73
            +++  F+S+ G D+     + L   L +E ++  + + +   G  I ++++  IE S  
Sbjct: 10  NLQFHAFISYSGHDSF-WVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYK 68

Query: 74  SIIIFSESYASSRWCLDELLKILECK-KEYAQIVVPVFYRVDPSHVRKQTGNFGDSFLK 131
           SI + S ++  S WC  EL         E +  ++ +     P +    + +   S + 
Sbjct: 69  SIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLMA 127

>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 = 72.8 bits (178), Expect = 7e-16
 Identities = 23/111 (20%), Positives = 40/111 (36%), Gaps = 5/111 (4%)

Query: 15  EIKYDVFLSFGGEDTRESFTSHLYSAL--SRETVETFIDD-DLRRGDEISQSLLDAIEAS 71
            I YD F+S+   D      + +   L       +  +   D   G  I  +++D+IE S
Sbjct: 3   NICYDAFVSYSERD-AYWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEKS 61

Query: 72  SISIIIFSESYASSRWCLDEL-LKILECKKEYAQIVVPVFYRVDPSHVRKQ 121
             ++ + SE++  S WC  EL         E     + +           Q
Sbjct: 62  HKTVFVLSENFVKSEWCKYELDFSHFRLFDENNDAAILILLEPIEKKAIPQ 112

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	538
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1fyva_	161	Toll-like receptor 1, TLR1 {Human (Homo sapiens) [	99.83
d1fyxa_	149	Toll-like receptor 2, TLR2 {Human (Homo sapiens) [	99.79
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.42
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.06
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.96
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.93
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.93
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.9
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.88
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.86
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.81
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.79
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.78
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.71
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.61
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.61
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.6
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.6
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.56
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.53
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.52
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.48
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.44
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.37
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.47
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	97.3
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.2
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.18
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.13
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.12
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.11
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.07
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.02
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.0
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.99
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.96
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.94
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.94
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.92
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.91
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.86
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.84
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.8
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.77
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.75
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.71
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.68
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.66
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.66
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.66
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.61
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.6
d1okkd2	207	GTPase domain of the signal recognition particle r	96.6
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.57
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.55
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.55
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.54
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.53
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.53
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.52
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.51
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.39
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.37
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.29
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.25
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.25
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.25
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.24
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.24
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.22
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.12
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.08
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.06
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.05
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.94
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.88
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.85
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.81
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.81
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.77
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.75
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.75
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	95.75
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.74
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.72
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.7
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.7
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.67
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.66
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.65
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.6
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.59
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.56
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.51
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.48
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.38
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.35
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.34
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.25
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.24
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.23
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.21
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.2
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.1
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.06
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.05
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	94.94
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.85
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.69
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.61
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	94.59
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.58
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.35
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.33
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.2
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.18
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.77
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	93.77
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.76
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	93.74
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.74
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	93.73
d1g2912	240	Maltose transport protein MalK, N-terminal domain	93.71
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.61
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.57
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	93.52
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	93.49
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.45
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.44
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.34
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	93.22
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.11
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.11
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.1
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	93.05
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.04
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	92.96
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.96
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.94
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	92.68
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.62
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.62
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.59
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	92.51
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.36
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.35
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.16
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	92.15
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.12
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	92.01
d1tuea_	205	Replication protein E1 helicase domain {Human papi	92.01
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	91.96
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	91.96
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.95
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	91.95
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.87
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.87
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	91.73
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	91.65
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	91.65
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	91.63
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.63
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	91.61
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.55
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	91.51
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.5
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.49
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	91.49
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.44
d1nrjb_	209	Signal recognition particle receptor beta-subunit	91.42
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	91.28
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.25
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	91.23
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	91.21
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.16
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	91.14
d2fh5b1	207	Signal recognition particle receptor beta-subunit	91.13
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	91.13
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.11
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	91.04
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	91.01
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	90.87
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	90.86
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.82
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	90.81
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	90.8
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.73
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	90.72
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	90.68
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	90.59
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	90.46
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	90.41
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	90.39
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	90.38
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	90.22
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.19
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	90.07
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	90.03
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	90.01
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.98
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.97
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	89.82
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	89.78
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	89.76
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	89.75
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	89.74
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	89.73
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	89.58
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	89.52
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	89.37
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	89.36
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.35
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	89.29
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	89.19
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.0
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	88.68
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	88.53
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	88.45
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.42
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.11
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	87.86
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	87.77
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	87.6
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	87.55
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	87.41
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	87.34
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	87.09
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.06
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.03
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	86.32
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	85.72
d1xpua3	289	Transcription termination factor Rho, ATPase domai	85.71
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	84.08
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	83.55
d1wu7a1	97	Histidyl-tRNA synthetase (HisRS), C-terminal domai	83.48
d2f62a1	152	Nucleoside 2-deoxyribosyltransferase {Trypanosoma	83.38
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.98
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	82.73
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	82.28
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	82.06
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	82.04
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	81.05
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	80.46
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.23

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=8.1e-37  Score=294.21  Aligned_cols=247  Identities=19%  Similarity=0.187  Sum_probs=193.6

Q ss_pred             CCCCceeccchhHHHHHhhhc-CCCCceEEEEeccCCCchhHHHHHHHHh----hccceeeEEEEeehhhhhhcCChHHH
Q 009306          186 ENEDLVGVRLPMKEIESLLRT-GSTNVYKLGIWGIGGIGKTTIAGAIFNK----ISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~----~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..+.++||+.++++|.++|.. .+.+.++|+|+||||+||||||++++++    ...+|++++|+...+.. ....+...
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~-~~~~l~~~   96 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTA-PKSTFDLF   96 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCS-TTHHHHHH
T ss_pred             CCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCC-CHHHHHHH
Confidence            446688999999999998865 4456889999999999999999999986    44568899998733221 12223333


Q ss_pred             HHHHHHHHhcCCCCC-------CchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEeccchhhh
Q 009306          261 RQQLLSTLLNDGNVK-------NFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITTRDRQVL  333 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~-------~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTtR~~~~~  333 (538)
                      +..++..+.......       .........+.+.+.++++|+||||||+..+++.+..      .+++||||||+..++
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~v~  170 (277)
T d2a5yb3          97 TDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEIS  170 (277)
T ss_dssp             HHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGGGG
T ss_pred             HHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHHHH
Confidence            334443333322111       1112223345677889999999999999999987753      489999999999998


Q ss_pred             hhcCCC-eeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHHHHHHHhcCCCHHHHHHHHHHhhc
Q 009306          334 ANCGVD-EVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALEVLGRYLYGKRREVWENAKSKWET  412 (538)
Q Consensus       334 ~~~~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~~~~L~~~~~~~~~~~l~~l~~  412 (538)
                      ..+... ..|+|++|+.+||++||..++|.... .+..++.+.+|+++|+|+||||+++|+.|+.++.+.|....+.+..
T Consensus       171 ~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~-~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~  249 (277)
T d2a5yb3         171 NAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV-GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLES  249 (277)
T ss_dssp             GGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHH
T ss_pred             HhcCCCCceEECCCCCHHHHHHHHHHHhCCccC-chhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHhc
Confidence            877554 67999999999999999999876543 3456788899999999999999999999999999999999998887


Q ss_pred             CCCCcHHHHHHHhHhCCCHHhHHHhhcc
Q 009306          413 APPKGIQDALKISYDGLDDKEQNIFLDI  440 (538)
Q Consensus       413 ~~~~~v~~~l~~s~~~L~~~~k~~l~~l  440 (538)
                      .....+..++..||+.||++.|.||.++
T Consensus       250 ~~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         250 RGLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HCSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             CcHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            7778899999999999999999999764

>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=99.83  E-value=1.1e-21  Score=171.23  Aligned_cols=103  Identities=20%  Similarity=0.426  Sum_probs=92.3

Q ss_pred             CCCCCCCCCcccEEEcCcccccccchH-HHHHHHHhhCCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccc
Q 009306            8 YASLTNPEIKYDVFLSFGGEDTRESFT-SHLYSALSRETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASS   85 (538)
Q Consensus         8 ~~~~~~~~~~~dvFiSy~~~D~~~~~~-~~l~~~l~~~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s   85 (538)
                      +.......++|||||||+++|  +.|| ..|...|+++|+++|+|+ ++.+|+.+.++|.++|++|+++|+|+|++|+.|
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 PLEELQRNLQFHAFISYSGHD--SFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQS   80 (161)
T ss_dssp             CSTTSSSCCCEEEEEECCGGG--HHHHHHTHHHHHHTTTCCEECTTTTCCTTSCHHHHHHHHHHHEEEEEEEESHHHHHH
T ss_pred             ChhHcCCCCeeEEEEecChhH--HHHHHHHHHHHHHhCCCcceEeccccccccccHHHHHHHHHhCCEEEEEecCccccC
Confidence            344556789999999999999  6677 579999999999999998 999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHHH-hhcCCeEEEEEEe
Q 009306           86 RWCLDELLKILECK-KEYAQIVVPVFYR  112 (538)
Q Consensus        86 ~~c~~El~~~~~~~-~~~~~~v~pv~~~  112 (538)
                      .||..|+..++.+. ..+..++|||+++
T Consensus        81 ~w~~~E~~~a~~~~~~~~~~~lIpV~l~  108 (161)
T d1fyva_          81 EWCHYELYFAHHNLFHEGSNSLILILLE  108 (161)
T ss_dssp             TSHHHHHHTTSCCCSCSSCSSEEEEESS
T ss_pred             hHHHHHHHHHHHHHHHcCCCceeEEEEe
Confidence            99999999988765 4455789999976

>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=99.79  E-value=1.2e-20  Score=162.54  Aligned_cols=97  Identities=23%  Similarity=0.404  Sum_probs=87.3

Q ss_pred             CCCcccEEEcCcccccccchHH-HHHHHHhh--CCCeeEeeC-CCCCCCcchHHHHHHHHhcceEEEEeccCcccchhhH
Q 009306           14 PEIKYDVFLSFGGEDTRESFTS-HLYSALSR--ETVETFIDD-DLRRGDEISQSLLDAIEASSISIIIFSESYASSRWCL   89 (538)
Q Consensus        14 ~~~~~dvFiSy~~~D~~~~~~~-~l~~~l~~--~g~~~~~d~-~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y~~s~~c~   89 (538)
                      .++.|||||||+++|  +.||. .|...|++  .|+++|+|+ ++.+|+.+.++|.++|++|+++|+|+||+|+.|.||.
T Consensus         2 ~~~~YDvFiSys~~D--~~~V~~~l~~~LE~~~~g~~~~~~~rd~~~G~~~~~~i~~~i~~S~~~i~vlS~~~l~s~wc~   79 (149)
T d1fyxa_           2 RNICYDAFVSYSERD--AYWVENLMVQELENFNPPFKLCLHKRDFIHGKWIIDNIIDSIEKSHKTVFVLSENFVKSEWCK   79 (149)
T ss_dssp             CSCCEEEEEECCGGG--HHHHHTHHHHHHTTSSSCCCEEEHHHHCCSSSCHHHHHHHHHHHEEEEEEEECHHHHHHHTHH
T ss_pred             CCCEEEEEEECchhh--HHHHHHHHHHHHHhcCCCceEEEecccccccchHHHHHHHHHHhCCEEEEEEcCccccccchH
Confidence            678999999999999  66774 68999976  499999998 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH-hhcCCeEEEEEEe
Q 009306           90 DELLKILECK-KEYAQIVVPVFYR  112 (538)
Q Consensus        90 ~El~~~~~~~-~~~~~~v~pv~~~  112 (538)
                      .|+..++... +.++.++|||+++
T Consensus        80 ~E~~~a~~~~~~~~~~~iIpV~l~  103 (149)
T d1fyxa_          80 YELDFSHFRLFDENNDAAILILLE  103 (149)
T ss_dssp             HHSCCSCCTTCGGGTTCCEEEESS
T ss_pred             HHHHHHHHHHHHcCCceEEEEEec
Confidence            9998877654 5667789999987

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.42  E-value=6.4e-13  Score=126.11  Aligned_cols=197  Identities=13%  Similarity=0.151  Sum_probs=113.2

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhh-hcCChHHH
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAE-ETCRLGDL  260 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~-~~~~~~~l  260 (538)
                      .+...++.|+||+.++++|.+.      ..+.+.|+|++|+|||+|+++++.+....+.   |+....... .......+
T Consensus         6 ~p~~~~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~---~i~~~~~~~~~~~~~~~~   76 (283)
T d2fnaa2           6 SPKDNRKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGINELNLPYI---YLDLRKFEERNYISYKDF   76 (283)
T ss_dssp             SCCCSGGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHHHHTCCEE---EEEGGGGTTCSCCCHHHH
T ss_pred             CCCCChhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeE---EEEeccccccccccHHHH
Confidence            3445678999999999998764      2357899999999999999999988755432   333211111 12223333


Q ss_pred             HHHHHHHHhcC-----------CC---------------CCCchhhcHHHHHH--HhcCCCeEEEEecCCCh--------
Q 009306          261 RQQLLSTLLND-----------GN---------------VKNFLNTDLNFQSR--RLTRKKVLIVFDDVDHP--------  304 (538)
Q Consensus       261 ~~~l~~~l~~~-----------~~---------------~~~~~~~~~~~l~~--~l~~k~~LlVlDdv~~~--------  304 (538)
                      ...+.......           ..               ...........+..  ....+++++++|+++..        
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~  156 (283)
T d2fnaa2          77 LLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNL  156 (283)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCC
T ss_pred             HHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHH
Confidence            33333221100           00               00011111222222  23568899999998432        


Q ss_pred             -HHHHHHhcCcCCCCCCCEEEEeccchhhhhhc------------CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchH
Q 009306          305 -RQIKILVGRLDLFASGSRIIITTRDRQVLANC------------GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHT  371 (538)
Q Consensus       305 -~~~~~l~~~l~~~~~~~~iiiTtR~~~~~~~~------------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~  371 (538)
                       ..+..+...    ......+++.+........            .....+.|++++.+++.+++.+..-......+   
T Consensus       157 ~~~l~~~~~~----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~---  229 (283)
T d2fnaa2         157 LPALAYAYDN----LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK---  229 (283)
T ss_dssp             HHHHHHHHHH----CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC---
T ss_pred             HHHHHHHHHh----hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHH---
Confidence             112222211    2344455554443222111            12356889999999999999876522111111   


Q ss_pred             HHHHHHHHHhcCCcHHHHHHHHHh
Q 009306          372 ELACKTIKYARGVPLALEVLGRYL  395 (538)
Q Consensus       372 ~~~~~i~~~~~G~PLal~~~~~~L  395 (538)
                       ...++++.++|+|.+|+.++..+
T Consensus       230 -~~~~i~~~~~G~P~~L~~~~~~~  252 (283)
T d2fnaa2         230 -DYEVVYEKIGGIPGWLTYFGFIY  252 (283)
T ss_dssp             -CHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             -HHHHHHHHhCCCHHHHHHHHHHH
Confidence             25689999999999999998766

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.06  E-value=3.2e-09  Score=99.59  Aligned_cols=193  Identities=13%  Similarity=0.076  Sum_probs=111.7

Q ss_pred             CCCCCceeccchhHHHHHhhhc----CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRT----GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~----~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..+..++||+.++++|.++|..    .+...+.+.|+|++|+|||++|+.+++.+.......+....   ..........
T Consensus        13 y~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~---~~~~~~~~~~   89 (276)
T d1fnna2          13 YVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN---GFIYRNFTAI   89 (276)
T ss_dssp             CCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE---TTTCCSHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEec---chhhhhhhhh
Confidence            4567799999999999998864    23345679999999999999999999988765443333221   2233455566


Q ss_pred             HHHHHHHHhcCCCCC-CchhhcHHHHHHHh--cCCCeEEEEecCCChHH-----HHHHhcCcCC-CCCCCEEEEeccchh
Q 009306          261 RQQLLSTLLNDGNVK-NFLNTDLNFQSRRL--TRKKVLIVFDDVDHPRQ-----IKILVGRLDL-FASGSRIIITTRDRQ  331 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~~~-----~~~l~~~l~~-~~~~~~iiiTtR~~~  331 (538)
                      ...+....+...... .........+.+.+  .....++++|++++...     ...+...... ......+|.++....
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  169 (276)
T d1fnna2          90 IGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDA  169 (276)
T ss_dssp             HHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH
T ss_pred             hhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchh
Confidence            666666655443222 33344444444433  23567778888764321     1222211111 122334555554433


Q ss_pred             hhhhc-------CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHH
Q 009306          332 VLANC-------GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKY  380 (538)
Q Consensus       332 ~~~~~-------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~  380 (538)
                      .....       .....+.+.+++.++..+++..++-.........++..+.+++.
T Consensus       170 ~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~  225 (276)
T d1fnna2         170 VLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADI  225 (276)
T ss_dssp             HHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHH
T ss_pred             hhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHH
Confidence            22211       12346789999999999999876522112222334555556554

>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=98.96  E-value=1.2e-09  Score=99.71  Aligned_cols=185  Identities=15%  Similarity=0.202  Sum_probs=112.3

Q ss_pred             ccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce-eeEEEEeehhhhhhcCChHH
Q 009306          181 DTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-SGSYFARNVREAEETCRLGD  259 (538)
Q Consensus       181 ~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~~~~~~~~~~~~~~~~~~~  259 (538)
                      ...|....++||.+..++.|..++..+.  .+.+.++|++|+||||+|+.+++.+...+ ...++..+   .+...+...
T Consensus         8 KyrP~~~~d~ig~~~~~~~L~~~~~~~~--~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n---~~~~~~~~~   82 (224)
T d1sxjb2           8 KYRPQVLSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN---ASDDRGIDV   82 (224)
T ss_dssp             HTCCSSGGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC---TTSCCSHHH
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHcCC--CCeEEEECCCCCCchhhHHHHHHHHhcccccccccccc---ccccCCcee
Confidence            3455666889999999999999998643  33478999999999999999998765432 22222222   122222222


Q ss_pred             HHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhhc
Q 009306          260 LRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLANC  336 (538)
Q Consensus       260 l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~  336 (538)
                      +...+..........              ...+.-++|+|+++..  .....+...+......+.+++++.+. .+...+
T Consensus        83 i~~~~~~~~~~~~~~--------------~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l  148 (224)
T d1sxjb2          83 VRNQIKHFAQKKLHL--------------PPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPL  148 (224)
T ss_dssp             HHTHHHHHHHBCCCC--------------CTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHH
T ss_pred             hhhHHHHHHHhhccC--------------CCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHH
Confidence            222222111111000              0234568899999743  22233322222224456666666543 222222


Q ss_pred             -CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          337 -GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       337 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                       .....+.+++++.++...++.+.+...  .-....+....|++.++|.+.
T Consensus       149 ~sr~~~i~~~~~~~~~i~~~l~~i~~~e--~~~i~~~~l~~I~~~s~Gd~R  197 (224)
T d1sxjb2         149 QSQCAILRYSKLSDEDVLKRLLQIIKLE--DVKYTNDGLEAIIFTAEGDMR  197 (224)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHhhhcccchhhhHHHHHHHHHhc--ccCCCHHHHHHHHHHcCCcHH
Confidence             345689999999999999998776321  223456778999999999875

>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=98.93  E-value=2.1e-09  Score=98.19  Aligned_cols=182  Identities=14%  Similarity=0.176  Sum_probs=111.3

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChHHH
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      ..|....++||.+..++.|..++..+.  .+.+.++|++|+||||+|+.+++.+... +...+...+   .+...+....
T Consensus         8 yrP~~~~divg~~~~~~~L~~~i~~~~--~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~---~~~~~~~~~~   82 (227)
T d1sxjc2           8 YRPETLDEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN---ASDDRGIDVV   82 (227)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC---TTSCCSHHHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEec---ccccCCeeee
Confidence            345566889999999999999997643  3347799999999999999999875432 222222221   1111222111


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhh-c
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLAN-C  336 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~-~  336 (538)
                      ........... .              ....+.-++|+|+++..  .....+...+......+.++++|... .+... .
T Consensus        83 ~~~~~~~~~~~-~--------------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~  147 (227)
T d1sxjc2          83 RNQIKDFASTR-Q--------------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALL  147 (227)
T ss_dssp             HTHHHHHHHBC-C--------------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHH
T ss_pred             ecchhhccccc-c--------------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHH
Confidence            11111111110 0              01234458899999643  34444444444445677777777654 22222 2


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      .....+.+.+++.++..+++.+.+...  .-....+....|++.++|..
T Consensus       148 sr~~~i~~~~~~~~~i~~~l~~I~~~e--~i~i~~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         148 SQCTRFRFQPLPQEAIERRIANVLVHE--KLKLSPNAEKALIELSNGDM  194 (227)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHHHTT--TCCBCHHHHHHHHHHHTTCH
T ss_pred             HHHhhhccccccccccccccccccccc--cccCCHHHHHHHHHHcCCcH
Confidence            345688999999999999998876332  22345677889999999875

>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=98.93  E-value=2.4e-08  Score=93.95  Aligned_cols=193  Identities=12%  Similarity=0.072  Sum_probs=106.9

Q ss_pred             CCCCCceeccchhHHHHHhhhc----CC---CCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehhhh
Q 009306          185 SENEDLVGVRLPMKEIESLLRT----GS---TNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVREA  251 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~----~~---~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~~~  251 (538)
                      ..|+.++||+.++++|.+.+..    +.   +...++.|+|++|+|||++++.+++.+....      ....++.    .
T Consensus        13 ~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~----~   88 (287)
T d1w5sa2          13 YIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN----A   88 (287)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE----G
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeec----c
Confidence            4668899999999999886632    21   1123466789999999999999998764321      2233333    3


Q ss_pred             hhcCChHHHHHHHHHHHhcCCCCC-CchhhcHHHHHHHh--cCCCeEEEEecCCCh--------HHHHHHh---cCcC-C
Q 009306          252 EETCRLGDLRQQLLSTLLNDGNVK-NFLNTDLNFQSRRL--TRKKVLIVFDDVDHP--------RQIKILV---GRLD-L  316 (538)
Q Consensus       252 ~~~~~~~~l~~~l~~~l~~~~~~~-~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~--------~~~~~l~---~~l~-~  316 (538)
                      ........................ .........+.+..  .....++++|.++..        +....+.   ..+. .
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~  168 (287)
T d1w5sa2          89 FNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSR  168 (287)
T ss_dssp             GGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCT
T ss_pred             ccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchh
Confidence            333444555555555554433222 33333334444333  356678888887532        1222221   1111 1


Q ss_pred             CC-CCCE-EEEeccchhh--------hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh
Q 009306          317 FA-SGSR-IIITTRDRQV--------LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA  381 (538)
Q Consensus       317 ~~-~~~~-iiiTtR~~~~--------~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~  381 (538)
                      .. .... |++++.....        .........+.+++++.++..+++..++-.........++..+.+++.+
T Consensus       169 ~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~  243 (287)
T d1w5sa2         169 DGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVY  243 (287)
T ss_dssp             TSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHH
T ss_pred             hcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHH
Confidence            11 1223 3344333211        0111235678999999999999999876221122223456666676655

>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=98.90  E-value=4.1e-09  Score=96.52  Aligned_cols=185  Identities=17%  Similarity=0.197  Sum_probs=110.5

Q ss_pred             cccCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEeehhhhhhcCChH
Q 009306          180 DDTFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFARNVREAEETCRLG  258 (538)
Q Consensus       180 ~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~~~~~~~~~~~~~  258 (538)
                      ....|....+++|.+..++.|..++..+  ..+.+.|+|++|+||||+|+.+++.+... +...+...+.........+.
T Consensus        16 ~ky~P~~~~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~~~~~   93 (231)
T d1iqpa2          16 EKYRPQRLDDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIR   93 (231)
T ss_dssp             HHTCCCSTTTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTH
T ss_pred             HHhCCCCHHHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcccchhHHH
Confidence            3344556689999999999999999864  34558899999999999999999876432 22222222111111001111


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhh
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLAN  335 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~  335 (538)
                      ...    .......              .....++.++++|+++..  .....+...+........+|.+|... .+...
T Consensus        94 ~~~----~~~~~~~--------------~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~  155 (231)
T d1iqpa2          94 EKV----KEFARTK--------------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEP  155 (231)
T ss_dssp             HHH----HHHHHSC--------------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHH
T ss_pred             HHH----HHHHhhh--------------hccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHh
Confidence            111    1111000              011346678999999642  33344443333223455556655443 22222


Q ss_pred             c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          336 C-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       336 ~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      + .....+.+.+.+..+....+.+.+...  .-....+..+.|++.++|...
T Consensus       156 l~sR~~~i~~~~~~~~~~~~~l~~~~~~e--~i~i~~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         156 IQSRCAIFRFRPLRDEDIAKRLRYIAENE--GLELTEEGLQAILYIAEGDMR  205 (231)
T ss_dssp             HHHTEEEEECCCCCHHHHHHHHHHHHHTT--TCEECHHHHHHHHHHHTTCHH
T ss_pred             HhCccccccccccchhhHHHHHHHHHHHh--CCCCCHHHHHHHHHHcCCCHH
Confidence            2 223678999999999999998887332  233456778899999998754

>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=98.88  E-value=1.2e-08  Score=93.75  Aligned_cols=195  Identities=15%  Similarity=0.124  Sum_probs=112.5

Q ss_pred             CCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQ  263 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~  263 (538)
                      |..-.+++|.+..++.|..++..+. -.+.+.|+|++|+||||+|+.+++.+......    .     ............
T Consensus         8 P~~~~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~----~-----~~~~~~~~~~~~   77 (239)
T d1njfa_           8 PQTFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGI----T-----ATPCGVCDNCRE   77 (239)
T ss_dssp             CSSGGGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHHHHCTTCS----C-----SSCCSCSHHHHH
T ss_pred             CCCHHHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCcccc----c-----cCccccchHHHH
Confidence            3455789999999999999987542 24568899999999999999998875432110    0     000000000111


Q ss_pred             HHHHHhcC-CCCCCchhhcHHHHHHHh--------cCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccchh-
Q 009306          264 LLSTLLND-GNVKNFLNTDLNFQSRRL--------TRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDRQ-  331 (538)
Q Consensus       264 l~~~l~~~-~~~~~~~~~~~~~l~~~l--------~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~~-  331 (538)
                      +....... .............+++.+        .++.-++|||+++..  .....|+..+.....++++|++|.+.. 
T Consensus        78 i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~  157 (239)
T d1njfa_          78 IEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQK  157 (239)
T ss_dssp             HHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGG
T ss_pred             HHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccc
Confidence            11000000 000000000111122111        234568999999754  344555555544456777777776542 


Q ss_pred             hhhhc-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH-HHHH
Q 009306          332 VLANC-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL-ALEV  390 (538)
Q Consensus       332 ~~~~~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL-al~~  390 (538)
                      +...+ .....+.+.+++.++..+.+...+-..  .....++.+..+++.++|.+- ||..
T Consensus       158 i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e--~~~~~~~~l~~i~~~s~Gd~R~ain~  216 (239)
T d1njfa_         158 LPVTILSRCLQFHLKALDVEQIRHQLEHILNEE--HIAHEPRALQLLARAAEGSLRDALSL  216 (239)
T ss_dssp             SCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHHHTTTCHHHHHHH
T ss_pred             cChhHhhhhcccccccCcHHHhhhHHHHHHhhh--ccCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            22222 234688999999999999888776221  223456778899999999985 4443

>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=98.86  E-value=6.8e-09  Score=95.34  Aligned_cols=191  Identities=10%  Similarity=0.098  Sum_probs=109.9

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce---eeEEEEeehhhhhhcCChH
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF---SGSYFARNVREAEETCRLG  258 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f---~~~~~~~~~~~~~~~~~~~  258 (538)
                      ..|..-++++|.+..++.|..++..+  ..+.+.|+|++|+||||+++.+++++....   ...+...    .+......
T Consensus         6 y~P~~~~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~----~~~~~~~~   79 (237)
T d1sxjd2           6 YRPKNLDEVTAQDHAVTVLKKTLKSA--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN----ASDERGIS   79 (237)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTTCT--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC----SSSCCCHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhee----ccccccch
Confidence            34555678999999999999999754  334488999999999999999998753321   1122222    11122222


Q ss_pred             HHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCCCCCCCEEEEeccch-hhhhh
Q 009306          259 DLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDLFASGSRIIITTRDR-QVLAN  335 (538)
Q Consensus       259 ~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~  335 (538)
                      .....+ ............    ...+......+.-++|+|+++..  .....+...+........+++++... .....
T Consensus        80 ~~~~~~-~~~~~~~~~~~~----~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~  154 (237)
T d1sxjd2          80 IVREKV-KNFARLTVSKPS----KHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDP  154 (237)
T ss_dssp             HHTTHH-HHHHHSCCCCCC----TTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHH
T ss_pred             HHHHHH-HHHhhhhhhhhh----HHHHhhccccCceEEEEecccccCHHHHHHHhhcccccccccccccccccccccccc
Confidence            222222 111111111111    11122222334447999999743  23333333222224456666665443 22211


Q ss_pred             c-CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          336 C-GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       336 ~-~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      + .....+.+.+++.++...++...+....  -....+....|++.++|.+
T Consensus       155 l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~--i~i~~~~l~~ia~~s~gd~  203 (237)
T d1sxjd2         155 LASQCSKFRFKALDASNAIDRLRFISEQEN--VKCDDGVLERILDISAGDL  203 (237)
T ss_dssp             HHHHSEEEECCCCCHHHHHHHHHHHHHTTT--CCCCHHHHHHHHHHTSSCH
T ss_pred             ccchhhhhccccccccccchhhhhhhhhhc--CcCCHHHHHHHHHHcCCCH
Confidence            1 1236789999999999999988774322  2345677889999998875

>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=98.81  E-value=2.1e-08  Score=92.66  Aligned_cols=152  Identities=13%  Similarity=0.166  Sum_probs=97.6

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEeehhhhhhcCChHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      +..+||+.++++|...|....  ..-+.|+|++|+|||+|+..++.++...      ....+|..+....-.        
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~--k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~lia--------   87 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLA--------   87 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---C--------
T ss_pred             CcccChHHHHHHHHHHHhcCc--cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhc--------
Confidence            468999999999999997543  2347799999999999999999875432      123455443221110        


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHh-cCCCeEEEEecCCCh----------HHHHHHh-cCcCCCCCCCEEEEeccc
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRL-TRKKVLIVFDDVDHP----------RQIKILV-GRLDLFASGSRIIITTRD  329 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------~~~~~l~-~~l~~~~~~~~iiiTtR~  329 (538)
                              +. ......++....+.+.+ ...++++++|++...          .++..++ +.+.  ....++|.+|..
T Consensus        88 --------g~-~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~  156 (268)
T d1r6bx2          88 --------GT-KYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTY  156 (268)
T ss_dssp             --------CC-CCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECH
T ss_pred             --------cC-ccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCH
Confidence                    11 01123333333333333 456789999998543          2344444 4443  456788888887


Q ss_pred             hhhhhhcC-------CCeeEEcCCCCHHHHHHHHHhhh
Q 009306          330 RQVLANCG-------VDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       330 ~~~~~~~~-------~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ........       ..+.+.+++++.+++.+++....
T Consensus       157 eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         157 QEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             HHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            76644332       23578999999999999997654

>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=98.79  E-value=1.3e-08  Score=88.71  Aligned_cols=148  Identities=12%  Similarity=0.107  Sum_probs=90.9

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEeehhhhhhcCChHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      +..+||+.+++++...|....  ..-+.++|++|+|||+++..++.++...      -...+|..+....-......   
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~--k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~r---   96 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYR---   96 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSH---
T ss_pred             CCCcCcHHHHHHHHHHHhccC--CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCcc---
Confidence            468999999999999998543  2347899999999999999999976532      13456655433321111110   


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHH-HHhc-CCCeEEEEecCCCh----------HHHHHHhcCcCCCCCCCEEEEeccc
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQS-RRLT-RKKVLIVFDDVDHP----------RQIKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~-~~l~-~k~~LlVlDdv~~~----------~~~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                                    ...++....+. +... ..++++++||+...          +....+.+.+.  ....++|.+|..
T Consensus        97 --------------G~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~  160 (195)
T d1jbka_          97 --------------GEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTL  160 (195)
T ss_dssp             --------------HHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECH
T ss_pred             --------------HHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCH
Confidence                          11122222222 2222 35789999998533          11233334433  345678888876


Q ss_pred             hhhhhhcC-------CCeeEEcCCCCHHHHHHHH
Q 009306          330 RQVLANCG-------VDEVYQMEELVHDDALRLF  356 (538)
Q Consensus       330 ~~~~~~~~-------~~~~~~l~~L~~~ea~~Lf  356 (538)
                      +.......       ..+.+.++.++.+++..++
T Consensus       161 eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         161 DEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             HHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            65544332       3367899999999887654

>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=98.78  E-value=2.6e-08  Score=92.23  Aligned_cols=197  Identities=12%  Similarity=0.083  Sum_probs=103.1

Q ss_pred             cCCCCCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccce------eeEEEEeehh------
Q 009306          182 TFHSENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHF------SGSYFARNVR------  249 (538)
Q Consensus       182 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f------~~~~~~~~~~------  249 (538)
                      ..|...++++|.+...+.|..++..+. ..+.+.|+|++|+||||+|+.+++.+....      ....+.....      
T Consensus         5 y~P~~~~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (252)
T d1sxje2           5 YRPKSLNALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELN   83 (252)
T ss_dssp             TCCCSGGGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------C
T ss_pred             cCCCCHHHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhh
Confidence            345556789999999999988886532 334478999999999999999998752210      1111100000      


Q ss_pred             -----------hhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCcCC
Q 009306          250 -----------EAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRLDL  316 (538)
Q Consensus       250 -----------~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l~~  316 (538)
                                 ..........................      ...-......+.-++|||+++..  .....+...+..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~  157 (252)
T d1sxje2          84 VVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVD------FQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEK  157 (252)
T ss_dssp             CEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSCHHHHHHHHHHHHH
T ss_pred             hccCCccceeeecccccCCcceeeehhhhhhhhhhhh------hhhcccccCCCceEEEeccccccccccchhhhccccc
Confidence                       00000001111111111111111000      00001112234558999999764  333334333333


Q ss_pred             CCCCCEEEEeccchh-hhhh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          317 FASGSRIIITTRDRQ-VLAN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       317 ~~~~~~iiiTtR~~~-~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      ....+++|+||.+.. +... ......+++.+++.++..+++...+-... ..-..++..+.++..+.|.+.
T Consensus       158 ~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~-~~~~~~~~l~~i~~~s~Gd~R  228 (252)
T d1sxje2         158 YSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNER-IQLETKDILKRIAQASNGNLR  228 (252)
T ss_dssp             STTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHT-CEECCSHHHHHHHHHHTTCHH
T ss_pred             ccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcC-CCCCcHHHHHHHHHHcCCcHH
Confidence            355677777775442 2111 12236789999999999999876652211 111123566788999999874

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.71  E-value=1.9e-07  Score=83.73  Aligned_cols=170  Identities=15%  Similarity=0.201  Sum_probs=96.8

Q ss_pred             Cceeccchh--HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHH
Q 009306          189 DLVGVRLPM--KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLS  266 (538)
Q Consensus       189 ~~vGR~~~l--~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~  266 (538)
                      .++|-..++  +.+.++....+.....+.|+|++|+|||.|+.++++........++++..          ..+...+..
T Consensus        12 F~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~----------~~~~~~~~~   81 (213)
T d1l8qa2          12 FIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSA----------DDFAQAMVE   81 (213)
T ss_dssp             CCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEH----------HHHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEech----------HHHHHHHHH
Confidence            345665544  33344444333334458899999999999999999988777666777651          222223332


Q ss_pred             HHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh---HHHH-HHhcCcC-CCCCCCEEEEeccchh---------h
Q 009306          267 TLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP---RQIK-ILVGRLD-LFASGSRIIITTRDRQ---------V  332 (538)
Q Consensus       267 ~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~~~-~l~~~l~-~~~~~~~iiiTtR~~~---------~  332 (538)
                      .+...         ....+.+.+. .--+|+|||++..   ..++ .+...+. ....+..||+||+...         +
T Consensus        82 ~~~~~---------~~~~~~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL  151 (213)
T d1l8qa2          82 HLKKG---------TINEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRL  151 (213)
T ss_dssp             HHHHT---------CHHHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHH
T ss_pred             HHHcc---------chhhHHHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHH
Confidence            22211         1112222232 3358999999643   2222 2222111 1146788999998642         2


Q ss_pred             hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHh
Q 009306          333 LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYA  381 (538)
Q Consensus       333 ~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~  381 (538)
                      ...+....++.++ ++.++-.+++.+++  ........++.+.-+++.+
T Consensus       152 ~SRL~~g~~~~i~-p~d~~~~~iL~~~a--~~rgl~l~~~v~~yl~~~~  197 (213)
T d1l8qa2         152 VSRFEGGILVEIE-LDNKTRFKIIKEKL--KEFNLELRKEVIDYLLENT  197 (213)
T ss_dssp             HHHHHTSEEEECC-CCHHHHHHHHHHHH--HHTTCCCCHHHHHHHHHHC
T ss_pred             HHHhhCceEEEEC-CCcHHHHHHHHHHH--HHcCCCCCHHHHHHHHHhc
Confidence            2223345678886 57788888888777  2223334456666666665

>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=98.61  E-value=3.2e-07  Score=84.11  Aligned_cols=174  Identities=14%  Similarity=0.186  Sum_probs=95.4

Q ss_pred             CCceeccchhHHHHHhhh---c-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          188 EDLVGVRLPMKEIESLLR---T-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~---~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      ++++|-+...++|.+.+.   .       +....+-+.++|++|+|||+||+.++++....    ++..+....      
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~----~~~i~~~~l------   78 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVP----FITASGSDF------   78 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCC----EEEEEHHHH------
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCC----EEEEEhHHh------
Confidence            567888887777665331   1       22334569999999999999999999876433    222211111      


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh----------------HHHHHHhcCcCCCC--C
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP----------------RQIKILVGRLDLFA--S  319 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----------------~~~~~l~~~l~~~~--~  319 (538)
                             .+..     .......+...+...-...|++|+|||++..                ..+..|+..+....  .
T Consensus        79 -------~~~~-----~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~  146 (247)
T d1ixza_          79 -------VEMF-----VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDT  146 (247)
T ss_dssp             -------HHSC-----TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTC
T ss_pred             -------hhcc-----ccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCC
Confidence                   1000     0000111111122222467899999998532                01233333222222  2


Q ss_pred             CCEEEEeccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          320 GSRIIITTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       320 ~~~iiiTtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      +.-||.||.....+ ..+    +....+++++.+.++-.+++...........+   .....+++.+.|..-
T Consensus       147 ~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~---~~~~~la~~t~g~s~  215 (247)
T d1ixza_         147 AIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED---VDLALLAKRTPGFVG  215 (247)
T ss_dssp             CEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTT---CCHHHHHHTCTTCCH
T ss_pred             CEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccc---cCHHHHHHHCCCCCH
Confidence            33334466554322 111    34578999999999999999888733221111   124567777777643

>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=98.61  E-value=2.7e-07  Score=85.47  Aligned_cols=179  Identities=17%  Similarity=0.149  Sum_probs=101.7

Q ss_pred             CCceeccchhHHHHHhhh----c-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLR----T-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~----~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .+++|.++..++|.+.+.    .       +....+-+.++|++|+|||++|+++++.....    ++........... 
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~----~~~i~~~~l~~~~-   78 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF----FFLINGPEIMSKL-   78 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCE----EEEECHHHHTTSC-
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCe----EEEEEchhhcccc-
Confidence            457788888888877532    1       22335669999999999999999999976543    2222121111100 


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH-------------HHHHHhcCc--CCCCCCC
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR-------------QIKILVGRL--DLFASGS  321 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~-------------~~~~l~~~l--~~~~~~~  321 (538)
                      ..                 .............-..+|++|+|||++...             ....+....  ....++.
T Consensus        79 ~g-----------------~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~v  141 (258)
T d1e32a2          79 AG-----------------ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV  141 (258)
T ss_dssp             TT-----------------HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCE
T ss_pred             cc-----------------cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCc
Confidence            00                 001111112222335689999999996420             122222111  1223344


Q ss_pred             EEEEeccchhhhhh-c----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH-HHHH
Q 009306          322 RIIITTRDRQVLAN-C----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA-LEVL  391 (538)
Q Consensus       322 ~iiiTtR~~~~~~~-~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa-l~~~  391 (538)
                      -||.||.....+.. +    +.+..++++..+.++-.++|.....+.....   ......+++.+.|+-.+ |..+
T Consensus       142 lvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~---~~~~~~la~~t~G~s~adl~~l  214 (258)
T d1e32a2         142 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLAD---DVDLEQVANETHGHVGADLAAL  214 (258)
T ss_dssp             EEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCT---TCCHHHHHHHCTTCCHHHHHHH
T ss_pred             cEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCccccc---ccchhhhhhcccCCCHHHHHHH
Confidence            56667766533221 1    3567899999999999999988763221111   11256788999887533 4433

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.60  E-value=4.6e-07  Score=80.86  Aligned_cols=176  Identities=13%  Similarity=0.112  Sum_probs=101.1

Q ss_pred             cchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhc---
Q 009306          194 RLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLN---  270 (538)
Q Consensus       194 ~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~---  270 (538)
                      +...++|...+..+. -...+.++|++|+||||+|+.++..+-..-...        ........+ ...+......   
T Consensus         8 ~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~--------~~~~~~~~~-~~~i~~~~~~~~~   77 (207)
T d1a5ta2           8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQG--------HKSCGHCRG-CQLMQAGTHPDYY   77 (207)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT--------TBCCSCSHH-HHHHHHTCCTTEE
T ss_pred             HHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccc--------cccccccch-hhhhhhccccccc
Confidence            345566666665432 244589999999999999999998653211000        000000000 0000000000   


Q ss_pred             ----CCCCC-CchhhcHHHHHHHh-----cCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccchh-hhhhc-
Q 009306          271 ----DGNVK-NFLNTDLNFQSRRL-----TRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDRQ-VLANC-  336 (538)
Q Consensus       271 ----~~~~~-~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~~-~~~~~-  336 (538)
                          ..... ...++. ..+.+.+     .+++-++|+||++.  ......++..+.....++.+|+||++.. +.+.+ 
T Consensus        78 ~~~~~~~~~~i~~~~i-r~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~  156 (207)
T d1a5ta2          78 TLAPEKGKNTLGVDAV-REVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLR  156 (207)
T ss_dssp             EECCCTTCSSBCHHHH-HHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHH
T ss_pred             hhhhhhcccccccchh-hHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhc
Confidence                00000 111111 1122222     23556999999975  4556677777666667888887777653 33333 


Q ss_pred             CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHH
Q 009306          337 GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLA  387 (538)
Q Consensus       337 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLa  387 (538)
                      .....+.+.+++.++....+....       ...++.+..+++.++|.|-.
T Consensus       157 SRc~~i~~~~~~~~~~~~~L~~~~-------~~~~~~~~~i~~~s~Gs~r~  200 (207)
T d1a5ta2         157 SRCRLHYLAPPPEQYAVTWLSREV-------TMSQDALLAALRLSAGSPGA  200 (207)
T ss_dssp             TTSEEEECCCCCHHHHHHHHHHHC-------CCCHHHHHHHHHHTTTCHHH
T ss_pred             ceeEEEecCCCCHHHHHHHHHHcC-------CCCHHHHHHHHHHcCCCHHH
Confidence            334789999999999999997654       23457788899999999853

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.60  E-value=8.7e-08  Score=88.63  Aligned_cols=188  Identities=16%  Similarity=0.168  Sum_probs=101.6

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---------------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeeh
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---------------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNV  248 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---------------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~  248 (538)
                      |....+++|.+..+++|..++..               +....+.+.|+|++|+||||+|+.+++.+...   .+++. .
T Consensus        10 P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~---~~~~~-~   85 (253)
T d1sxja2          10 PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYD---ILEQN-A   85 (253)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCE---EEEEC-T
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhh---hhccc-c
Confidence            44558899999999999988743               12235679999999999999999999876533   22332 1


Q ss_pred             hhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-----HHHHHHhcCcCCCCCCCEE
Q 009306          249 REAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-----RQIKILVGRLDLFASGSRI  323 (538)
Q Consensus       249 ~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-----~~~~~l~~~l~~~~~~~~i  323 (538)
                         +...... ....................  ..........+..++++|+++..     ..+..+.....  .....+
T Consensus        86 ---~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~--~~~~~i  157 (253)
T d1sxja2          86 ---SDVRSKT-LLNAGVKNALDNMSVVGYFK--HNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR--KTSTPL  157 (253)
T ss_dssp             ---TSCCCHH-HHHHTGGGGTTBCCSTTTTT--C----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHH--HCSSCE
T ss_pred             ---ccchhhH-HHHHHHHHHhhcchhhhhhh--hhhhcccccccceEEEeeeccccccchhhhhHHHhhhhc--cccccc
Confidence               1111111 11221111111110000000  00011112346678899998532     11222222111  122334


Q ss_pred             EEecc--chhhhhh-cCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCc
Q 009306          324 IITTR--DRQVLAN-CGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVP  385 (538)
Q Consensus       324 iiTtR--~~~~~~~-~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~P  385 (538)
                      ++|+.  ....... ......+++.+++.++....+...+-....  ....+....|++.++|..
T Consensus       158 i~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i--~i~~~~l~~i~~~s~GDi  220 (253)
T d1sxja2         158 ILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKF--KLDPNVIDRLIQTTRGDI  220 (253)
T ss_dssp             EEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTC--CCCTTHHHHHHHHTTTCH
T ss_pred             ccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCC--CCCHHHHHHHHHhCCCcH
Confidence            44432  2222222 234568999999999999988876522111  122356788999999976

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.56  E-value=5.2e-07  Score=82.45  Aligned_cols=173  Identities=14%  Similarity=0.174  Sum_probs=101.6

Q ss_pred             CCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHH
Q 009306          185 SENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       185 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      ..-+++||.+..+++|..++..   .....+.+.++||+|+||||+|+.+++.+...+-   .+.    .........+.
T Consensus         6 ~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~---~~~----~~~~~~~~~~~   78 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIH---VTS----GPVLVKQGDMA   78 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEE---EEE----TTTCCSHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCCcc---ccc----CcccccHHHHH
Confidence            3457899999999999988753   1223456889999999999999999998665432   222    11111111111


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH--HHHHHh---cC---------------cCCCCCCC
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR--QIKILV---GR---------------LDLFASGS  321 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--~~~~l~---~~---------------l~~~~~~~  321 (538)
                      . +                    +.  ...++..+++|+++...  .-+.+.   ..               .....+..
T Consensus        79 ~-~--------------------~~--~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (238)
T d1in4a2          79 A-I--------------------LT--SLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPF  135 (238)
T ss_dssp             H-H--------------------HH--HCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCC
T ss_pred             H-H--------------------HH--hhccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCe
Confidence            1 1                    11  12455677888775431  111111   00               00012244


Q ss_pred             EEEEeccch-hhhh--hcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          322 RIIITTRDR-QVLA--NCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       322 ~iiiTtR~~-~~~~--~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      .+|.+|... ....  .......+.++..+.++...++...+  .........+....+++.++|.+-.+.
T Consensus       136 ~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~l~~i~~~s~gd~R~ai  204 (238)
T d1in4a2         136 TLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAA--SLMDVEIEDAAAEMIAKRSRGTPRIAI  204 (238)
T ss_dssp             EEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHH--HHTTCCBCHHHHHHHHHTSTTCHHHHH
T ss_pred             EEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhh--hhccchhhHHHHHHHHHhCCCCHHHHH
Confidence            555555443 2211  22344678899999999999998776  223334556778899999999876543

>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=98.53  E-value=2.4e-07  Score=90.28  Aligned_cols=152  Identities=13%  Similarity=0.154  Sum_probs=88.2

Q ss_pred             CCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc------eeeEEEEeehhhhhhcCChHHHH
Q 009306          188 EDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH------FSGSYFARNVREAEETCRLGDLR  261 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~------f~~~~~~~~~~~~~~~~~~~~l~  261 (538)
                      +.++||+.+++++...|.......  +.|+|++|+|||+|+..++.++...      ....+|..+....-....     
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k~n--~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~-----   94 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTKNN--PVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAK-----   94 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSCCC--CEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-------------
T ss_pred             CCCcCcHHHHHHHHHHHhcCCCCC--CeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccC-----
Confidence            568999999999999997533222  5778999999999999998875432      234566554322111000     


Q ss_pred             HHHHHHHhcCCCCCCchhhcHHHHHHHh-c-CCCeEEEEecCCChH---------H-HHHHhcCcCCCCCCCEEEEeccc
Q 009306          262 QQLLSTLLNDGNVKNFLNTDLNFQSRRL-T-RKKVLIVFDDVDHPR---------Q-IKILVGRLDLFASGSRIIITTRD  329 (538)
Q Consensus       262 ~~l~~~l~~~~~~~~~~~~~~~~l~~~l-~-~k~~LlVlDdv~~~~---------~-~~~l~~~l~~~~~~~~iiiTtR~  329 (538)
                                  .....+.....+...+ . ..+++|++|++...-         + ...|.+.+.  ....++|-+|..
T Consensus        95 ------------~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~  160 (387)
T d1qvra2          95 ------------YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTL  160 (387)
T ss_dssp             ---------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHH--TTCCCEEEEECH
T ss_pred             ------------cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCH
Confidence                        0012222222222223 2 347899999996541         1 223333332  245677777766


Q ss_pred             hhhhhh------cCCCeeEEcCCCCHHHHHHHHHhhh
Q 009306          330 RQVLAN------CGVDEVYQMEELVHDDALRLFSRHA  360 (538)
Q Consensus       330 ~~~~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~  360 (538)
                      ...-..      ....+.+.+++.+.+++..++....
T Consensus       161 ~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         161 DEYREIEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             HHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence            544321      1234678999999999999988654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.52  E-value=6.2e-07  Score=81.96  Aligned_cols=175  Identities=16%  Similarity=0.144  Sum_probs=100.4

Q ss_pred             CCCCCCceeccchhHHHHHhhhc---CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHH
Q 009306          184 HSENEDLVGVRLPMKEIESLLRT---GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDL  260 (538)
Q Consensus       184 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l  260 (538)
                      |..-+++||.+..+++|..++..   .....+-+.++||+|+||||+|+.+++.....|   ....    ..........
T Consensus         5 P~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~---~~~~----~~~~~~~~~~   77 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNL---RVTS----GPAIEKPGDL   77 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCE---EEEE----TTTCCSHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCe---Eecc----CCccccchhh
Confidence            33457899999988988888753   223356688999999999999999998765442   1222    1111111111


Q ss_pred             HHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh--HHHHHHhcCc--------C----------CCCCC
Q 009306          261 RQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP--RQIKILVGRL--------D----------LFASG  320 (538)
Q Consensus       261 ~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~l--------~----------~~~~~  320 (538)
                                           ...+.+. .+.+.++++|+++..  ..-+.+...+        .          ...+.
T Consensus        78 ---------------------~~~~~~~-~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~  135 (239)
T d1ixsb2          78 ---------------------AAILANS-LEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPR  135 (239)
T ss_dssp             ---------------------HHHHHTT-CCTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCC
T ss_pred             ---------------------HHHHHhh-ccCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCC
Confidence                                 1111111 233457778988643  1111111100        0          00223


Q ss_pred             CEEEEec-cchhh--hhhcCCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcHHHH
Q 009306          321 SRIIITT-RDRQV--LANCGVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPLALE  389 (538)
Q Consensus       321 ~~iiiTt-R~~~~--~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~  389 (538)
                      ..++.+| +....  .........+.+...+.++..+++.+.+....  .....+....+++.+.|.+-...
T Consensus       136 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--i~~~~~~l~~ia~~s~gd~R~a~  205 (239)
T d1ixsb2         136 FTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLG--VRITEEAALEIGRRSRGTMRVAK  205 (239)
T ss_dssp             CEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGC--CCBCHHHHHHHHHHTTSSHHHHH
T ss_pred             EEEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhC--CccchHHHHHHHHHcCCCHHHHH
Confidence            3444444 32211  11223456888999999999998887763222  23456788999999999875443

>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=98.48  E-value=3.6e-07  Score=84.16  Aligned_cols=174  Identities=17%  Similarity=0.134  Sum_probs=97.8

Q ss_pred             CCceeccchhHHHHHhhh---c-------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCCh
Q 009306          188 EDLVGVRLPMKEIESLLR---T-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRL  257 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~---~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~  257 (538)
                      .+++|.++..++|.+.+.   .       +....+.+.++|++|+|||++|+.+++.....+   +.+. .......   
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~---~~i~-~~~l~~~---   84 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPF---FTIS-GSDFVEM---   84 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCE---EEEC-SCSSTTS---
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCE---EEEE-hHHhhhc---
Confidence            577888887777765432   1       223356789999999999999999998875432   1222 1110000   


Q ss_pred             HHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCCh-------------H---HHHHHhcCcCCC--CC
Q 009306          258 GDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHP-------------R---QIKILVGRLDLF--AS  319 (538)
Q Consensus       258 ~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-------------~---~~~~l~~~l~~~--~~  319 (538)
                                     ........+...+...-+..|++|+|||+|..             .   .+..++..+...  ..
T Consensus        85 ---------------~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~  149 (256)
T d1lv7a_          85 ---------------FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNE  149 (256)
T ss_dssp             ---------------CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSS
T ss_pred             ---------------chhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCC
Confidence                           00011111222222333568899999998521             1   122333222211  23


Q ss_pred             CCEEEEeccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          320 GSRIIITTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       320 ~~~iiiTtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      +.-||.||.....+ +.+    ..+..+.++..+.++-.++|....-+.....   ......+++.+.|+.-
T Consensus       150 ~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~---~~~~~~la~~t~G~s~  218 (256)
T d1lv7a_         150 GIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAP---DIDAAIIARGTPGFSG  218 (256)
T ss_dssp             CEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCT---TCCHHHHHHTCTTCCH
T ss_pred             CEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCc---ccCHHHHHHhCCCCCH
Confidence            44455577654332 211    3467899999999999999988773322111   1224567778888753

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.44  E-value=3.2e-07  Score=85.24  Aligned_cols=174  Identities=16%  Similarity=0.148  Sum_probs=99.0

Q ss_pred             CCceeccchhHHHHHhhhc-----------CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCC
Q 009306          188 EDLVGVRLPMKEIESLLRT-----------GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCR  256 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~  256 (538)
                      .+++|.+...++|.+.+..           +....+.+.++|++|+|||+||++++......    ++.........   
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~----~~~~~~~~l~~---   79 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN----FISIKGPELLT---   79 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCE----EEEECHHHHHT---
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCc----EEEEEHHHhhh---
Confidence            5678888888777765421           22335679999999999999999999987544    23322111110   


Q ss_pred             hHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCCeEEEEecCCChH----------------HHHHHhcCcCCC--C
Q 009306          257 LGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKKVLIVFDDVDHPR----------------QIKILVGRLDLF--A  318 (538)
Q Consensus       257 ~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----------------~~~~l~~~l~~~--~  318 (538)
                                    . ........+...+...-...|++|+|||++...                .+..++..+...  .
T Consensus        80 --------------~-~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  144 (265)
T d1r7ra3          80 --------------M-WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  144 (265)
T ss_dssp             --------------S-CTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC-----
T ss_pred             --------------c-cccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCC
Confidence                          0 000111111122222334688999999996320                123444444322  2


Q ss_pred             CCCEEEEeccchhhh-hhc----CCCeeEEcCCCCHHHHHHHHHhhhcCCCCCCCchHHHHHHHHHHhcCCcH
Q 009306          319 SGSRIIITTRDRQVL-ANC----GVDEVYQMEELVHDDALRLFSRHAFGGDHPHESHTELACKTIKYARGVPL  386 (538)
Q Consensus       319 ~~~~iiiTtR~~~~~-~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~i~~~~~G~PL  386 (538)
                      .+.-||.||.....+ +.+    .....++++..+.++-.++|....-+.....   ......+++++.|...
T Consensus       145 ~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~---~~~l~~la~~t~g~s~  214 (265)
T d1r7ra3         145 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAK---DVDLEFLAKMTNGFSG  214 (265)
T ss_dssp             -CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-------CCCCHHHHHHHCSSCC
T ss_pred             CCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchh---hhhHHHHHhcCCCCCH
Confidence            345567777655332 111    3456899999999999999987652211111   1123567778877653

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.37  E-value=3.8e-06  Score=76.76  Aligned_cols=51  Identities=16%  Similarity=0.103  Sum_probs=36.4

Q ss_pred             CCceeccchhHHHHHhhh-------c-CCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          188 EDLVGVRLPMKEIESLLR-------T-GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~-------~-~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+||..+.++.+.+-..       . .....+.|.++|++|+|||++|+.+++.....
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~   67 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFP   67 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCS
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhccccc
Confidence            457887776665544322       1 12235678999999999999999999986544

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.47  E-value=0.0003  Score=61.39  Aligned_cols=130  Identities=9%  Similarity=0.052  Sum_probs=76.2

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc---eeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCC
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH---FSGSYFARNVREAEETCRLGDLRQQLLSTLLNDG  272 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~---f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~  272 (538)
                      +++.|..++..+  ....+.++|++|+|||++|..+.+.+...   ++...++...   ...-++..+ +.+...+....
T Consensus         2 ~~~~l~~~i~~~--~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~---~~~I~Id~I-R~i~~~~~~~~   75 (198)
T d2gnoa2           2 QLETLKRIIEKS--EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE---GENIGIDDI-RTIKDFLNYSP   75 (198)
T ss_dssp             HHHHHHHHHHTC--SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS---SSCBCHHHH-HHHHHHHTSCC
T ss_pred             HHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCC---cCCCCHHHH-HHHHHHHhhCc
Confidence            566677777643  56789999999999999999999865332   2334444310   011122222 22333322111


Q ss_pred             CCCCchhhcHHHHHHHhcCCCeEEEEecCCC--hHHHHHHhcCcCCCCCCCEEEEeccch-hhhhhcC-CCeeEEcCCC
Q 009306          273 NVKNFLNTDLNFQSRRLTRKKVLIVFDDVDH--PRQIKILVGRLDLFASGSRIIITTRDR-QVLANCG-VDEVYQMEEL  347 (538)
Q Consensus       273 ~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~l~~~~~~~~iiiTtR~~-~~~~~~~-~~~~~~l~~L  347 (538)
                                      ..+++-++|+|+++.  .....+|+..+...+.++.+|++|.+. .+.+... ....+.+.+.
T Consensus        76 ----------------~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p  138 (198)
T d2gnoa2          76 ----------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP  138 (198)
T ss_dssp             ----------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC
T ss_pred             ----------------ccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc
Confidence                            123445999999974  456677777766556677777666554 3443332 2356667644

>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=97.30  E-value=0.0021  Score=57.90  Aligned_cols=47  Identities=28%  Similarity=0.225  Sum_probs=36.2

Q ss_pred             CceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          189 DLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|||....++++.+.+..-......|.|+|+.|+|||++|+.+...-
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            47888888888888776522223348999999999999999998643

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.20  E-value=0.0019  Score=60.47  Aligned_cols=49  Identities=14%  Similarity=0.209  Sum_probs=35.8

Q ss_pred             CCceeccchhHHHHHhhhc-------CCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          188 EDLVGVRLPMKEIESLLRT-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       188 ~~~vGR~~~l~~l~~~L~~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..++|.+..++.+...+..       ......++.++|++|+|||.||+.++..+.
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc
Confidence            4577888777777654421       122245788999999999999999998764

>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=97.18  E-value=0.00015  Score=61.86  Aligned_cols=36  Identities=17%  Similarity=0.151  Sum_probs=28.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccce-eeEEEE
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHF-SGSYFA  245 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~~~~~  245 (538)
                      ...+|.|+|++|+||||+|+.++.++...| ....+.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~~~~~~~~~   41 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLL   41 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcCCCchhhh
Confidence            456899999999999999999999886554 334443

>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=97.13  E-value=0.00011  Score=63.08  Aligned_cols=26  Identities=15%  Similarity=0.235  Sum_probs=23.5

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++.|+|.|++|+||||||+.++.++.
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            57799999999999999999998764

>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=97.12  E-value=0.00023  Score=66.84  Aligned_cols=26  Identities=27%  Similarity=0.336  Sum_probs=22.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +.+.++||+|+|||.||+++++....
T Consensus        50 ~~iLl~GPpG~GKT~lAkalA~~~~~   75 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIARRLAKLANA   75 (309)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             ceEEEECCCCCCHHHHHHHHhhcccc
Confidence            45789999999999999999987643

>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=97.11  E-value=0.0001  Score=61.91  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +.|.|+|++|+||||+|+.++.++.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            3588999999999999999999864

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.07  E-value=0.00067  Score=60.97  Aligned_cols=48  Identities=13%  Similarity=0.123  Sum_probs=39.1

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .|.+.|..+-+...++.|+|++|+|||+||.+++.....+...++|+.
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            456666655556778999999999999999999998877777777776

>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=97.02  E-value=0.00017  Score=61.07  Aligned_cols=25  Identities=24%  Similarity=0.308  Sum_probs=22.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|.|+|++|+||||+|+.++..+.
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            5799999999999999999987754

>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=97.00  E-value=0.00034  Score=60.66  Aligned_cols=38  Identities=24%  Similarity=0.276  Sum_probs=29.0

Q ss_pred             CCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEE
Q 009306          207 GSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYF  244 (538)
Q Consensus       207 ~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~  244 (538)
                      +..+.-+|+|.|++|+||||||+.+...+.........
T Consensus        18 ~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~   55 (198)
T d1rz3a_          18 KTAGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCV   55 (198)
T ss_dssp             CCSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             cCCCCEEEEEECCCCCCHHHHHHHHHHHhcccccccee
Confidence            34456689999999999999999999877655433333

>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=96.99  E-value=0.00021  Score=60.33  Aligned_cols=28  Identities=21%  Similarity=0.302  Sum_probs=24.8

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .++++|+|.+|+|||||+..+..++..+
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            3689999999999999999999887655

>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=96.96  E-value=0.00015  Score=62.93  Aligned_cols=37  Identities=24%  Similarity=0.237  Sum_probs=29.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ...+|.|+|++|+||||+|+.++.++...+....++.
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~~~~~~~~~~   54 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   54 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCCccchh
Confidence            3567889999999999999999998776655555543

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.94  E-value=0.00022  Score=60.65  Aligned_cols=28  Identities=14%  Similarity=0.146  Sum_probs=24.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .++|.|+|++|+||||+|+.+++++...
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~   30 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEP   30 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            4689999999999999999999987543

>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=96.94  E-value=0.00023  Score=58.98  Aligned_cols=24  Identities=29%  Similarity=0.224  Sum_probs=20.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ++|.|+|++|+||||||+++....
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

>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=96.92  E-value=0.00021  Score=60.52  Aligned_cols=24  Identities=29%  Similarity=0.457  Sum_probs=21.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|+|+|++|+||||+|+.++.++.
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478999999999999999998764

>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=96.91  E-value=0.00017  Score=61.76  Aligned_cols=27  Identities=22%  Similarity=0.247  Sum_probs=23.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +.|.|+|++|+|||||+++++..+...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            458999999999999999999876544

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.86  E-value=0.00034  Score=59.16  Aligned_cols=28  Identities=18%  Similarity=0.393  Sum_probs=24.7

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ...+++.|+|++|+||||+|+.++.++.
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            3578899999999999999999998764

>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=96.84  E-value=0.0012  Score=57.50  Aligned_cols=38  Identities=21%  Similarity=0.389  Sum_probs=29.0

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      .+...++.++|+.|+||||.+.+++.+++..-..+..+
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   43 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA   43 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            34567899999999999999999998876554444444

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.80  E-value=0.00043  Score=63.39  Aligned_cols=29  Identities=28%  Similarity=0.378  Sum_probs=25.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      ..+.|.++|++|+||||||+.++..+...
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~~~~   59 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEETQGN   59 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTTTC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhhcc
Confidence            45678999999999999999999987544

>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=96.77  E-value=0.0012  Score=61.80  Aligned_cols=48  Identities=19%  Similarity=0.329  Sum_probs=32.2

Q ss_pred             CceeccchhHHHHHhhhc-------CCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          189 DLVGVRLPMKEIESLLRT-------GSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       189 ~~vGR~~~l~~l~~~L~~-------~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++|.+..++.+...+..       ......++.++|++|+|||.||+.+++.+-
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~   78 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF   78 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhc
Confidence            355666666555443321       111234688999999999999999998763

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.00075  Score=61.40  Aligned_cols=49  Identities=20%  Similarity=0.190  Sum_probs=37.5

Q ss_pred             HHHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          198 KEIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       198 ~~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..|..+|. .+-+..+++-|+|++|+||||||.+++......-..++|++
T Consensus        40 ~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyid   89 (263)
T d1u94a1          40 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   89 (263)
T ss_dssp             HHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEc
Confidence            35555664 33345678999999999999999999987766666678876

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.71  E-value=0.00039  Score=58.95  Aligned_cols=27  Identities=37%  Similarity=0.274  Sum_probs=23.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +.++|.|.|++|+||||+|+.++.++.
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~lg   29 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLPG   29 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCSS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999987653

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.68  E-value=0.00048  Score=58.98  Aligned_cols=28  Identities=18%  Similarity=0.302  Sum_probs=24.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ++|+|.|++|+||||+++.++.++....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~~   29 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKEG   29 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            5899999999999999999999876554

>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=96.66  E-value=0.0012  Score=57.71  Aligned_cols=39  Identities=21%  Similarity=0.289  Sum_probs=30.1

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      .....++.++|+.|+||||.+.+++.++..+...+..+.
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit   46 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA   46 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEe
Confidence            345678999999999999998888887765555555554

>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=96.66  E-value=0.00065  Score=57.77  Aligned_cols=25  Identities=32%  Similarity=0.550  Sum_probs=22.5

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      |+|+|++|+|||||++.++..+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~~   27 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCCC
Confidence            7999999999999999999877654

>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=96.66  E-value=0.0029  Score=57.45  Aligned_cols=95  Identities=19%  Similarity=0.167  Sum_probs=58.4

Q ss_pred             HHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC---
Q 009306          199 EIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV---  274 (538)
Q Consensus       199 ~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~---  274 (538)
                      .|...|. .+-+..+++-|+|++|+||||||..++......-..++|++.    ...... +.++++    +...+.   
T Consensus        47 ~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDt----E~~~~~-e~a~~~----GvD~d~il~  117 (269)
T d1mo6a1          47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDA----EHALDP-DYAKKL----GVDTDSLLV  117 (269)
T ss_dssp             HHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEES----SCCCCH-HHHHHH----TCCGGGCEE
T ss_pred             HHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEEC----CccCCH-HHHHHh----CCCHHHeEE
Confidence            4555664 455667899999999999999999888765555566788772    222222 223333    322111   


Q ss_pred             --CCchhhcHHHHHHHhc-CCCeEEEEecCC
Q 009306          275 --KNFLNTDLNFQSRRLT-RKKVLIVFDDVD  302 (538)
Q Consensus       275 --~~~~~~~~~~l~~~l~-~k~~LlVlDdv~  302 (538)
                        ....++..+.+..... ++.-|||+|.+.
T Consensus       118 ~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         118 SQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             ECCSSHHHHHHHHHHHHHTTCEEEEEEECST
T ss_pred             ecCCCHHHHHHHHHHHHhcCCCCEEEEeccc
Confidence              1344555555444443 446789999884

>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=96.61  E-value=0.00058  Score=57.76  Aligned_cols=27  Identities=30%  Similarity=0.372  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..-.|.|+|++|+||||+|+.+++++.
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            344589999999999999999998753

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.60  E-value=0.00051  Score=57.92  Aligned_cols=25  Identities=24%  Similarity=0.344  Sum_probs=21.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      |.+.|++|+||||+++.++.++.-.
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~   28 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVG   28 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCC
Confidence            5566999999999999999987544

>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=96.60  E-value=0.0031  Score=54.80  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=29.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.+++.++|+.|+||||.+.+++..+..+-..+.++.
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            4678999999999999999989887765545555554

>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=96.57  E-value=0.0017  Score=60.37  Aligned_cols=27  Identities=22%  Similarity=0.229  Sum_probs=22.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .++.++|++|+|||.||+.++.++..+
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~  150 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGK  150 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTT
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCC
Confidence            346679999999999999999987644

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.55  E-value=0.00058  Score=57.34  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=20.9

Q ss_pred             EEEeccCCCchhHHHHHHHHhhc
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      |.|.||+|+||||+++.++.++.
T Consensus         3 I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            77889999999999999999874

>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=96.55  E-value=0.0027  Score=57.66  Aligned_cols=94  Identities=18%  Similarity=0.102  Sum_probs=56.8

Q ss_pred             HHHHhhh-cCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC---
Q 009306          199 EIESLLR-TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV---  274 (538)
Q Consensus       199 ~l~~~L~-~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~---  274 (538)
                      .|..+|. .+-+..+++-|+|++|+|||+||..++......-..++|++.-    ..... .    .+..++-..+.   
T Consensus        44 ~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE----~~~~~-~----~a~~~Gvd~d~i~~  114 (268)
T d1xp8a1          44 SLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE----HALDP-V----YARALGVNTDELLV  114 (268)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS----CCCCH-H----HHHHTTCCGGGCEE
T ss_pred             HHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECC----ccCCH-H----HHHHhCCCchhEEE
Confidence            4555554 3335577899999999999999999988755544567777622    22222 2    23333332211   


Q ss_pred             --CCchhhcHHHHHHHhcC-CCeEEEEecC
Q 009306          275 --KNFLNTDLNFQSRRLTR-KKVLIVFDDV  301 (538)
Q Consensus       275 --~~~~~~~~~~l~~~l~~-k~~LlVlDdv  301 (538)
                        ..+.++..+.+...... ..-|||+|-+
T Consensus       115 ~~~~~~E~~~~~~~~l~~~~~~~liIiDSi  144 (268)
T d1xp8a1         115 SQPDNGEQALEIMELLVRSGAIDVVVVDSV  144 (268)
T ss_dssp             ECCSSHHHHHHHHHHHHTTTCCSEEEEECT
T ss_pred             EcCCCHHHHHHHHHHHHhcCCCcEEEEecc
Confidence              13455555555554433 4678999987

>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=96.54  E-value=0.0015  Score=57.06  Aligned_cols=38  Identities=21%  Similarity=0.197  Sum_probs=25.1

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ....++.++|+.|+||||.+.+++.+++..-..+..+.
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            35778999999999999998888887765544455544

>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=96.53  E-value=0.00081  Score=58.35  Aligned_cols=27  Identities=22%  Similarity=0.235  Sum_probs=24.3

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +..++|+|.|++|+||||+|+.+++++
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            467899999999999999999998875

>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=96.53  E-value=0.00075  Score=56.80  Aligned_cols=29  Identities=21%  Similarity=0.064  Sum_probs=25.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      ++++|+|..|+|||||+..+..+++.+..
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~g~   30 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVREGW   30 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTC
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhCCC
Confidence            57899999999999999999998876643

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.52  E-value=0.00053  Score=58.12  Aligned_cols=24  Identities=21%  Similarity=0.329  Sum_probs=21.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|.|.|++|+||||+|+.+++++.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            377889999999999999998874

>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=96.51  E-value=0.00079  Score=58.30  Aligned_cols=27  Identities=22%  Similarity=0.219  Sum_probs=23.6

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..+.+|.|.|++|+||||+|+.+++.+
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            356789999999999999999998765

>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=96.39  E-value=0.0023  Score=57.72  Aligned_cols=25  Identities=32%  Similarity=0.328  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|+|+.|+|||||++.+..-
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl   64 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRF   64 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcc
Confidence            3457999999999999999988763

>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=96.37  E-value=0.0012  Score=56.51  Aligned_cols=34  Identities=18%  Similarity=0.167  Sum_probs=26.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      +++.|.|++|+||||+++.++.++....-....+
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~   35 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            5789999999999999999999886553333333

>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=96.29  E-value=0.00096  Score=56.61  Aligned_cols=26  Identities=23%  Similarity=0.198  Sum_probs=22.3

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHh
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +...+|.++|++|+||||+|+.++..
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            35678999999999999999988764

>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=96.25  E-value=0.0027  Score=56.70  Aligned_cols=25  Identities=32%  Similarity=0.336  Sum_probs=21.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...++|+|+.|+|||||++.+..-+
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcC
Confidence            4569999999999999999888643

>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=96.25  E-value=0.0014  Score=57.21  Aligned_cols=27  Identities=19%  Similarity=0.155  Sum_probs=23.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+|.++|.+|+||||+|++++..+...
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~~~   29 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            468999999999999999999876543

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.25  E-value=0.0088  Score=52.67  Aligned_cols=24  Identities=29%  Similarity=0.248  Sum_probs=20.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...+++|.|++|+|||||.+.++.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCcchhhHhccC
Confidence            345799999999999999997765

>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=96.24  E-value=0.0013  Score=57.56  Aligned_cols=38  Identities=18%  Similarity=0.234  Sum_probs=28.7

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccce-eeEEEEe
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHF-SGSYFAR  246 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f-~~~~~~~  246 (538)
                      ....+|.|+|++|+||||||+++..++...+ ...+++.
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   60 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEc
Confidence            3567899999999999999999998765433 2344443

>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=96.24  E-value=0.0011  Score=56.99  Aligned_cols=31  Identities=29%  Similarity=0.393  Sum_probs=25.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGS  242 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~  242 (538)
                      +.|+|+|++|+|||||++.++.+....|..+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~~~~   32 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSFGFS   32 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEEEC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcceeEE
Confidence            4589999999999999999998877666433

>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=96.22  E-value=0.0058  Score=53.06  Aligned_cols=37  Identities=19%  Similarity=0.100  Sum_probs=29.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.+++.++|++|+||||.+.+++.+++.+...+..+.
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            4578999999999999999999988776644455544

>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=96.12  E-value=0.0014  Score=57.54  Aligned_cols=27  Identities=19%  Similarity=0.458  Sum_probs=23.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      -+|+|.|++|+||||+|+.+...+...
T Consensus         3 ~iIgI~G~~gSGKSTla~~L~~~l~~~   29 (213)
T d1uj2a_           3 FLIGVSGGTASGKSSVCAKIVQLLGQN   29 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhchh
Confidence            479999999999999999999876543

>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=96.08  E-value=0.0015  Score=57.62  Aligned_cols=26  Identities=27%  Similarity=0.328  Sum_probs=23.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .++|+|-||+|+||||+|+.+++++.
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~g   28 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQ   28 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35899999999999999999998863

>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=96.06  E-value=0.0013  Score=56.74  Aligned_cols=28  Identities=29%  Similarity=0.456  Sum_probs=24.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      .|+|.||+|+|||||++.++......|.
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~~   29 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIFG   29 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCcee
Confidence            4889999999999999999988766554

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.05  E-value=0.009  Score=54.51  Aligned_cols=26  Identities=31%  Similarity=0.360  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ....++|+|+.|+|||||++.++..+
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            44579999999999999999998744

>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=95.94  E-value=0.002  Score=55.59  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=21.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+|.|.|++|+||||+|+.+++.+
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            468999999999999999999865

>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=95.88  E-value=0.0019  Score=55.05  Aligned_cols=31  Identities=23%  Similarity=0.418  Sum_probs=25.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGS  242 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~  242 (538)
                      ++|+|+||+|+|||||++.+..+....|..+
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            5699999999999999999998776666533

>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=95.85  E-value=0.0077  Score=58.20  Aligned_cols=114  Identities=11%  Similarity=0.055  Sum_probs=65.9

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCC
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNV  274 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~  274 (538)
                      ..++.+.+++..   ...+|.|+|+.|+||||....+.+.+......++-+.+.-+    ..+...        ......
T Consensus       145 ~~~~~l~~l~~~---~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE----~~~~~~--------~q~~v~  209 (401)
T d1p9ra_         145 HNHDNFRRLIKR---PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIE----FDIDGI--------GQTQVN  209 (401)
T ss_dssp             HHHHHHHHHHTS---SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCC----SCCSSS--------EEEECB
T ss_pred             HHHHHHHHHHhh---hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcc----cccCCC--------Ceeeec
Confidence            344555666542   45689999999999999999999876443233333332111    100000        000000


Q ss_pred             CCchhhcHHHHHHHhcCCCeEEEEecCCChHHHHHHhcCcCCCCCCCEEEEec
Q 009306          275 KNFLNTDLNFQSRRLTRKKVLIVFDDVDHPRQIKILVGRLDLFASGSRIIITT  327 (538)
Q Consensus       275 ~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~l~~~~~~~~iiiTt  327 (538)
                      ..........++..++..|=+|++.++.+.+........    ...++.++||
T Consensus       210 ~~~~~~~~~~l~~~lR~dPDvi~igEiRd~~ta~~a~~a----a~tGhlV~tT  258 (401)
T d1p9ra_         210 PRVDMTFARGLRAILRQDPDVVMVGEIRDLETAQIAVQA----SLTGHLVMST  258 (401)
T ss_dssp             GGGTBCHHHHHHHHGGGCCSEEEESCCCSHHHHHHHHHH----HHTTCEEEEE
T ss_pred             CCcCCCHHHHHHHHHhhcCCEEEecCcCChHHHHHHHHH----HhcCCeEEEE
Confidence            111223456677888889999999999988776555433    1234455555

>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=95.81  E-value=0.0023  Score=54.44  Aligned_cols=22  Identities=36%  Similarity=0.445  Sum_probs=20.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |.|.|++|+||||+|+.++.++
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            7899999999999999998875

>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=95.81  E-value=0.0044  Score=57.97  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=32.9

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEEe
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFAR  246 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~~  246 (538)
                      ++.+.+........+|+|+|++|.|||||...+...+... +...+-..
T Consensus        39 ~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViav   87 (323)
T d2qm8a1          39 DLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAV   87 (323)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeec
Confidence            3333333344567889999999999999999999876543 33333333

>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=95.77  E-value=0.0024  Score=54.86  Aligned_cols=23  Identities=35%  Similarity=0.242  Sum_probs=20.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|.|.|++|+||||+|+.+++++
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999998876

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=95.75  E-value=0.0034  Score=59.78  Aligned_cols=33  Identities=21%  Similarity=0.079  Sum_probs=27.8

Q ss_pred             cCCCCceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          206 TGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       206 ~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+.+..+.+.++||+|+|||++|+.+++.+...
T Consensus       149 ~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~  181 (362)
T d1svma_         149 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGK  181 (362)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCE
T ss_pred             hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            355667789999999999999999999987643

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.75  E-value=0.0046  Score=56.56  Aligned_cols=49  Identities=20%  Similarity=0.249  Sum_probs=36.0

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++..+.+.+..  ++.++|.++|-||+||||++..++..+......+..+.
T Consensus         7 ~~~~~~~~~~~--~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD   55 (279)
T d1ihua2           7 SLSALVDDIAR--NEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTT   55 (279)
T ss_dssp             CHHHHHHHHHT--TSCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cHHHHHHHhhc--CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            45556666653  46789999999999999999999887766544444444

>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=95.75  E-value=0.0032  Score=56.67  Aligned_cols=24  Identities=25%  Similarity=0.317  Sum_probs=20.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ....++|+|+.|+|||||++.+..
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHh
Confidence            345799999999999999998765

>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=95.74  E-value=0.0026  Score=54.94  Aligned_cols=26  Identities=27%  Similarity=0.193  Sum_probs=23.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..++|.|.|++|+||||+|+.+++++
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            45689999999999999999998865

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.72  E-value=0.0048  Score=55.34  Aligned_cols=38  Identities=24%  Similarity=0.318  Sum_probs=30.5

Q ss_pred             HHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          199 EIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       199 ~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .|..+|..+-+..+++.|+|++|+|||++|.+++....
T Consensus        24 ~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          24 SLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             HHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             HHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            45556655556678999999999999999999987654

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=95.70  E-value=0.0034  Score=53.90  Aligned_cols=25  Identities=28%  Similarity=0.355  Sum_probs=20.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.++| |.|++|+||||+|+.++.++
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            45555 68999999999999999875

>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=95.70  E-value=0.0048  Score=57.76  Aligned_cols=33  Identities=30%  Similarity=0.319  Sum_probs=27.6

Q ss_pred             CCCceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          208 STNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       208 ~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      .++..+|+|+|++|+|||||...+...+.....
T Consensus        51 ~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~   83 (327)
T d2p67a1          51 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGL   83 (327)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTC
T ss_pred             cCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCC
Confidence            346788999999999999999999987766543

>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=95.67  E-value=0.003  Score=55.70  Aligned_cols=24  Identities=29%  Similarity=0.397  Sum_probs=21.4

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      +|+|-|++|+||||+|+.++.++.
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg   28 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFG   28 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999998763

>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=95.66  E-value=0.0026  Score=54.18  Aligned_cols=22  Identities=32%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |+|.|++|+||||+|+.+++.+
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7888999999999999999876

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.65  E-value=0.0026  Score=54.70  Aligned_cols=23  Identities=30%  Similarity=0.485  Sum_probs=20.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .|.|.|++|+||||+|+.++.++
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHB
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            36677999999999999999875

>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=95.60  E-value=0.0028  Score=54.04  Aligned_cols=22  Identities=36%  Similarity=0.510  Sum_probs=20.3

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |.|.|++|+||||+|+.++.++
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7789999999999999999876

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=95.59  E-value=0.0042  Score=56.53  Aligned_cols=35  Identities=23%  Similarity=0.348  Sum_probs=28.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.|+|+|-||+||||+|..++..+......+..++
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID   36 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVG   36 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            57899999999999999999998877644455554

>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=95.56  E-value=0.0032  Score=55.09  Aligned_cols=40  Identities=25%  Similarity=0.261  Sum_probs=30.1

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      ..|..+|..+-....++.|.|++|+|||+||.+++.....
T Consensus        10 ~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~~~   49 (242)
T d1n0wa_          10 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQL   49 (242)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTS
T ss_pred             HHHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            3455566544345678999999999999999999876443

>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=95.51  E-value=0.026  Score=51.29  Aligned_cols=31  Identities=19%  Similarity=0.240  Sum_probs=25.5

Q ss_pred             CCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          209 TNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       209 ~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ...-+|+|.|..|+|||||+..+...+...+
T Consensus        25 ~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~   55 (286)
T d1odfa_          25 KCPLFIFFSGPQGSGKSFTSIQIYNHLMEKY   55 (286)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeECCCCCCHHHHHHHHHHHHHHHh
Confidence            3455889999999999999999988765543

>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=95.48  E-value=0.0038  Score=53.20  Aligned_cols=25  Identities=20%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ++|+|+||+|+|||||++.+..+..
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            5789999999999999999988764

>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=95.38  E-value=0.0041  Score=52.86  Aligned_cols=22  Identities=27%  Similarity=0.354  Sum_probs=19.5

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |.|.|++|+||||+|+.++.++
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5577999999999999999875

>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=95.35  E-value=0.027  Score=51.76  Aligned_cols=39  Identities=31%  Similarity=0.336  Sum_probs=29.1

Q ss_pred             HHhhhcC-CCCceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          201 ESLLRTG-STNVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       201 ~~~L~~~-~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      ...|... ....-+|+|.|.+|+||||+|+.+...+...+
T Consensus        69 ~~fl~~~~~k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~  108 (308)
T d1sq5a_          69 EQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWP  108 (308)
T ss_dssp             HHHHTCC-CCCCEEEEEEECTTSSHHHHHHHHHHHHTTST
T ss_pred             HHHhcccCCCCCEEEEEeCCCCCCCcHHHHHHHHHHhhhc
Confidence            3344432 23467899999999999999999998876543

>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=95.34  E-value=0.0043  Score=52.60  Aligned_cols=22  Identities=32%  Similarity=0.273  Sum_probs=19.9

Q ss_pred             EEEeccCCCchhHHHHHHHHhh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      |+|.|++|+||||+|+.+++++
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999998775

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.25  E-value=0.0073  Score=54.08  Aligned_cols=38  Identities=21%  Similarity=0.265  Sum_probs=30.8

Q ss_pred             HHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          198 KEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       198 ~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..|.++|..+-+...++.|+|++|+|||++|.+++...
T Consensus        24 ~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          24 QEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             HHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             HHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            34556666666678899999999999999999998753

>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=95.24  E-value=0.0065  Score=55.94  Aligned_cols=37  Identities=24%  Similarity=0.217  Sum_probs=30.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ..+++.++|-||+||||+|..++..+..+...+..++
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD   43 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS   43 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEe
Confidence            4678889999999999999999998877655555554

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.23  E-value=0.0041  Score=55.13  Aligned_cols=51  Identities=16%  Similarity=0.151  Sum_probs=34.6

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhcccee-eEEEEe
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKISRHFS-GSYFAR  246 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~-~~~~~~  246 (538)
                      -+..|.++|..+-+...++.|+|++|+|||+||.+++......-. .+.|+.
T Consensus        11 Gi~~LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          11 MIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             CCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            344566666655456678999999999999999987765333322 344444

>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=95.21  E-value=0.029  Score=48.67  Aligned_cols=35  Identities=11%  Similarity=0.076  Sum_probs=27.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      ..+|+|.|+-|+||||+++.+.+.+..+...+.+.
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            35789999999999999999999876654334443

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.20  E-value=0.012  Score=55.89  Aligned_cols=36  Identities=22%  Similarity=0.132  Sum_probs=25.1

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      .+...+...+.     .++..|+|++|.||||++..+...+
T Consensus       152 ~Q~~A~~~al~-----~~~~vI~G~pGTGKTt~i~~~l~~l  187 (359)
T d1w36d1         152 WQKVAAAVALT-----RRISVISGGPGTGKTTTVAKLLAAL  187 (359)
T ss_dssp             HHHHHHHHHHT-----BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc-----CCeEEEEcCCCCCceehHHHHHHHH
Confidence            34444554442     3579999999999999887665443

>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=95.10  E-value=0.0043  Score=55.33  Aligned_cols=38  Identities=18%  Similarity=0.246  Sum_probs=30.0

Q ss_pred             hHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          197 MKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       197 l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +..|..+|..+-+..+++.|+|++|+||||||.+++..
T Consensus        20 i~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          20 SKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             CHHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CHHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            34556666655556779999999999999999998764

>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=95.06  E-value=0.0053  Score=55.97  Aligned_cols=29  Identities=17%  Similarity=0.243  Sum_probs=22.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +.++|+|+|.+|+||||+++.+.+.+...
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~~   31 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRRE   31 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhhc
Confidence            45689999999999999999998877544

>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=95.05  E-value=0.006  Score=54.39  Aligned_cols=41  Identities=24%  Similarity=0.261  Sum_probs=31.3

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      -+..|.++|..+-....++.|.|++|+|||++|.+++....
T Consensus        19 G~~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          19 SSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             SCHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCHHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            34455666654445578899999999999999999997654

>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=94.94  E-value=0.022  Score=51.30  Aligned_cols=52  Identities=33%  Similarity=0.506  Sum_probs=32.9

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLS  266 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~  266 (538)
                      +.++|.|.+|+|||+|+..++..... +-+.++|+- +.+  ......++.+.+..
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~-iGe--r~~ev~~~~~~~~~  121 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG-VGE--RTREGNDLYHEMIE  121 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEE-ESC--CHHHHHHHHHHHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEEE-ecc--ChHHHHHHHHHHHh
Confidence            34999999999999999999887443 333445543 222  12234455555554

>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=94.85  E-value=0.0067  Score=51.94  Aligned_cols=22  Identities=36%  Similarity=0.419  Sum_probs=19.0

Q ss_pred             ceEEEEeccCCCchhHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      .-+|+|+|+.|+||||+|..+.
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            3478999999999999998764

>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=94.69  E-value=0.0072  Score=56.88  Aligned_cols=47  Identities=17%  Similarity=0.093  Sum_probs=32.5

Q ss_pred             CCCCceeccchhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          186 ENEDLVGVRLPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       186 ~~~~~vGR~~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +....+|.+.....|.-.+-..  +..-+.|.|++|+||||||+.+..-
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~--~~h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhcc--CCCeEEEECCCCccHHHHHHHHHHh
Confidence            3467899987666554322211  1123899999999999999999863

>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=94.61  E-value=0.011  Score=52.54  Aligned_cols=27  Identities=26%  Similarity=0.420  Sum_probs=22.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccce
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +++|.|+.|.|||||...+.+......
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~~~   28 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLEDNY   28 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTTTS
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhCC
Confidence            689999999999999999987654443

>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=94.59  E-value=0.011  Score=54.23  Aligned_cols=35  Identities=23%  Similarity=0.372  Sum_probs=27.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.|+|+|-||+||||+|..++..+......+.-++
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID   37 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVG   37 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            46788999999999999999988776644455444

>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=94.58  E-value=0.0075  Score=52.12  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|+|||||.+.++.-+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            34569999999999999999998744

>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=94.35  E-value=0.029  Score=48.87  Aligned_cols=30  Identities=23%  Similarity=0.293  Sum_probs=26.0

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhccce
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISRHF  239 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~~f  239 (538)
                      +.+.|+|-|+-|+||||+++.+.+++..++
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L~~~~   31 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKLQPNC   31 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHTTTSE
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHHHhCC
Confidence            356799999999999999999999887654

>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=94.33  E-value=0.011  Score=51.20  Aligned_cols=25  Identities=16%  Similarity=0.212  Sum_probs=22.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+++|+||+|+|||||.+.+..+..
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            5789999999999999999988764

>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=94.20  E-value=0.044  Score=50.87  Aligned_cols=87  Identities=14%  Similarity=0.025  Sum_probs=51.6

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhhcCChHHHHHHHHHHHhcCCCCCCchhhcHHHHHHHhcCCC
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEETCRLGDLRQQLLSTLLNDGNVKNFLNTDLNFQSRRLTRKK  293 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~k~  293 (538)
                      +.|+|+.|+||||+.++++..+..... .+-+.+..+.......         .....  .....-.....++..++..+
T Consensus       169 ili~G~tgSGKTT~l~al~~~i~~~~r-ivtiEd~~El~l~~~~---------~~~~~--~~~~~~~~~~ll~~~lR~~p  236 (323)
T d1g6oa_         169 VIVCGGTGSGKTTYIKSIMEFIPKEER-IISIEDTEEIVFKHHK---------NYTQL--FFGGNITSADCLKSCLRMRP  236 (323)
T ss_dssp             EEEEESTTSSHHHHHHHHGGGSCTTCC-EEEEESSCCCCCSSCS---------SEEEE--ECBTTBCHHHHHHHHTTSCC
T ss_pred             EEEEeeccccchHHHHHHhhhcccccc-eeeccchhhhhccccc---------cccee--ccccchhHHHHHHHHhccCC
Confidence            899999999999999999987655432 3333322221100000         00000  00011123456677788889


Q ss_pred             eEEEEecCCChHHHHHHhc
Q 009306          294 VLIVFDDVDHPRQIKILVG  312 (538)
Q Consensus       294 ~LlVlDdv~~~~~~~~l~~  312 (538)
                      =.||+.++.+.+.+..+..
T Consensus       237 d~iivgEiR~~ea~~~l~a  255 (323)
T d1g6oa_         237 DRIILGELRSSEAYDFYNV  255 (323)
T ss_dssp             SEEEESCCCSTHHHHHHHH
T ss_pred             CcccCCccCchhHHHHHHH
Confidence            9999999988777765543

>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=94.18  E-value=0.01  Score=50.97  Aligned_cols=26  Identities=27%  Similarity=0.150  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..-+|+|-|.-|+||||+++.+.+.+
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            45589999999999999999887665

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.77  E-value=0.022  Score=53.95  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=21.4

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+...||.|+|||.||+.++...
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcceeeeCCCCccHHHHHHHHHhhc
Confidence            3448888999999999999998764

>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=93.77  E-value=0.13  Score=46.04  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=21.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .+..|+|++|+|||||+.+++..+.
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            4688999999999999999887654

>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=93.76  E-value=0.021  Score=49.27  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=23.1

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccc
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      +|+|-|+-|+||||+++.+.+.+..+
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            48899999999999999999887654

>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=93.74  E-value=0.024  Score=49.97  Aligned_cols=25  Identities=32%  Similarity=0.227  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.+..-
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl   55 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGL   55 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            3457999999999999999988864

>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=93.74  E-value=0.017  Score=50.84  Aligned_cols=24  Identities=25%  Similarity=0.199  Sum_probs=21.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...+++|.|+.|+|||||.+.++-
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            345799999999999999998876

>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=93.73  E-value=0.023  Score=49.95  Aligned_cols=35  Identities=23%  Similarity=0.262  Sum_probs=28.4

Q ss_pred             eEEEEe-ccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIW-GIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~-G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|+|+ |-||+||||+|..++..++.....+..+.
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            577777 78999999999999998877655666665

>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=93.71  E-value=0.023  Score=50.21  Aligned_cols=24  Identities=29%  Similarity=0.173  Sum_probs=21.2

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        29 Ge~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          29 GEFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcC
Confidence            457999999999999999999863

>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=93.61  E-value=0.015  Score=51.44  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|++|+|||||++.++--
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl   54 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLL   54 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCC
Confidence            3457999999999999999988763

>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=93.57  E-value=0.12  Score=46.39  Aligned_cols=54  Identities=11%  Similarity=-0.042  Sum_probs=34.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc-ceeeEEEEeehhhhhhcCChHHHHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR-HFSGSYFARNVREAEETCRLGDLRQQLLSTLL  269 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~-~f~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~  269 (538)
                      ...++.|.|.+|+|||+++.+++..+.. +-..++|+..      ......+...++....
T Consensus        34 ~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~------E~~~~~~~~r~~~~~~   88 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML------EESVEETAEDLIGLHN   88 (277)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES------SSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee------ccchhhHHhHHHHHhh
Confidence            4567899999999999999999876542 2233444441      2334445555554443

>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=93.52  E-value=0.023  Score=50.39  Aligned_cols=28  Identities=21%  Similarity=0.248  Sum_probs=24.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      +++.|+|-|+-|+||||+++.+.+.+..
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            3578999999999999999999987654

>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=93.49  E-value=0.023  Score=50.73  Aligned_cols=25  Identities=28%  Similarity=0.275  Sum_probs=21.6

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ....++|+|+.|+|||||++.+..-
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcc
Confidence            4457999999999999999988764

>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=93.45  E-value=0.027  Score=49.62  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.5

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +++|.|+.|+|||||.+.++.-.
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCChHHHHHHHHHcCC
Confidence            68899999999999999998744

>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=93.44  E-value=0.018  Score=51.14  Aligned_cols=24  Identities=25%  Similarity=0.196  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ....++|+|+.|+|||||++.+..
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            456799999999999999999876

>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=93.34  E-value=0.02  Score=46.72  Aligned_cols=21  Identities=29%  Similarity=0.257  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |.|.|.+|+|||||...+...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998763

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.22  E-value=0.03  Score=49.20  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=28.2

Q ss_pred             eEEEEe-ccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIW-GIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~-G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      ++|+|+ +-||+||||+|..++..+......+..++
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            678888 67999999999999998876655566655

>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=93.11  E-value=0.046  Score=47.17  Aligned_cols=34  Identities=24%  Similarity=0.355  Sum_probs=26.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccc-eeeEEEE
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRH-FSGSYFA  245 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~-f~~~~~~  245 (538)
                      +.|+|-|+-|+||||+++.+.+.+... +..+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~~~~   37 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFT   37 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEe
Confidence            578999999999999999999887654 3444443

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=93.11  E-value=0.023  Score=49.20  Aligned_cols=20  Identities=35%  Similarity=0.380  Sum_probs=17.9

Q ss_pred             EEEEeccCCCchhHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~  232 (538)
                      +|+|+|+.|+||||.|+.+.
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            79999999999999998654

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=93.10  E-value=0.021  Score=49.35  Aligned_cols=21  Identities=48%  Similarity=0.556  Sum_probs=18.2

Q ss_pred             eEEEEeccCCCchhHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIF  232 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~  232 (538)
                      -+|+|+|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            369999999999999998663

>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=93.05  E-value=0.021  Score=51.28  Aligned_cols=25  Identities=28%  Similarity=0.217  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||++.+.--
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            4457999999999999999998763

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.04  E-value=0.023  Score=50.21  Aligned_cols=25  Identities=40%  Similarity=0.480  Sum_probs=21.7

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||++.+..-
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl   54 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGL   54 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            3457999999999999999999873

>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=92.96  E-value=0.02  Score=50.17  Aligned_cols=25  Identities=28%  Similarity=0.150  Sum_probs=21.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|+|||||.+.++--
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl   49 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGF   49 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcC
Confidence            3457999999999999999999864

>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=92.96  E-value=0.033  Score=48.32  Aligned_cols=35  Identities=14%  Similarity=0.059  Sum_probs=28.5

Q ss_pred             eEEEEeccC-CCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIG-GIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~-GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.+.|+|-+ |+||||++..++..+..+...+.++.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEEC
Confidence            458899998 99999999999998877755555554

>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=92.94  E-value=0.036  Score=46.40  Aligned_cols=31  Identities=23%  Similarity=0.231  Sum_probs=22.4

Q ss_pred             HhhhcCCCCceEEEEeccCCCchhHHHHHHHH
Q 009306          202 SLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       202 ~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +.+.......+ |+|+|.+|+|||||...+..
T Consensus         5 ~~~~~~~k~~k-I~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_           5 QFLGLYKKTGK-LVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             HHHTCTTCCEE-EEEEEETTSSHHHHHHHHSC
T ss_pred             HhccccCCCCE-EEEECCCCCCHHHHHHHHhC
Confidence            34433333344 78999999999999998865

>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=92.68  E-value=0.032  Score=48.89  Aligned_cols=25  Identities=32%  Similarity=0.355  Sum_probs=22.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++..|+|.-|.|||||.+.+...
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5688999999999999999998875

>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=92.62  E-value=0.019  Score=50.81  Aligned_cols=27  Identities=22%  Similarity=0.218  Sum_probs=23.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      .+.|+|-|+-|+||||+++.+.+.+..
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            468999999999999999988876543

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=92.62  E-value=0.037  Score=46.23  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.5

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +-+.|.|.+|+||||+|.++..+
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            45899999999999999998875

>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=92.59  E-value=0.029  Score=46.13  Aligned_cols=21  Identities=38%  Similarity=0.428  Sum_probs=19.3

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|+|.+|+|||||...+...
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999874

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=92.51  E-value=0.066  Score=43.69  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=22.8

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ..-+|.+.|.=|.||||+++.+++.+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhc
Confidence            45579999999999999999999854

>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=92.36  E-value=0.037  Score=47.10  Aligned_cols=24  Identities=17%  Similarity=0.459  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..+.|+|+|.+|+|||||...+..
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcC
Confidence            456799999999999999999985

>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=92.35  E-value=0.039  Score=46.10  Aligned_cols=23  Identities=35%  Similarity=0.411  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .-+.|.|++|+||||||..+..+
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            45899999999999999998875

>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=92.16  E-value=0.036  Score=45.77  Aligned_cols=20  Identities=20%  Similarity=0.438  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |++.|.+|+|||||+..+.+
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            77899999999999998886

>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=92.15  E-value=0.043  Score=49.05  Aligned_cols=26  Identities=27%  Similarity=0.207  Sum_probs=22.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      ..+++|.|+.|.|||||++.++--++
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCCCc
Confidence            45799999999999999999987543

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.12  E-value=0.041  Score=48.67  Aligned_cols=23  Identities=26%  Similarity=0.261  Sum_probs=20.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ++|+|+|..|+||||+|..+.++
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            57999999999999999988765

>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=92.01  E-value=0.45  Score=42.51  Aligned_cols=34  Identities=12%  Similarity=0.098  Sum_probs=24.6

Q ss_pred             HHHHHHHHhcceEEEEeccCcccchhhHHHHHHHH
Q 009306           62 QSLLDAIEASSISIIIFSESYASSRWCLDELLKIL   96 (538)
Q Consensus        62 ~~i~~~i~~s~~~i~v~S~~y~~s~~c~~El~~~~   96 (538)
                      .++.+.|+.+|++|.|+--.---|.+|. ++...+
T Consensus         7 r~i~~~i~~~DvIl~V~DaR~P~ss~~~-~l~~~~   40 (273)
T d1puja_           7 REVTEKLKLIDIVYELVDARIPMSSRNP-MIEDIL   40 (273)
T ss_dssp             HHHHHHGGGCSEEEEEEETTSTTTTSCH-HHHHHC
T ss_pred             HHHHHHHHhCCEEEEEEECCCCCCCCCH-HHHHHH
Confidence            5678889999999999987765666653 344444

>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=92.01  E-value=0.054  Score=45.94  Aligned_cols=41  Identities=20%  Similarity=0.263  Sum_probs=32.3

Q ss_pred             chhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhhc
Q 009306          195 LPMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKIS  236 (538)
Q Consensus       195 ~~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~  236 (538)
                      .-+..|..+|. +.+....+.|+|+++.|||++|..+.+-+.
T Consensus        38 ~Fl~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          38 TFLGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            34556666774 456778899999999999999999888653

>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=91.96  E-value=0.049  Score=45.15  Aligned_cols=23  Identities=30%  Similarity=0.370  Sum_probs=20.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .-|.|.|.+|+||||+|.++..+
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            45899999999999999988876

>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=91.96  E-value=0.051  Score=47.95  Aligned_cols=26  Identities=35%  Similarity=0.353  Sum_probs=22.3

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||.+.++...
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999988743

>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=91.95  E-value=0.056  Score=44.98  Aligned_cols=22  Identities=23%  Similarity=0.421  Sum_probs=19.1

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      --|+|.|.+|+|||||...+..
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3488999999999999998865

>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=91.95  E-value=0.047  Score=48.27  Aligned_cols=26  Identities=31%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHhh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      ...+++|.|+.|.|||||.+.++--+
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34579999999999999999998643

>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=91.87  E-value=0.04  Score=45.39  Aligned_cols=21  Identities=19%  Similarity=0.251  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |.|.|.+|+|||||+..+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999863

>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=91.87  E-value=0.04  Score=45.95  Aligned_cols=21  Identities=29%  Similarity=0.336  Sum_probs=18.8

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|+|.+|+|||||+..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            778999999999999998763

>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=91.73  E-value=0.042  Score=45.38  Aligned_cols=21  Identities=29%  Similarity=0.325  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|+..+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999998863

>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=91.65  E-value=0.17  Score=45.45  Aligned_cols=35  Identities=17%  Similarity=0.049  Sum_probs=25.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      +.++|.|.+|+|||+|+.........+...++|.-
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            34899999999999999987665555544555543

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.65  E-value=0.24  Score=43.24  Aligned_cols=24  Identities=25%  Similarity=-0.036  Sum_probs=21.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +.+++.|+|+...||||+.+.++-
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEeccCchhhHHHHHHHHH
Confidence            457899999999999999998876

>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=91.63  E-value=0.044  Score=45.46  Aligned_cols=20  Identities=25%  Similarity=0.257  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |++.|.+|+|||||...+..
T Consensus         8 i~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999876

>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=91.63  E-value=0.046  Score=45.40  Aligned_cols=21  Identities=24%  Similarity=0.366  Sum_probs=19.3

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .|+|.|.+|+|||||...+..
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

>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=91.61  E-value=0.044  Score=45.54  Aligned_cols=20  Identities=25%  Similarity=0.453  Sum_probs=18.8

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=91.55  E-value=0.042  Score=45.61  Aligned_cols=20  Identities=25%  Similarity=0.728  Sum_probs=18.3

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67889999999999998886

>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=91.51  E-value=0.046  Score=45.29  Aligned_cols=21  Identities=33%  Similarity=0.700  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|...+...
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999999874

>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=91.50  E-value=0.063  Score=46.67  Aligned_cols=34  Identities=24%  Similarity=0.397  Sum_probs=25.7

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -++.|.++|.     .+..++.|.+|+|||||...+..+
T Consensus        85 g~~~L~~~l~-----~kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          85 GIEELKEYLK-----GKISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             THHHHHHHHS-----SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hHhhHHHHhc-----CCeEEEECCCCCCHHHHHHhhcch
Confidence            3566777774     235788999999999999987654

>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=91.49  E-value=0.047  Score=45.16  Aligned_cols=20  Identities=25%  Similarity=0.390  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||+|+..+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=91.49  E-value=0.047  Score=45.13  Aligned_cols=21  Identities=24%  Similarity=0.545  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999999874

>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=91.44  E-value=0.043  Score=45.23  Aligned_cols=21  Identities=33%  Similarity=0.416  Sum_probs=18.8

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            789999999999999988763

>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=91.42  E-value=0.049  Score=46.74  Aligned_cols=23  Identities=22%  Similarity=0.176  Sum_probs=20.6

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +.|+|.|.+|+|||||...+...
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            46899999999999999999864

>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=91.28  E-value=0.04  Score=48.47  Aligned_cols=25  Identities=24%  Similarity=0.256  Sum_probs=21.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...+++|.|+.|.|||||.+.++.-
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            3457999999999999999988863

>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=91.25  E-value=0.051  Score=44.72  Aligned_cols=20  Identities=25%  Similarity=0.380  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||+|+..+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            68889999999999999886

>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=91.23  E-value=0.051  Score=45.23  Aligned_cols=20  Identities=35%  Similarity=0.511  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999875

>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=91.21  E-value=0.051  Score=44.81  Aligned_cols=21  Identities=19%  Similarity=0.371  Sum_probs=19.0

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |++.|.+|+|||||...++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>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=91.16  E-value=0.052  Score=45.05  Aligned_cols=21  Identities=29%  Similarity=0.525  Sum_probs=19.0

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|...+...
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999988763

>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=91.14  E-value=0.052  Score=45.19  Aligned_cols=21  Identities=33%  Similarity=0.574  Sum_probs=19.0

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      -|+|.|.+|+|||+|...+..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999999886

>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=91.13  E-value=0.054  Score=46.53  Aligned_cols=23  Identities=17%  Similarity=0.163  Sum_probs=20.2

Q ss_pred             eEEEEeccCCCchhHHHHHHHHh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +.|+|.|.+|+|||||...+...
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            35899999999999999998863

>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=91.13  E-value=0.053  Score=44.95  Aligned_cols=20  Identities=20%  Similarity=0.390  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||+..+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78899999999999999886

>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=91.11  E-value=0.054  Score=44.77  Aligned_cols=20  Identities=25%  Similarity=0.448  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            77889999999999999886

>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=91.04  E-value=0.051  Score=45.01  Aligned_cols=21  Identities=24%  Similarity=0.370  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|+..+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            778999999999999988763

>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=91.01  E-value=0.047  Score=46.02  Aligned_cols=20  Identities=35%  Similarity=0.340  Sum_probs=18.4

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||+..+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78899999999999998885

>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=90.87  E-value=0.058  Score=43.83  Aligned_cols=21  Identities=33%  Similarity=0.431  Sum_probs=19.2

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998874

>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=90.86  E-value=0.058  Score=44.52  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=19.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .-|+|.|.+|+|||||...+..
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            3478899999999999999876

>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=90.82  E-value=0.1  Score=43.22  Aligned_cols=22  Identities=36%  Similarity=0.323  Sum_probs=19.3

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|.|+|.+|+|||||...+...
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999988763

>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=90.81  E-value=0.058  Score=45.02  Aligned_cols=21  Identities=33%  Similarity=0.249  Sum_probs=18.7

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|...+...
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999988864

>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=90.80  E-value=0.06  Score=44.46  Aligned_cols=21  Identities=29%  Similarity=0.583  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|+|.+|+|||+|...+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            788999999999999998863

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=90.73  E-value=0.063  Score=52.09  Aligned_cols=50  Identities=18%  Similarity=0.261  Sum_probs=32.0

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEEeehhhhhh----cCChHHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFARNVREAEE----TCRLGDLRQQLLS  266 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~~~~~~~~----~~~~~~l~~~l~~  266 (538)
                      -|.+.||+|+|||-||+.++..+.--    +...+.....+    ..++.++.+.++.
T Consensus        51 NILliGPTGvGKTlLAr~LAk~l~VP----Fv~~daT~fTeaGYvG~DVesii~~L~~  104 (443)
T d1g41a_          51 NILMIGPTGVGKTEIARRLAKLANAP----FIKVEATKFTEVGYVGKEVDSIIRDLTD  104 (443)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHTTCC----EEEEEGGGGC----CCCCTHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCC----EEEeecceeeecceeecchhHHHHHHHH
Confidence            38999999999999999999865322    22222222211    3456666666654

>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=90.72  E-value=0.06  Score=44.75  Aligned_cols=20  Identities=20%  Similarity=0.383  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |++.|.+|+|||||+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>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=90.68  E-value=0.069  Score=44.60  Aligned_cols=24  Identities=21%  Similarity=0.290  Sum_probs=21.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|.|.+|+|||||...++..
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999864

>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=90.59  E-value=0.063  Score=44.24  Aligned_cols=21  Identities=29%  Similarity=0.623  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788899999999999998863

>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=90.46  E-value=0.066  Score=44.31  Aligned_cols=20  Identities=25%  Similarity=0.348  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||+|+..+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999998876

>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=90.41  E-value=0.068  Score=44.23  Aligned_cols=21  Identities=24%  Similarity=0.406  Sum_probs=18.8

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|...+...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998863

>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=90.39  E-value=0.084  Score=44.26  Aligned_cols=22  Identities=27%  Similarity=0.309  Sum_probs=19.6

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      -|+|.|.+|+|||+|...+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3889999999999999998874

>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=90.38  E-value=0.068  Score=44.53  Aligned_cols=20  Identities=20%  Similarity=0.413  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||+..+..
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998876

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=90.22  E-value=0.12  Score=46.22  Aligned_cols=40  Identities=20%  Similarity=0.184  Sum_probs=31.9

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHhh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      -+..+..+|....+....+.++|+|+.|||+++..+..-+
T Consensus        89 f~~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          89 AASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3445666776555677889999999999999999988876

>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=90.19  E-value=0.073  Score=43.74  Aligned_cols=21  Identities=33%  Similarity=0.376  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678899999999999988763

>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=90.07  E-value=0.071  Score=44.27  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=18.3

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |.+.|.+|+|||+|+..+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78899999999999998875

>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=90.03  E-value=0.074  Score=44.76  Aligned_cols=21  Identities=29%  Similarity=0.335  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |.|.|.+|+|||+|...+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999998863

>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=90.01  E-value=0.075  Score=44.60  Aligned_cols=20  Identities=35%  Similarity=0.547  Sum_probs=18.7

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||+..+.+
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=89.98  E-value=0.075  Score=45.14  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=19.0

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||+..+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999998863

>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=89.97  E-value=0.063  Score=44.94  Aligned_cols=22  Identities=23%  Similarity=0.294  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .|+|+|.+|+|||||...+..+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999863

>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=89.82  E-value=0.077  Score=43.28  Aligned_cols=21  Identities=24%  Similarity=0.349  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||..++...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999853

>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=89.78  E-value=0.082  Score=43.68  Aligned_cols=21  Identities=29%  Similarity=0.531  Sum_probs=18.9

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      -|+|.|.+|+|||||+..+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999999876

>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=89.76  E-value=0.12  Score=46.17  Aligned_cols=39  Identities=23%  Similarity=0.446  Sum_probs=27.2

Q ss_pred             hhHHHHHhhhcCCCCceEEEEeccCCCchhHHHHHHHHh
Q 009306          196 PMKEIESLLRTGSTNVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       196 ~l~~l~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      .+.++...+.......-.|+|.|.+|+|||||...++.+
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            334444444443334445889999999999999999864

>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=89.75  E-value=0.11  Score=43.50  Aligned_cols=21  Identities=38%  Similarity=0.479  Sum_probs=18.1

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      -|+|.|.+|+|||||...+..
T Consensus        19 KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            377999999999999998754

>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=89.74  E-value=0.092  Score=43.63  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=21.1

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHh
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ...|+|.|.+|+|||||..++..+
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            456899999999999999999863

>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=89.73  E-value=0.082  Score=44.26  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=19.0

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |++.|.+|+|||+|+..+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999988874

>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=89.58  E-value=0.086  Score=43.76  Aligned_cols=20  Identities=25%  Similarity=0.552  Sum_probs=18.5

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||+..+..
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999998876

>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=89.52  E-value=0.086  Score=44.60  Aligned_cols=21  Identities=24%  Similarity=0.273  Sum_probs=18.7

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||+|...+...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999988863

>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=89.37  E-value=0.092  Score=43.41  Aligned_cols=21  Identities=38%  Similarity=0.680  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |.+.|.+|+|||||...+...
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            677899999999999998873

>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=89.36  E-value=0.069  Score=44.66  Aligned_cols=20  Identities=25%  Similarity=0.507  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999875

>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=89.35  E-value=0.08  Score=44.89  Aligned_cols=18  Identities=28%  Similarity=0.466  Sum_probs=17.0

Q ss_pred             EEEeccCCCchhHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAI  231 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~  231 (538)
                      |.|.|.+|+|||||...+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            788999999999999988

>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=89.29  E-value=0.093  Score=43.71  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=18.6

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998876

>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=89.19  E-value=0.084  Score=44.42  Aligned_cols=20  Identities=35%  Similarity=0.410  Sum_probs=18.0

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |++.|.+|+|||+|...+..
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            78899999999999998765

>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=89.00  E-value=0.07  Score=44.81  Aligned_cols=20  Identities=25%  Similarity=0.587  Sum_probs=18.4

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||||...+..
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999998864

>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=88.68  E-value=0.055  Score=44.92  Aligned_cols=20  Identities=40%  Similarity=0.514  Sum_probs=17.2

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |+|.|.+|+|||+|...+..
T Consensus         6 i~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC-
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            77889999999999987765

>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=88.53  E-value=0.12  Score=46.56  Aligned_cols=24  Identities=29%  Similarity=0.115  Sum_probs=20.3

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhh
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.++|.|.+|+|||+|+..+....
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~   92 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQ   92 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHT
T ss_pred             CEEEeecCCCCChHHHHHHHHHhH
Confidence            348999999999999999887654

>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=88.45  E-value=0.11  Score=43.16  Aligned_cols=21  Identities=24%  Similarity=0.457  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |++.|.+|+|||||...+...
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999988874

>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=88.42  E-value=0.11  Score=43.80  Aligned_cols=21  Identities=29%  Similarity=0.300  Sum_probs=18.9

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |.|.|.+|+|||+|...+...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            788999999999999998764

>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=88.11  E-value=0.089  Score=43.63  Aligned_cols=23  Identities=26%  Similarity=0.288  Sum_probs=19.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ..+ |.|.|.+|+|||||...+..
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhc
Confidence            455 67899999999999998875

>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=87.86  E-value=0.065  Score=46.74  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=17.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..++.|.+|+|||||...+..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            3568899999999999977643

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=87.77  E-value=0.46  Score=41.07  Aligned_cols=22  Identities=23%  Similarity=-0.002  Sum_probs=19.8

Q ss_pred             eEEEEeccCCCchhHHHHHHHH
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      +++.|+|+...||||+.+.++-
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHH
Confidence            3689999999999999998876

>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=87.60  E-value=0.1  Score=43.55  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=20.4

Q ss_pred             CceEEEEeccCCCchhHHHHHHHH
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      ...-|+|.|.+++|||||..++..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            455699999999999999987754

>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=87.55  E-value=0.13  Score=42.93  Aligned_cols=21  Identities=43%  Similarity=0.634  Sum_probs=19.1

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||..++...
T Consensus        11 V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            889999999999999998863

>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=87.41  E-value=0.07  Score=43.49  Aligned_cols=21  Identities=29%  Similarity=0.514  Sum_probs=19.3

Q ss_pred             EEEeccCCCchhHHHHHHHHh
Q 009306          214 LGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      |+|.|.+|+|||||...+..+
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999864

>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=87.34  E-value=0.085  Score=43.77  Aligned_cols=20  Identities=30%  Similarity=0.343  Sum_probs=8.3

Q ss_pred             EEEeccCCCchhHHHHHHHH
Q 009306          214 LGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~  233 (538)
                      |.|.|.+|+|||||...+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78889999999999988775

>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=87.09  E-value=0.23  Score=45.90  Aligned_cols=30  Identities=23%  Similarity=0.307  Sum_probs=24.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhcccee
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRHFS  240 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~f~  240 (538)
                      +-.|.|-|+=|+||||+++.+.+.+..+..
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            345788899999999999999998765543

>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=87.03  E-value=0.15  Score=44.31  Aligned_cols=21  Identities=33%  Similarity=0.434  Sum_probs=18.5

Q ss_pred             EEEEeccCCCchhHHHHHHHH
Q 009306          213 KLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      -|.|.|.+|+|||||.+.+..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999998754

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.32  E-value=0.48  Score=32.97  Aligned_cols=65  Identities=17%  Similarity=0.014  Sum_probs=52.6

Q ss_pred             HHhhccccccCCCCHHHHHHHHHhCCCChHHHHHHHhhCCceeEecCCcEEecHHHHHHHHHHHh
Q 009306          435 NIFLDIACFFIDEDRDTATKFLDDCEFFATSAIEVLVDKHLITISVLNKIEMHYLLRAMGREIVR  499 (538)
Q Consensus       435 ~~l~~la~f~~~~~~~~l~~l~~~~~~~~~~~l~~L~~~~Li~~~~~~~~~~H~lv~~~~~~~~~  499 (538)
                      .++..++--+.+.+..++...++.+.......+..|.+.|++..+++|+|.+-+-+-+++...++
T Consensus         9 ~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~g~y~lG~~l~~lg~~~l~   73 (75)
T d1mkma1           9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLR   73 (75)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCEEECTHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCCEeecHHHHHHHHHHHh
Confidence            44555555566788888888887776777889999999999999878899999988888877764

>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=85.72  E-value=0.26  Score=45.45  Aligned_cols=33  Identities=24%  Similarity=0.272  Sum_probs=26.2

Q ss_pred             EEEEeccCCCchhHHHHHHHHhhccceeeEEEE
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKISRHFSGSYFA  245 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~  245 (538)
                      .|.|-|.=|+||||+++.+.+.+..+...+.++
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~   39 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAITPNRILLI   39 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCceEEE
Confidence            478889999999999999999876654444444

>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=85.71  E-value=0.21  Score=44.96  Aligned_cols=28  Identities=21%  Similarity=0.046  Sum_probs=23.6

Q ss_pred             ceEEEEeccCCCchhHHHHHHHHhhccc
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFNKISRH  238 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~~~~~~  238 (538)
                      .+.++|.|.+|+|||+|+..+++.....
T Consensus        43 GQr~~I~g~~g~GKT~l~~~i~~~~~~~   70 (289)
T d1xpua3          43 GQRGLIVAPPKAGKTMLLQNIAQSIAYN   70 (289)
T ss_dssp             TCEEEEEECSSSSHHHHHHHHHHHHHHH
T ss_pred             CCeeeEeCCCCCCHHHHHHHHHHHHhhc
Confidence            4458999999999999999999876544

>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=84.08  E-value=0.28  Score=43.94  Aligned_cols=25  Identities=28%  Similarity=0.267  Sum_probs=22.1

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      ..|-|+|.|-+|.|||||+.++...
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~~   29 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILYY   29 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHHh
Confidence            5677999999999999999998763

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=83.55  E-value=0.37  Score=37.79  Aligned_cols=25  Identities=20%  Similarity=0.199  Sum_probs=20.5

Q ss_pred             CceEEEEeccCCCchhHHHHHHHHh
Q 009306          210 NVYKLGIWGIGGIGKTTIAGAIFNK  234 (538)
Q Consensus       210 ~~~~v~I~G~~GiGKTtLa~~~~~~  234 (538)
                      +.++..|+++.|.|||+++..++.+
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~   31 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA   31 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH
Confidence            4677899999999999998766644

>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=83.48  E-value=1  Score=32.87  Aligned_cols=61  Identities=18%  Similarity=0.154  Sum_probs=47.7

Q ss_pred             CcccEEEcCcccccccchHHHHHHHHhhCCCeeEeeCCCCCCCcchHHHHHHHHhcceEEEEecc
Q 009306           16 IKYDVFLSFGGEDTRESFTSHLYSALSRETVETFIDDDLRRGDEISQSLLDAIEASSISIIIFSE   80 (538)
Q Consensus        16 ~~~dvFiSy~~~D~~~~~~~~l~~~l~~~g~~~~~d~~~~~g~~~~~~i~~~i~~s~~~i~v~S~   80 (538)
                      .+.+|||..-|.+.. .++..|...|+.+|++|.+|.   .+..+...+..|-..--.+++++.+
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            467999999888755 689999999999999999875   2456777788877666666666664

>d2f62a1 c.23.14.1 (A:9-160) Nucleoside 2-deoxyribosyltransferase {Trypanosoma brucei [TaxId: 5691]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: N-(deoxy)ribosyltransferase-like
family: N-deoxyribosyltransferase
domain: Nucleoside 2-deoxyribosyltransferase
species: Trypanosoma brucei [TaxId: 5691]

Probab=83.38  E-value=1.6  Score=34.85  Aligned_cols=70  Identities=16%  Similarity=0.080  Sum_probs=51.9

Q ss_pred             ccchHHHHHHHHhhCCCeeEeeC--CCCCCCcchHHHHHHHHhcceEEEEeccCc--ccchhhHHHHHHHHHHH
Q 009306           30 RESFTSHLYSALSRETVETFIDD--DLRRGDEISQSLLDAIEASSISIIIFSESY--ASSRWCLDELLKILECK   99 (538)
Q Consensus        30 ~~~~~~~l~~~l~~~g~~~~~d~--~~~~g~~~~~~i~~~i~~s~~~i~v~S~~y--~~s~~c~~El~~~~~~~   99 (538)
                      ...+.+.+...|+..|+.++.-.  .......|-+.-.+.|++|+.+|++++|--  -.+.=+..|+-.+....
T Consensus        17 ~~~~~~~i~~~l~~~g~~~~~P~d~~~~~~~~If~~d~~~i~~~D~VIA~Ld~frg~~~D~GTa~EiG~A~alg   90 (152)
T d2f62a1          17 GASYYNKVRELLKKENVMPLIPTDNEATEALDIRQKNIQMIKDCDAVIADLSPFRGHEPDCGTAFEVGCAAALN   90 (152)
T ss_dssp             THHHHHHHHHHHHTTTCEEECTTTTCCSSHHHHHHHHHHHHHHCSEEEEECCCCSSSSCCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHCCCEEeccccccchhHHHHHHHHHHHHHhCCEEEEEccccCCCCCCchHHHHHHHHHHCC
Confidence            35688999999999999999733  333334466777788999999999998521  12345778998888665

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.73  E-value=0.41  Score=36.59  Aligned_cols=26  Identities=4%  Similarity=0.139  Sum_probs=22.4

Q ss_pred             eEEEEeccCCCchhHHHHHHHHhhcc
Q 009306          212 YKLGIWGIGGIGKTTIAGAIFNKISR  237 (538)
Q Consensus       212 ~~v~I~G~~GiGKTtLa~~~~~~~~~  237 (538)
                      =.|.++|..|.||+|||.++...+.+
T Consensus         7 f~i~~tg~~~~gk~~ia~al~~~l~q   32 (122)
T d1g8fa3           7 FSIVLGNSLTVSREQLSIALLSTFLQ   32 (122)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            35889999999999999999887644

>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=82.28  E-value=0.34  Score=43.83  Aligned_cols=20  Identities=0%  Similarity=-0.094  Sum_probs=16.7

Q ss_pred             CCcEEecHHHHHHHHHHHhh
Q 009306          481 LNKIEMHYLLRAMGREIVRQ  500 (538)
Q Consensus       481 ~~~~~~H~lv~~~~~~~~~~  500 (538)
                      ...|+.|+-|-+++-.++..
T Consensus       273 ~~nyRs~~~I~~~an~l~~~  292 (306)
T d1uaaa1         273 EQNYRSSGRILKAANILIAN  292 (306)
T ss_dssp             CCBSSSCHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHc
Confidence            45689999999999888765

>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=82.06  E-value=0.41  Score=42.59  Aligned_cols=23  Identities=30%  Similarity=0.534  Sum_probs=20.3

Q ss_pred             ceEEEEeccCCCchhHHHHHHHH
Q 009306          211 VYKLGIWGIGGIGKTTIAGAIFN  233 (538)
Q Consensus       211 ~~~v~I~G~~GiGKTtLa~~~~~  233 (538)
                      .|-|+|.|-.|.|||||+..+..
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~   24 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLY   24 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHHH
Confidence            36699999999999999998864

>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=81.05  E-value=0.15  Score=43.00  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=19.7

Q ss_pred             EEEEeccCCCchhHHHHHHHHhh
Q 009306          213 KLGIWGIGGIGKTTIAGAIFNKI  235 (538)
Q Consensus       213 ~v~I~G~~GiGKTtLa~~~~~~~  235 (538)
                      +.+|+|+.|+|||||..++..-+
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            46788999999999999998654

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=80.46  E-value=0.79  Score=36.92  Aligned_cols=33  Identities=21%  Similarity=0.110  Sum_probs=21.6

Q ss_pred             EEEeccCCCchhHHHHHHHHhhccceeeEEEEe
Q 009306          214 LGIWGIGGIGKTTIAGAIFNKISRHFSGSYFAR  246 (538)
Q Consensus       214 v~I~G~~GiGKTtLa~~~~~~~~~~f~~~~~~~  246 (538)
                      |-|+=-.|=||||-|.-.+-|...+-..++.+.
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~G~rV~ivQ   37 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQ   37 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcCCCEEEEEE
Confidence            334434678999999888877655544455554

>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=80.23  E-value=0.43  Score=43.49  Aligned_cols=22  Identities=5%  Similarity=0.066  Sum_probs=17.7

Q ss_pred             CCcEEecHHHHHHHHHHHhhcC
Q 009306          481 LNKIEMHYLLRAMGREIVRQES  502 (538)
Q Consensus       481 ~~~~~~H~lv~~~~~~~~~~~~  502 (538)
                      ...|++++-|.+++..+++...
T Consensus       283 ~~nyRs~~~I~~~an~ll~~~~  304 (318)
T d1pjra1         283 EQNYRSTKRILQAANEVIEHNV  304 (318)
T ss_dssp             CBCSSSCHHHHHHHHHHHTTCS
T ss_pred             CCCCCCcHHHHHHHHHHHHcCc
Confidence            4558899999999999987653