Citrus Sinensis ID: 013128

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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-------45
Protein Sequence
MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQKATN
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccccEEEEEEEcccccccHHHHHHHHHHHcccccccccccEEEccccccccEEEEEccccEEEEEEccEEEEEEEEEEEccccccccccccccccccccccEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHccEEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHccHHHHHHHcccccccEEEEccccccHHHHHHHHHcccccEEEEEEccccccHHHHHHHHHHccccEEEEEEcccccccccccccccccccccccccccHHHHHHHcccccccccccEEEEEEcccccccccccccccccEEEEEEccccHHHHHHHHHHHccccccccHHHHHHHcccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHHHHHHccccHHHccEEEEccccccccEEEEEccccEEEEEEccEEEEEEEEEEccccccccccccccccccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEccccccccccEcccccccHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccEEEEccccccHHHHHHHHHHHccccEEEEEccEccccHHHHHHHHcccccEEEEEEEcccEEEcccccccccccccccccEEEEHHHHHHHcccHccccccEEEEEEcccHHcccHHHccccccccEEEEccccHHHHHHHHHHHcccccccHHHHHHHHHHHccccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYylgnkatttsaqrfrvgksekEKTFEIALDRNEETFDVFKDVTLKWKLVYTQvpssmeyrnpnlgdynaslRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANnivlkhpmtfktLALDSELKREITEDLENFMNGKEYYTRIGRAWKrgyllygppgtgkSSLIAAMANQLKFdiydldlsavqSNSELRFLLLtmpsrsmlviEDIDCSvklqnressevqatnqeeNKVTLSGLLNFIDGLwsccgegriivfttnhkekldpallrpgrmdmhlhmSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQKATN
Flexible Loop (DISEMBL)
MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNkatttsaqrfrvgksekEKTFeialdrneetfdvfkdvtlKWKLVYTqvpssmeyrnpnLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEdlenfmngkeyyTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESsevqatnqeenkvTLSGLLNFIDGLWSCCGEGRIIVfttnhkekldpALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHakmtqqqkatn
Low Complexity Region (SEG)
MSKAKTVlstaaslsasaMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQKATN
Disordered region (IsUnstruct)
***************ASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFR********TFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKL*****************VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLH***********
Disordered Region (DISOPRED)
****KTV*STAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTS*******************DRNEETFDVFKDVTLKWKLVYTQ*******************RSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNI*LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDC*************************GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKF*************
Disordered Region (DISEMBL)
***********ASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQN************ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAK*********
Disordered Region (DISPRO)
*SKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYR***********RSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQN************ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQ******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQKATN
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	449	2.2.26 [Sep-21-2011]
Q54DY9	458	Probable mitochondrial ch	yes	no	0.574	0.563	0.321	3e-34
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.547	0.585	0.325	2e-32
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.498	0.498	0.344	9e-32
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.561	0.601	0.330	3e-31
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.559	0.599	0.316	7e-30
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.559	0.600	0.324	1e-29
P32839	456	Mitochondrial chaperone B	yes	no	0.342	0.337	0.432	2e-28
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.481	0.515	0.328	5e-28
Q54HY8	421	Probable mitochondrial ch	no	no	0.492	0.524	0.342	8e-28
Q5UR45	196	Putative AAA family ATPas	N/A	no	0.358	0.821	0.340	4e-16

>sp|Q54DY9|BCS1B_DICDI Probable mitochondrial chaperone BCS1-B OS=Dictyostelium discoideum GN=bcsl1b PE=3 SV=1

 Score =  146 bits (369), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 96/299 (32%), Positives = 157/299 (52%), Gaps = 41/299 (13%)

Query: 170 HVLEKAKAI---KEESKVVKLHTVMHMRWDANNIVLKHPM---TFKTLALDSELKREITE 223
           +++E+AK +   KEE K + ++T M   W        HP       ++ LD      I +
Sbjct: 167 NLIEEAKEMALEKEEGKTL-IYTSMGTDWRR----FGHPRRKRPISSVILDKGKSELIIQ 221

Query: 224 DLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-SN 282
           D++ F+N  ++Y   G  ++RGYLLYGPPGTGKSS I A+A +L+  I  L+L+    S+
Sbjct: 222 DVKKFLNNSDWYNDRGIPYRRGYLLYGPPGTGKSSFITALAGELQLSICILNLAGKSVSD 281

Query: 283 SELRFLLLTMPSRSMLVIEDIDCSVKLQNRE-SSEVQATNQEE----------------- 324
           + L  LL T P RS++++EDID +++  N + S++  + N                    
Sbjct: 282 TSLNQLLATAPQRSIILLEDIDSAIQTGNHDLSAKSNSANAPSISSGGLQYQGYYGNPSV 341

Query: 325 ----NKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT 380
               + +T SGLLN +DG+     EGRI+  TTNH EKLD  L+RPGR+D+ + +  C++
Sbjct: 342 SSGGSALTFSGLLNALDGV--AASEGRILFMTTNHLEKLDKVLIRPGRVDLQIEIGLCSS 399

Query: 381 SVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEV----SLNGLVK 435
              +Q+   +       L +Q  E ++    +PA++    M  +N  +    +LN L+K
Sbjct: 400 YQMEQMFLKFYPTDFD-LAKQFVEKLENYKFSPAQLQAYFMTYSNNSIEAINNLNELIK 457

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.
Dictyostelium discoideum (taxid: 44689)

>sp|Q7ZV60|BCS1_DANRE Mitochondrial chaperone BCS1 OS=Danio rerio GN=bcs1l PE=2 SV=2

 Score =  140 bits (352), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/258 (32%), Positives = 140/258 (54%), Gaps = 12/258 (4%)

Query: 171 VLEKAK--AIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENF 228
           +L++A+  A+K+E     ++T M   W       +      ++ L+S +   I +D++ F
Sbjct: 150 ILQEARELALKQEEGRTVMYTAMGAEWRPFGFPRRR-RPLSSVVLESGVAERIVDDVKEF 208

Query: 229 MNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-SNSELRF 287
           +   ++YT  G  ++RGYLLYGPPG GKSS I A+A +L + I  + LS    S+  L  
Sbjct: 209 IGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGYSICLMSLSDRSLSDDRLNH 268

Query: 288 LLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGR 347
           LL   P +S++++ED+D +   +    +E     Q   ++T SGLLN +DG+ S   E R
Sbjct: 269 LLSVAPQQSIILLEDVDAAFVSRELLPTENPLAYQGMGRLTFSGLLNALDGVASS--EAR 326

Query: 348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN----TSVFKQLAFNYLGISHHYLFEQIE 403
           I+  TTN  E+LDPAL+RPGR+D+  ++ +C+    T +F++           +  EQ  
Sbjct: 327 IVFMTTNFIERLDPALVRPGRVDLKQYVGHCSHWQLTQMFRRFYPQESAAEADHFSEQ-- 384

Query: 404 ELIKEVNVTPAEVAGELM 421
            L    +++ A+V G  M
Sbjct: 385 ALAAHTDLSAAQVQGHFM 402

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Danio rerio (taxid: 7955)

>sp|Q9P6Q3|BCS1_SCHPO Probable mitochondrial chaperone bcs1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.07 PE=2 SV=1

 Score =  138 bits (348), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 137/238 (57%), Gaps = 14/238 (5%)

Query: 186 KLHTVMHMRWDANNIVLKHPMTFKTLA---LDSELKREITEDLENFMNGKEYYTRIGRAW 242
           K  T ++  W        HP + + L+   L+S +K+ IT+D+ +F+   ++Y   G  +
Sbjct: 182 KNKTTIYTAWATEWKPFGHPRSKRMLSSVVLESNVKKMITDDVHDFLRNSQWYDTRGIPY 241

Query: 243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-SNSELRFLLLTMPSRSMLVIE 301
           +RGYLLYGPPG+GK+S + A+A +L +DI  L+L+    ++  L  LL  +P ++++++E
Sbjct: 242 RRGYLLYGPPGSGKTSFLYALAGELDYDICVLNLAEKGLTDDRLNHLLSNVPPKAVVLLE 301

Query: 302 DIDCSVKLQNRE-SSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLD 360
           D+D +   Q RE S EV         VT SGLLN +DG+ S   + RII  TTNH EKLD
Sbjct: 302 DVDSA--FQGRERSGEVGF----HANVTFSGLLNALDGVTSS--DERIIFMTTNHPEKLD 353

Query: 361 PALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAG 418
           PAL+RPGR+D+  ++        +++   + G S   + + + +++   N + A + G
Sbjct: 354 PALVRPGRVDVKAYLGNATPEQVREMFTRFYGHSPE-MADDLSDIVCPKNTSMASLQG 410

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

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

>sp|Q9Y276|BCS1_HUMAN Mitochondrial chaperone BCS1 OS=Homo sapiens GN=BCS1L PE=1 SV=1

 Score =  136 bits (342), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 89/269 (33%), Positives = 145/269 (53%), Gaps = 17/269 (6%)

Query: 170 HVLEKAKAI---KEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLE 226
           ++LE+A+ +   +EE K V ++T +   W       +      ++ L   L   I  D++
Sbjct: 149 NILEEARELALQQEEGKTV-MYTAVGSEWRPFGYPRRR-RPLNSVVLQQGLADRIVRDVQ 206

Query: 227 NFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-YDLDLSAVQSNSEL 285
            F++  ++YT  G  ++RGYLLYGPPG GKSS I A+A +L+  I       +  S+  L
Sbjct: 207 EFIDNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSDDRL 266

Query: 286 RFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE 345
             LL   P +S++++ED+D +  L    + E     Q   ++T SGLLN +DG+ S   E
Sbjct: 267 NHLLSVAPQQSLVLLEDVDAAF-LSRDLAVENPVKYQGLGRLTFSGLLNALDGVAST--E 323

Query: 346 GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN----TSVFKQLAFNYLGISHHYLFEQ 401
            RI+  TTNH ++LDPAL+RPGR+D+  ++ YC+    T +F++    Y G +       
Sbjct: 324 ARIVFMTTNHVDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRF---YPGQAPSLAENF 380

Query: 402 IEELIKEVN-VTPAEVAGELMKSTNAEVS 429
            E +++  N ++PA+V G  M   N  V 
Sbjct: 381 AEHVLRATNQISPAQVQGYFMLYKNDPVG 409

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Homo sapiens (taxid: 9606)

>sp|Q5E9H5|BCS1_BOVIN Mitochondrial chaperone BCS1 OS=Bos taurus GN=BCS1L PE=2 SV=1

 Score =  132 bits (331), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 83/262 (31%), Positives = 139/262 (53%), Gaps = 11/262 (4%)

Query: 170 HVLEKAKAI---KEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLE 226
           ++LE+A+ +   +EE K V ++T +   W       +      ++ L+  +   I  D+ 
Sbjct: 149 NILEEARELALQQEEGKTV-MYTAVGSEWRPFGYPRRR-RPLNSVVLEQGVTERIVRDIR 206

Query: 227 NFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-YDLDLSAVQSNSEL 285
            F++  ++Y   G  ++RGYLLYGPPG GKSS I A+A +L+  I       +  S+  L
Sbjct: 207 EFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELQHSICLLSLTDSSLSDDRL 266

Query: 286 RFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE 345
             LL   P +S++++ED+D +  L    ++E     Q   ++T SGLLN +DG+ S   E
Sbjct: 267 NHLLSVAPQQSLVLLEDVDAAF-LSRDLAAENPIKYQGLGRLTFSGLLNALDGVAST--E 323

Query: 346 GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEEL 405
            RI+  TTNH ++LDPAL+RPGR+DM  ++ +C+     Q+   +       L E   + 
Sbjct: 324 ARIVFMTTNHIDRLDPALIRPGRVDMKEYVGHCSRWQLTQMFQRFYPGQATSLAENFADR 383

Query: 406 IKEV--NVTPAEVAGELMKSTN 425
           + +    ++PA+V G  M   N
Sbjct: 384 VLQATTQISPAQVQGYFMLYKN 405

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Bos taurus (taxid: 9913)

>sp|Q9CZP5|BCS1_MOUSE Mitochondrial chaperone BCS1 OS=Mus musculus GN=Bcs1l PE=1 SV=1

 Score =  131 bits (330), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/262 (32%), Positives = 139/262 (53%), Gaps = 11/262 (4%)

Query: 170 HVLEKAKAI---KEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLE 226
           ++LE+A+A+   +EE K V ++T +   W       +      ++ L   L   I +D+ 
Sbjct: 149 NILEEARALALQQEEGKTV-MYTAVGSEWRTFGYPRRR-RPLDSVVLQQGLADRIVKDIR 206

Query: 227 NFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-YDLDLSAVQSNSEL 285
            F++  ++Y   G  ++RGYLLYGPPG GKSS I A+A +L+  I       +  S+  L
Sbjct: 207 EFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSDDRL 266

Query: 286 RFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE 345
             LL   P +S++++ED+D +  L    + E     Q   ++T SGLLN +DG+ S   E
Sbjct: 267 NHLLSVAPQQSLVLLEDVDAAF-LSRDLAVENPIKYQGLGRLTFSGLLNALDGVAST--E 323

Query: 346 GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEEL 405
            RI+  TTN+ ++LDPAL+RPGR+D+  ++ YC+     Q+   +       L E   E 
Sbjct: 324 ARIVFMTTNYIDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRFYPGQAPSLAENFAEH 383

Query: 406 IKEVN--VTPAEVAGELMKSTN 425
           + +    ++PA+V G  M   N
Sbjct: 384 VLKATSEISPAQVQGYFMLYKN 405

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Mus musculus (taxid: 10090)

>sp|P32839|BCS1_YEAST Mitochondrial chaperone BCS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BCS1 PE=1 SV=2

 Score =  127 bits (318), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 70/162 (43%), Positives = 103/162 (63%), Gaps = 8/162 (4%)

Query: 210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF 269
           ++ LDS +K  I +D+ +FM   ++Y+  G  ++RGYLLYGPPG+GK+S I A+A +L +
Sbjct: 227 SVILDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPGSGKTSFIQALAGELDY 286

Query: 270 DIYDLDLSAVQ-SNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVT 328
           +I  L+LS    ++  L  L+  MP RS+L++EDID +     R  +  Q  +   + VT
Sbjct: 287 NICILNLSENNLTDDRLNHLMNNMPERSILLLEDIDAA--FNKRSQTGEQGFH---SSVT 341

Query: 329 LSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
            SGLLN +DG+ S   E  I   TTNH EKLD A++RPGR+D
Sbjct: 342 FSGLLNALDGVTSS--EETITFMTTNHPEKLDAAIMRPGRID 381

Essential for the expression of the Rieske iron-sulfur protein.

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

>sp|Q7ZTL7|BCS1_XENLA Mitochondrial chaperone BCS1 OS=Xenopus laevis GN=bcs1l PE=2 SV=1

 Score =  125 bits (315), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 127/225 (56%), Gaps = 9/225 (4%)

Query: 170 HVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLA---LDSELKREITEDLE 226
           ++L++A+ +  + +V K  TVM+    A       P   + L+   L+  +  +I +D++
Sbjct: 149 NILQEARELALKQQVGK--TVMYNAVGAEWRQFGFPRRRRPLSSVVLEQGISEKIVQDVK 206

Query: 227 NFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-YDLDLSAVQSNSEL 285
            F+   ++Y+  G  ++RGYLLYGPPG GKSS I A+A +L++ I       +  S+  L
Sbjct: 207 GFIENPKWYSDRGIPYRRGYLLYGPPGCGKSSFITALAGELEYSICLMSLSDSSLSDDRL 266

Query: 286 RFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE 345
             LL   P +S++++ED+D +   ++       A  Q   ++T SGLLN +DG+ S   E
Sbjct: 267 NHLLSVAPQQSIILLEDVDAAFVSRDLNKQNPTAY-QGMGRLTFSGLLNALDGVAST--E 323

Query: 346 GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNY 390
            RI+  TTNH ++LDPAL+RPGR+D+  ++ +C      Q+   +
Sbjct: 324 ARIVFMTTNHIDRLDPALIRPGRVDVKQYVGHCTNWQLSQMFLRF 368

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Xenopus laevis (taxid: 8355)

>sp|Q54HY8|BCS1A_DICDI Probable mitochondrial chaperone BCS1-A OS=Dictyostelium discoideum GN=bcs1la PE=3 SV=1

 Score =  125 bits (313), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 130/228 (57%), Gaps = 7/228 (3%)

Query: 204 HPMTFKTLA---LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLI 260
           +P + ++L+   L  +LK ++ ED+++F+  + +Y   G  ++RGYLLYG PG GKSSLI
Sbjct: 179 NPRSIRSLSSVILADDLKSKLIEDIKSFITNESWYRNRGIPYRRGYLLYGEPGNGKSSLI 238

Query: 261 AAMANQLKFDIYDLDLSAVQ-SNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQA 319
            A+A +L  DI  + LS+    + ++  LL   P +S+L+IEDID + K           
Sbjct: 239 NAIAGELNLDICIVSLSSKDIDDKQINHLLNNAPPKSILLIEDIDAAFKSHRDNVDSNNN 298

Query: 320 TNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN 379
            +   N +T SGLLN +DG+     EGRI+  TTN  E LD AL+R GR+D+ + +S   
Sbjct: 299 NSNNNNSLTYSGLLNALDGV--ASQEGRILFMTTNKIELLDSALIREGRIDLKIKVSNAT 356

Query: 380 TSVFKQLAFNYLGI-SHHYLFEQIEELIKEVNVTPAEVAGELMKSTNA 426
            S   QL  ++  + + + L  +  E + +  ++ +++ G L+K  N+
Sbjct: 357 KSQAAQLFTHFYNLPTDNQLAIRFSENLHDHQLSMSQIQGFLLKYINS 404

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|Q5UR45|YL572_MIMIV Putative AAA family ATPase L572 OS=Acanthamoeba polyphaga mimivirus GN=MIMI_L572 PE=3 SV=1

 Score = 86.3 bits (212), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/191 (34%), Positives = 105/191 (54%), Gaps = 30/191 (15%)

Query: 259 LIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSR-SMLVIEDIDCS---VKLQNRES 314
           +I A++   K  I+ L L+ +Q ++EL  LL  +  + ++LV+EDIDC+   VK + +E 
Sbjct: 1   MIKAISTHTKRHIHYLILNNIQDDNELINLLNAVNCKETILVLEDIDCASEAVKSRAKEE 60

Query: 315 SEV--QATNQE---ENKV--------------TLSGLLNFIDGLWSCCGEGRIIVFTTNH 355
             V  + T+ +   ENK+              TLSG+LN +DG+++   EGRI++ TTNH
Sbjct: 61  ETVVEKVTDDKSTLENKILADQLKKVEKVSKLTLSGILNSLDGIFN--SEGRIVIMTTNH 118

Query: 356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI-SHHYLFEQIEELIKEVNVTPA 414
            E LDPAL+R GR+DM +  S C+     ++  N+ G  +   +  +I   I     +PA
Sbjct: 119 SEVLDPALIRRGRIDMQIEFSNCDRYQIAKMYENFYGKNADSDILSKIPSDI----YSPA 174

Query: 415 EVAGELMKSTN 425
            V+G L+   N
Sbjct: 175 HVSGLLLSYRN 185

Acanthamoeba polyphaga (taxid: 5757)

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	449
356542322	572	PREDICTED: uncharacterized protein LOC10	0.971	0.762	0.617	1e-148
359483290	431	PREDICTED: mitochondrial chaperone BCS1-	0.859	0.895	0.605	1e-146
225443401	500	PREDICTED: probable mitochondrial chaper	0.982	0.882	0.552	1e-139
449460285	461	PREDICTED: probable mitochondrial chaper	0.962	0.937	0.547	1e-138
225443403	437	PREDICTED: probable mitochondrial chaper	0.897	0.922	0.574	1e-137
297735750	1186	unnamed protein product [Vitis vinifera]	0.897	0.339	0.574	1e-137
225431310	522	PREDICTED: uncharacterized protein LOC10	0.962	0.827	0.553	1e-136
357452221	458	Mitochondrial chaperone BCS1 [Medicago t	0.966	0.947	0.556	1e-136
255561048	528	ATP binding protein, putative [Ricinus c	0.982	0.835	0.532	1e-134
357452271	468	Mitochondrial chaperone BCS1 [Medicago t	0.977	0.938	0.538	1e-134

>gi|356542322|ref|XP_003539617.1| PREDICTED: uncharacterized protein LOC100778503 [Glycine max]

 Score =  530 bits (1364), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 275/445 (61%), Positives = 341/445 (76%), Gaps = 9/445 (2%)

Query: 1   MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
           MS + T++S  ASL+ASAMLIRS+ NDF+P EI D+  SKI+ +S+ FSSQLTI++EEFQ
Sbjct: 1   MSNSTTLISAVASLAASAMLIRSITNDFIPLEILDFFYSKIYYLSRQFSSQLTIIIEEFQ 60

Query: 61  GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
           G S NQV+EAA  YLG KAT  SA R +  KSE +K    ++DR+E+  D ++ V +KWK
Sbjct: 61  GVSRNQVYEAAEVYLGTKATL-SALRVKASKSEDDKKLAFSVDRDEDISDDYEGVQVKWK 119

Query: 121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
           L   ++      R+ N  D NA+ +SEVR YELSFHKKHK+ + N YLP+VLE+AK IK+
Sbjct: 120 LS-CEILEPYGSRHSN--DRNANFKSEVRSYELSFHKKHKEKIFNSYLPYVLERAKDIKQ 176

Query: 181 ESKVVKLHTVMH-MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIG 239
           E+  VKLHT+ +   W+ N++   HPMTFKTLA+D+ELKRE+  DL+ F+ GKE+Y R G
Sbjct: 177 ENMEVKLHTIEYDCYWNGNSVKFSHPMTFKTLAIDAELKREVVSDLDKFVKGKEFYKRTG 236

Query: 240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLV 299
           +AWKRGYLLYGPPGTGKSSLIAAMAN L +DIYDLDL+ V +N++L+ LLL M +RS+LV
Sbjct: 237 KAWKRGYLLYGPPGTGKSSLIAAMANYLNYDIYDLDLTIVTNNNDLKNLLLGMSNRSILV 296

Query: 300 IEDIDCSVKLQNRESS----EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH 355
            EDIDCS+KLQNRE      + +  N +E+KVTLSGLLN IDGLWSCCGE RII+FTTNH
Sbjct: 297 FEDIDCSIKLQNREEEEEEEQKKGDNNKESKVTLSGLLNVIDGLWSCCGEERIIIFTTNH 356

Query: 356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAE 415
           KE+LDPALLRPGRMDMH+H+SYC  S FKQL  NYLGIS H LFEQIE L+ EVNVTPAE
Sbjct: 357 KERLDPALLRPGRMDMHIHLSYCTFSAFKQLVLNYLGISQHKLFEQIEGLLGEVNVTPAE 416

Query: 416 VAGELMKSTNAEVSLNGLVKFLHAK 440
           VAGEL KS++    L  LV FLH+K
Sbjct: 417 VAGELTKSSDTRDPLQDLVNFLHSK 441

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483290|ref|XP_003632935.1| PREDICTED: mitochondrial chaperone BCS1-like [Vitis vinifera]

 Score =  523 bits (1347), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 255/421 (60%), Positives = 321/421 (76%), Gaps = 35/421 (8%)

Query: 21  IRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKAT 80
           IRS+AND LP E++DY  S +H +S+YFSSQLTIV++EFQG S+N++FEAA+ YLG +  
Sbjct: 29  IRSIANDLLPNEVHDYFSSTLHNLSRYFSSQLTIVIDEFQGLSMNKLFEAADVYLGTR-M 87

Query: 81  TTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDY 140
           T S ++ RV K ++EK    AL R                               N  + 
Sbjct: 88  TPSVRKIRVVKGDEEKKLA-ALGRG------------------------------NSRNR 116

Query: 141 NASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNI 200
             + R EVR YELSF+K ++D+VL+ YLP++LE+A+AIKEE+KVVKLHTV +  WD  +I
Sbjct: 117 GETPRLEVRSYELSFNKNYRDIVLDSYLPYILERARAIKEENKVVKLHTVNYSNWDLGSI 176

Query: 201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLI 260
           +L HPMTF+TLA+DSELK+E+ EDL+NF+NGK+YY RIG+AWKRGYLLYGPPGTGKSSLI
Sbjct: 177 LLDHPMTFQTLAMDSELKKELVEDLDNFVNGKDYYRRIGKAWKRGYLLYGPPGTGKSSLI 236

Query: 261 AAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQAT 320
           AAMAN L +DIYDLDL+ V SNS+LR LLL M S+S+LVIEDIDC +KLQNR+S E    
Sbjct: 237 AAMANHLNYDIYDLDLTNVNSNSDLRALLLAMSSKSILVIEDIDCMIKLQNRDSEERWQP 296

Query: 321 NQEENKVTLSGLLNFIDGLWSCCGE-GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN 379
           ++  N+VTLSGLLNFIDG+WSCCG+ GRIIVF+TNH+++LDPALLRPGRMDMH+HMSYC 
Sbjct: 297 HK--NQVTLSGLLNFIDGIWSCCGDQGRIIVFSTNHRDQLDPALLRPGRMDMHIHMSYCT 354

Query: 380 TSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHA 439
            S FKQLA NYLG+  H LF+Q+E L+ EV VTPAEVAGEL+KS + +VSL GL+ FLH+
Sbjct: 355 ISAFKQLALNYLGVWQHPLFDQVEGLMGEVKVTPAEVAGELIKSKDPDVSLQGLLGFLHS 414

Query: 440 K 440
           K
Sbjct: 415 K 415

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443401|ref|XP_002267368.1| PREDICTED: probable mitochondrial chaperone BCS1-B-like [Vitis vinifera]

 Score =  500 bits (1287), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 264/478 (55%), Positives = 338/478 (70%), Gaps = 37/478 (7%)

Query: 3   KAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEF--- 59
           +A TVLS AASL+ASAML R++A+D +P E+Y Y  S +H + +Y SSQ TI++EEF   
Sbjct: 9   RAATVLSAAASLAASAMLFRTIASDLVPGEVYGYFSSTLHNIFRYLSSQHTIIIEEFKGN 68

Query: 60  QGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKW 119
           QG ++N++ EAA  YLG K T+ + ++ RVGK E+EK   + +D +EE  DVF+DV + W
Sbjct: 69  QGHTVNELIEAAEVYLGTK-TSPAVRKLRVGKDEEEKKLAVTIDGDEEIVDVFEDVKVTW 127

Query: 120 KLVYTQVPS------SMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLE 173
           + +  QV S        E R   L D + ++ SE R YELSF+KKHKD VLN Y P++LE
Sbjct: 128 RSISRQVESLGFGNMGGEGRTFWLEDPDETVWSEERSYELSFNKKHKDKVLNSYFPYILE 187

Query: 174 KAKAIKEESKVVKLHTV--MHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNG 231
           +AKAIKEESKVVKLH V   H  W  + I+L HPMTF+TLA+DSELK  + EDL+NF+ G
Sbjct: 188 RAKAIKEESKVVKLHAVNTHHGCW-RDAIILDHPMTFQTLAMDSELKMALLEDLDNFVKG 246

Query: 232 KEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLT 291
           K +Y R+G+ W+RGYLLYGP GTGKSSLIAAMAN L +DIYD+DL+ V+SN +LR LLL 
Sbjct: 247 KAFYKRMGKTWRRGYLLYGPSGTGKSSLIAAMANHLNYDIYDMDLTGVRSNDDLRLLLLA 306

Query: 292 MPSRSMLVIEDIDCSVKLQNR------ESSEVQATNQE------------------ENKV 327
           MPS+++LVIED+DC V LQN+           +AT  E                  EN+V
Sbjct: 307 MPSKAILVIEDVDCVVNLQNQEDNEEDREDREEATTGEPYNPWDEDGWVTEDEVEAENQV 366

Query: 328 TLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLA 387
           TLSG LN I+GL SCC E +I+VFTTNH+E+LDPALLRPG +DM +HMSYC  S FKQLA
Sbjct: 367 TLSGFLNLINGLLSCCSEEQILVFTTNHREQLDPALLRPGCIDMEIHMSYCTMSAFKQLA 426

Query: 388 FNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQ 445
           +NYLG+  H LFEQIE L+ EV VTPAEVAGELMKS +A VSL G+++F H K+ Q +
Sbjct: 427 WNYLGLYDHPLFEQIERLMGEVKVTPAEVAGELMKSKDAGVSLQGVIEFFHKKIEQNE 484

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460285|ref|XP_004147876.1| PREDICTED: probable mitochondrial chaperone BCS1-B-like [Cucumis sativus] gi|449511627|ref|XP_004164010.1| PREDICTED: probable mitochondrial chaperone BCS1-B-like [Cucumis sativus]

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 244/446 (54%), Positives = 323/446 (72%), Gaps = 14/446 (3%)

Query: 1   MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
           +   KT+ S  ASL+ASA+L R+  N+ +P  + DY  S++H     FSSQL IV+EE  
Sbjct: 8   LPSPKTIPSLMASLTASAVLFRTFYNELIPDAVRDYFVSRLHDFYTRFSSQLIIVIEELD 67

Query: 61  GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
           G ++NQ+F+AAN YLG K ++ S +R +V K +KEK   + +DRN+E  D+F+ V  KW 
Sbjct: 68  GLTVNQMFDAANVYLGTKVSS-STRRIKVHKPQKEKELAVTIDRNQELIDIFQGVNFKWV 126

Query: 121 LVYTQV--PSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAI 178
           LV +++  P S + RN N+ ++     S+VRH+ELSFHKKH+++ L  YLPH+L +A  I
Sbjct: 127 LVSSRIERPISSKNRNANVHEH-----SDVRHFELSFHKKHREMALRFYLPHILREANTI 181

Query: 179 KEESKVVKLHTVMH---MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYY 235
            +E K +KLHT+ +     W   +I L HP TF T+A++ E K+ + +DL  F+  KEYY
Sbjct: 182 GDEKKAMKLHTIDYNGTHYW--GSIDLNHPATFDTIAMNPETKKALIDDLNTFIERKEYY 239

Query: 236 TRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSR 295
            R+GRAWKRGYLLYGPPGTGKSSLIAAMAN LKFDIYD+DL  VQ NS+LR LL+   +R
Sbjct: 240 RRVGRAWKRGYLLYGPPGTGKSSLIAAMANYLKFDIYDMDLKEVQYNSDLRRLLIGTGNR 299

Query: 296 SMLVIEDIDCSVKLQNRES-SEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN 354
           S+LVIEDIDCS++LQ+R S S+ Q  + E+ K+TLSGLLNFIDGLWS CG+ RI+VFTTN
Sbjct: 300 SILVIEDIDCSIELQDRSSDSKNQTKSTEDEKITLSGLLNFIDGLWSSCGDERIVVFTTN 359

Query: 355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPA 414
           H ++LDPALLRPGRMDMHLHMSYC+   FK LA+NYL I  H LFE+I+E + +V  TPA
Sbjct: 360 HMDRLDPALLRPGRMDMHLHMSYCDFGGFKILAYNYLLIQEHPLFEKIKEFLNKVEATPA 419

Query: 415 EVAGELMKSTNAEVSLNGLVKFLHAK 440
           E+AGELMKS +   SL G+++ LH K
Sbjct: 420 ELAGELMKSDDTISSLQGIIQLLHDK 445

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443403|ref|XP_002267398.1| PREDICTED: probable mitochondrial chaperone bcs1-like [Vitis vinifera]

 Score =  496 bits (1277), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 246/428 (57%), Positives = 318/428 (74%), Gaps = 25/428 (5%)

Query: 19  MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ-GFSINQVFEAANYYLGN 77
           +LIR +  +F+P+E++            + SSQLTI++EEFQ G ++N++FEAA+ YLG 
Sbjct: 25  ILIRKITKNFMPSEVH----------GCFSSSQLTIIIEEFQAGVAVNKLFEAADIYLGA 74

Query: 78  KATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNL 137
                S ++ +V K  KEK  E+ +DRNEE  DVF+++ +KW LV        E +NPN 
Sbjct: 75  D-MAGSVRKVKVLKDRKEKKMEVTMDRNEEMTDVFENIRVKWTLV------CKEAKNPN- 126

Query: 138 GDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDA 197
              N  L+SE R YELSF K+HK +VLN YLP++LE++KAIKE +K +KLHTVM   W A
Sbjct: 127 --GNLDLQSEERSYELSFSKEHKGLVLNSYLPYILERSKAIKEGNKALKLHTVMSRSWQA 184

Query: 198 NNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKS 257
           + I + HPMTF+TLA+DSELK+ + +DL+NF+NGK+YY RIG+AWKRGYL+YGPPGTGKS
Sbjct: 185 DAINIDHPMTFQTLAMDSELKKALVDDLDNFINGKDYYRRIGKAWKRGYLVYGPPGTGKS 244

Query: 258 SLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVK-LQNRESSE 316
           SLIAAMAN LK+DIYDLDL A+ +NS+L+ LLL M SRS+LV+E +DC    LQ++E   
Sbjct: 245 SLIAAMANHLKYDIYDLDLRAIYNNSDLKLLLLAMSSRSILVMEHVDCMFNILQSQEEDC 304

Query: 317 VQATNQEENKVTLSGLLNFIDGLWSCCG-EGRIIVFTTNHKEKLDPALLRPGRMDMHLHM 375
             A  +  N+VTLSGLLNFIDG+WS CG +GRII+ TTNH++KLDPALLRPGRMDMH+HM
Sbjct: 305 SWAPRK--NQVTLSGLLNFIDGVWSFCGDQGRIIIITTNHRDKLDPALLRPGRMDMHIHM 362

Query: 376 SYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVK 435
           SYC  S FKQLAFN LG+ HH LF+QIE LI +V VTPAEV+GELMKS +   SL GL+ 
Sbjct: 363 SYCTVSAFKQLAFNCLGVRHHPLFQQIEGLISKVEVTPAEVSGELMKSKDPGTSLQGLIN 422

Query: 436 FLHAKMTQ 443
           FL  K+ +
Sbjct: 423 FLCNKIKE 430

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735750|emb|CBI18437.3| unnamed protein product [Vitis vinifera]

 Score =  494 bits (1273), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 246/428 (57%), Positives = 318/428 (74%), Gaps = 25/428 (5%)

Query: 19  MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ-GFSINQVFEAANYYLGN 77
           +LIR +  +F+P+E++            + SSQLTI++EEFQ G ++N++FEAA+ YLG 
Sbjct: 462 ILIRKITKNFMPSEVH----------GCFSSSQLTIIIEEFQAGVAVNKLFEAADIYLGA 511

Query: 78  KATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNL 137
                S ++ +V K  KEK  E+ +DRNEE  DVF+++ +KW LV        E +NPN 
Sbjct: 512 D-MAGSVRKVKVLKDRKEKKMEVTMDRNEEMTDVFENIRVKWTLV------CKEAKNPN- 563

Query: 138 GDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDA 197
              N  L+SE R YELSF K+HK +VLN YLP++LE++KAIKE +K +KLHTVM   W A
Sbjct: 564 --GNLDLQSEERSYELSFSKEHKGLVLNSYLPYILERSKAIKEGNKALKLHTVMSRSWQA 621

Query: 198 NNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKS 257
           + I + HPMTF+TLA+DSELK+ + +DL+NF+NGK+YY RIG+AWKRGYL+YGPPGTGKS
Sbjct: 622 DAINIDHPMTFQTLAMDSELKKALVDDLDNFINGKDYYRRIGKAWKRGYLVYGPPGTGKS 681

Query: 258 SLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVK-LQNRESSE 316
           SLIAAMAN LK+DIYDLDL A+ +NS+L+ LLL M SRS+LV+E +DC    LQ++E   
Sbjct: 682 SLIAAMANHLKYDIYDLDLRAIYNNSDLKLLLLAMSSRSILVMEHVDCMFNILQSQEEDC 741

Query: 317 VQATNQEENKVTLSGLLNFIDGLWSCCG-EGRIIVFTTNHKEKLDPALLRPGRMDMHLHM 375
             A  +  N+VTLSGLLNFIDG+WS CG +GRII+ TTNH++KLDPALLRPGRMDMH+HM
Sbjct: 742 SWAPRK--NQVTLSGLLNFIDGVWSFCGDQGRIIIITTNHRDKLDPALLRPGRMDMHIHM 799

Query: 376 SYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVK 435
           SYC  S FKQLAFN LG+ HH LF+QIE LI +V VTPAEV+GELMKS +   SL GL+ 
Sbjct: 800 SYCTVSAFKQLAFNCLGVRHHPLFQQIEGLISKVEVTPAEVSGELMKSKDPGTSLQGLIN 859

Query: 436 FLHAKMTQ 443
           FL  K+ +
Sbjct: 860 FLCNKIKE 867

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431310|ref|XP_002269184.1| PREDICTED: uncharacterized protein LOC100241950 [Vitis vinifera] gi|147815615|emb|CAN63838.1| hypothetical protein VITISV_041357 [Vitis vinifera]

 Score =  493 bits (1268), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 250/452 (55%), Positives = 324/452 (71%), Gaps = 20/452 (4%)

Query: 1   MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
           ++ AKTV STAASL A+AM+ RSV  DFLP E      S I  +   FS Q+T+V++EF 
Sbjct: 13  LASAKTVFSTAASLLATAMVFRSVLQDFLPYEAQQIFCSGIRRLFNRFSPQMTMVIDEFD 72

Query: 61  GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
           G + NQ+FEAA  YLG+K    S+QR RV +  KE+ F I ++R++E  DVF+ V  +W 
Sbjct: 73  GIAYNQIFEAAETYLGSKVC--SSQRLRVSRPAKERKFNINVERDQEIVDVFRGVKFRWL 130

Query: 121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
           L+  +  S   Y NP   D+N+++RSEVR +ELSFHKKH D+VLN Y P++L+++ ++ +
Sbjct: 131 LICIKTESRSIY-NPR--DFNSTIRSEVRSFELSFHKKHLDMVLNSYFPYILKESVSLIQ 187

Query: 181 ESKVVKLHTV--------MHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGK 232
           E K +KL TV        M   W  ++I L HP TF T+A+DSELK +I EDL+ F+  +
Sbjct: 188 EKKTLKLFTVDFEKMFGKMSDAW--SSISLDHPSTFDTIAMDSELKSKILEDLKRFVRRR 245

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTM 292
           +YY ++G+AWKRGYLLYGPPGTGKSSLIAA+AN L FDIYDL+L+ ++ NSELR LLL  
Sbjct: 246 DYYKKVGKAWKRGYLLYGPPGTGKSSLIAAIANYLNFDIYDLELTELRCNSELRRLLLAT 305

Query: 293 PSRSMLVIEDIDCSVKLQNRESSEVQATN----QEENKVTLSGLLNFIDGLWSCCGEGRI 348
            +RS+LV+EDIDC+++LQ+R S+E Q  N    Q E +VTLSGLLNFIDGLWS CG+ RI
Sbjct: 306 ANRSILVVEDIDCTIQLQDR-SAESQVMNPRSFQFEKQVTLSGLLNFIDGLWSSCGDERI 364

Query: 349 IVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE 408
           I+FTTNHK+KLDPALLRPGRMDMH+HMSYC    FK LA NYLGI +HYLF  IE LI+ 
Sbjct: 365 IIFTTNHKDKLDPALLRPGRMDMHIHMSYCTPYGFKILAANYLGIINHYLFSYIENLIQT 424

Query: 409 VNVTPAEVAGELMKSTNAEVSLNGLVKFLHAK 440
             VTPAEVA  L++S   E +L  L+KFL  K
Sbjct: 425 TEVTPAEVAEHLLQSDEPEKALRDLIKFLEVK 456

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357452221|ref|XP_003596387.1| Mitochondrial chaperone BCS1 [Medicago truncatula] gi|355485435|gb|AES66638.1| Mitochondrial chaperone BCS1 [Medicago truncatula]

 Score =  492 bits (1266), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 247/444 (55%), Positives = 320/444 (72%), Gaps = 10/444 (2%)

Query: 4   AKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFS 63
           +K VLS  AS++    L+R+V N+ +P E+ +++ S +H V + F++Q TIV+EEFQG +
Sbjct: 11  SKPVLSAVASIA----LMRTVTNELIPREVLNFVQSGLHHVFRQFNAQFTIVIEEFQGMT 66

Query: 64  INQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVY 123
            NQVFEAA  YLG KAT  SA+R +  KS + K     LDR+EE  DVF+ V++KWKL+ 
Sbjct: 67  RNQVFEAAEAYLGTKATV-SAERVKATKSMEHKKLSFNLDRDEEVSDVFEGVSVKWKLIC 125

Query: 124 TQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESK 183
            QV SS   R+ + G   +S  SE+R YEL+FHKKHK+ +++ YLP+V+E AK IK+   
Sbjct: 126 IQVDSS-RVRHFDRG---SSPVSEIRSYELTFHKKHKNKIIDSYLPYVMEIAKQIKQGIV 181

Query: 184 VVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWK 243
            +K+H+  + RW  + I   HPM+F TLA+D EL+REI  DL+ F+  KE+Y R G+AWK
Sbjct: 182 TLKIHSNEYNRWCHDPIKFNHPMSFTTLAIDEELQREIKNDLDKFVRAKEFYRRTGKAWK 241

Query: 244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDI 303
           RGYLLYGPPGTGKSSLIAAMAN L +DIYDLDL+ V  N  L+ L+L+M +RS+LVIEDI
Sbjct: 242 RGYLLYGPPGTGKSSLIAAMANYLNYDIYDLDLTNVGDNKSLKQLILSMSNRSILVIEDI 301

Query: 304 DCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPAL 363
           DCSVKLQNRE  E +  +   N +TLSGLLN +DGLWSCCGE  IIVFTTNHK++LDPAL
Sbjct: 302 DCSVKLQNREEDE-EVVHNGHNNMTLSGLLNAVDGLWSCCGEEHIIVFTTNHKDRLDPAL 360

Query: 364 LRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKS 423
           LRPGRMD  +H+SYCN S FKQL  NYL I+ H LFE+IE L+ EV VTPAE+A  L K 
Sbjct: 361 LRPGRMDKQIHLSYCNFSAFKQLVVNYLCITEHELFEKIEVLLGEVQVTPAEIAEVLTKD 420

Query: 424 TNAEVSLNGLVKFLHAKMTQQQKA 447
            +A   L  L+KFL AK   Q+++
Sbjct: 421 VDATECLQDLIKFLQAKKMVQEES 444

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561048|ref|XP_002521536.1| ATP binding protein, putative [Ricinus communis] gi|223539214|gb|EEF40807.1| ATP binding protein, putative [Ricinus communis]

 Score =  485 bits (1249), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 246/462 (53%), Positives = 329/462 (71%), Gaps = 21/462 (4%)

Query: 1   MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
           ++ AKTVLSTAAS++A+ ML RSVA D LP E +DY    I  +   FSSQ+T+VV+EF 
Sbjct: 10  LATAKTVLSTAASVAATVMLARSVAQDILPYEFHDYFLFNIRKILGRFSSQITMVVDEFD 69

Query: 61  GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
           GF  NQ++EAA  YL +   + S +RF+V K EKEK   + ++ NEE  DV++ V  KW 
Sbjct: 70  GFVHNQIYEAAETYLASN-ISPSTRRFKVSKPEKEKNLTVKMEGNEEIIDVYRGVKFKWI 128

Query: 121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
            V +QV  S    +P   D+NA+LRSEVR +E+SF KKHK++ L  YLPH++ +A+++ +
Sbjct: 129 FVCSQV-ESRNLHHP--FDHNATLRSEVRSFEVSFPKKHKEMALESYLPHIVREAESMVQ 185

Query: 181 ESKVVKLHTV--------MHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGK 232
           E K +++ +V        +   W   N  L HP TF+TLALD++LK  I EDLE F+  K
Sbjct: 186 EKKTLRIFSVDYDNIYGNLADAWKPVN--LDHPATFQTLALDAQLKGTILEDLERFVKRK 243

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTM 292
           +YY ++G+AWKRGYLLYGPPGTGKSSLIAAMAN LKFDIYDL+L+ ++ NSELR LL+  
Sbjct: 244 DYYRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDIYDLELTELRCNSELRKLLIAT 303

Query: 293 PSRSMLVIEDIDCSVKLQNR----ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI 348
            +RS+LV+EDIDC+++ Q+R     ++E  A    + +VTLSGLLNFIDGLWS CG+ RI
Sbjct: 304 ANRSILVVEDIDCTIEFQDRLAEANAAEFHAHYPPQKQVTLSGLLNFIDGLWSSCGDERI 363

Query: 349 IVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE 408
           I+FTTNHKEKLDPALLRPGRMD+H+HMSYC    F+ LA NYLGI  H+LF +IE+LI  
Sbjct: 364 IIFTTNHKEKLDPALLRPGRMDVHVHMSYCTPCGFRLLAANYLGIKDHHLFGRIEDLILT 423

Query: 409 VNVTPAEVAGELMKSTNAEVSLNGLVKFLHAK---MTQQQKA 447
             VTPAEVA +L++S   E  L+ L++FL  +   +T+Q+KA
Sbjct: 424 AQVTPAEVAEQLLRSDELETVLSELIQFLEVRKKEITEQEKA 465

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357452271|ref|XP_003596412.1| Mitochondrial chaperone BCS1 [Medicago truncatula] gi|355485460|gb|AES66663.1| Mitochondrial chaperone BCS1 [Medicago truncatula]

 Score =  484 bits (1245), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 242/449 (53%), Positives = 310/449 (69%), Gaps = 10/449 (2%)

Query: 1   MSKAKTVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
           M  +KT+LS  AS+    +L+R++ N+ +P EI +++ S +H   + FS+Q TIV+EEFQ
Sbjct: 1   MFDSKTLLSAMASI----VLVRNITNEVIPHEILNFVQSGLHHFCRQFSAQFTIVIEEFQ 56

Query: 61  GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
           G + NQVFEAA  YLG KAT  S +R +V KS   K     +DR EE  D F+ + +KWK
Sbjct: 57  GMAKNQVFEAAETYLGTKATV-STERVKVSKSHDHKKLSFNIDRGEEVSDDFEGIRVKWK 115

Query: 121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
           L+  Q   S    N    D  AS  SE+R YEL+FHKKHK+ +++ YLP+V+E AK IKE
Sbjct: 116 LICIQEDGSRIRHN----DMYASSMSEIRSYELTFHKKHKNKIIDSYLPYVMEMAKQIKE 171

Query: 181 ESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGR 240
            +  +K+H+  +  W    +   HPM+F TLA+D EL+REI  DL+NF+  KE+Y R G+
Sbjct: 172 ANMAIKIHSNDYGCWSHEPVKFNHPMSFNTLAIDEELQREIMNDLDNFVKAKEFYRRTGK 231

Query: 241 AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVI 300
           AW+RGYLLYGPPGTGKSSLIAAMAN L +DIYDLDL+ VQ N  L+ L+L M +RS+LVI
Sbjct: 232 AWQRGYLLYGPPGTGKSSLIAAMANYLNYDIYDLDLTDVQDNKILKQLILGMSNRSILVI 291

Query: 301 EDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLD 360
           EDIDC++ LQNRE  +    +   NKVTLSGLLN +DGLWSCCGE  IIVFTTNHK+KLD
Sbjct: 292 EDIDCTINLQNREEDK-DVVDNGYNKVTLSGLLNAVDGLWSCCGEEHIIVFTTNHKDKLD 350

Query: 361 PALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGEL 420
           PALLRPGRMD  +H+SYCN S  KQL  NYL I+ H LFE+IE L+ EV VTPAE+A EL
Sbjct: 351 PALLRPGRMDKQIHLSYCNFSALKQLVVNYLCITQHELFEEIEVLLGEVQVTPAEIAEEL 410

Query: 421 MKSTNAEVSLNGLVKFLHAKMTQQQKATN 449
            K  +A   L  L+K L AK   ++   N
Sbjct: 411 TKDCDATECLEDLIKSLQAKKMIKEDINN 439

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	449
TAIR|locus:2077997	576	BCS1 "cytochrome BC1 synthesis	0.986	0.769	0.508	6.5e-123
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.966	0.962	0.535	4e-122
TAIR|locus:2175986	505	AT5G17760 [Arabidopsis thalian	0.948	0.843	0.474	2.3e-103
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.908	0.824	0.477	3.1e-99
TAIR|locus:2053109	494	AT2G18190 [Arabidopsis thalian	0.910	0.827	0.479	3.2e-97
TAIR|locus:2175946	470	AT5G17730 [Arabidopsis thalian	0.937	0.895	0.437	1.6e-95
TAIR|locus:2175956	533	AT5G17740 [Arabidopsis thalian	0.937	0.789	0.446	2.1e-93
TAIR|locus:2098658	530	AT3G28510 [Arabidopsis thalian	0.677	0.573	0.360	2.8e-84
TAIR|locus:2095532	477	AT3G28600 [Arabidopsis thalian	0.837	0.788	0.433	9.3e-84
TAIR|locus:2098648	510	AT3G28540 [Arabidopsis thalian	0.654	0.576	0.371	9.3e-84

TAIR|locus:2077997 BCS1 "cytochrome BC1 synthesis" [Arabidopsis thaliana (taxid:3702)]

 Score = 1180 (420.4 bits), Expect = 6.5e-123, Sum P(2) = 6.5e-123
 Identities = 234/460 (50%), Positives = 323/460 (70%)

Query:     1 MSKAKTVXXXXXXXXXXXMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
             ++ AKTV           ML RS+  D+LP E++ Y+      +  YFSSQ+TI++EEF+
Sbjct:    55 LATAKTVLTTAASVAATAMLARSLVQDYLPDEVHHYISYGFRSIFGYFSSQMTIIIEEFE 114

Query:    61 GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
             GF+ N+VFEAA  YL  K + ++ +R +V K EKE  + + ++R+EE  D +  V  +W 
Sbjct:   115 GFAHNEVFEAAEAYLATKISPSN-KRIKVSKHEKENNYNVTVERDEEVVDTYNGVKFQW- 172

Query:   121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
             +++ +   S  + NP   D N++LRSEVR +EL+FHKK KDV L  YLP ++++A  +K+
Sbjct:   173 ILHCRHVESKHFHNPR--DLNSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRATLMKQ 230

Query:   181 ESKVVKLHTV----MHMRW-DA-NNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEY 234
             E K +K+ T+    M+  + DA  ++ L HP TFKTLA+DS++K  + EDL+ F+  +++
Sbjct:   231 EKKTLKIFTLSPENMYGNYSDAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFVKRRDF 290

Query:   235 YTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPS 294
             Y R+G+AWKRGYLLYGPPGTGKSSLIAAMAN L FDIYDL+L+AV +NSELR LL+   +
Sbjct:   291 YKRVGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLLIATAN 350

Query:   295 RSMLVIEDIDCSVKLQNRESSEV--QATNQEE---NKVTLSGLLNFIDGLWSCCGEGRII 349
             RS+L++EDIDCS++L++R S E   ++ + E+    KVTLSGLLNFIDGLWS CG+ RII
Sbjct:   351 RSILIVEDIDCSLELKDRTSDEPPRESDDIEDPRYKKVTLSGLLNFIDGLWSSCGDERII 410

Query:   350 VFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV 409
             +FTTN+KEKLD ALLRPGRMDMH+HMSYC  S FK LA NYL I  H LF +IEE I+  
Sbjct:   411 IFTTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKEHRLFSKIEEGIEAT 470

Query:   410 NVTPAEVAGELMKSTNAEVSLNGLVKFLHAKM--TQQQKA 447
              VTPAEVA +LM++ + +  L GL++FL  K    +Q KA
Sbjct:   471 EVTPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKA 510

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0052542 "defense response by callose deposition" evidence=RCA

TAIR|locus:2078007 AT3G50940 [Arabidopsis thaliana (taxid:3702)]

 Score = 1201 (427.8 bits), Expect = 4.0e-122, P = 4.0e-122
 Identities = 236/441 (53%), Positives = 312/441 (70%)

Query:     1 MSKAKTVXXXXXXXXXXXMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQ 60
             ++ AKT            +L RSV  D++P E+++Y+         YFS Q+T V+EEF 
Sbjct:     9 LATAKTALTAVASVAAAAILARSVVQDYMPNEVHEYISHGFRRFFSYFSYQMTAVIEEFG 68

Query:    61 GFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWK 120
             GF  NQVFEAA  YL  K +  S +R +V K EK+  + + ++R+EE  D+F  V L W 
Sbjct:    69 GFEHNQVFEAAEAYLSTKISN-STRRIKVNKLEKQSNYSVTVERDEEVVDIFDGVKLSWI 127

Query:   121 LVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKE 180
             LV   V    ++RNP   D N++L+SEVR YELSF KK K++VL  YLP V+E+A +IK+
Sbjct:   128 LVCRHVDKK-DFRNPR--DLNSTLKSEVRSYELSFRKKFKNMVLESYLPFVVEQAASIKQ 184

Query:   181 ESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGR 240
             + K +K+ TV     +  ++ L HP TF+TLALD E+K+ + EDL+ F+  K +Y R+G+
Sbjct:   185 KFKTLKIFTVDSYSVEWTSVTLDHPSTFRTLALDPEVKKNLVEDLDRFVQRKGFYGRVGK 244

Query:   241 AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVI 300
             AWKRGYLLYGPPGTGKSSLIAA+AN L FDIYDLDL+++ +N+ELR LL++  +RS+LV+
Sbjct:   245 AWKRGYLLYGPPGTGKSSLIAAIANHLNFDIYDLDLTSLNNNAELRRLLMSTANRSILVV 304

Query:   301 EDIDCSVKLQNRESSEVQATNQEENK-VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL 359
             EDIDCS++L++R +   Q  N   +K VTLSGLLNF+DGLWS CG  RIIVFTTN++EKL
Sbjct:   305 EDIDCSIELKDRSTD--QENNDPLHKTVTLSGLLNFVDGLWSSCGNERIIVFTTNYREKL 362

Query:   360 DPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGE 419
             DPALLRPGRMDMH+HMSYC  + FK LA NYL I  H LFEQIEE I+E+ VTPAEVA +
Sbjct:   363 DPALLRPGRMDMHIHMSYCTPAAFKVLASNYLEIQDHILFEQIEEFIREIEVTPAEVAEQ 422

Query:   420 LMKSTNAEVSLNGLVKFLHAK 440
             LM+S + +  L GLV+FL AK
Sbjct:   423 LMRSDSVDKVLQGLVEFLKAK 443

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175986 AT5G17760 [Arabidopsis thaliana (taxid:3702)]

 Score = 1024 (365.5 bits), Expect = 2.3e-103, P = 2.3e-103
 Identities = 211/445 (47%), Positives = 302/445 (67%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIH-LVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGN 77
             M+IRS+A++ +PA + D++   +  L  +  SS LT+ +++      N+++ AA  YL  
Sbjct:    25 MMIRSMAHELIPAPLQDFIYRTLRSLFFRSSSSTLTLTIDDDNMGMNNEIYRAAQTYLST 84

Query:    78 KATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSS-----MEY 132
             K +   A R R+ K  K+K   + L   E   DV++DV L W+ V            +  
Sbjct:    85 KISP-DAVRLRISKGHKDKHVNLYLSDGEIVNDVYEDVQLVWRFVTDGGDKKGGGGGVGG 143

Query:   133 RNPNLGDYNASLRSEVR--HYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTV 190
             R    G     +  + +  ++ELSF KKHKD++LN Y+P++  KAK I++E +++ LH++
Sbjct:   144 RGGG-GGRRGGMDDDGKSEYFELSFDKKHKDLILNSYVPYIESKAKEIRDERRILMLHSL 202

Query:   191 MHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYG 250
               +RW++  ++L+HP TF+T+A++ +LKR++ EDL+ F+  KE+Y R+G+AWKRGYLLYG
Sbjct:   203 NSLRWES--VILEHPSTFETMAMEDDLKRDVIEDLDRFIRRKEFYKRVGKAWKRGYLLYG 260

Query:   251 PPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQ 310
             PPGTGKSSL+AAMAN LKFD+YDL L++V  +S+LR LLL   +RS+LVIEDIDC+V L 
Sbjct:   261 PPGTGKSSLVAAMANYLKFDVYDLQLASVMRDSDLRRLLLATRNRSILVIEDIDCAVDLP 320

Query:   311 NRESSEVQATNQEENK--VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGR 368
             NR    V+  N+ E++  +TLSGLLNFIDGLWS CG+ RII+FTTNHK++LDPALLRPGR
Sbjct:   321 NRIEQPVEGKNRGESQGPLTLSGLLNFIDGLWSSCGDERIIIFTTNHKDRLDPALLRPGR 380

Query:   369 MDMHLHMSYCNTSVFKQLAFNYLGISH----HYLFEQIEELIKEVNVTPAEVAGELMKST 424
             MDMH++M +C+   FK LA NYLG+S     H LF +IE LI    +TPA+VA ELMKS 
Sbjct:   381 MDMHIYMGHCSFQGFKTLASNYLGLSDAAMPHRLFPEIERLIDGEVMTPAQVAEELMKSE 440

Query:   425 NAEVSLNGLVKFLHAKMTQQQKATN 449
             +A+V+L GLV  L  KM  + K +N
Sbjct:   441 DADVALEGLVNVLE-KMRLKSKESN 464

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:1005716649 AT2G18193 [Arabidopsis thaliana (taxid:3702)]

 Score = 985 (351.8 bits), Expect = 3.1e-99, P = 3.1e-99
 Identities = 211/442 (47%), Positives = 296/442 (66%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYF---SSQLTIVVEEFQGFSINQVFEAANYYL 75
             ML RS+ +DF+P ++  Y  S   L+ ++F   S  LT++++E  G + NQVF+AA  YL
Sbjct:    26 MLFRSMLHDFVPEKLRSYFSS---LLDRFFTPKSKYLTVIIDENFGLNRNQVFDAAEMYL 82

Query:    76 GNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNP 135
              +K    + +R RVGK  K+K F I+++R EE  D F++  +KW  V ++        N 
Sbjct:    83 RSKIGPET-ERLRVGKIPKQKHFTISIERGEEILDTFEESEVKWSYVQSE--------NE 133

Query:   136 NLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRW 195
               GD         R+YEL+F KK +D VLN YL HV+ +++ IK   +VVKL++      
Sbjct:   134 K-GD------KVKRYYELTFEKKLRDKVLNSYLTHVVAESEEIKRNLRVVKLYSRDVYAS 186

Query:   196 DANN---------IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGY 246
             D ++         I L+HP TF TLA+D   K++I +DLE F+  KE+Y R+G+AWKRGY
Sbjct:   187 DDDDGMAGGNWGCINLEHPSTFDTLAMDPNAKKKIIDDLERFLKRKEFYKRVGKAWKRGY 246

Query:   247 LLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCS 306
             LLYGPPGTGKSSLIAAMAN LKFD++DL+LS++  N EL+ +LL+  +RS+LVIEDIDC+
Sbjct:   247 LLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYDNGELKRVLLSTTNRSILVIEDIDCN 306

Query:   307 VKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRP 366
              ++++RE+ E Q   Q + KVTLSG+LNFIDGLWS  G+ RIIVFTTNHKE+LDPALLRP
Sbjct:   307 AEVRDREA-ENQEDEQIKGKVTLSGILNFIDGLWSSFGDERIIVFTTNHKERLDPALLRP 365

Query:   367 GRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHYLFEQIEELIKEVNVTPAEVAGELMKST 424
             GRMD+H++MSYC    F+ L  NYLG+   +H L E+IE L+    VTPAE+A ELM+  
Sbjct:   366 GRMDVHINMSYCTGLGFRTLVSNYLGLDGLNHPLCEEIEALVDSTEVTPAELAEELMQDD 425

Query:   425 NAEVSLNGLVKFLHAKMTQQQK 446
             + +V L G++ F+  +  ++ K
Sbjct:   426 DTDVVLRGVISFVEKRKVERSK 447

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2053109 AT2G18190 [Arabidopsis thaliana (taxid:3702)]

 Score = 966 (345.1 bits), Expect = 3.2e-97, P = 3.2e-97
 Identities = 213/444 (47%), Positives = 294/444 (66%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYF---SSQLTIVVEEFQGFSINQVFEAANYYL 75
             ML RS+ ND +P  +  Y+     L++++F   S  LT+V++E  GF  NQVF+AA  YL
Sbjct:    27 MLFRSLFNDEVPERLRSYITD---LLNRFFTPKSKNLTMVIDEIIGFKRNQVFDAAEVYL 83

Query:    76 GNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNP 135
              NK    +A R RVGK  K+K F I +++ EE  D F++  L+W    T V S  E    
Sbjct:    84 RNKIGPETA-RLRVGKLPKQKHFTIYIEKGEEILDTFENSELRW----TYVESENE---- 134

Query:   136 NLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHT--VMHM 193
                   AS + E R+YEL+F KK +D V+N YL HV+ +++  K + + VKL++  V   
Sbjct:   135 ------AS-QKEKRYYELTFEKKLRDKVMNSYLSHVVAESEETKRDLRAVKLYSRDVRAS 187

Query:   194 RWDANN-------IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGY 246
             + D          I L+HP TF+TLA+D   K++I +D+E F+  +E+Y R+G+AWKRGY
Sbjct:   188 KDDDGMAGAGWGCINLEHPSTFETLAMDPGAKKKIIDDMERFLKRREFYKRVGKAWKRGY 247

Query:   247 LLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCS 306
             LLYGPPGTGKSSLIAAMAN LKFD++DL+LS++  N++L+ +LL+  +RS+LVIEDIDCS
Sbjct:   248 LLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYENAQLKSILLSTTNRSILVIEDIDCS 307

Query:   307 -VKLQNRESSEVQATNQEE-NKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALL 364
               ++ +RE+ E Q   +    +VTLSGLLNF+DGLWS  G+ RIIVFTTNHKE+LDPALL
Sbjct:   308 SAEVVDREADEYQEYEEGYYGRVTLSGLLNFVDGLWSSFGDERIIVFTTNHKERLDPALL 367

Query:   365 RPGRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHYLFEQIEELIKEVNVTPAEVAGELMK 422
             RPGRMDMH++MSYC    F+ L  NYLG+   +H L E+IE LI    VTPAE+A ELM+
Sbjct:   368 RPGRMDMHINMSYCTGLGFRTLVSNYLGLGGLNHPLCEEIEALIDSTEVTPAELAEELMQ 427

Query:   423 STNAEVSLNGLVKFLHAKMTQQQK 446
               + +V L G+V F+  +  +  K
Sbjct:   428 EDDTDVVLRGVVSFVENRKVEISK 451

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175946 AT5G17730 [Arabidopsis thaliana (taxid:3702)]

 Score = 950 (339.5 bits), Expect = 1.6e-95, P = 1.6e-95
 Identities = 190/434 (43%), Positives = 283/434 (65%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEE-FQGFSINQVFEAANYYLGN 77
             M+I+      +P  + +Y+ S ++       S LT+++++  +    N+++ AA  Y+  
Sbjct:    25 MMIKPFLEMTIPPPLQNYMISYLNSFLHSTPSTLTLIIDDHIKNGMYNELYGAAQVYIST 84

Query:    78 KATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNL 137
             K    +A+R R+ +   EK   I     E   D+++ + +KW+       S+M +     
Sbjct:    85 KVNH-NAERLRISRDRSEKNVNIHFSVGEVVSDIYQGIEVKWRFCVDSNKSNMVHY---F 140

Query:   138 GDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTV--MHMRW 195
             G++   L  +    ELSF KKH ++VLN Y+P+V  KAK I  E K++K+++   M+++W
Sbjct:   141 GEH-FKLNPDRECVELSFEKKHTELVLNSYIPYVESKAKVINNERKILKMYSYCCMYLKW 199

Query:   196 DANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTG 255
              + N  L+HP TF T+A++ ELKR +  DL+ F+  K++Y R+G+ WKRGYLLYGPPGTG
Sbjct:   200 QSVN--LEHPSTFDTMAMNEELKRSVMGDLDRFIRRKDFYKRVGKPWKRGYLLYGPPGTG 257

Query:   256 KSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESS 315
             K+SL+AA+AN LKFDIYDL L++V+ +++LR LLL   + S+L++EDIDC+V L  R   
Sbjct:   258 KTSLVAAIANYLKFDIYDLQLASVREDADLRRLLLGTTNSSILLVEDIDCAVDLHTRLQP 317

Query:   316 EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHM 375
             + Q   +  + +TLSGLL  IDGLWS CG+ RI++FTT HKE+LDPALLRPGRMDMH+HM
Sbjct:   318 KTQDDTKGSSMLTLSGLLTCIDGLWSSCGDERIVIFTTTHKERLDPALLRPGRMDMHIHM 377

Query:   376 SYCNTSVFKQLAFNYLGISH---HYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNG 432
              +C   VFK LA NYLG+SH   H+L+ +IE LIK   +TPA+VA ELMK+ + +V+L G
Sbjct:   378 GHCCFDVFKTLASNYLGLSHDDPHHLYPEIERLIKGEVLTPAQVAEELMKNEDPDVALEG 437

Query:   433 LVKFLHAKMTQQQK 446
             LVK L  K  + +K
Sbjct:   438 LVKVLKRKRLELEK 451

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175956 AT5G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 930 (332.4 bits), Expect = 2.1e-93, P = 2.1e-93
 Identities = 197/441 (44%), Positives = 279/441 (63%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSI-NQVFEAANYYLGN 77
             M+I+ + N  +P  + +++ S +   +   SS LT+ +++     I ++++ AA  YL  
Sbjct:    25 MIIKPMINTIIPRPVQNFVFSYLKSFAGSRSSTLTLTIDQMSSMYIPDELYAAAQAYLST 84

Query:    78 KATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSM--EYRNP 135
             K +  S  R  + +   EK  ++ L   E   DV+  + LKW+ +     ++M  EY   
Sbjct:    85 KISPNSV-RLIMARDPAEKKVKLYLSDGEVVSDVYNGIKLKWRFLARNKNNTMVEEYGQ- 142

Query:   136 NLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRW 195
                 Y  +++ E    ELSF KKH+D+V+N Y+P+V  KAK +  + +++K+H   HM  
Sbjct:   143 ---SYQGNIQRE--SLELSFDKKHRDLVVNSYIPYVESKAKEVNNKRRILKMHCYSHMAQ 197

Query:   196 DANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTG 255
                ++  KHP TF T+A++ +LKR + EDL+ F+  K++Y R+G+AWKRGYLLYGPPGTG
Sbjct:   198 TWQSVNFKHPSTFDTMAMNDDLKRSMIEDLDRFVGRKDFYKRVGKAWKRGYLLYGPPGTG 257

Query:   256 KSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNR--- 312
             KSSL+AAMAN LKFDIYDL L++VQ ++ LR LLL   + S+L+IEDIDCSV L  R   
Sbjct:   258 KSSLVAAMANYLKFDIYDLQLASVQGDAHLRSLLLATNNSSILLIEDIDCSVDLPTRLQP 317

Query:   313 --ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
               E+S+     Q    +TLSGLLN IDGLWS CG  RII+FTTN+KEKLDPALLRPGRMD
Sbjct:   318 PTETSQPLGAVQVSKPLTLSGLLNCIDGLWSSCGNERIIIFTTNNKEKLDPALLRPGRMD 377

Query:   371 MHLHMSYCNTSVFKQLAFNYLGISH-----HYLFEQIEELIKEVNVTPAEVAGELMKSTN 425
             MH++M +C+   FK LA NYLG+S      H L   I+ LI    +TPA+VA ELMK  +
Sbjct:   378 MHIYMGHCSFQGFKTLASNYLGLSDENDDTHPLCPDIKHLIDGHVLTPAQVAEELMKDED 437

Query:   426 AEVSLNGLVKFLHAKMTQQQK 446
             A+ +L GLVK L  K  + +K
Sbjct:   438 ADAALEGLVKVLKRKRLEPKK 458

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2098658 AT3G28510 [Arabidopsis thaliana (taxid:3702)]

 Score = 545 (196.9 bits), Expect = 2.8e-84, Sum P(2) = 2.8e-84
 Identities = 116/322 (36%), Positives = 190/322 (59%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEF--QGFSINQVFEAANYYLG 76
             M   ++   ++PA    Y++   H +  + S  + I   E+  +G   +Q +++   YL 
Sbjct:    19 MFFWAIYKQYVPAHFRAYVERYFHKMIGWISYYVDIKFTEYTDEGLKRSQAYDSIRNYLA 78

Query:    77 NKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPN 136
             +K+T   A+R +  +++  K+   ++D +EE  D F+ V +KW   Y    S+++   P 
Sbjct:    79 SKSTAL-AKRLKANETKNSKSLVFSMDDHEEIEDEFEGVKVKW---Y----SNVKVIQPQ 130

Query:   137 LGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMR-- 194
               +Y      E RH+ LSFH++H+ +++  YL HVL + KAI   ++  KL+T    +  
Sbjct:   131 -SNYGQRSSEERRHFTLSFHRRHRGMIIETYLDHVLREGKAIGLMNRERKLYTNNSSQEW 189

Query:   195 --WDA---NNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLY 249
               W +   +N+   HP TF+TLA+D E K  I +DL  F  GK+YY ++G+ WKRGYLL+
Sbjct:   190 YPWRSGKWSNVPFHHPATFETLAMDPEKKEGIKKDLIKFSKGKDYYKKVGKPWKRGYLLF 249

Query:   250 GPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKL 309
             GPPGTGKS++IAA+AN L +D+YDL+L+ V+ NSEL+ LLL   S+S++VIEDIDCS+ L
Sbjct:   250 GPPGTGKSTMIAAIANFLDYDVYDLELTTVKDNSELKKLLLDTTSKSIIVIEDIDCSLDL 309

Query:   310 QNRESSEVQATNQEENKVTLSG 331
               +   + +   +E+ +    G
Sbjct:   310 TGQRKKKKEEDEEEDGEEKKEG 331

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0001666 "response to hypoxia" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2095532 AT3G28600 [Arabidopsis thaliana (taxid:3702)]

 Score = 820 (293.7 bits), Expect = 9.3e-84, Sum P(2) = 9.3e-84
 Identities = 181/418 (43%), Positives = 259/418 (61%)

Query:    47 YFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNE 106
             +FS  + I   +++ +  N  F A   YLG KAT   A+  R  + ++ K   + L R+E
Sbjct:    57 FFSPYVEISFSQYEDYQFNHAFAAIETYLGAKATD-KAKHLRASQVKESKG--LVLKRDE 113

Query:   107 -ETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLN 165
              +  D ++  T+ W++       S  YR                 ++L+FH++ +D+V +
Sbjct:   114 TKVRDEYEGGTVWWEME----TDSTGYRT----------------FKLTFHRRSRDIVTD 153

Query:   166 LYLPHVLEKAKAIKEESKVVKLHTVM-HMRWDANN------IVLKHPMTFKTLALDSELK 218
              Y+ +V E+ K+I+ +SK +KL T      W  +       I  +HP +F TLA+D++ K
Sbjct:   154 SYIKYVFEEGKSIQAKSKQMKLFTNNPSSHWGTSKKSFWRYIDFEHPASFHTLAMDTKKK 213

Query:   219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA 278
              EI  DL  F NGKEYY +IG+AWKRGYLL+GPPGTGKS++IAAMAN L + IYDL+L+A
Sbjct:   214 EEILNDLAAFSNGKEYYKKIGKAWKRGYLLHGPPGTGKSTMIAAMANHLNYSIYDLELTA 273

Query:   279 VQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEV----------QATNQEENKVT 328
             +++NSELR LL    S+S++VIEDIDCS+ L  +   E           Q T ++++ VT
Sbjct:   274 IRNNSELRKLLTATSSKSIIVIEDIDCSLDLTGKRKKEKNLMTSREDGEQGTEEDKSFVT 333

Query:   329 LSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAF 388
             LSGLLNFIDG+WS CG+ RII+FTTNH EKLDPAL+R GRMDMH+ +SYC+   FK LA 
Sbjct:   334 LSGLLNFIDGIWSACGQERIIIFTTNHFEKLDPALIRRGRMDMHIELSYCSFEAFKILAK 393

Query:   389 NYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQQQK 446
             NYL +  H LF++IE L+KE  + PA+VA  LMK  N E+  +G +K L   +  ++K
Sbjct:   394 NYLDLDTHPLFKKIESLLKETKIAPADVAENLMKK-NTEIDADGSLKDLIQALEGKKK 450

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2098648 AT3G28540 [Arabidopsis thaliana (taxid:3702)]

 Score = 525 (189.9 bits), Expect = 9.3e-84, Sum P(2) = 9.3e-84
 Identities = 119/320 (37%), Positives = 189/320 (59%)

Query:    19 MLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEF---QGFSINQVFEAANYYL 75
             M   SV   F+P +I DYL+   + +    S+ + I   E+   +G   +Q ++    YL
Sbjct:    19 MFFWSVYRQFVPYQIRDYLEKCFYKMFGLVSNSVHIKFTEYTEDKGLKKSQAYDLIRNYL 78

Query:    76 GNKATTTSAQRFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNP 135
              +K+T   AQR +  +S+  K+  ++LD +E   DVF+ V + W L       S+ +++ 
Sbjct:    79 SSKSTAR-AQRLKANESKNSKSLVLSLDNHEAVEDVFQGVKVVWSL-------SV-WKSN 129

Query:   136 NLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVM---- 191
             +  D      SE R+  LSFH ++++++   YL HVL + K I  +++  KL+T      
Sbjct:   130 DQAD-----SSEKRYLTLSFHNRYREMITTTYLDHVLREGKEIGLKNRERKLYTNNSSQD 184

Query:   192 HMRWDA---NNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLL 248
             +  W     +N+   HP TF+TLA+D E K  + +DL  F  GK+YY ++G+ WKRGYLL
Sbjct:   185 YSAWREGRWSNVPFDHPATFETLAMDLEKKEGMKKDLIKFTKGKDYYRKVGKPWKRGYLL 244

Query:   249 YGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVK 308
             +GPPGTGKS++I+AMAN L++D+YDL+L+ V+ NSEL+ L+L    +S++VIEDIDCS+ 
Sbjct:   245 FGPPGTGKSTMISAMANFLEYDVYDLELTTVKDNSELKKLMLDTKGKSIVVIEDIDCSLD 304

Query:   309 L--QNRESSEVQATNQEENK 326
             L  Q ++  E     +EE K
Sbjct:   305 LTGQRKKKKEEDEDEEEEEK 324

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

GO:0017111 "nucleoside-triphosphatase activity" 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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00029625001 SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (459 aa) (Vitis vinifera)

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	449
pfam14363	100	pfam14363, AAA_assoc, Domain associated at C-termi	3e-25
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	6e-20
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-14
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	4e-13
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-12
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	5e-12
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	9e-12
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	2e-11
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	3e-11
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	7e-11
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-10
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	1e-09
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	1e-09
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	2e-09
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	2e-07
smart00382	148	smart00382, AAA, ATPases associated with a variety	4e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-06
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	8e-05
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	8e-05
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-04
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	2e-04
pfam13207	114	pfam13207, AAA_17, AAA domain	0.001
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.002
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.003
TIGR00678	188	TIGR00678, holB, DNA polymerase III, delta' subuni	0.003
PRK08939	306	PRK08939, PRK08939, primosomal protein DnaI; Revie	0.004
CHL00206	2281	CHL00206, ycf2, Ycf2; Provisional	0.004

>gnl|CDD|222710 pfam14363, AAA_assoc, Domain associated at C-terminal with AAA

 Score = 98.8 bits (247), Expect = 3e-25
 Identities = 40/98 (40%), Positives = 58/98 (59%), Gaps = 4/98 (4%)

Query: 28  FLPAEIYDYLDSKIH-LVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQR 86
            LP E+ +YL S +  L    FS  LTIV++E+ GFS NQ+++AA  YL  K  + SA+R
Sbjct: 1   LLPHELREYLSSLLRRLFGSRFSPYLTIVIDEYDGFSRNQLYDAAEAYLSTK-ISPSARR 59

Query: 87  FRVGKSEKEKT--FEIALDRNEETFDVFKDVTLKWKLV 122
            +  K++K K     ++LD  EE  DVF+ V + W  V
Sbjct: 60  LKASKAKKSKNSSLVLSLDDGEEVTDVFEGVKVWWTSV 97

This domain is found in association with the AAA family, pfam00004. Length = 100

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

 Score = 85.0 bits (211), Expect = 6e-20
 Identities = 41/140 (29%), Positives = 65/140 (46%), Gaps = 17/140 (12%)

Query: 246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV------QSNSELR--FLLLTMPSRSM 297
            LLYGPPGTGK++L  A+A +L     ++  S +      +S   LR  F      +  +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 298 LVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE 357
           + I++ID     +             E++  ++ LL  +DG  +      I++  TN  +
Sbjct: 61  IFIDEIDALAGSRGSGGD-------SESRRVVNQLLTELDGF-TSSLSKVIVIAATNRPD 112

Query: 358 KLDPALLRPGRMDMHLHMSY 377
           KLDPALLR GR D  +    
Sbjct: 113 KLDPALLR-GRFDRIIEFPL 131

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

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score = 74.9 bits (184), Expect = 2e-14
 Identities = 57/164 (34%), Positives = 81/164 (49%), Gaps = 19/164 (11%)

Query: 216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           E K +I E +E  M   E +  +G    +G LLYGPPGTGK+ L  A+AN+       ++
Sbjct: 185 EAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISIN 244

Query: 276 ----LSAVQSNSELR----FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKV 327
               +S     SE R    F      + S++ I++ID     +   + EV+       K 
Sbjct: 245 GPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVE-------KR 297

Query: 328 TLSGLLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMD 370
            ++ LL  +DGL    G GR+IV   TN  + LDPAL RPGR D
Sbjct: 298 VVAQLLTLMDGLK---GRGRVIVIGATNRPDALDPALRRPGRFD 338

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. Length = 733

>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated

 Score = 71.2 bits (175), Expect = 4e-13
 Identities = 55/175 (31%), Positives = 86/175 (49%), Gaps = 21/175 (12%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TF+ +A   E K E  E++ +F+   E +T +G    +G LL GPPGTGK+ L  A+A +
Sbjct: 181 TFRDIAGIEEAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE 239

Query: 267 LKFDIYDLDLSAVQ------SNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNRESSEVQ 318
            +   + +  S           + +R L       S  ++ I++ID +V  Q    + + 
Sbjct: 240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEID-AVGRQ--RGAGIG 296

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGR---IIVFTTNHKEKLDPALLRPGRMD 370
             N E  + TL+ LL  +DG      +G    I++  TN  + LD ALLRPGR D
Sbjct: 297 GGNDEREQ-TLNQLLTEMDGF-----KGNKGVIVIAATNRVDILDAALLRPGRFD 345

Length = 638

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

 Score = 69.5 bits (170), Expect = 1e-12
 Identities = 48/172 (27%), Positives = 79/172 (45%), Gaps = 17/172 (9%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           T   +    E K E+ E +E  +   E + ++G    +G LLYGPPGTGK+ L  A+A +
Sbjct: 240 TLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE 299

Query: 267 LK--------FDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            +         ++    +   + N    F      + S++ I++ID    L +       
Sbjct: 300 SRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEID---SLASGRGP--- 353

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
            +     +  +  LL  +DG+     EG +++  TN  + LDPALLRPGR D
Sbjct: 354 -SEDGSGRRVVGQLLTELDGI--EKAEGVLVIAATNRPDDLDPALLRPGRFD 402

Length = 494

>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional

 Score = 67.1 bits (164), Expect = 5e-12
 Identities = 59/170 (34%), Positives = 82/170 (48%), Gaps = 34/170 (20%)

Query: 219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA 278
           +EI E +E  +   E Y  IG    +G +LYGPPGTGK+ L  A+AN+         L  
Sbjct: 193 QEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATF----LRV 248

Query: 279 VQSNSEL--------------RFLLLTMPSRSMLVIEDIDC-SVKLQNRESS---EVQAT 320
           V   SEL               F +    + S++ I++ID    K  +  S    E+Q T
Sbjct: 249 V--GSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRT 306

Query: 321 NQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
             E        LLN +DG  S  G+ ++I+  TN  E LDPAL+RPGR+D
Sbjct: 307 MLE--------LLNQLDGFDS-RGDVKVIM-ATNRIESLDPALIRPGRID 346

Length = 438

>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score = 66.6 bits (162), Expect = 9e-12
 Identities = 51/172 (29%), Positives = 80/172 (46%), Gaps = 15/172 (8%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TF  +A   E K E+ E L  ++     + ++G    +G L+ GPPGTGK+ L  A+A +
Sbjct: 150 TFADVAGCDEAKEEVAE-LVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 208

Query: 267 LKF--------DIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            K         D  ++ +    S     F      +  ++ I++ID       R+     
Sbjct: 209 AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAV----GRQRGAGL 264

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
               +E + TL+ +L  +DG      EG I++  TN  + LDPALLRPGR D
Sbjct: 265 GGGHDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFD 314

Length = 644

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

 Score = 65.0 bits (159), Expect = 2e-11
 Identities = 59/179 (32%), Positives = 83/179 (46%), Gaps = 41/179 (22%)

Query: 213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--FD 270
           LD ++ +EI E +E  +   E +  +G    +G LLYGPPGTGK+ L  A+ANQ    F 
Sbjct: 156 LDEQI-QEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATF- 213

Query: 271 IYDLDLSAVQSNSEL------------R--FLLLTMPSRSMLVIEDIDCSVKLQNRESS- 315
              + +      SEL            R  F L    + S++ I++ID     +    + 
Sbjct: 214 ---IRVVG----SELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTS 266

Query: 316 ---EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI-IVFTTNHKEKLDPALLRPGRMD 370
              EVQ T  E        LLN +DG       G + ++  TN  + LDPALLRPGR D
Sbjct: 267 GDREVQRTMLE--------LLNQLDGFDP---RGNVKVIMATNRPDILDPALLRPGRFD 314

Length = 406

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score = 65.3 bits (159), Expect = 3e-11
 Identities = 46/163 (28%), Positives = 78/163 (47%), Gaps = 16/163 (9%)

Query: 216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           E+K+E+ E +E  +   E + ++G    +G LL+GPPGTGK+ L  A+A +   +   + 
Sbjct: 460 EVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVR 519

Query: 276 ----LSAVQSNSELRFLLLTMPSR----SMLVIEDIDCSVKLQNRESSEVQATNQEENKV 327
               LS     SE     +   +R    +++  ++ID     +         T++  N+ 
Sbjct: 520 GPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDT-SVTDRIVNQ- 577

Query: 328 TLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
               LL  +DG+        +++  TN  + LDPALLRPGR D
Sbjct: 578 ----LLTEMDGIQE--LSNVVVIAATNRPDILDPALLRPGRFD 614

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. Length = 733

>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score = 63.5 bits (155), Expect = 7e-11
 Identities = 58/182 (31%), Positives = 88/182 (48%), Gaps = 23/182 (12%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TFK +A   E K E+ E ++ F+     +T++G    +G LL GPPGTGK+ L  A+A +
Sbjct: 53  TFKDVAGIDEAKEELMEIVD-FLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE 111

Query: 267 LK---FDIYDLD-------LSAVQSNSELRFLLLTMPSR--SMLVIEDIDCSVKLQNRES 314
                F I   D       + A    S +R L          ++ I++ID +V    R+ 
Sbjct: 112 AGVPFFSISGSDFVEMFVGVGA----SRVRDLFEQAKKNAPCIIFIDEID-AV---GRQR 163

Query: 315 SEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLH 374
                   +E + TL+ LL  +DG  +    G I++  TN  + LDPALLRPGR D  + 
Sbjct: 164 GAGLGGGNDEREQTLNQLLVEMDGFGT--NTGVIVIAATNRPDVLDPALLRPGRFDRQVV 221

Query: 375 MS 376
           + 
Sbjct: 222 VD 223

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 [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional

 Score = 62.9 bits (153), Expect = 1e-10
 Identities = 55/169 (32%), Positives = 75/169 (44%), Gaps = 30/169 (17%)

Query: 218 KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS 277
           K+EI E +E  +   E Y +IG    RG LLYGPPGTGK+ L  A+A+          + 
Sbjct: 154 KQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATF----IR 209

Query: 278 AVQSNSELRFL------------LLTMPSRSMLVIEDIDC----SVKLQNRESSEVQATN 321
            V S    ++L            L    + S++ I+++D         Q     EVQ   
Sbjct: 210 VVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQR-- 267

Query: 322 QEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
                  L  LLN +DG         I+   TN  + LDPALLRPGR+D
Sbjct: 268 ------ILLELLNQMDGFDQTTNVKVIM--ATNRADTLDPALLRPGRLD 308

Length = 398

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

 Score = 56.8 bits (137), Expect = 1e-09
 Identities = 33/149 (22%), Positives = 51/149 (34%), Gaps = 30/149 (20%)

Query: 243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV-----------QSNSELRFL 288
            +  LLYGPPGTGK++L  A+AN+L         L+ S +                L F 
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78

Query: 289 LLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI 348
           L       +L I++ID    L     + +              L    D       E   
Sbjct: 79  LAEKAKPGVLFIDEID---SLSRGAQNALLRV-----------LETLNDLRIDR--ENVR 122

Query: 349 IVFTTNHKEKLDPALLRPGRMDMHLHMSY 377
           ++  TN     D       R+D+ + +  
Sbjct: 123 VIGATNRPLLGDLDRALYDRLDIRIVIPL 151

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

>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

 Score = 60.0 bits (146), Expect = 1e-09
 Identities = 55/177 (31%), Positives = 83/177 (46%), Gaps = 19/177 (10%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TF  +A   E K E++E ++   N K+Y   +G    +G LL GPPGTGK+ L  A+A +
Sbjct: 148 TFADVAGVDEAKEELSELVDFLKNPKKY-QALGAKIPKGVLLVGPPGTGKTLLAKAVAGE 206

Query: 267 LKFDIYDLDLSAVQS--------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSE 316
               +    +S             S +R L       +  ++ I++ID       R+   
Sbjct: 207 A--GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEID----AVGRQRGA 260

Query: 317 VQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHL 373
                 +E + TL+ LL  +DG      EG I++  TN  + LDPALLRPGR D  +
Sbjct: 261 GLGGGNDEREQTLNQLLVEMDG--FGGNEGVIVIAATNRPDVLDPALLRPGRFDRQI 315

Length = 596

>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family

 Score = 59.0 bits (143), Expect = 2e-09
 Identities = 51/160 (31%), Positives = 81/160 (50%), Gaps = 14/160 (8%)

Query: 219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA 278
           REI E +E  +   E +  +G    +G LLYGPPGTGK+ L  A+A++       +  S 
Sbjct: 132 REIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSE 191

Query: 279 V------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS 330
           +      +    +R  F L    + S++ I++ID    +  + +    + ++E  + TL 
Sbjct: 192 LVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDA---IAAKRTDSGTSGDREVQR-TLM 247

Query: 331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
            LL  +DG +   G  ++I   TN  + LDPALLRPGR D
Sbjct: 248 QLLAELDG-FDPRGNVKVIA-ATNRPDILDPALLRPGRFD 285

Many proteins may score above the trusted cutoff because an internal. Length = 364

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

 Score = 52.5 bits (127), Expect = 2e-07
 Identities = 58/179 (32%), Positives = 84/179 (46%), Gaps = 41/179 (22%)

Query: 213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--FD 270
           L+ ++ RE+ E +E  +   E +  +G    +G LLYGPPGTGK+ L  A+A++    F 
Sbjct: 136 LEEQI-REVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATF- 193

Query: 271 IYDLDLSAVQSNSEL------------R--FLLLTMPSRSMLVIEDIDCSVKLQNRESS- 315
           I           SEL            R  F L    + S++ I++ID ++  +  +S  
Sbjct: 194 IR-------VVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEID-AIAAKRTDSGT 245

Query: 316 ----EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
               EVQ         TL  LL  +DG     G  +II   TN  + LDPA+LRPGR D
Sbjct: 246 SGDREVQR--------TLMQLLAEMDGFDP-RGNVKIIA-ATNRIDILDPAILRPGRFD 294

Length = 389

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

 Score = 46.2 bits (109), Expect = 4e-06
 Identities = 31/146 (21%), Positives = 55/146 (37%), Gaps = 16/146 (10%)

Query: 243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIY-----DLDLSAVQSNSELRFLLLTMPSRSM 297
               L+ GPPG+GK++L  A+A +L          D +    +   +L  +++     S 
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 298 LVIEDIDCSVKLQNRESS--------EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII 349
                +   + L              E+ +    E +  L  L      L     +   +
Sbjct: 62  SGELRLR--LALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTV 119

Query: 350 VFTTNHKEKLDPALLRPGRMDMHLHM 375
           + TTN ++ L PALLR  R D  + +
Sbjct: 120 ILTTNDEKDLGPALLRR-RFDRRIVL 144

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

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

 Score = 48.0 bits (115), Expect = 7e-06
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 9/73 (12%)

Query: 205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
           P T   +  + + K ++ E +E+++ GK          K+  LLYGPPG GK+SL  A+A
Sbjct: 10  PKTLSDVVGNEKAKEQLREWIESWLKGKP---------KKALLLYGPPGVGKTSLAHALA 60

Query: 265 NQLKFDIYDLDLS 277
           N   +++ +L+ S
Sbjct: 61  NDYGWEVIELNAS 73

Length = 482

>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated

 Score = 43.9 bits (104), Expect = 8e-05
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 10/69 (14%)

Query: 209 KTLALDSELKREITEDLENFMNGKEYYTRIGRA----WK------RGYLLYGPPGTGKSS 258
           K+ +L  E  R  T +   F  G E   +I R     ++       G LL+G  GTGK+ 
Sbjct: 70  KSNSLLDEKFRNSTFENFLFDKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTY 129

Query: 259 LIAAMANQL 267
           L A +AN+L
Sbjct: 130 LAACIANEL 138

Length = 268

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

 Score = 44.3 bits (106), Expect = 8e-05
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 7/54 (12%)

Query: 238 IGRAWKRGYL----LYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN-SELR 286
           + R  + G L    L+GPPGTGK++L   +A           LSAV S   +LR
Sbjct: 27  LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFE--ALSAVTSGVKDLR 78

Length = 413

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

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 52/189 (27%), Positives = 84/189 (44%), Gaps = 23/189 (12%)

Query: 229 MNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-----YDLDLSAVQSNS 283
           +   E + ++G    +G LL+GPPGTGK+ L  A+AN+    +       L     +S  
Sbjct: 4   LKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANEGAEFLSINGPEILSKYVGESEL 63

Query: 284 ELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS 341
            LR  F      + S++ I++ID     ++ +  EV      E +V  + LL  +DGL  
Sbjct: 64  RLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEV------ERRVV-AQLLALMDGL-- 114

Query: 342 CCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE 400
               G++IV   TN  + LDPA  RPGR D  + ++  +    +      L I    +F 
Sbjct: 115 --KRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPD----EAGRLEILQIHTRLMFL 168

Query: 401 QIEELIKEV 409
                 K +
Sbjct: 169 GPPGTGKTL 177

Length = 494

>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 47/162 (29%), Positives = 71/162 (43%), Gaps = 32/162 (19%)

Query: 232 KEYYTRIGRAWKRGYLLYGPPGTGKS--------SLIAAMANQLKFDIYDLD------LS 277
            E Y   G    +G LLYGPPG GK+        SL A +  +     Y L+      L+
Sbjct: 205 PELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLN 264

Query: 278 AVQSNSELRFLLLTMPSRS-----MLVIEDID-CSVKLQNRE---SSEVQATNQEENKVT 328
                +E +  L+   +R        VI   D      + R    SS+V+ T        
Sbjct: 265 KYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVSSDVETT-------V 317

Query: 329 LSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
           +  LL  IDG+ S   +  I++  +N ++ +DPA+LRPGR+D
Sbjct: 318 VPQLLAEIDGVESL--DNVIVIGASNREDMIDPAILRPGRLD 357

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 [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

>gnl|CDD|221983 pfam13207, AAA_17, AAA domain

 Score = 38.4 bits (89), Expect = 0.001
 Identities = 13/30 (43%), Positives = 19/30 (63%)

Query: 246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
            L+ GPPG+GKS+L   +A +L   +  LD
Sbjct: 2   ILITGPPGSGKSTLAKKLAEKLGIPVISLD 31

Length = 114

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

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 3/40 (7%)

Query: 248 LYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN-SELR 286
           L+GPPGTGK++L   +A           LSAV S   +LR
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFE--ALSAVTSGVKDLR 90

Length = 436

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

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 12/39 (30%), Positives = 16/39 (41%)

Query: 232 KEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD 270
            +   R         LL GP GTGK+SL+  +   L   
Sbjct: 13  LDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVA 51

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

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

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 5/38 (13%)

Query: 235 YTRIGRAWKRG-----YLLYGPPGTGKSSLIAAMANQL 267
           Y ++ RA ++G     YL  GP G GK  L  A+A  L
Sbjct: 1   YQQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKAL 38

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

>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed

 Score = 38.7 bits (91), Expect = 0.004
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 9/50 (18%)

Query: 219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK 268
               + LE +  G+           +G  LYG  G GKS L+AA+AN+L 
Sbjct: 141 MAALDFLEAYPPGE---------KVKGLYLYGDFGVGKSYLLAAIANELA 181

Length = 306

>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 43/183 (23%), Positives = 70/183 (38%), Gaps = 47/183 (25%)

Query: 231  GKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA-----------------NQLKF---- 269
            GK +  R+  +  RG L+ G  GTG+S L+  +A                 N+ K     
Sbjct: 1618 GKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLID 1677

Query: 270  -----DIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDID----------------CSVK 308
                 D  D+D S          LL  M + +M ++  ID                C + 
Sbjct: 1678 DIDIDDSDDIDDSDDIDRDLDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIW 1737

Query: 309  LQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH-KEKLDPALLRPG 367
            + N     V     E N ++L  L+N +      C    I+V  + H  +K+DPAL+ P 
Sbjct: 1738 IPNIHDLNVN----ESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPN 1793

Query: 368  RMD 370
            +++
Sbjct: 1794 KLN 1796

Length = 2281

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	449
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.98
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.98
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.97
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.97
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.97
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.97
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.97
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.97
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.97
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.97
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.97
CHL00195	489	ycf46 Ycf46; Provisional	99.97
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.96
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.96
PF14363	98	AAA_assoc: Domain associated at C-terminal with AA	99.96
CHL00176	638	ftsH cell division protein; Validated	99.96
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.96
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.95
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.95
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.95
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.95
CHL00206	2281	ycf2 Ycf2; Provisional	99.95
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.94
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.92
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.92
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.92
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.92
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.91
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.85
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.83
PF00004	132	AAA: ATPase family associated with various cellula	99.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.8
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.78
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.76
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.75
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.75
CHL00181	287	cbbX CbbX; Provisional	99.75
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.74
PRK04195	482	replication factor C large subunit; Provisional	99.72
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.71
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.71
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.7
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.7
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.69
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.67
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.67
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.66
PLN03025	319	replication factor C subunit; Provisional	99.66
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.66
PHA02544	316	44 clamp loader, small subunit; Provisional	99.66
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.64
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.64
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.62
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.62
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.62
PRK06893	229	DNA replication initiation factor; Validated	99.61
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.61
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.61
PRK13342	413	recombination factor protein RarA; Reviewed	99.61
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.6
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.59
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.59
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.58
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.58
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.58
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.57
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.57
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.57
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.56
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.56
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.56
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.56
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.55
PRK12402	337	replication factor C small subunit 2; Reviewed	99.55
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.55
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.54
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.54
PRK10865	857	protein disaggregation chaperone; Provisional	99.54
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.53
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.53
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.53
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.51
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.51
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.51
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.51
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.51
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.51
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.5
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.5
PRK08084	235	DNA replication initiation factor; Provisional	99.5
PRK13341	725	recombination factor protein RarA/unknown domain f	99.5
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.49
PRK08727	233	hypothetical protein; Validated	99.49
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.49
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.49
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.49
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.49
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.48
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.48
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.48
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.46
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.45
CHL00095	821	clpC Clp protease ATP binding subunit	99.45
PRK05642	234	DNA replication initiation factor; Validated	99.43
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.42
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.42
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.42
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.41
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.41
KOG2028	554	consensus ATPase related to the helicase subunit o	99.4
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.4
PRK12422	445	chromosomal replication initiation protein; Provis	99.39
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.39
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.39
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.37
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.36
COG0714	329	MoxR-like ATPases [General function prediction onl	99.35
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.35
PRK06620	214	hypothetical protein; Validated	99.35
PHA02244	383	ATPase-like protein	99.34
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.32
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.31
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.3
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.3
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.3
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.29
PRK10865	857	protein disaggregation chaperone; Provisional	99.28
PRK09087	226	hypothetical protein; Validated	99.27
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.26
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.25
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.24
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.24
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.23
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.22
CHL00095	821	clpC Clp protease ATP binding subunit	99.22
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.22
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.22
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.21
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.21
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.18
PRK07952	244	DNA replication protein DnaC; Validated	99.17
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.16
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.16
PF07726	131	AAA_3: ATPase family associated with various cellu	99.16
PRK08116	268	hypothetical protein; Validated	99.14
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.13
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.12
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.1
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.1
PRK13531	498	regulatory ATPase RavA; Provisional	99.09
smart00382	148	AAA ATPases associated with a variety of cellular	99.07
PRK08181	269	transposase; Validated	99.06
smart00350	509	MCM minichromosome maintenance proteins.	99.06
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.05
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.04
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.04
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.03
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.01
PRK12377	248	putative replication protein; Provisional	99.01
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.99
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.98
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.98
PRK08939	306	primosomal protein DnaI; Reviewed	98.98
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.97
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.97
COG0593	408	DnaA ATPase involved in DNA replication initiation	98.97
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.96
PRK06526	254	transposase; Provisional	98.96
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.96
PRK04132	846	replication factor C small subunit; Provisional	98.94
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.94
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.92
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.92
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.91
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.9
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.86
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.86
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.84
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.84
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.84
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.83
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.82
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.82
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.79
PRK09183	259	transposase/IS protein; Provisional	98.79
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.77
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.77
PRK06835	329	DNA replication protein DnaC; Validated	98.76
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.76
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.75
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.75
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.74
PRK06921	266	hypothetical protein; Provisional	98.74
PF13173	128	AAA_14: AAA domain	98.73
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.71
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.65
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.64
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.62
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.62
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.61
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.6
PRK09862	506	putative ATP-dependent protease; Provisional	98.58
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.58
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.56
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.56
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.55
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.52
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.52
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.51
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.5
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.49
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.47
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.46
PF05729	166	NACHT: NACHT domain	98.45
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.44
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.42
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.42
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.41
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.41
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.39
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.37
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.37
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.36
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.34
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.32
PRK15115	444	response regulator GlrR; Provisional	98.32
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.31
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.3
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.27
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.27
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.24
COG2204	464	AtoC Response regulator containing CheY-like recei	98.24
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.23
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.2
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.19
PHA02774	613	E1; Provisional	98.17
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.16
PHA02624	647	large T antigen; Provisional	98.15
PHA00729	226	NTP-binding motif containing protein	98.06
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.04
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	98.01
PRK15455	644	PrkA family serine protein kinase; Provisional	98.0
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.99
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.98
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.95
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.93
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.93
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.88
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	97.86
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.84
PRK00131	175	aroK shikimate kinase; Reviewed	97.83
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.83
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.8
PF14516	331	AAA_35: AAA-like domain	97.79
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.76
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.73
PRK08118	167	topology modulation protein; Reviewed	97.72
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.72
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	97.71
PRK14737	186	gmk guanylate kinase; Provisional	97.7
COG1241	682	MCM2 Predicted ATPase involved in replication cont	97.69
PF08740	187	BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA A	97.68
PRK07261	171	topology modulation protein; Provisional	97.67
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.66
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.66
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.65
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.64
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.64
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.63
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.63
PRK13947	171	shikimate kinase; Provisional	97.62
PRK06067	234	flagellar accessory protein FlaH; Validated	97.61
PRK03839	180	putative kinase; Provisional	97.61
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.61
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.6
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	97.59
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.59
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.59
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.59
PRK00625	173	shikimate kinase; Provisional	97.57
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.56
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.56
PRK04040	188	adenylate kinase; Provisional	97.55
COG1485	367	Predicted ATPase [General function prediction only	97.55
PRK13949	169	shikimate kinase; Provisional	97.55
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.54
PRK04841	903	transcriptional regulator MalT; Provisional	97.51
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.49
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.49
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.47
PRK13948	182	shikimate kinase; Provisional	97.47
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.45
PRK05973	237	replicative DNA helicase; Provisional	97.44
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.43
PTZ00202	550	tuzin; Provisional	97.43
PRK06217	183	hypothetical protein; Validated	97.43
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.41
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.41
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.41
PRK14532	188	adenylate kinase; Provisional	97.4
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.4
PRK12608	380	transcription termination factor Rho; Provisional	97.39
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.39
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.39
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	97.39
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.37
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.37
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.36
PRK14531	183	adenylate kinase; Provisional	97.36
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.35
PRK13765	637	ATP-dependent protease Lon; Provisional	97.35
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.35
PRK05057	172	aroK shikimate kinase I; Reviewed	97.34
PRK13946	184	shikimate kinase; Provisional	97.34
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.34
PRK09376	416	rho transcription termination factor Rho; Provisio	97.31
PRK08233	182	hypothetical protein; Provisional	97.31
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.31
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	97.28
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	97.28
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.27
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.27
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.26
PRK03731	171	aroL shikimate kinase II; Reviewed	97.26
PRK11823	446	DNA repair protein RadA; Provisional	97.25
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.24
PRK14530	215	adenylate kinase; Provisional	97.24
PRK13808	333	adenylate kinase; Provisional	97.24
PRK09354	349	recA recombinase A; Provisional	97.24
PRK06547	172	hypothetical protein; Provisional	97.23
PRK06762	166	hypothetical protein; Provisional	97.23
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.23
cd01128	249	rho_factor Transcription termination factor rho is	97.22
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.19
PLN02674	244	adenylate kinase	97.19
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.18
PRK13764	602	ATPase; Provisional	97.18
TIGR00767	415	rho transcription termination factor Rho. Members	97.17
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.17
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.16
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.16
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.14
PRK02496	184	adk adenylate kinase; Provisional	97.14
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.14
PF13245	76	AAA_19: Part of AAA domain	97.13
PRK14528	186	adenylate kinase; Provisional	97.13
PLN02199	303	shikimate kinase	97.12
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.11
COG1855	604	ATPase (PilT family) [General function prediction	97.1
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.1
PTZ00088	229	adenylate kinase 1; Provisional	97.1
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.09
PRK04296	190	thymidine kinase; Provisional	97.08
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	97.08
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.07
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.07
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.07
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.06
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.06
PLN02200	234	adenylate kinase family protein	97.05
PRK00279	215	adk adenylate kinase; Reviewed	97.05
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.04
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.03
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.03
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.03
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.03
COG4650	531	RtcR Sigma54-dependent transcription regulator con	97.02
PF13479	213	AAA_24: AAA domain	97.02
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.0
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.99
PRK14527	191	adenylate kinase; Provisional	96.99
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.97
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.97
PRK04182	180	cytidylate kinase; Provisional	96.96
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.96
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.95
PRK06696	223	uridine kinase; Validated	96.95
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	96.95
PLN02459	261	probable adenylate kinase	96.95
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.93
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.93
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.92
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.92
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.91
KOG2383	467	consensus Predicted ATPase [General function predi	96.91
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.91
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.9
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.9
PRK01184	184	hypothetical protein; Provisional	96.89
PTZ00035	337	Rad51 protein; Provisional	96.89
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.88
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.87
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.86
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.86
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.86
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.83
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.83
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.83
PHA02530	300	pseT polynucleotide kinase; Provisional	96.83
PRK14526	211	adenylate kinase; Provisional	96.8
PRK04220	301	2-phosphoglycerate kinase; Provisional	96.77
PHA00350	399	putative assembly protein	96.77
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.77
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.76
cd03246	173	ABCC_Protease_Secretion This family represents the	96.76
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.76
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.76
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	96.74
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.73
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.73
PRK10867	433	signal recognition particle protein; Provisional	96.73
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.71
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.71
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.69
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.69
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.67
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.67
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.67
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.65
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.65
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.64
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.64
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.63
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.63
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.62
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.61
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.6
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.6
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.58
PRK00889	175	adenylylsulfate kinase; Provisional	96.57
COG4133	209	CcmA ABC-type transport system involved in cytochr	96.57
PRK05541	176	adenylylsulfate kinase; Provisional	96.57
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.56
PRK10646	153	ADP-binding protein; Provisional	96.56
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.56
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	96.56
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.55
PLN02165	334	adenylate isopentenyltransferase	96.54
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.54
PRK10416	318	signal recognition particle-docking protein FtsY;	96.53
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.52
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.52
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	96.52
PRK14529	223	adenylate kinase; Provisional	96.51
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.51
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	96.5
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.5
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	96.49
TIGR00959	428	ffh signal recognition particle protein. This mode	96.48
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.48
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.48
PTZ00301	210	uridine kinase; Provisional	96.47
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	96.45
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	96.45
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.44
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.43
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.42
PRK12338	319	hypothetical protein; Provisional	96.41
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.4
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	96.4
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	96.4
PRK04328	249	hypothetical protein; Provisional	96.4
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.38
PRK10436	462	hypothetical protein; Provisional	96.36
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.35
COG3378	517	Phage associated DNA primase [General function pre	96.35
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.34
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.34
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.32
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	96.32
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.32
PRK09825	176	idnK D-gluconate kinase; Provisional	96.31
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.3
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.3
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.3
PRK05480	209	uridine/cytidine kinase; Provisional	96.29
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.29
PRK11545	163	gntK gluconate kinase 1; Provisional	96.28
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	96.28
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.27
PRK12337	475	2-phosphoglycerate kinase; Provisional	96.27

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9e-101  Score=761.92  Aligned_cols=428  Identities=50%  Similarity=0.816  Sum_probs=402.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHHHhhcccCCceEEEEcccCCCCcchHHHHHHHhhccCCCcccch
Q 013128            6 TVLSTAASLSASAMLIRSVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQ   85 (449)
Q Consensus         6 ~~~~~~~S~~a~~~~~~~~~~~~~P~~l~~~~~~~~~~~~~~~~~~~ti~i~e~~~~~~n~~y~a~~~YL~t~~~~~~~~   85 (449)
                      ++|+.+||++|++|++|+|+++++|.+++.|+.+++++|++.+++|.++.|.|++|+.+||+|.|+|.||++++++ .++
T Consensus         2 ~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~y~~~~~~~l~g~~s~~~~~~~~e~~g~~~n~~~~aie~yl~~k~~~-~~~   80 (457)
T KOG0743|consen    2 SVFTAYASLLGSLMFIKSMLQDIIPPSINPYFISALRGLFGVFSSYALIRIGEQDGVFRNQLYVAIEVYLSSKSSA-IAK   80 (457)
T ss_pred             CccchhHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHhhccCcccEEEEeehhccchHHHHHHHHHHhhhccchh-hhh
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999999 889


Q ss_pred             heeccccCCCCceEEeccCCCeEEeeecCeeeEEEEEEeecCCCCccCCCCCCCCcccCCCcceEEEEEEcCCchhHHHH
Q 013128           86 RFRVGKSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLN  165 (449)
Q Consensus        86 rl~~~~~~~~~~~~~~~~~~~~v~D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~~  165 (449)
                      |++.+.+.+++++++.+++|++|.|+|+||++||.+++...+ ....         .+...+.|+|+|+|++++++.|+.
T Consensus        81 rl~~~~~~~s~~~~l~~~~~~~i~d~f~gv~~~w~~~~~~~~-~~~~---------~~~~~~~r~~~L~f~k~~~e~V~~  150 (457)
T KOG0743|consen   81 RLTQNLSKNSKSLVLGLDDNEEISDEFEGVPVKWRHFVDYNE-KWIF---------VEREREKRYFELTFHKKPRELVTL  150 (457)
T ss_pred             hhhhhhccccccceEEecCCcEEEEEEeceEEEEEEEEEecC-cccc---------cccCCcceEEEEEecCccHHHhHH
Confidence            999999999999999999999999999999999999998766 3321         134678999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCceeEEeeec---------cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHh
Q 013128          166 LYLPHVLEKAKAIKEESKVVKLHTVM---------HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYT  236 (449)
Q Consensus       166 ~yl~~v~~~~~~~~~~~~~~~~~~~~---------~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~  236 (449)
                      +||+++.+++++|+.+++.+++|++.         +..|.+  +.++||.+|++|+|+++.|+.|++||..|++++++|+
T Consensus       151 syl~~v~~~~k~I~~~~r~~kl~t~~~~~~~~~~~~~~W~~--v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~Yk  228 (457)
T KOG0743|consen  151 SYLPYVVSKAKEILEENRELKLYTNSGKTVIYTAKGGEWRS--VGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYK  228 (457)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccCCccee--cCCCCCCCccccccChhHHHHHHHHHHHHHhcchHHH
Confidence            99999999999999999999999886         458998  9999999999999999999999999999999999999


Q ss_pred             hhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchh
Q 013128          237 RIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSE  316 (449)
Q Consensus       237 ~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~  316 (449)
                      ++|++|+||||||||||||||||++||||+|++++|+++++++..+.+|++++..++++|||+||||||.+..+++....
T Consensus       229 rvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~  308 (457)
T KOG0743|consen  229 RVGKAWKRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLATPNKSILLIEDIDCSFDLRERRKKK  308 (457)
T ss_pred             hcCcchhccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhCCCCcEEEEeecccccccccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999877776654


Q ss_pred             hhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC-
Q 013128          317 VQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH-  395 (449)
Q Consensus       317 ~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~-  395 (449)
                      ..........+++|||||++||+||+||+++||||||||+++|||||+||||||+||+|++|++++++.|+++||+.++ 
T Consensus       309 ~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~  388 (457)
T KOG0743|consen  309 KENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEED  388 (457)
T ss_pred             cccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCC
Confidence            3222223567999999999999999999999999999999999999999999999999999999999999999999975 


Q ss_pred             CCCHHHHHHHHHccCCCHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHHhhhh
Q 013128          396 HYLFEQIEELIKEVNVTPAEVAGELMKST-NAEVSLNGLVKFLHAKMTQQQK  446 (449)
Q Consensus       396 ~~l~~~i~~l~~~~~~tpa~i~~~l~~~~-~~~~al~~l~~~l~~~~~~~~~  446 (449)
                      |.|+++|++++++..+|||||++.||++. |++.|++.|+++|++++.+..+
T Consensus       389 h~L~~eie~l~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~~~~~~  440 (457)
T KOG0743|consen  389 HRLFDEIERLIEETEVTPAQVAEELMKNKNDADVALKGLVEALESKKEKRNK  440 (457)
T ss_pred             cchhHHHHHHhhcCccCHHHHHHHHhhccccHHHHHHHHHHHHHhhhhhhcc
Confidence            99999999999999999999999999987 8999999999999999875443

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

Probab=100.00  E-value=5.4e-41  Score=324.56  Aligned_cols=239  Identities=24%  Similarity=0.311  Sum_probs=195.1

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...+..++++++|.++++++|++.++.++.+|+.|.++|+.+|+|+|||||||||||.||+|+|++.++.|+.+..|++
T Consensus       142 v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSEl  221 (406)
T COG1222         142 VEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSEL  221 (406)
T ss_pred             eccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHH
Confidence            34456679999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cC-----hHH-HHHHHH--cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 QS-----NSE-LRFLLL--TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~~-----~~~-l~~~~~--~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      ..     ... .+.+|.  +...||||||||||++...|-..+.    ..+.+.++|+-+||+.|||+..  .+++=||+
T Consensus       222 VqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t----~gDrEVQRTmleLL~qlDGFD~--~~nvKVI~  295 (406)
T COG1222         222 VQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGT----SGDREVQRTMLELLNQLDGFDP--RGNVKVIM  295 (406)
T ss_pred             HHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCC----CchHHHHHHHHHHHHhccCCCC--CCCeEEEE
Confidence            32     333 344444  4458999999999999875543322    2356788999999999999977  47899999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc-------C
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK-------S  423 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~-------~  423 (449)
                      +||+++.|||||+||||||++|+||+|+.++|++|++-+...-+..-.-+++.++.. .++|.|||...|..       .
T Consensus       296 ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~  375 (406)
T COG1222         296 ATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRE  375 (406)
T ss_pred             ecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHh
Confidence            999999999999999999999999999999999999988775433222334555544 35999999999974       2


Q ss_pred             CCHHHHHHHHHHHHHHHHHhh
Q 013128          424 TNAEVSLNGLVKFLHAKMTQQ  444 (449)
Q Consensus       424 ~~~~~al~~l~~~l~~~~~~~  444 (449)
                      +......+++.++.++.....
T Consensus       376 ~R~~Vt~~DF~~Av~KV~~~~  396 (406)
T COG1222         376 RRDEVTMEDFLKAVEKVVKKK  396 (406)
T ss_pred             ccCeecHHHHHHHHHHHHhcc
Confidence            334556666777666655443

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=6.9e-37  Score=315.30  Aligned_cols=212  Identities=25%  Similarity=0.350  Sum_probs=186.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc--
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV--  279 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~--  279 (449)
                      ..++.+|++++|.+++|+++.+.+..++++++.|.++|+.+++|||||||||||||++|+|+|++.+.+|+.+.+.++  
T Consensus       427 e~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~s  506 (693)
T KOG0730|consen  427 EMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFS  506 (693)
T ss_pred             cCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHH
Confidence            346789999999999999999999999999999999999999999999999999999999999999999999987766  


Q ss_pred             ----cChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          280 ----QSNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       280 ----~~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                          .++..++.+|.++.  .||||||||||++...|+...       .....+++++||++|||+..  ..+++||++|
T Consensus       507 k~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~-------~~v~~RVlsqLLtEmDG~e~--~k~V~ViAAT  577 (693)
T KOG0730|consen  507 KYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSS-------SGVTDRVLSQLLTEMDGLEA--LKNVLVIAAT  577 (693)
T ss_pred             HhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCc-------cchHHHHHHHHHHHcccccc--cCcEEEEecc
Confidence                35677888888875  699999999999988655222       25567899999999999976  4689999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhc
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMK  422 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~  422 (449)
                      |+|+.||+||+||||||..|++|.|+.+.|.+|++.++..-...-.-+++++++.+ +||.|||.++|-.
T Consensus       578 NRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~  647 (693)
T KOG0730|consen  578 NRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQE  647 (693)
T ss_pred             CChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHH
Confidence            99999999999999999999999999999999999999865433334567777665 5999999998853

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

Probab=100.00  E-value=5e-36  Score=305.01  Aligned_cols=209  Identities=23%  Similarity=0.340  Sum_probs=183.0

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc---
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV---  279 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~---  279 (449)
                      -+..+|+++++.++++.++...+.+++++++.|+++|+..|.|+|||||||||||.||+|+||+.+.+|+.+..-++   
T Consensus       505 VPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlNk  584 (802)
T KOG0733|consen  505 VPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLNK  584 (802)
T ss_pred             cCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHHH
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999987665   


Q ss_pred             ---cChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          280 ---QSNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       280 ---~~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                         .++..++.+|.++  ..|||||+||||++.+.|+.+.       .....+++++||..|||+..  ..++.||++||
T Consensus       585 YVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~-------s~~s~RvvNqLLtElDGl~~--R~gV~viaATN  655 (802)
T KOG0733|consen  585 YVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEG-------SSVSSRVVNQLLTELDGLEE--RRGVYVIAATN  655 (802)
T ss_pred             HhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCC-------chhHHHHHHHHHHHhccccc--ccceEEEeecC
Confidence               3456778888876  4799999999999998766554       24567899999999999976  46799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-----HHHHHHHHHccCCCHHHHHHHH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-----FEQIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-----~~~i~~l~~~~~~tpa~i~~~l  420 (449)
                      +|+.+|||++||||||..++++.|+.++|..|++........++     .++|....+-.+||.||++.++
T Consensus       656 RPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLv  726 (802)
T KOG0733|consen  656 RPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALV  726 (802)
T ss_pred             CCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHH
Confidence            99999999999999999999999999999999999998644444     3455554455689999998776

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1e-35  Score=298.59  Aligned_cols=207  Identities=28%  Similarity=0.373  Sum_probs=177.4

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc---
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ---  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~---  280 (449)
                      ...+|+++-|.++.|+++.+.+ .|++.|..|.++|=..|+|+||.||||||||.||+|+|.+.+.+||....+++.   
T Consensus       299 ~nv~F~dVkG~DEAK~ELeEiV-efLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~  377 (752)
T KOG0734|consen  299 KNVTFEDVKGVDEAKQELEEIV-EFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMF  377 (752)
T ss_pred             cccccccccChHHHHHHHHHHH-HHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhh
Confidence            3568999999999999997755 799999999999999999999999999999999999999999999999988873   


Q ss_pred             ---ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          281 ---SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       281 ---~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                         ....++.+|..+  ..||||||||||++...|...       +....+.++++||..|||+..  ++++|||++||.
T Consensus       378 VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~-------~~~y~kqTlNQLLvEmDGF~q--NeGiIvigATNf  448 (752)
T KOG0734|consen  378 VGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPS-------DQHYAKQTLNQLLVEMDGFKQ--NEGIIVIGATNF  448 (752)
T ss_pred             hcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCcc-------HHHHHHHHHHHHHHHhcCcCc--CCceEEEeccCC
Confidence               457888888876  479999999999998754432       223678999999999999976  578999999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHH
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGEL  420 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l  420 (449)
                      |+.||+||.||||||+||.+|.|+...|.+|++.|+..-.+.-.-+..-+++. .+|+.||+++..
T Consensus       449 pe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlV  514 (752)
T KOG0734|consen  449 PEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLV  514 (752)
T ss_pred             hhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHH
Confidence            99999999999999999999999999999999999986433322233334444 479999997765

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

Probab=100.00  E-value=7.6e-34  Score=289.15  Aligned_cols=209  Identities=22%  Similarity=0.294  Sum_probs=179.2

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc-----
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV-----  279 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~-----  279 (449)
                      ..+|++++|.+....++.+.+.. +.+|+.|..+|+.++||+|||||||||||+||+|+|++++.+|+.++..++     
T Consensus       186 nv~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSGvS  264 (802)
T KOG0733|consen  186 NVSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSGVS  264 (802)
T ss_pred             CcchhhccChHHHHHHHHHHHHH-hcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcccC
Confidence            35799999999999999988766 999999999999999999999999999999999999999999999998776     


Q ss_pred             -cChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc--CCCCeEEEEEcC
Q 013128          280 -QSNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC--CGEGRIIVFTTN  354 (449)
Q Consensus       280 -~~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--~~~~~iiI~tTN  354 (449)
                       .++..++.+|..+.  .|||+||||||++.+.|...+.       +-.++++++||+.||++...  .|..|+||++||
T Consensus       265 GESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqr-------eMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATn  337 (802)
T KOG0733|consen  265 GESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQR-------EMERRIVAQLLTSMDELSNEKTKGDPVLVIGATN  337 (802)
T ss_pred             cccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHH-------HHHHHHHHHHHHhhhcccccccCCCCeEEEecCC
Confidence             35688999999875  7999999999999886554332       33568999999999998654  347799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      +|+.|||||+|+||||..|.+..|+..+|..|++.....-.+...-++.+++.- -+|-.||+..++-
T Consensus       338 RPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~  405 (802)
T KOG0733|consen  338 RPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCR  405 (802)
T ss_pred             CCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHH
Confidence            999999999999999999999999999999999998886555554455555553 3588888876663

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9.3e-34  Score=300.19  Aligned_cols=213  Identities=28%  Similarity=0.389  Sum_probs=181.4

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc--
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ--  280 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~--  280 (449)
                      ..+.+|++++|.++.|++|.+.+ .|+++|+.|.++|...|+|+||.||||||||.||+|+|.+.+.+|+.++.+++.  
T Consensus       305 ~t~V~FkDVAG~deAK~El~E~V-~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~  383 (774)
T KOG0731|consen  305 NTGVKFKDVAGVDEAKEELMEFV-KFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEM  383 (774)
T ss_pred             CCCCccccccCcHHHHHHHHHHH-HHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHH
Confidence            34589999999999999999876 799999999999999999999999999999999999999999999999999873  


Q ss_pred             ----ChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          281 ----SNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       281 ----~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                          ..+..+.+|..+.  .||||+|||||++...+.....   ...+.+...++++||..|||..+.  .++|++++||
T Consensus       384 ~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~---~~~~~e~e~tlnQll~emDgf~~~--~~vi~~a~tn  458 (774)
T KOG0731|consen  384 FVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGT---GGGQDEREQTLNQLLVEMDGFETS--KGVIVLAATN  458 (774)
T ss_pred             hcccchHHHHHHHHHhhccCCeEEEeccccccccccccccc---CCCChHHHHHHHHHHHHhcCCcCC--CcEEEEeccC
Confidence                3677888888765  7999999999999875531011   113466788999999999999774  7899999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC-CHHHHHHHHH-ccCCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY-LFEQIEELIK-EVNVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~-~~~~tpa~i~~~l~  421 (449)
                      +++.||+||+||||||++|+++.|+...|.+|++.++...... -..++..+.. ..++++|||++++.
T Consensus       459 r~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~n  527 (774)
T KOG0731|consen  459 RPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCN  527 (774)
T ss_pred             CccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhh
Confidence            9999999999999999999999999999999999999876443 2223344443 35799999999886

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

Probab=100.00  E-value=3.4e-33  Score=258.42  Aligned_cols=214  Identities=25%  Similarity=0.340  Sum_probs=177.2

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      ++..++.+++|.+-+|++|++.++.++...+.|+++|+.+|+|+|||||||||||+|++|+|++....|+.+..+++.. 
T Consensus       149 kpdvsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgsefvqk  228 (408)
T KOG0727|consen  149 KPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  228 (408)
T ss_pred             CCCccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHHH
Confidence            4456899999999999999999999999999999999999999999999999999999999999999999999888732 


Q ss_pred             -----hHHHHHHH--HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLL--LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~--~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           ....+..|  .+.+.|+||||||||++...+-..+    .+.+.+.++++-+|||.|||+..  ..++-+|++||
T Consensus       229 ylgegprmvrdvfrlakenapsiifideidaiatkrfdaq----tgadrevqril~ellnqmdgfdq--~~nvkvimatn  302 (408)
T KOG0727|consen  229 YLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQ----TGADREVQRILIELLNQMDGFDQ--TTNVKVIMATN  302 (408)
T ss_pred             HhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhcccc----ccccHHHHHHHHHHHHhccCcCc--ccceEEEEecC
Confidence                 23344444  4456899999999999976443222    22346678899999999999976  46789999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK  422 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~  422 (449)
                      +.+.|||||+||||+|++|+||+|+..+++-++......-+..-.-+++.++.+ -.+|.|+|..+|..
T Consensus       303 radtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqe  371 (408)
T KOG0727|consen  303 RADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQE  371 (408)
T ss_pred             cccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHH
Confidence            999999999999999999999999999999888877665433333345555544 46999999888853

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=8.7e-33  Score=287.59  Aligned_cols=212  Identities=23%  Similarity=0.313  Sum_probs=174.0

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc---
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV---  279 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~---  279 (449)
                      -+..+|++++|.+++|.+|++.+..++++++.+.. |...+.|+|||||||||||.+|+|+|-++...|+.+..-++   
T Consensus       666 IPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfss-glrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPELLNM  744 (953)
T KOG0736|consen  666 IPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPELLNM  744 (953)
T ss_pred             CCccchhcccCHHHHHHHHHHHhcCcccChhhhhc-cccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHHHHHH
Confidence            45578999999999999999999999999998865 66667899999999999999999999999999999986665   


Q ss_pred             ---cChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          280 ---QSNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       280 ---~~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                         +++.+++..|.++.  +|||||+||+|.+++.|++.+++     .+...+++|+||.+|||+.......+.||++||
T Consensus       745 YVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDS-----GGVMDRVVSQLLAELDgls~~~s~~VFViGATN  819 (953)
T KOG0736|consen  745 YVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDS-----GGVMDRVVSQLLAELDGLSDSSSQDVFVIGATN  819 (953)
T ss_pred             HhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCc-----cccHHHHHHHHHHHhhcccCCCCCceEEEecCC
Confidence               46788999999875  79999999999999988776543     366789999999999999875678899999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCH-HHHHHHHHHHhCcCCCCCHHHHHHHHHc--cCCCHHHHHHHH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNT-SVFKQLAFNYLGISHHYLFEQIEELIKE--VNVTPAEVAGEL  420 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~-~~r~~l~~~~l~~~~~~l~~~i~~l~~~--~~~tpa~i~~~l  420 (449)
                      +||.|||||+||||||+-++++.+.. +.+..+++..-..-...-.-++.++++.  .++|.||+-.+|
T Consensus       820 RPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLC  888 (953)
T KOG0736|consen  820 RPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLC  888 (953)
T ss_pred             CccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHH
Confidence            99999999999999999999998865 4455566544332111111223344443  469999987766

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

Probab=100.00  E-value=1e-31  Score=273.98  Aligned_cols=233  Identities=24%  Similarity=0.304  Sum_probs=184.6

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc-
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-  280 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~-  280 (449)
                      ..+..+|++|+|.+.+|++|.+.+..++.+++.|.++|+++++|+|||||||||||++|+++|++++.+++.+..+.+. 
T Consensus       138 ~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~  217 (398)
T PTZ00454        138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQ  217 (398)
T ss_pred             CCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHH
Confidence            4566799999999999999999999999999999999999999999999999999999999999999999999876552 


Q ss_pred             -----ChHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          281 -----SNSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       281 -----~~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                           ....++.+|..  ..+|+||||||||.++..+.....    ........++..||+.+|++...  .+++||+||
T Consensus       218 k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~----~~d~~~~r~l~~LL~~ld~~~~~--~~v~VI~aT  291 (398)
T PTZ00454        218 KYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQT----GADREVQRILLELLNQMDGFDQT--TNVKVIMAT  291 (398)
T ss_pred             HhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccC----CccHHHHHHHHHHHHHhhccCCC--CCEEEEEec
Confidence                 12344555443  468999999999999764422111    11234567889999999998653  568999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc-------CCC
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK-------STN  425 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~-------~~~  425 (449)
                      |+++.||||++||||||.+|++|+|+.++|..|++.++...+....-++..++.. .++|++||..++..       ...
T Consensus       292 N~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r~~~  371 (398)
T PTZ00454        292 NRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNR  371 (398)
T ss_pred             CCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999875443323345556554 37999999888753       222


Q ss_pred             HHHHHHHHHHHHHHH
Q 013128          426 AEVSLNGLVKFLHAK  440 (449)
Q Consensus       426 ~~~al~~l~~~l~~~  440 (449)
                      .....+++.++++..
T Consensus       372 ~~i~~~df~~A~~~v  386 (398)
T PTZ00454        372 YVILPKDFEKGYKTV  386 (398)
T ss_pred             CccCHHHHHHHHHHH
Confidence            344555666666554

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

Probab=99.98  E-value=8.7e-33  Score=260.20  Aligned_cols=235  Identities=26%  Similarity=0.325  Sum_probs=183.8

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...+..+|.++.|.+.+.++|.+.++.++.+|++|...|+.+|+|++|||+||||||.||+|+||.....|+.+-.+++
T Consensus       176 ~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseL  255 (440)
T KOG0726|consen  176 VEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSEL  255 (440)
T ss_pred             cccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHH
Confidence            34456678999999999999999999999999999999999999999999999999999999999999999998877766


Q ss_pred             c-----ChHHH-HHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 Q-----SNSEL-RFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~-----~~~~l-~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      .     +...| +.+|.-  ...|||+||||||++...+=...+    ....+.++++-+|||.+||+.+  .+.+-||+
T Consensus       256 iQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~S----ggerEiQrtmLELLNQldGFds--rgDvKvim  329 (440)
T KOG0726|consen  256 IQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNS----GGEREIQRTMLELLNQLDGFDS--RGDVKVIM  329 (440)
T ss_pred             HHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCCC----ccHHHHHHHHHHHHHhccCccc--cCCeEEEE
Confidence            2     33344 344433  358999999999999764422221    2345667888899999999988  46799999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHH-HccCCCHHHHHHHHhcC-------
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELI-KEVNVTPAEVAGELMKS-------  423 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~-~~~~~tpa~i~~~l~~~-------  423 (449)
                      +||+.+.|||||+||||+|+.|+||.|+...++.|+..+-..-...-.-.++.++ .+..+|.|||..+|...       
T Consensus       330 ATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictEaGllAlRe  409 (440)
T KOG0726|consen  330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTEAGLLALRE  409 (440)
T ss_pred             ecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHHHhHHHHHH
Confidence            9999999999999999999999999999999999987555432211122345554 34569999999888642       


Q ss_pred             CCHHHHHHHHHHHHHHH
Q 013128          424 TNAEVSLNGLVKFLHAK  440 (449)
Q Consensus       424 ~~~~~al~~l~~~l~~~  440 (449)
                      +.-.+..+++.++.+..
T Consensus       410 rRm~vt~~DF~ka~e~V  426 (440)
T KOG0726|consen  410 RRMKVTMEDFKKAKEKV  426 (440)
T ss_pred             HHhhccHHHHHHHHHHH
Confidence            22334445555555443

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=99.98  E-value=5.8e-32  Score=250.01  Aligned_cols=215  Identities=25%  Similarity=0.319  Sum_probs=176.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      .-+..+++-+.|.+.+.++|.+-++.+.++|+.|..+|++.|+|+|||||||||||.||+|+|++....|+.++.+++..
T Consensus       140 KvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvsgselvq  219 (404)
T KOG0728|consen  140 KVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQ  219 (404)
T ss_pred             hCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHH
Confidence            34556889999999999999999999999999999999999999999999999999999999999999999999988742


Q ss_pred             -----h-HHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 -----N-SELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 -----~-~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                           . .-.+.+|..  ...|+|||+||||.+...+...+.    +.+++.+++.-+|||.+||+...  .++-+|++|
T Consensus       220 k~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~~~----ggdsevqrtmlellnqldgfeat--knikvimat  293 (404)
T KOG0728|consen  220 KYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGS----GGDSEVQRTMLELLNQLDGFEAT--KNIKVIMAT  293 (404)
T ss_pred             HHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccCCC----CccHHHHHHHHHHHHhccccccc--cceEEEEec
Confidence                 2 334455544  458999999999999764433222    23567788999999999999774  678899999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK  422 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~  422 (449)
                      |+.+.|||||+||||+|+.|+||+|+.++|.+|++..-..-+..-.-.++.++++ .+.|.||+...|..
T Consensus       294 nridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vcte  363 (404)
T KOG0728|consen  294 NRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTE  363 (404)
T ss_pred             cccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhhh
Confidence            9999999999999999999999999999999999876543322222234444444 35888888888764

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

Probab=99.97  E-value=1.6e-31  Score=260.37  Aligned_cols=207  Identities=23%  Similarity=0.320  Sum_probs=170.3

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC---
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS---  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~---  281 (449)
                      ...|++|+|.++.|+-|.+.+..++.-|++|+-+-.|| +|+|++||||||||+||+|+|.+++..||.|+.+.+.+   
T Consensus       208 ~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPW-kgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltSKwR  286 (491)
T KOG0738|consen  208 NIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPW-KGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKWR  286 (491)
T ss_pred             CcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhccccc-ceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhhhhc
Confidence            36799999999999999999999999999999999888 79999999999999999999999999999999888753   


Q ss_pred             --hHHHHHHHH---cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC-C-eEEEEEcC
Q 013128          282 --NSELRFLLL---TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE-G-RIIVFTTN  354 (449)
Q Consensus       282 --~~~l~~~~~---~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~-~-~iiI~tTN  354 (449)
                        ...+.+++.   +...|++|||||||.++..|++.+      +++.+++.-++||..|||+...... . |+|+++||
T Consensus       287 GeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~------EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN  360 (491)
T KOG0738|consen  287 GESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSS------EHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATN  360 (491)
T ss_pred             cchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCcc------chhHHHHHHHHHHHHhhccccccccceeEEEEeccC
Confidence              233444433   335899999999999997555442      4567788999999999999765332 2 66778999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      .|+.||.||+|  ||.+.|++|.|+.++|+.|++..|......-.-.++.+.++. ++|.+||...|
T Consensus       361 ~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvC  425 (491)
T KOG0738|consen  361 FPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVC  425 (491)
T ss_pred             CCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHH
Confidence            99999999999  999999999999999999999999864322222334444443 58999998877

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=5.3e-31  Score=275.01  Aligned_cols=231  Identities=26%  Similarity=0.356  Sum_probs=193.1

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc---
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ---  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~---  280 (449)
                      ...+|.+++|.++.|+++.+.+ .|++.|..|.++|...|+|+||+||||||||+||+|+|.+.+.+++.++.+++.   
T Consensus       145 ~~v~F~DVAG~dEakeel~EiV-dfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVemf  223 (596)
T COG0465         145 VKVTFADVAGVDEAKEELSELV-DFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMF  223 (596)
T ss_pred             cCcChhhhcCcHHHHHHHHHHH-HHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhhh
Confidence            4468999999999999998865 799999999999999999999999999999999999999999999999999873   


Q ss_pred             ---ChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          281 ---SNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       281 ---~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                         ..+..+.+|.++.  .||||||||||+....|+...    ...+.+...++++||.+|||...  ++++|+|++||+
T Consensus       224 VGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~----GggnderEQTLNQlLvEmDGF~~--~~gviviaaTNR  297 (596)
T COG0465         224 VGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGL----GGGNDEREQTLNQLLVEMDGFGG--NEGVIVIAATNR  297 (596)
T ss_pred             cCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCC----CCCchHHHHHHHHHHhhhccCCC--CCceEEEecCCC
Confidence               4688899998886  599999999999987554431    12356677899999999999974  478999999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc------------
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK------------  422 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~------------  422 (449)
                      |+-+||||+||||||++|.++.|+...|+++++.++......-.-.+..+++. .+++.|++++.+..            
T Consensus       298 pdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAal~aar~n~~~  377 (596)
T COG0465         298 PDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNKKE  377 (596)
T ss_pred             cccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHHHHHHHHhcCee
Confidence            99999999999999999999999999999999977765433322233334444 36999999888842            


Q ss_pred             --CCCHHHHHHHHHHHHHHHH
Q 013128          423 --STNAEVSLNGLVKFLHAKM  441 (449)
Q Consensus       423 --~~~~~~al~~l~~~l~~~~  441 (449)
                        ..+.+.|.+.++...+++-
T Consensus       378 i~~~~i~ea~drv~~G~erks  398 (596)
T COG0465         378 ITMRDIEEAIDRVIAGPERKS  398 (596)
T ss_pred             EeccchHHHHHHHhcCcCcCC
Confidence              2478888888887766554

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=8.7e-31  Score=243.47  Aligned_cols=230  Identities=23%  Similarity=0.298  Sum_probs=177.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc-
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-  280 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~-  280 (449)
                      -.+..++++++|.+.+.+++.+.+..++.+++.|.++|+.+|+|+|+|||||||||.||+|.|...+..|..+-...+. 
T Consensus       164 ekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQ  243 (424)
T KOG0652|consen  164 EKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQ  243 (424)
T ss_pred             cCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHHHh
Confidence            3455689999999999999999999999999999999999999999999999999999999999999888777554442 


Q ss_pred             ----ChHHH-HH--HHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          281 ----SNSEL-RF--LLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       281 ----~~~~l-~~--~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                          +...| +.  .+.+...|+||||||+|++...+-...    .....+.+++.-+|||.+||+.+  .+.+-||++|
T Consensus       244 MfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSe----k~GDREVQRTMLELLNQLDGFss--~~~vKviAAT  317 (424)
T KOG0652|consen  244 MFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSE----KAGDREVQRTMLELLNQLDGFSS--DDRVKVIAAT  317 (424)
T ss_pred             hhhcchHHHHHHHHHHhhccCCeEEEEechhhhcccccccc----ccccHHHHHHHHHHHHhhcCCCC--ccceEEEeec
Confidence                23333 33  344556899999999999976432221    12346678899999999999977  4788999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC---CCCCHHHHHHHHHccCCCHHHHHHHHhc-------C
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS---HHYLFEQIEELIKEVNVTPAEVAGELMK-------S  423 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~tpa~i~~~l~~-------~  423 (449)
                      |+.+-|||||+|.||+|+.|+||.|+.+.|..|++.+-..-   +..-++++.+-.+  .|..|+....|..       +
T Consensus       318 NRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTd--dFNGAQcKAVcVEAGMiALRr  395 (424)
T KOG0652|consen  318 NRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTD--DFNGAQCKAVCVEAGMIALRR  395 (424)
T ss_pred             ccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhccc--ccCchhheeeehhhhHHHHhc
Confidence            99999999999999999999999999999999998766543   2333444443332  3777777655542       3


Q ss_pred             CCHHHHHHHHHHHHHH
Q 013128          424 TNAEVSLNGLVKFLHA  439 (449)
Q Consensus       424 ~~~~~al~~l~~~l~~  439 (449)
                      +-.+...+.+.+.+.+
T Consensus       396 ~atev~heDfmegI~e  411 (424)
T KOG0652|consen  396 GATEVTHEDFMEGILE  411 (424)
T ss_pred             ccccccHHHHHHHHHH
Confidence            3334444555444443

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

Probab=99.97  E-value=2.1e-30  Score=267.59  Aligned_cols=207  Identities=22%  Similarity=0.285  Sum_probs=180.7

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc------
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV------  279 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~------  279 (449)
                      ..|++++|..++|+.+.+.+..+.+++..|...+.+.+.|+|||||||||||.||.|+|...+..++.+..-++      
T Consensus       664 i~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPElL~KyIG  743 (952)
T KOG0735|consen  664 IRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPELLSKYIG  743 (952)
T ss_pred             CCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHHHHHHhc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999987665      


Q ss_pred             cChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC
Q 013128          280 QSNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE  357 (449)
Q Consensus       280 ~~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  357 (449)
                      .++..++.+|.++.  +|||||+||+|.+++.|+..+       .+...+++++||..|||...  -.++.|+++|.+|+
T Consensus       744 aSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDs-------TGVTDRVVNQlLTelDG~Eg--l~GV~i~aaTsRpd  814 (952)
T KOG0735|consen  744 ASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDS-------TGVTDRVVNQLLTELDGAEG--LDGVYILAATSRPD  814 (952)
T ss_pred             ccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCC-------CCchHHHHHHHHHhhccccc--cceEEEEEecCCcc
Confidence            35678888888774  799999999999998655433       24456899999999999876  47899999999999


Q ss_pred             CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          358 KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       358 ~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      .|||||+||||+|++++-|.|++.+|.+|++..-.....+-.-+++-++..+ +||.||++.+|.
T Consensus       815 liDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~  879 (952)
T KOG0735|consen  815 LIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLY  879 (952)
T ss_pred             ccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHH
Confidence            9999999999999999999999999999999776654444444555555544 699999998884

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.97  E-value=3e-30  Score=263.95  Aligned_cols=237  Identities=24%  Similarity=0.302  Sum_probs=186.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+..+|++++|.+++++++.+.+..++.+++.|+.+|..+++|+|||||||||||++|+++|++++.+++.++++.+..
T Consensus       124 ~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~~  203 (389)
T PRK03992        124 ESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQ  203 (389)
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHhH
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999887632


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...++.+|..+  ..|+||||||||.++..+......    .......++..|++.+|++..  ..++.||+||
T Consensus       204 ~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~----~~~~~~~~l~~lL~~ld~~~~--~~~v~VI~aT  277 (389)
T PRK03992        204 KFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS----GDREVQRTLMQLLAEMDGFDP--RGNVKIIAAT  277 (389)
T ss_pred             hhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCC----ccHHHHHHHHHHHHhccccCC--CCCEEEEEec
Confidence                  23445555543  479999999999998643322111    123445678889999998754  3578999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc-------CCC
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK-------STN  425 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~-------~~~  425 (449)
                      |+++.+|+|++|||||+..|++|.|+.++|.+|++.++..........+..++.. .+++++||..++..       ...
T Consensus       278 n~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~~~  357 (389)
T PRK03992        278 NRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDR  357 (389)
T ss_pred             CChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999875433222234555544 36999999888753       222


Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q 013128          426 AEVSLNGLVKFLHAKMTQQ  444 (449)
Q Consensus       426 ~~~al~~l~~~l~~~~~~~  444 (449)
                      .....+.+.++++..+...
T Consensus       358 ~~i~~~d~~~A~~~~~~~~  376 (389)
T PRK03992        358 TEVTMEDFLKAIEKVMGKE  376 (389)
T ss_pred             CCcCHHHHHHHHHHHhccc
Confidence            3456667777776654433

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.97  E-value=2.9e-30  Score=268.41  Aligned_cols=183  Identities=22%  Similarity=0.389  Sum_probs=150.9

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc----------EE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD----------IY  272 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~----------~~  272 (449)
                      .++.+|++|+|.+++++.|.+.+..++.+++.|+..|+++++|+|||||||||||++|+++|++++.+          ++
T Consensus       176 ~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl  255 (512)
T TIGR03689       176 VPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFL  255 (512)
T ss_pred             CCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999765          33


Q ss_pred             EEeccccc------ChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc
Q 013128          273 DLDLSAVQ------SNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW  340 (449)
Q Consensus       273 ~l~~s~~~------~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  340 (449)
                      .+..+.+.      .+..++.+|..+      ..|+||||||+|.++..++....      .......+++||+.|||+.
T Consensus       256 ~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s------~d~e~~il~~LL~~LDgl~  329 (512)
T TIGR03689       256 NIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVS------SDVETTVVPQLLSELDGVE  329 (512)
T ss_pred             eccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCcc------chHHHHHHHHHHHHhcccc
Confidence            33333321      223444444433      36999999999999864432211      1223567899999999987


Q ss_pred             ccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          341 SCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       341 ~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +.  ++++||+|||+++.|||||+||||||.+|+|++|+.+++++|++.|+..
T Consensus       330 ~~--~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~  380 (512)
T TIGR03689       330 SL--DNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD  380 (512)
T ss_pred             cC--CceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc
Confidence            63  5799999999999999999999999999999999999999999999874

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.

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

Probab=99.97  E-value=4.6e-30  Score=263.58  Aligned_cols=235  Identities=24%  Similarity=0.289  Sum_probs=183.9

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...++.+|++|+|.++++++|.+.+..++.+++.|..+|+.+++|+|||||||||||++|+++|++++.+++.+..+.+
T Consensus       174 ~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL  253 (438)
T PTZ00361        174 VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSEL  253 (438)
T ss_pred             cccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchh
Confidence            33456689999999999999999999999999999999999999999999999999999999999999999999987776


Q ss_pred             cC------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 QS------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~~------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      .+      ...++.+|..  ...|+||||||||.++..+.....    ........++..||+.+||+..  ..++.||+
T Consensus       254 ~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~s----gg~~e~qr~ll~LL~~Ldg~~~--~~~V~VI~  327 (438)
T PTZ00361        254 IQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATS----GGEKEIQRTMLELLNQLDGFDS--RGDVKVIM  327 (438)
T ss_pred             hhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCC----cccHHHHHHHHHHHHHHhhhcc--cCCeEEEE
Confidence            32      2234444433  357999999999999864322111    1123345677889999999854  35689999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc-------C
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK-------S  423 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~-------~  423 (449)
                      |||+++.||+|++||||||.+|+||.|+.++|.+|++.++......-.-.++.++.. .++|++||..++..       .
T Consensus       328 ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~~Alr~  407 (438)
T PTZ00361        328 ATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRE  407 (438)
T ss_pred             ecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999875433222244555543 46999999888753       2


Q ss_pred             CCHHHHHHHHHHHHHHH
Q 013128          424 TNAEVSLNGLVKFLHAK  440 (449)
Q Consensus       424 ~~~~~al~~l~~~l~~~  440 (449)
                      .......+.+.++++..
T Consensus       408 ~r~~Vt~~D~~~A~~~v  424 (438)
T PTZ00361        408 RRMKVTQADFRKAKEKV  424 (438)
T ss_pred             cCCccCHHHHHHHHHHH
Confidence            22345556666666654

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.97  E-value=8.8e-30  Score=268.66  Aligned_cols=231  Identities=26%  Similarity=0.382  Sum_probs=183.0

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc--
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ--  280 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~--  280 (449)
                      .+..+|++++|.+++|+++.+.+ .++..++.|.+.|...++|+|||||||||||++++++|++++.+++.++++++.  
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~-~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~~  127 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIV-DFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM  127 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHH-HHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHHH
Confidence            45679999999999999998765 468899999999999999999999999999999999999999999999887653  


Q ss_pred             ----ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          281 ----SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       281 ----~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                          ....++.+|..+  ..||||||||||.+...+.....    ........+++.||+.||++..  ..+++||+|||
T Consensus       128 ~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~----~~~~~~~~~~~~lL~~~d~~~~--~~~v~vI~aTn  201 (495)
T TIGR01241       128 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLG----GGNDEREQTLNQLLVEMDGFGT--NTGVIVIAATN  201 (495)
T ss_pred             HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcC----CccHHHHHHHHHHHhhhccccC--CCCeEEEEecC
Confidence                345677777664  57899999999999864432211    0123445788999999999865  35689999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhc-------CCCH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMK-------STNA  426 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~-------~~~~  426 (449)
                      +++.||||++||||||.+|+++.|+.++|.+|++.++.........++..++... ++|++||..++-.       ....
T Consensus       202 ~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~  281 (495)
T TIGR01241       202 RPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKT  281 (495)
T ss_pred             ChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCC
Confidence            9999999999999999999999999999999999999865443334566666654 5999999877642       1222


Q ss_pred             HHHHHHHHHHHHHH
Q 013128          427 EVSLNGLVKFLHAK  440 (449)
Q Consensus       427 ~~al~~l~~~l~~~  440 (449)
                      ....+.+.++++..
T Consensus       282 ~i~~~~l~~a~~~~  295 (495)
T TIGR01241       282 EITMNDIEEAIDRV  295 (495)
T ss_pred             CCCHHHHHHHHHHH
Confidence            34455555555543

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.

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

Probab=99.97  E-value=6e-30  Score=237.85  Aligned_cols=206  Identities=20%  Similarity=0.325  Sum_probs=172.3

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      ....+||+++|.++.|+... .+..|+.+|+.|.++.   |+++|+|||||||||++|+|+|++.+.+++.+...++.. 
T Consensus       115 ~~~it~ddViGqEeAK~kcr-li~~yLenPe~Fg~WA---PknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGe  190 (368)
T COG1223         115 ISDITLDDVIGQEEAKRKCR-LIMEYLENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGE  190 (368)
T ss_pred             hccccHhhhhchHHHHHHHH-HHHHHhhChHHhcccC---cceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHH
Confidence            35678999999999998764 5668899998887764   789999999999999999999999999999999887742 


Q ss_pred             -----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           ...++.++..+  ..|||+||||+|++.-  +|+-++-    .+....+++.||..|||+..  +++++.|++||
T Consensus       191 hVGdgar~Ihely~rA~~~aPcivFiDE~DAiaL--dRryQel----RGDVsEiVNALLTelDgi~e--neGVvtIaaTN  262 (368)
T COG1223         191 HVGDGARRIHELYERARKAAPCIVFIDELDAIAL--DRRYQEL----RGDVSEIVNALLTELDGIKE--NEGVVTIAATN  262 (368)
T ss_pred             HhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhh--hhhHHHh----cccHHHHHHHHHHhccCccc--CCceEEEeecC
Confidence                 24566676665  4799999999999875  3332221    23445688999999999976  68899999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHhc
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMK  422 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~~  422 (449)
                      +|+.||||+.+  ||...|+|..|+.++|..|++.|...-..++...++.+... .++|..||.+-.++
T Consensus       263 ~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK  329 (368)
T COG1223         263 RPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLK  329 (368)
T ss_pred             ChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHH
Confidence            99999999999  99999999999999999999999987766666667776655 46999999998875

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.97  E-value=2e-29  Score=277.37  Aligned_cols=209  Identities=22%  Similarity=0.315  Sum_probs=176.3

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc---
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ---  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~---  280 (449)
                      +..+|++++|.+++|+.+.+.+..++.+++.|.++|..+++|+|||||||||||++|+++|++++.+++.++++++.   
T Consensus       448 ~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~~  527 (733)
T TIGR01243       448 PNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKW  527 (733)
T ss_pred             cccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhcc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999987653   


Q ss_pred             ---ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          281 ---SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       281 ---~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                         ++..++.+|..+  ..||||||||||.+++.++...      ........+++||..|||+..  ..+++||+|||+
T Consensus       528 vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~------~~~~~~~~~~~lL~~ldg~~~--~~~v~vI~aTn~  599 (733)
T TIGR01243       528 VGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARF------DTSVTDRIVNQLLTEMDGIQE--LSNVVVIAATNR  599 (733)
T ss_pred             cCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCC------CccHHHHHHHHHHHHhhcccC--CCCEEEEEeCCC
Confidence               345677777654  5799999999999987443221      123356788999999999865  467999999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHH
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      ++.||||++||||||.+|++|+|+.++|.+||+.++......-..++..+++.. ++|++||..++
T Consensus       600 ~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~  665 (733)
T TIGR01243       600 PDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVC  665 (733)
T ss_pred             hhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999999888754433333456666554 59999998766

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.97  E-value=3.6e-29  Score=260.49  Aligned_cols=205  Identities=21%  Similarity=0.242  Sum_probs=164.0

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc---
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ---  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~---  280 (449)
                      .+.+|++|+|.+.+|+.+.+....|.   ....+.|.+.++|+|||||||||||++|+++|++++.+++.++++.+.   
T Consensus       223 ~~~~~~dvgGl~~lK~~l~~~~~~~~---~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~~  299 (489)
T CHL00195        223 VNEKISDIGGLDNLKDWLKKRSTSFS---KQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGI  299 (489)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHhh---HHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhcccc
Confidence            45689999999999998887665543   234567899999999999999999999999999999999999987653   


Q ss_pred             ---ChHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          281 ---SNSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       281 ---~~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                         ++..++.+|..  ..+||||+|||||.++..+...+      +.......++.|+..|+..    ...++||+|||+
T Consensus       300 vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~------d~~~~~rvl~~lL~~l~~~----~~~V~vIaTTN~  369 (489)
T CHL00195        300 VGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKG------DSGTTNRVLATFITWLSEK----KSPVFVVATANN  369 (489)
T ss_pred             cChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCC------CchHHHHHHHHHHHHHhcC----CCceEEEEecCC
Confidence               34566666653  45899999999999875322111      2234567888899998853    456899999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC--HHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL--FEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l--~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      ++.||||++||||||..++++.|+.++|++|++.++.......  ..++..+++.. ++|++||...+.
T Consensus       370 ~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~  438 (489)
T CHL00195        370 IDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSII  438 (489)
T ss_pred             hhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999998743221  23456666654 799999987764

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=1.2e-29  Score=236.64  Aligned_cols=215  Identities=24%  Similarity=0.296  Sum_probs=176.4

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...+..|+.++.|-.++.+.+++-++.++.+|+.|-++|+.+|+|+|||||||||||.+|+|+||..+..|+.+-.|++
T Consensus       168 veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvigsel  247 (435)
T KOG0729|consen  168 VEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSEL  247 (435)
T ss_pred             eecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHHH
Confidence            44556689999999999999999999999999999999999999999999999999999999999999999999988877


Q ss_pred             cC------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 QS------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~~------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      ..      ....+.+|..+  .+-||||+||||++.+.+-..+.    +...+.+++.-+|++.+||+..  .+++-|++
T Consensus       248 vqkyvgegarmvrelf~martkkaciiffdeidaiggarfddg~----ggdnevqrtmleli~qldgfdp--rgnikvlm  321 (435)
T KOG0729|consen  248 VQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFDDGA----GGDNEVQRTMLELINQLDGFDP--RGNIKVLM  321 (435)
T ss_pred             HHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCccccCCC----CCcHHHHHHHHHHHHhccCCCC--CCCeEEEe
Confidence            32      23455555544  56899999999999875433221    2346678899999999999966  46788999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC---CCCCHHHHHHHHHccCCCHHHHHHHHhc
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS---HHYLFEQIEELIKEVNVTPAEVAGELMK  422 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~tpa~i~~~l~~  422 (449)
                      +||+|+.|||||+||||+|++++|..|+-+.|..|++.+...-   ..--++-+.++..  +-|.|||...|..
T Consensus       322 atnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcp--nstgaeirsvcte  393 (435)
T KOG0729|consen  322 ATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCP--NSTGAEIRSVCTE  393 (435)
T ss_pred             ecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCC--CCcchHHHHHHHH
Confidence            9999999999999999999999999999999999987655432   1222444555554  3788999888864

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

Probab=99.96  E-value=1e-29  Score=240.13  Aligned_cols=204  Identities=23%  Similarity=0.335  Sum_probs=172.6

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      .+...|++++|.+..|+.+.+.+..+++.|.+|.--.+|| +|+|||||||||||.||+|+|-+.+..|+.++.+++.+ 
T Consensus       127 KPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~Pw-rgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvSK  205 (439)
T KOG0739|consen  127 KPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPW-RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSK  205 (439)
T ss_pred             CCCCchhhhccchhHHHHHHhheeecccchhhhcCCCCcc-eeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHHHH
Confidence            3456789999999999999999999999999998776777 89999999999999999999999999999999888743 


Q ss_pred             -----hHHHHHHHH--cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLLL--TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~~--~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           +.-+..+|.  +..+|+||||||||.+++.++...       .+..+++-.+||-.|.|+-.. .++++|+++||
T Consensus       206 WmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enE-------seasRRIKTEfLVQMqGVG~d-~~gvLVLgATN  277 (439)
T KOG0739|consen  206 WMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENE-------SEASRRIKTEFLVQMQGVGND-NDGVLVLGATN  277 (439)
T ss_pred             HhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCc-------hHHHHHHHHHHHHhhhccccC-CCceEEEecCC
Confidence                 233344444  446899999999999887444332       345667888999999998654 57899999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHcc-CCCHHHHH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEV-NVTPAEVA  417 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~-~~tpa~i~  417 (449)
                      -|+.||.|++|  ||+..|++|.|...+|..|++..++...|.|. +++.+|...+ ++|.+||+
T Consensus       278 iPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDis  340 (439)
T KOG0739|consen  278 IPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDIS  340 (439)
T ss_pred             CchhHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceE
Confidence            99999999999  99999999999999999999999999988884 5677777664 58888874

>PF14363 AAA_assoc: Domain associated at C-terminal with AAA

Probab=99.96  E-value=2.6e-29  Score=206.93  Aligned_cols=97  Identities=40%  Similarity=0.663  Sum_probs=93.2

Q ss_pred             hCcHHHHHHHHHHHHHhhc-ccCCceEEEEcccCCCCcchHHHHHHHhhccCCCcccchheeccccCCCCceEEeccCCC
Q 013128           28 FLPAEIYDYLDSKIHLVSQ-YFSSQLTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIALDRNE  106 (449)
Q Consensus        28 ~~P~~l~~~~~~~~~~~~~-~~~~~~ti~i~e~~~~~~n~~y~a~~~YL~t~~~~~~~~rl~~~~~~~~~~~~~~~~~~~  106 (449)
                      |||++||+++.++++++++ +++||+||+|+|++|+++|++|+||++||++++++ +++||++++++++++++++|++||
T Consensus         1 ~~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g~~~N~ly~a~~~YL~s~~s~-~a~rL~~~~~~~~~~~~l~l~~~e   79 (98)
T PF14363_consen    1 LLPHELRSYLRSLLRRLFSSRFSPYLTIVIPEFDGLSRNELYDAAQAYLSSKISP-SARRLKASKSKNSKNLVLSLDDGE   79 (98)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCCcEEEEEEeCCCccccHHHHHHHHHHhhccCc-ccceeeecccCCCCceEEecCCCC
Confidence            6899999999999988776 89999999999999999999999999999999999 889999999999999999999999


Q ss_pred             eEEeeecCeeeEEEEEEee
Q 013128          107 ETFDVFKDVTLKWKLVYTQ  125 (449)
Q Consensus       107 ~v~D~f~G~~~~W~~~~~~  125 (449)
                      +|+|+|+||++||.+++++
T Consensus        80 ~V~D~F~Gv~v~W~~~~~e   98 (98)
T PF14363_consen   80 EVVDVFEGVKVWWSSVCTE   98 (98)
T ss_pred             EEEEEECCEEEEEEEEccC
Confidence            9999999999999999864

>CHL00176 ftsH cell division protein; Validated

Probab=99.96  E-value=2.4e-28  Score=261.75  Aligned_cols=212  Identities=27%  Similarity=0.373  Sum_probs=173.6

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc--
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ--  280 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~--  280 (449)
                      ....+|++++|.++.|+++.+. ..+++.++.|..+|...++|+||+||||||||++|+++|++++.+++.++++.+.  
T Consensus       177 ~~~~~f~dv~G~~~~k~~l~ei-v~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~~  255 (638)
T CHL00176        177 DTGITFRDIAGIEEAKEEFEEV-VSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEM  255 (638)
T ss_pred             CCCCCHHhccChHHHHHHHHHH-HHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHHH
Confidence            3457999999999999988765 4678889999999999999999999999999999999999999999999988763  


Q ss_pred             ----ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          281 ----SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       281 ----~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                          ....++.+|..+  ..||||||||||++...++....    ........+++.||..|||+..  ..+++||+|||
T Consensus       256 ~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~----~~~~e~~~~L~~LL~~~dg~~~--~~~ViVIaaTN  329 (638)
T CHL00176        256 FVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIG----GGNDEREQTLNQLLTEMDGFKG--NKGVIVIAATN  329 (638)
T ss_pred             hhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCC----CCcHHHHHHHHHHHhhhccccC--CCCeeEEEecC
Confidence                234556666654  47999999999999764432211    1234456789999999999865  46789999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      +++.+|+||+||||||.+|+++.|+.++|.+|++.++..........+..++... +++++||...+-
T Consensus       330 ~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvn  397 (638)
T CHL00176        330 RVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLN  397 (638)
T ss_pred             chHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999874433344566666654 599999987764

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

Probab=99.96  E-value=3.8e-28  Score=256.50  Aligned_cols=228  Identities=27%  Similarity=0.391  Sum_probs=187.7

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc--
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ--  280 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~--  280 (449)
                      ....+|++++|.++.|+.+.+.+..++..++.|.+.|..+++|+|||||||||||+||+|+|++++.+|+.++.+++.  
T Consensus       236 ~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~sk  315 (494)
T COG0464         236 DEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSK  315 (494)
T ss_pred             CCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHhcc
Confidence            445789999999999999999999999999999999999999999999999999999999999999999999988764  


Q ss_pred             ----ChHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          281 ----SNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       281 ----~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                          ++..++.+|..+.  +||||||||+|.++..++....       ......+++||..|||+..  ..+++||+|||
T Consensus       316 ~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~-------~~~~r~~~~lL~~~d~~e~--~~~v~vi~aTN  386 (494)
T COG0464         316 WVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSED-------GSGRRVVGQLLTELDGIEK--AEGVLVIAATN  386 (494)
T ss_pred             ccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCc-------hHHHHHHHHHHHHhcCCCc--cCceEEEecCC
Confidence                3567777777664  7999999999999875543321       1226889999999999866  46799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH--HHHHHHH-ccCCCHHHHHHHHhcC-------C
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE--QIEELIK-EVNVTPAEVAGELMKS-------T  424 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~--~i~~l~~-~~~~tpa~i~~~l~~~-------~  424 (449)
                      +|+.+|+|++||||||..+++|.|+.++|..+++.++......+.+  .++.+++ ..+++.+||...+.+.       .
T Consensus       387 ~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~  466 (494)
T COG0464         387 RPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREA  466 (494)
T ss_pred             CccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999966554332  3344444 3459999998887531       1


Q ss_pred             -CHHHHHHHHHHHHHH
Q 013128          425 -NAEVSLNGLVKFLHA  439 (449)
Q Consensus       425 -~~~~al~~l~~~l~~  439 (449)
                       ..+..++.+.++++.
T Consensus       467 ~~~~~~~~~~~~a~~~  482 (494)
T COG0464         467 RRREVTLDDFLDALKK  482 (494)
T ss_pred             ccCCccHHHHHHHHHh
Confidence             224555666665554

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.95  E-value=5.7e-28  Score=235.50  Aligned_cols=221  Identities=20%  Similarity=0.290  Sum_probs=181.5

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhc-CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh--
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIG-RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN--  282 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g-~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~--  282 (449)
                      .+|++++|.+++++.+.+.+..++.+++.|...+ ..+++|+|||||||||||.+|+|+|++.+..++.+..+.+.+.  
T Consensus        89 v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~KWf  168 (386)
T KOG0737|consen   89 VSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTSKWF  168 (386)
T ss_pred             eehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccchhhH
Confidence            4899999999999999999999999999997433 3457899999999999999999999999999999999988642  


Q ss_pred             ---HH-HHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          283 ---SE-LRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       283 ---~~-l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                         .. +..+|.-  .-+||||||||+|.++..| + ..     +++.....-++|...-||+.+..+..++|+++||+|
T Consensus       169 gE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R-~-s~-----dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP  241 (386)
T KOG0737|consen  169 GEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQR-R-ST-----DHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRP  241 (386)
T ss_pred             HHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhc-c-cc-----hHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCC
Confidence               22 2333333  3479999999999998865 2 11     345556677889999999998766678888999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhcCCCHHHHHHHHHH
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMKSTNAEVSLNGLVK  435 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~~~~~~~al~~l~~  435 (449)
                      ..||.|++|  ||...++++.|+.++|++|++-+|..++..-.-++.++...+ ++|..||.+.|     ...|+..+.+
T Consensus       242 ~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC-----~~Aa~~~ire  314 (386)
T KOG0737|consen  242 FDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELC-----RLAALRPIRE  314 (386)
T ss_pred             ccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHH-----HHHhHhHHHH
Confidence            999999999  999999999999999999999999987654444455555543 69999999998     4567777777


Q ss_pred             HHHHH
Q 013128          436 FLHAK  440 (449)
Q Consensus       436 ~l~~~  440 (449)
                      +++..
T Consensus       315 ~~~~~  319 (386)
T KOG0737|consen  315 LLVSE  319 (386)
T ss_pred             HHHhc
Confidence            77765

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

Probab=99.95  E-value=6.3e-28  Score=229.49  Aligned_cols=210  Identities=26%  Similarity=0.329  Sum_probs=171.1

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh--
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN--  282 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~--  282 (449)
                      ..+|+.+.|.-++..++++-+.-++.+++.+.++|+.+|.|++||||||||||.+|+++|..++.+++.+..+.+.+.  
T Consensus       128 ~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~kyi  207 (388)
T KOG0651|consen  128 NISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYI  207 (388)
T ss_pred             ccCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhhhhhhc
Confidence            348999999999999999999999999999999999999999999999999999999999999999999998887542  


Q ss_pred             ----HHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          283 ----SELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       283 ----~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                          .-++..|..+.  .|||||+||||+..+.+..++.    ..+...+.||-.|+|.|||...  -..+-+|+|||+|
T Consensus       208 GEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~se~T----s~dreiqrTLMeLlnqmdgfd~--l~rVk~ImatNrp  281 (388)
T KOG0651|consen  208 GESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGT----SSDREIQRTLMELLNQMDGFDT--LHRVKTIMATNRP  281 (388)
T ss_pred             ccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEecccc----chhHHHHHHHHHHHHhhccchh--cccccEEEecCCc
Confidence                33455555544  6899999999999874432222    2356678899999999999866  3678899999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC---CCCCHHHHHHHHHccCCCHHHHHHHHhc
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS---HHYLFEQIEELIKEVNVTPAEVAGELMK  422 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~tpa~i~~~l~~  422 (449)
                      +.|||||+||||+|+.+++|.|+...|..+++-.-..-   +.--.+.+..+.+.  +..+|+...+.+
T Consensus       282 dtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~--f~gad~rn~~tE  348 (388)
T KOG0651|consen  282 DTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDG--FNGADLRNVCTE  348 (388)
T ss_pred             cccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhc--cChHHHhhhccc
Confidence            99999999999999999999999999998776433321   11224555555554  778887777654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.95  E-value=3e-27  Score=240.37  Aligned_cols=215  Identities=24%  Similarity=0.287  Sum_probs=170.2

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      ...+..+|++++|.+++++.|.+.+..++.+++.|..+|..+++|+|||||||||||++|+++|++++.+++.+..+.+.
T Consensus       114 ~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l~  193 (364)
T TIGR01242       114 EERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV  193 (364)
T ss_pred             ccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHHH
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999988766553


Q ss_pred             C------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 S------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      .      ...++.++..  ...|+||||||+|.+...+......    .......++..+++.+|++..  ..++.||+|
T Consensus       194 ~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~----~~~~~~~~l~~ll~~ld~~~~--~~~v~vI~t  267 (364)
T TIGR01242       194 RKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTS----GDREVQRTLMQLLAELDGFDP--RGNVKVIAA  267 (364)
T ss_pred             HHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCC----ccHHHHHHHHHHHHHhhCCCC--CCCEEEEEe
Confidence            2      1223444433  3578999999999987533221111    123445678889999998744  356899999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      ||+++.+|++++|||||+..|+++.|+.++|.+|++.++..........+..+.... +++++||..++.
T Consensus       268 tn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~  337 (364)
T TIGR01242       268 TNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICT  337 (364)
T ss_pred             cCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999988654322212344444443 699999987764

Many proteins may score above the trusted cutoff because an internal

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

Probab=99.95  E-value=2.6e-27  Score=233.11  Aligned_cols=168  Identities=16%  Similarity=0.135  Sum_probs=131.4

Q ss_pred             hHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc------ChHHHHHHHHcC-------CCCceEE
Q 013128          233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ------SNSELRFLLLTM-------PSRSMLV  299 (449)
Q Consensus       233 ~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~------~~~~l~~~~~~~-------~~~~Il~  299 (449)
                      .+....|+.+|++++||||||||||++|+++|++++.+++.++.+++.      ++..++.+|..+       .+|||||
T Consensus       138 n~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLF  217 (413)
T PLN00020        138 NFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLF  217 (413)
T ss_pred             hhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEE
Confidence            334447888999999999999999999999999999999999988874      356777777654       3699999


Q ss_pred             eeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc--------c--ccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          300 IEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL--------W--SCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       300 iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--------~--~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                      |||||.+++.++..+      .....+.+...||+.+|+.        |  ......++||+|||+|+.|||||+|||||
T Consensus       218 IDEIDA~~g~r~~~~------~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRf  291 (413)
T PLN00020        218 INDLDAGAGRFGTTQ------YTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRM  291 (413)
T ss_pred             EehhhhcCCCCCCCC------cchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCC
Confidence            999999987543211      1112344558899998863        4  12245689999999999999999999999


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc
Q 013128          370 DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV  409 (449)
Q Consensus       370 d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~  409 (449)
                      |..+  +.|+.++|..|++.++...+.. ..++..+++..
T Consensus       292 Dk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f  328 (413)
T PLN00020        292 EKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLVDTF  328 (413)
T ss_pred             Ccee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHHHcC
Confidence            9965  6899999999999998865433 45666666553

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.95  E-value=4.4e-27  Score=264.92  Aligned_cols=179  Identities=18%  Similarity=0.193  Sum_probs=138.9

Q ss_pred             cChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh---------------------------
Q 013128          230 NGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN---------------------------  282 (449)
Q Consensus       230 ~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~---------------------------  282 (449)
                      .++..+.++|..+++|+||+||||||||+||+|+|.+++++++.++++++...                           
T Consensus      1617 ~~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~ 1696 (2281)
T CHL00206       1617 HGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRD 1696 (2281)
T ss_pred             cCcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccc
Confidence            34667788999999999999999999999999999999999999987765421                           


Q ss_pred             ----------------------HHHHHHHH--cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC
Q 013128          283 ----------------------SELRFLLL--TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG  338 (449)
Q Consensus       283 ----------------------~~l~~~~~--~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  338 (449)
                                            ..++.+|.  +..+||||+|||||++...             .....+++.||+.|||
T Consensus      1697 ~~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~-------------ds~~ltL~qLLneLDg 1763 (2281)
T CHL00206       1697 LDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVN-------------ESNYLSLGLLVNSLSR 1763 (2281)
T ss_pred             cchhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCC-------------ccceehHHHHHHHhcc
Confidence                                  11343444  3468999999999999642             1123468999999998


Q ss_pred             cccc-CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH---HHHHHHHHc-cCCCH
Q 013128          339 LWSC-CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF---EQIEELIKE-VNVTP  413 (449)
Q Consensus       339 ~~~~-~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~---~~i~~l~~~-~~~tp  413 (449)
                      .... ...+++||+|||+|+.|||||+||||||++|+++.|+..+|++++...+...+..+.   ..+..++.. .++|+
T Consensus      1764 ~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSG 1843 (2281)
T CHL00206       1764 DCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNA 1843 (2281)
T ss_pred             ccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCH
Confidence            6432 246799999999999999999999999999999999999999888755432222222   134555554 47999


Q ss_pred             HHHHHHHh
Q 013128          414 AEVAGELM  421 (449)
Q Consensus       414 a~i~~~l~  421 (449)
                      ||++.++-
T Consensus      1844 ADLanLvN 1851 (2281)
T CHL00206       1844 RDLVALTN 1851 (2281)
T ss_pred             HHHHHHHH
Confidence            99987763

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.94  E-value=3.5e-26  Score=247.25  Aligned_cols=210  Identities=25%  Similarity=0.365  Sum_probs=169.2

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc----
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ----  280 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~----  280 (449)
                      ..+|+++.|.+..++++.+.+. +...+..|..++...++|+||+||||||||++++++|++++.+++.++++++.    
T Consensus       148 ~~~~~di~g~~~~~~~l~~i~~-~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~~~  226 (644)
T PRK10733        148 KTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFV  226 (644)
T ss_pred             hCcHHHHcCHHHHHHHHHHHHH-HhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHhhh
Confidence            4579999999999999877654 56777788888888899999999999999999999999999999999987653    


Q ss_pred             --ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          281 --SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       281 --~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                        ....++.+|..+  ..||||||||||.+...++....    ........++++||..|||+..  .+++++|+|||++
T Consensus       227 g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~----g~~~~~~~~ln~lL~~mdg~~~--~~~vivIaaTN~p  300 (644)
T PRK10733        227 GVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLG----GGHDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRP  300 (644)
T ss_pred             cccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCC----CCchHHHHHHHHHHHhhhcccC--CCCeeEEEecCCh
Confidence              234555555554  47999999999999764432111    1123456789999999999866  4679999999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      +.||||++||||||++|+++.|+.++|.+|++.++........-++..+.+. .++|++||.+++-
T Consensus       301 ~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~  366 (644)
T PRK10733        301 DVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  366 (644)
T ss_pred             hhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999976533222234445554 4799999988875

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=99.92  E-value=6.4e-25  Score=238.71  Aligned_cols=210  Identities=20%  Similarity=0.276  Sum_probs=170.6

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-----CcEEEEecc
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-----FDIYDLDLS  277 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-----~~~~~l~~s  277 (449)
                      ..-.+|++++|.++++..+.+-+..++.+++.|.++++.++||+|+|||||||||++|+|+|..+.     ..++.-+..
T Consensus       259 ~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkga  338 (1080)
T KOG0732|consen  259 DSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGA  338 (1080)
T ss_pred             hcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCc
Confidence            345689999999999999999999999999999999999999999999999999999999999993     333322222


Q ss_pred             cc------cChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEE
Q 013128          278 AV------QSNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII  349 (449)
Q Consensus       278 ~~------~~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  349 (449)
                      +.      ..+.+++-+|..+  .+|+|||+||||-+.+.++...       ......+++.||..|||+-+  .+.++|
T Consensus       339 D~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSskq-------Eqih~SIvSTLLaLmdGlds--RgqVvv  409 (1080)
T KOG0732|consen  339 DCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQ-------EQIHASIVSTLLALMDGLDS--RGQVVV  409 (1080)
T ss_pred             hhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccchH-------HHhhhhHHHHHHHhccCCCC--CCceEE
Confidence            21      2456677777766  4799999999999988664432       23455678999999999977  478999


Q ss_pred             EEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHH-HHHHHc-cCCCHHHHHHHHh
Q 013128          350 VFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQI-EELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       350 I~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i-~~l~~~-~~~tpa~i~~~l~  421 (449)
                      |++||+++.+||||+||||||..++||+|+-++|.+|+...-.....++.... ..+.+. .++-.||+..++.
T Consensus       410 igATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCT  483 (1080)
T KOG0732|consen  410 IGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCT  483 (1080)
T ss_pred             EcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHH
Confidence            99999999999999999999999999999999999999877766556665444 334333 3677788776664

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.92  E-value=1.8e-24  Score=238.25  Aligned_cols=208  Identities=26%  Similarity=0.344  Sum_probs=168.7

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      +..+|++|+|.+++++.|.+.+..++.+++.|+.+|+.+++|+|||||||||||++++++|++++.+++.+++..+.+  
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~~  252 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKY  252 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhccc
Confidence            456899999999999999999999999999999999999999999999999999999999999999999998776532  


Q ss_pred             ----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          282 ----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       282 ----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                          ...++.+|..+  ..|+||||||||.+.+.++...       .......++.|++.||++..  ...++||+|||+
T Consensus       253 ~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~-------~~~~~~~~~~Ll~~ld~l~~--~~~vivI~atn~  323 (733)
T TIGR01243       253 YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVT-------GEVEKRVVAQLLTLMDGLKG--RGRVIVIGATNR  323 (733)
T ss_pred             ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCc-------chHHHHHHHHHHHHhhcccc--CCCEEEEeecCC
Confidence                34566666553  4789999999999986432211       12235678899999999865  356888999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHH
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGEL  420 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l  420 (449)
                      ++.||+++.|||||+..++++.|+.++|.+|++.+.......-...+..+++. .+++++++...+
T Consensus       324 ~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~  389 (733)
T TIGR01243       324 PDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALA  389 (733)
T ss_pred             hhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999987764322212234444443 468888887654

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.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.92  E-value=3.1e-24  Score=222.08  Aligned_cols=206  Identities=23%  Similarity=0.298  Sum_probs=178.5

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc----
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV----  279 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~----  279 (449)
                      ++.+ ++++|...+...+.+.+..++..+..+...|.++++|+|+|||||||||.+++|+|++.+..++.+++.++    
T Consensus       180 ~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~  258 (693)
T KOG0730|consen  180 PEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKF  258 (693)
T ss_pred             cccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhc
Confidence            5666 78899999999999999999999999999999999999999999999999999999999999999998876    


Q ss_pred             --cChHHHHHHHHcCC--C-CceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          280 --QSNSELRFLLLTMP--S-RSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       280 --~~~~~l~~~~~~~~--~-~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                        .+++.|+..|..+.  + |+||+|||||.+++.+....        ....++.++|+..+||+..  ...+|++++||
T Consensus       259 ~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~--------~~e~Rv~sqlltL~dg~~~--~~~vivl~atn  328 (693)
T KOG0730|consen  259 PGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGAD--------DVESRVVSQLLTLLDGLKP--DAKVIVLAATN  328 (693)
T ss_pred             ccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccc--------hHHHHHHHHHHHHHhhCcC--cCcEEEEEecC
Confidence              35688898888764  4 99999999999998554332        1356789999999999864  47799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHH-ccCCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIK-EVNVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~tpa~i~~~l~  421 (449)
                      +|+.|||++.| ||||..++++.|+..+|.++++.+....++.-..+++.+.. ..+++.+|+...+-
T Consensus       329 rp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~  395 (693)
T KOG0730|consen  329 RPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCR  395 (693)
T ss_pred             CccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHH
Confidence            99999999999 99999999999999999999999998766664455555554 46899999988874

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.92  E-value=6.3e-25  Score=221.01  Aligned_cols=214  Identities=21%  Similarity=0.324  Sum_probs=160.3

Q ss_pred             cccCCCCCcccc--cCCHHH-HHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-cEEEEe
Q 013128          200 IVLKHPMTFKTL--ALDSEL-KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-DIYDLD  275 (449)
Q Consensus       200 ~~~~~p~~f~~l--~g~~~~-k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-~~~~l~  275 (449)
                      ....+...|+++  .|.+.. -+-.+.....-.-.|+...++|++.-+|+|||||||||||.+|+.|...|+. +--.++
T Consensus       210 ~ii~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVN  289 (744)
T KOG0741|consen  210 SIINPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVN  289 (744)
T ss_pred             cccCCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccC
Confidence            334555678876  344333 3333444444555789999999999999999999999999999999999975 333344


Q ss_pred             cccc------cChHHHHHHHHcCC----------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          276 LSAV------QSNSELRFLLLTMP----------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       276 ~s~~------~~~~~l~~~~~~~~----------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                      .-++      .++.+++.+|..+.          .-.||++||||+++..|+....     .......++++||.-|||.
T Consensus       290 GPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g-----~TGVhD~VVNQLLsKmDGV  364 (744)
T KOG0741|consen  290 GPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAG-----STGVHDTVVNQLLSKMDGV  364 (744)
T ss_pred             cHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCC-----CCCccHHHHHHHHHhcccH
Confidence            3333      35778888888762          3469999999999986655433     2355678899999999999


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC--CCCCHH--HHHHHHHc-cCCCHH
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHYLFE--QIEELIKE-VNVTPA  414 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~--~~~l~~--~i~~l~~~-~~~tpa  414 (449)
                      ..-  ++++||+.||+++.||+||+||||+.++++++.|++..|.+|++.+-..-  +..+..  ++++++.. .++|.|
T Consensus       365 eqL--NNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGA  442 (744)
T KOG0741|consen  365 EQL--NNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGA  442 (744)
T ss_pred             Hhh--hcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchh
Confidence            774  67999999999999999999999999999999999999999998666541  222222  34455443 359999


Q ss_pred             HHHHHH
Q 013128          415 EVAGEL  420 (449)
Q Consensus       415 ~i~~~l  420 (449)
                      ||....
T Consensus       443 EleglV  448 (744)
T KOG0741|consen  443 ELEGLV  448 (744)
T ss_pred             HHHHHH
Confidence            996554

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.91  E-value=1.9e-24  Score=217.71  Aligned_cols=211  Identities=21%  Similarity=0.242  Sum_probs=178.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++..|++++|.+..|+.+.+.+..++.+++.|..+. ++.+|+||.||||||||+|++|+|.+.+..++.+..+++.+
T Consensus       146 ~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr-~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLts  224 (428)
T KOG0740|consen  146 TLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLR-EPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTS  224 (428)
T ss_pred             cCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccc-cccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhh
Confidence            44567899999999999999999999999998887764 45689999999999999999999999999999999988853


Q ss_pred             ------hHHHHHHH--HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLL--LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~--~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            +.-++.+|  ++..+|+||||||||.++..+...       ..+...+...++|..+++..+...+.++||+||
T Consensus       225 K~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~-------e~e~srr~ktefLiq~~~~~s~~~drvlvigaT  297 (428)
T KOG0740|consen  225 KYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDN-------EHESSRRLKTEFLLQFDGKNSAPDDRVLVIGAT  297 (428)
T ss_pred             hccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCc-------ccccchhhhhHHHhhhccccCCCCCeEEEEecC
Confidence                  23334443  445689999999999999855222       234556778889999999988877889999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHcc-CCCHHHHHHHHhc
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEV-NVTPAEVAGELMK  422 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~-~~tpa~i~~~l~~  422 (449)
                      |.|+.+|.|++|  ||...+++|.|+.+.|..+|++++....+.+. .+++.+++-+ +++..||...|..
T Consensus       298 N~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~ke  366 (428)
T KOG0740|consen  298 NRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKE  366 (428)
T ss_pred             CCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHH
Confidence            999999999999  99999999999999999999999998866664 6777777654 5999999888864

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.85  E-value=1e-20  Score=185.78  Aligned_cols=223  Identities=22%  Similarity=0.225  Sum_probs=161.1

Q ss_pred             EEcCCchhHHHHHHHHHHHHHHHHHHHhCceeEEeeecccccc-----ccccccCCCCCcccccCCHHHHHHHHHHHHHH
Q 013128          154 SFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWD-----ANNIVLKHPMTFKTLALDSELKREITEDLENF  228 (449)
Q Consensus       154 ~~~~~~~~~v~~~yl~~v~~~~~~~~~~~~~~~~~~~~~~~w~-----~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~  228 (449)
                      -|.++.-..|.++|++.++-+...|++.++...-|...-....     ...........|+++++.+.+++.|.+....-
T Consensus       295 vYTtkeg~~V~w~yi~r~LGqPSLiREsSrg~~pw~gsls~~k~~i~~~~~~s~~gk~pl~~ViL~psLe~Rie~lA~aT  374 (630)
T KOG0742|consen  295 VYTTKEGTLVTWRYIERRLGQPSLIRESSRGRFPWIGSLSALKHPIQGSRSASSRGKDPLEGVILHPSLEKRIEDLAIAT  374 (630)
T ss_pred             heeccccchhHHHHHHHHcCCchhhhhhccccCCCcccHHHHhchhhhhHhhhhcCCCCcCCeecCHHHHHHHHHHHHHh
Confidence            3566777889999999999999999998886533322100000     00011122345999999999999987655443


Q ss_pred             HcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-----hHHHHHHHH---cCCCCceEEe
Q 013128          229 MNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-----NSELRFLLL---TMPSRSMLVI  300 (449)
Q Consensus       229 ~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-----~~~l~~~~~---~~~~~~Il~i  300 (449)
                      .+.+     ....+-|++|+|||||||||+.|+.||.+.|.++-.+..+++..     -..+..+|.   +....-+|||
T Consensus       375 aNTK-----~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGLllFI  449 (630)
T KOG0742|consen  375 ANTK-----KHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGLLLFI  449 (630)
T ss_pred             cccc-----cccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccceEEEe
Confidence            3322     23455689999999999999999999999999988887777642     233444443   3446779999


Q ss_pred             eccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCH
Q 013128          301 EDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT  380 (449)
Q Consensus       301 DeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~  380 (449)
                      ||.|+++..++...      ..+.....|+.||-- .|-.|   ..++++.+||+|.++|.|+-.  |+|..|+||.|..
T Consensus       450 DEADAFLceRnkty------mSEaqRsaLNAlLfR-TGdqS---rdivLvlAtNrpgdlDsAV~D--Ride~veFpLPGe  517 (630)
T KOG0742|consen  450 DEADAFLCERNKTY------MSEAQRSALNALLFR-TGDQS---RDIVLVLATNRPGDLDSAVND--RIDEVVEFPLPGE  517 (630)
T ss_pred             hhhHHHHHHhchhh------hcHHHHHHHHHHHHH-hcccc---cceEEEeccCCccchhHHHHh--hhhheeecCCCCh
Confidence            99999987554432      123445667776643 23322   457889999999999999999  9999999999999


Q ss_pred             HHHHHHHHHHhCc
Q 013128          381 SVFKQLAFNYLGI  393 (449)
Q Consensus       381 ~~r~~l~~~~l~~  393 (449)
                      ++|..|+..||..
T Consensus       518 EERfkll~lYlnk  530 (630)
T KOG0742|consen  518 EERFKLLNLYLNK  530 (630)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999999863

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

Probab=99.83  E-value=3.6e-19  Score=165.42  Aligned_cols=191  Identities=19%  Similarity=0.216  Sum_probs=130.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      .-+|.+|++++|+++++..+.-.+.......+        .-.++|||||||+||||||+.||++++.++..++...+..
T Consensus        17 ~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~--------~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k   88 (233)
T PF05496_consen   17 RLRPKSLDEFIGQEHLKGNLKILIRAAKKRGE--------ALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEK   88 (233)
T ss_dssp             HTS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS-----------EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--S
T ss_pred             hcCCCCHHHccCcHHHHhhhHHHHHHHHhcCC--------CcceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhh
Confidence            45899999999999999887655555443222        1357999999999999999999999999999998887877


Q ss_pred             hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc-----cCC---------CCe
Q 013128          282 NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS-----CCG---------EGR  347 (449)
Q Consensus       282 ~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~-----~~~---------~~~  347 (449)
                      ..++..++.....+.|||||||+.+..                  ....-|+..|+...-     .+.         ...
T Consensus        89 ~~dl~~il~~l~~~~ILFIDEIHRlnk------------------~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~F  150 (233)
T PF05496_consen   89 AGDLAAILTNLKEGDILFIDEIHRLNK------------------AQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPF  150 (233)
T ss_dssp             CHHHHHHHHT--TT-EEEECTCCC--H------------------HHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----
T ss_pred             HHHHHHHHHhcCCCcEEEEechhhccH------------------HHHHHHHHHhccCeEEEEeccccccceeeccCCCc
Confidence            888999999988999999999999843                  223347777763221     111         235


Q ss_pred             EEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHHHHHH
Q 013128          348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       348 iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i~~~l  420 (449)
                      -+|++|++...|.+.|..  ||....++.+.+.++..+|+++.....+..+.++ ..+++....=||.-..++|
T Consensus       151 TligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll  222 (233)
T PF05496_consen  151 TLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLL  222 (233)
T ss_dssp             EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHH
T ss_pred             eEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            789999999999999999  9999999999999999999998877777777554 4555566667775443333

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.

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

Probab=99.82  E-value=4.9e-20  Score=159.14  Aligned_cols=123  Identities=33%  Similarity=0.488  Sum_probs=99.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------hHHHHHHHHcC--C-CCceEEeeccchhhhcccccchh
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------NSELRFLLLTM--P-SRSMLVIEDIDCSVKLQNRESSE  316 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------~~~l~~~~~~~--~-~~~Il~iDeiD~l~~~~~~~~~~  316 (449)
                      +||+||||||||++|+++|++++.+++.+++..+.+      ...+...+...  . .|+||+|||+|.+......    
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~~~----   76 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKSQP----   76 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHCST----
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccccc----
Confidence            689999999999999999999999999999988862      34555555553  3 4899999999999874411    


Q ss_pred             hhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCC
Q 013128          317 VQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       317 ~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~  377 (449)
                         .........+..|++.++..... +.++++|+|||.++.++++++| +||+..|++|.
T Consensus        77 ---~~~~~~~~~~~~L~~~l~~~~~~-~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   77 ---SSSSFEQRLLNQLLSLLDNPSSK-NSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             ---SSSHHHHHHHHHHHHHHHTTTTT-SSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             ---ccccccccccceeeecccccccc-cccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence               12345567788999999987653 3568999999999999999998 89999999874

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 ....

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

Probab=99.80  E-value=1.3e-19  Score=173.75  Aligned_cols=179  Identities=21%  Similarity=0.303  Sum_probs=136.6

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhh-cCCCCcceEEeCCCCCCHHHHHHHHHHHcC---------CcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRI-GRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------FDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~-g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---------~~~~~l~~  276 (449)
                      -|+.|+.+.++|+++.++....+.-.+.-... -+.|.|-+|||||||||||+|++|+|+.|.         ..++.+++
T Consensus       140 lWEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  140 LWESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             hHHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh
Confidence            47889999999999999887766544322221 257788899999999999999999999993         35677887


Q ss_pred             ccccC------hHHHHHHHHcC-------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC
Q 013128          277 SAVQS------NSELRFLLLTM-------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC  343 (449)
Q Consensus       277 s~~~~------~~~l~~~~~~~-------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~  343 (449)
                      .++.+      ..-+..+|.+.       ..-..++|||++.+...|....+   ...+...-++++.+|..||.+... 
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S---~~EpsDaIRvVNalLTQlDrlK~~-  295 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASS---RNEPSDAIRVVNALLTQLDRLKRY-  295 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhc---CCCCchHHHHHHHHHHHHHHhccC-
Confidence            76632      22233333332       23456789999999875533221   123455678899999999999764 


Q ss_pred             CCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          344 GEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       344 ~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                       .+++|.+|+|-.+.||-|+..  |-|...++++|+.+++..|++..+.
T Consensus       296 -~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~Ilkscie  341 (423)
T KOG0744|consen  296 -PNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIE  341 (423)
T ss_pred             -CCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHH
Confidence             678999999999999999999  9999999999999999999988774

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.78  E-value=8.7e-18  Score=168.63  Aligned_cols=191  Identities=17%  Similarity=0.194  Sum_probs=143.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+|.+|++++|.++.++.+...+.......        ..++++|||||||||||++|+++|++++.++..++...+..
T Consensus        18 ~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~--------~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~   89 (328)
T PRK00080         18 SLRPKSLDEFIGQEKVKENLKIFIEAAKKRG--------EALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEK   89 (328)
T ss_pred             hcCcCCHHHhcCcHHHHHHHHHHHHHHHhcC--------CCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccC
Confidence            4578899999999999998887775543321        23568999999999999999999999999988887776666


Q ss_pred             hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-----cc---------CCCCe
Q 013128          282 NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-----SC---------CGEGR  347 (449)
Q Consensus       282 ~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-----~~---------~~~~~  347 (449)
                      ...+..++.....++||+|||||.+...                  ....|.+.|+...     ..         .-...
T Consensus        90 ~~~l~~~l~~l~~~~vl~IDEi~~l~~~------------------~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~  151 (328)
T PRK00080         90 PGDLAAILTNLEEGDVLFIDEIHRLSPV------------------VEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPF  151 (328)
T ss_pred             hHHHHHHHHhcccCCEEEEecHhhcchH------------------HHHHHHHHHHhcceeeeeccCccccceeecCCCc
Confidence            6778888888888999999999987430                  0111233333211     00         01236


Q ss_pred             EEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHHHHHH
Q 013128          348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       348 iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i~~~l  420 (449)
                      .+|++||++..++++|.+  ||+..+.+++++.++..+++++..+..+..+.++ +..+++...-+|..+...|
T Consensus       152 ~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l  223 (328)
T PRK00080        152 TLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLL  223 (328)
T ss_pred             eEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHH
Confidence            789999999999999988  9999999999999999999999888766666543 4555666666665555554

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.76  E-value=1.6e-17  Score=161.41  Aligned_cols=177  Identities=15%  Similarity=0.183  Sum_probs=124.6

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCC---CcceEEeCCCCCCHHHHHHHHHHHc-------CCcEEEEecc
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAW---KRGYLLYGPPGTGKSSLIAAMANQL-------KFDIYDLDLS  277 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~---~rg~LL~GPpGtGKT~la~aiA~~l-------~~~~~~l~~s  277 (449)
                      +++++|.+++|+.|.+.+...... ....+.|...   ..++||+||||||||++|+++|+.+       ..+++.++++
T Consensus         5 l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            578999999999998877555433 3333455543   3458999999999999999999876       2366677766


Q ss_pred             cccC------hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          278 AVQS------NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       278 ~~~~------~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      ++..      ...+..++..+ .++||||||+|.+..  +..        .......+..|++.|+..    ...+++|+
T Consensus        84 ~l~~~~~g~~~~~~~~~~~~a-~~~VL~IDE~~~L~~--~~~--------~~~~~~~i~~Ll~~~e~~----~~~~~vil  148 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVIKKA-LGGVLFIDEAYSLAR--GGE--------KDFGKEAIDTLVKGMEDN----RNEFVLIL  148 (261)
T ss_pred             HhhhhhccchHHHHHHHHHhc-cCCEEEEechhhhcc--CCc--------cchHHHHHHHHHHHHhcc----CCCEEEEe
Confidence            6532      23445555554 468999999999853  110        112234567788888763    23455666


Q ss_pred             EcCCC-----CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHH
Q 013128          352 TTNHK-----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQI  402 (449)
Q Consensus       352 tTN~~-----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i  402 (449)
                      +++..     ..++|+|.+  ||+.+|++|.++.+++.+++++++...+..+.++.
T Consensus       149 a~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a  202 (261)
T TIGR02881       149 AGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEA  202 (261)
T ss_pred             cCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHH
Confidence            55432     247899999  99999999999999999999999976555555443

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.75  E-value=3.9e-17  Score=162.07  Aligned_cols=182  Identities=17%  Similarity=0.207  Sum_probs=133.0

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR  286 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~  286 (449)
                      +|++++|.+++++.+...+......+        ..+.+++||||||||||++++++|++++.++..++.+.......+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~--------~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~   73 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQ--------EALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLA   73 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHH
Confidence            68999999999999888776544432        1246799999999999999999999999998877766665556677


Q ss_pred             HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc--------------ccCCCCeEEEEE
Q 013128          287 FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW--------------SCCGEGRIIVFT  352 (449)
Q Consensus       287 ~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--------------~~~~~~~iiI~t  352 (449)
                      ..+.....+.||||||||.+.+.                  ....|++.|+...              .......++|++
T Consensus        74 ~~l~~~~~~~vl~iDEi~~l~~~------------------~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~  135 (305)
T TIGR00635        74 AILTNLEEGDVLFIDEIHRLSPA------------------VEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGA  135 (305)
T ss_pred             HHHHhcccCCEEEEehHhhhCHH------------------HHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEe
Confidence            77777778899999999988531                  1122344433211              001123788899


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHH
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEV  416 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i  416 (449)
                      ||++..+++++.+  ||...+.++.++.++..++++...+..+..+.++ +..+++...=+|..+
T Consensus       136 t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~  198 (305)
T TIGR00635       136 TTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIA  198 (305)
T ss_pred             cCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchH
Confidence            9999999999998  9999999999999999999998877555555443 344444444444443

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.

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

Probab=99.75  E-value=8e-17  Score=151.66  Aligned_cols=172  Identities=22%  Similarity=0.309  Sum_probs=145.8

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |....|..+++|+|.+.+|+.+.+....|+.+..         .+++||||++|||||++++|+.+++   |..++.++-
T Consensus        18 i~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~p---------annvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k   88 (249)
T PF05673_consen   18 IKHPDPIRLDDLIGIERQKEALIENTEQFLQGLP---------ANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSK   88 (249)
T ss_pred             cCCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCCC---------CcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECH
Confidence            6677888999999999999999999999998653         5789999999999999999999988   788999999


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      .++..-..+...+...+.+.|||+||+-  +.               ........|-..|||--...+++++|.+|+|+.
T Consensus        89 ~~L~~l~~l~~~l~~~~~kFIlf~DDLs--Fe---------------~~d~~yk~LKs~LeGgle~~P~NvliyATSNRR  151 (249)
T PF05673_consen   89 EDLGDLPELLDLLRDRPYKFILFCDDLS--FE---------------EGDTEYKALKSVLEGGLEARPDNVLIYATSNRR  151 (249)
T ss_pred             HHhccHHHHHHHHhcCCCCEEEEecCCC--CC---------------CCcHHHHHHHHHhcCccccCCCcEEEEEecchh
Confidence            9999989999999988999999999964  22               123355778899998887778999999999986


Q ss_pred             CCCCc-----------------------cccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          357 EKLDP-----------------------ALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       357 ~~ld~-----------------------aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ..+..                       +|-.  ||...|.|..|+.++..+|++.++...+..+.
T Consensus       152 HLv~E~~~d~~~~~~~eih~~d~~eEklSLsD--RFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~  215 (249)
T PF05673_consen  152 HLVPESFSDREDIQDDEIHPSDTIEEKLSLSD--RFGLWLSFYPPDQEEYLAIVRHYAERYGLELD  215 (249)
T ss_pred             hccchhhhhccCCCccccCcchHHHHHHhHHH--hCCcEEEecCCCHHHHHHHHHHHHHHcCCCCC
Confidence            44432                       2223  99999999999999999999999977666654

>CHL00181 cbbX CbbX; Provisional

Probab=99.75  E-value=4.3e-17  Score=160.18  Aligned_cols=176  Identities=18%  Similarity=0.221  Sum_probs=126.6

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCc-c--eEEeCCCCCCHHHHHHHHHHHcC-------CcEEEEeccc
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKR-G--YLLYGPPGTGKSSLIAAMANQLK-------FDIYDLDLSA  278 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~r-g--~LL~GPpGtGKT~la~aiA~~l~-------~~~~~l~~s~  278 (449)
                      ++++|.+++|++|.+.+.. +.....+.+.|...+. |  +||+||||||||++|+++|+.+.       .+++.++.+.
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~-~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~  101 (287)
T CHL00181         23 EELVGLAPVKTRIREIAAL-LLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD  101 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHH-HHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH
Confidence            4799999999999887644 4455666777775542 3  89999999999999999999862       2577777655


Q ss_pred             cc------ChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          279 VQ------SNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       279 ~~------~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      +.      +......++..+ .++||||||+|.+...++  .       .......+..|+..|+..    ...++||++
T Consensus       102 l~~~~~g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~~~~--~-------~~~~~e~~~~L~~~me~~----~~~~~vI~a  167 (287)
T CHL00181        102 LVGQYIGHTAPKTKEVLKKA-MGGVLFIDEAYYLYKPDN--E-------RDYGSEAIEILLQVMENQ----RDDLVVIFA  167 (287)
T ss_pred             HHHHHhccchHHHHHHHHHc-cCCEEEEEccchhccCCC--c-------cchHHHHHHHHHHHHhcC----CCCEEEEEe
Confidence            42      222334455543 568999999998854111  0       112345667788888753    245677777


Q ss_pred             cCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH
Q 013128          353 TNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ  401 (449)
Q Consensus       353 TN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~  401 (449)
                      ++...     .++|+|.+  ||+.+|+|+.++.+++.+|+..++......+.++
T Consensus       168 g~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~  219 (287)
T CHL00181        168 GYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPE  219 (287)
T ss_pred             CCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChh
Confidence            65421     34699999  9999999999999999999999998765555443

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.74  E-value=3.2e-17  Score=161.06  Aligned_cols=175  Identities=15%  Similarity=0.190  Sum_probs=128.1

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCC---CcceEEeCCCCCCHHHHHHHHHHHcC-------CcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAW---KRGYLLYGPPGTGKSSLIAAMANQLK-------FDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~---~rg~LL~GPpGtGKT~la~aiA~~l~-------~~~~~l~~s~~  279 (449)
                      +++|.+++|++|.+.+.. +..+..+.+.|...   ..++||+||||||||++|+++|..+.       .+++.+++.++
T Consensus        23 ~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l  101 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAAL-LLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDL  101 (284)
T ss_pred             hccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHH
Confidence            689999999999887655 66666777788764   34799999999999999999999873       26788876554


Q ss_pred             c------ChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          280 Q------SNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       280 ~------~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                      .      +......++..+ .++||||||++.+...+.         ........+..|++.|+..    ..+++||+++
T Consensus       102 ~~~~~g~~~~~~~~~~~~a-~~gvL~iDEi~~L~~~~~---------~~~~~~~~~~~Ll~~le~~----~~~~~vI~a~  167 (284)
T TIGR02880       102 VGQYIGHTAPKTKEILKRA-MGGVLFIDEAYYLYRPDN---------ERDYGQEAIEILLQVMENQ----RDDLVVILAG  167 (284)
T ss_pred             hHhhcccchHHHHHHHHHc-cCcEEEEechhhhccCCC---------ccchHHHHHHHHHHHHhcC----CCCEEEEEeC
Confidence            2      223344555544 569999999998853111         0112345667788888753    2456777776


Q ss_pred             CCC--C---CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH
Q 013128          354 NHK--E---KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ  401 (449)
Q Consensus       354 N~~--~---~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~  401 (449)
                      +..  +   .++|+|.+  ||+.+|+||.++.+++..|+.+++......+.++
T Consensus       168 ~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~  218 (284)
T TIGR02880       168 YKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAE  218 (284)
T ss_pred             CcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHH
Confidence            542  2   35899999  9999999999999999999999998765545443

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=99.72  E-value=1.9e-16  Score=166.78  Aligned_cols=170  Identities=20%  Similarity=0.320  Sum_probs=128.5

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .|..    .++|.+|++++|.++.++.+.+.+..+..+.        + ++++|||||||||||++|+++|++++++++.
T Consensus         3 ~W~e----KyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~--------~-~~~lLL~GppG~GKTtla~ala~el~~~~ie   69 (482)
T PRK04195          3 PWVE----KYRPKTLSDVVGNEKAKEQLREWIESWLKGK--------P-KKALLLYGPPGVGKTSLAHALANDYGWEVIE   69 (482)
T ss_pred             Cchh----hcCCCCHHHhcCCHHHHHHHHHHHHHHhcCC--------C-CCeEEEECCCCCCHHHHHHHHHHHcCCCEEE
Confidence            5754    8899999999999999999999888776422        1 5789999999999999999999999999999


Q ss_pred             EecccccChHHHHHHHHcC--------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          274 LDLSAVQSNSELRFLLLTM--------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       274 l~~s~~~~~~~l~~~~~~~--------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      ++.++..+...+.......        ..+.||+|||+|.+....              ....+..|++.++.      .
T Consensus        70 lnasd~r~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~--------------d~~~~~aL~~~l~~------~  129 (482)
T PRK04195         70 LNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNE--------------DRGGARAILELIKK------A  129 (482)
T ss_pred             EcccccccHHHHHHHHHHhhccCcccCCCCeEEEEecCccccccc--------------chhHHHHHHHHHHc------C
Confidence            9998876655454433222        257899999999885311              11234556676653      1


Q ss_pred             CeEEEEEcCCCCCCCc-cccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          346 GRIIVFTTNHKEKLDP-ALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       346 ~~iiI~tTN~~~~ld~-aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ...+|+++|.+..+++ .|.+  | ...|+|+.|+.++...+++..+..++..+.
T Consensus       130 ~~~iIli~n~~~~~~~k~Lrs--r-~~~I~f~~~~~~~i~~~L~~i~~~egi~i~  181 (482)
T PRK04195        130 KQPIILTANDPYDPSLRELRN--A-CLMIEFKRLSTRSIVPVLKRICRKEGIECD  181 (482)
T ss_pred             CCCEEEeccCccccchhhHhc--c-ceEEEecCCCHHHHHHHHHHHHHHcCCCCC
Confidence            2356778899888877 5554  4 367999999999999999988866554443

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

Probab=99.71  E-value=1.9e-16  Score=166.11  Aligned_cols=200  Identities=21%  Similarity=0.217  Sum_probs=138.3

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH--
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR--  286 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~--  286 (449)
                      .+..|.+++|++|+++|.--...+.       -.+.-++|.||||+|||||+++||..+|..|+.++++.+.++.+++  
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~-------~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGH  395 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKK-------LKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGH  395 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhcc-------CCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhccc
Confidence            4678999999999998864433322       2234588999999999999999999999999999999999887765  


Q ss_pred             -------------HHHHcC-CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc----------
Q 013128          287 -------------FLLLTM-PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC----------  342 (449)
Q Consensus       287 -------------~~~~~~-~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----------  342 (449)
                                   +-+.++ ....+++|||||.+..  +-++.            .-+.||..+|--...          
T Consensus       396 RRTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~s--s~rGD------------PaSALLEVLDPEQN~~F~DhYLev~  461 (782)
T COG0466         396 RRTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGS--SFRGD------------PASALLEVLDPEQNNTFSDHYLEVP  461 (782)
T ss_pred             cccccccCChHHHHHHHHhCCcCCeEEeechhhccC--CCCCC------------hHHHHHhhcCHhhcCchhhccccCc
Confidence                         122222 3577999999999864  22222            224567666622111          


Q ss_pred             -CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC---CCCCHHHHHHHHHccCCCHHHHHH
Q 013128          343 -CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS---HHYLFEQIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       343 -~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~tpa~i~~  418 (449)
                       .-..|++|+|+|..+.|+.+|+.  ||. .|+++-.+.++..+|+++||-..   .|-|..      .+..++..-| .
T Consensus       462 yDLS~VmFiaTANsl~tIP~PLlD--RME-iI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~------~el~i~d~ai-~  531 (782)
T COG0466         462 YDLSKVMFIATANSLDTIPAPLLD--RME-VIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKK------GELTITDEAI-K  531 (782)
T ss_pred             cchhheEEEeecCccccCChHHhc--cee-eeeecCCChHHHHHHHHHhcchHHHHHcCCCc------cceeecHHHH-H
Confidence             01468999999999999999999  995 59999999999999999998532   111110      1122443333 4


Q ss_pred             HHhcCCCHHHHHHHHHHHHHH
Q 013128          419 ELMKSTNAEVSLNGLVKFLHA  439 (449)
Q Consensus       419 ~l~~~~~~~~al~~l~~~l~~  439 (449)
                      .+++....+..+++|.+.+..
T Consensus       532 ~iI~~YTREAGVR~LeR~i~k  552 (782)
T COG0466         532 DIIRYYTREAGVRNLEREIAK  552 (782)
T ss_pred             HHHHHHhHhhhhhHHHHHHHH
Confidence            445545555555555555543

>TIGR00763 lon ATP-dependent protease La

Probab=99.71  E-value=3.2e-16  Score=173.56  Aligned_cols=159  Identities=23%  Similarity=0.215  Sum_probs=116.3

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChH------
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNS------  283 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~------  283 (449)
                      +++|.+++|+.|.+.+.......       ...+.++||+||||||||++|+++|+.++.+++.++++.+.+..      
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~-------~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~  393 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRG-------KMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHR  393 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhc-------CCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCC
Confidence            47899999999988776443221       22234799999999999999999999999999999877654322      


Q ss_pred             ---------HHHHHHHcC-CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc----cc-------c
Q 013128          284 ---------ELRFLLLTM-PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL----WS-------C  342 (449)
Q Consensus       284 ---------~l~~~~~~~-~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~----~~-------~  342 (449)
                               .+...+... ..+.||+|||||.+...  .++            ...+.||..+|..    ..       .
T Consensus       394 ~~~~g~~~g~i~~~l~~~~~~~~villDEidk~~~~--~~~------------~~~~aLl~~ld~~~~~~f~d~~~~~~~  459 (775)
T TIGR00763       394 RTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGSS--FRG------------DPASALLEVLDPEQNNAFSDHYLDVPF  459 (775)
T ss_pred             CceeCCCCchHHHHHHHhCcCCCEEEEechhhcCCc--cCC------------CHHHHHHHhcCHHhcCccccccCCcee
Confidence                     233344432 34559999999998641  111            1234567766631    00       0


Q ss_pred             CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          343 CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       343 ~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      ...++++|+|||.++.++++|++  ||+ .|+|+.++.+++.+|+++|+.
T Consensus       460 d~s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~  506 (775)
T TIGR00763       460 DLSKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLI  506 (775)
T ss_pred             ccCCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHH
Confidence            11467899999999999999999  995 689999999999999999883

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.

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

Probab=99.70  E-value=4.1e-16  Score=147.90  Aligned_cols=192  Identities=18%  Similarity=0.218  Sum_probs=150.9

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      .-+|.+|++.+|.+++|+.+.=.+.....+.+        ..-++|||||||.||||||..||+++|.++-..+...+..
T Consensus        19 ~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e--------~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK   90 (332)
T COG2255          19 SLRPKTLDEFIGQEKVKEQLQIFIKAAKKRGE--------ALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEK   90 (332)
T ss_pred             ccCcccHHHhcChHHHHHHHHHHHHHHHhcCC--------CcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccC
Confidence            45789999999999999988777666555443        2357999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc----------cc----CCCCe
Q 013128          282 NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW----------SC----CGEGR  347 (449)
Q Consensus       282 ~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~----------~~----~~~~~  347 (449)
                      ...+..++.......|||||||+.+.+.                  +-.-|...|+.+.          +.    .-...
T Consensus        91 ~gDlaaiLt~Le~~DVLFIDEIHrl~~~------------------vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppF  152 (332)
T COG2255          91 PGDLAAILTNLEEGDVLFIDEIHRLSPA------------------VEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPF  152 (332)
T ss_pred             hhhHHHHHhcCCcCCeEEEehhhhcChh------------------HHHHhhhhhhheeEEEEEccCCccceEeccCCCe
Confidence            9999999999999999999999998541                  1111334444211          10    00235


Q ss_pred             EEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH-HHHHHHHccCCCHHHHHHHHhc
Q 013128          348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE-QIEELIKEVNVTPAEVAGELMK  422 (449)
Q Consensus       348 iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~-~i~~l~~~~~~tpa~i~~~l~~  422 (449)
                      -+|++|.+...|...|..  ||.+..++.+.+.++..+|+.+.-..-+..+.+ ...+++.+..=||. |+..|++
T Consensus       153 TLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPR-IAnRLLr  225 (332)
T COG2255         153 TLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPR-IANRLLR  225 (332)
T ss_pred             eEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcH-HHHHHHH
Confidence            789999999999999998  999999999999999999999988776666644 45566666777774 5555553

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

Probab=99.70  E-value=4.1e-16  Score=162.73  Aligned_cols=201  Identities=19%  Similarity=0.244  Sum_probs=138.1

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH--
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR--  286 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~--  286 (449)
                      ++..|+.++|++|++.+.--.-       .|...+.-++|+||||+|||+++++||..||..|+.++.+.+.+..+++  
T Consensus       411 eDHYgm~dVKeRILEfiAV~kL-------rgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKL-------RGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGH  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhh-------cccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhccc
Confidence            5678999999999998752211       1233345688999999999999999999999999999999887654443  


Q ss_pred             -------------HHHHcC-CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc----------
Q 013128          287 -------------FLLLTM-PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC----------  342 (449)
Q Consensus       287 -------------~~~~~~-~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----------  342 (449)
                                   +.+... ...-+++|||||.+..  +-+++.            -+.||..+|--...          
T Consensus       484 RRTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~--g~qGDP------------asALLElLDPEQNanFlDHYLdVp  549 (906)
T KOG2004|consen  484 RRTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGS--GHQGDP------------ASALLELLDPEQNANFLDHYLDVP  549 (906)
T ss_pred             ceeeeccCChHHHHHHHhhCCCCceEEeehhhhhCC--CCCCCh------------HHHHHHhcChhhccchhhhccccc
Confidence                         333333 3577999999999862  222221            23355444421110          


Q ss_pred             -CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC---CCCCHHHHHHHHHccCCCHHHHHH
Q 013128          343 -CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS---HHYLFEQIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       343 -~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~tpa~i~~  418 (449)
                       .-..+++|+|.|..+.|+++|+.  ||.+ |+++=...++...|+.+||-..   ++-+.++      ...++-+- ..
T Consensus       550 ~DLSkVLFicTAN~idtIP~pLlD--RMEv-IelsGYv~eEKv~IA~~yLip~a~~~~gl~~e------~v~is~~a-l~  619 (906)
T KOG2004|consen  550 VDLSKVLFICTANVIDTIPPPLLD--RMEV-IELSGYVAEEKVKIAERYLIPQALKDCGLKPE------QVKISDDA-LL  619 (906)
T ss_pred             cchhheEEEEeccccccCChhhhh--hhhe-eeccCccHHHHHHHHHHhhhhHHHHHcCCCHH------hcCccHHH-HH
Confidence             01468999999999999999999  9965 9999999999999999998542   2222211      11233222 24


Q ss_pred             HHhcCCCHHHHHHHHHHHHHHH
Q 013128          419 ELMKSTNAEVSLNGLVKFLHAK  440 (449)
Q Consensus       419 ~l~~~~~~~~al~~l~~~l~~~  440 (449)
                      .|++....+..+++|++.++.-
T Consensus       620 ~lI~~YcrEaGVRnLqk~iekI  641 (906)
T KOG2004|consen  620 ALIERYCREAGVRNLQKQIEKI  641 (906)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHH
Confidence            4555556677777777766653

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

Probab=99.69  E-value=1.9e-16  Score=156.65  Aligned_cols=153  Identities=24%  Similarity=0.309  Sum_probs=110.4

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN  282 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~  282 (449)
                      -+|.++++++|++.+... -..|...+...         .-.+++|||||||||||+|+.||+..+.+|..++...- +.
T Consensus        18 mRP~~lde~vGQ~HLlg~-~~~lrr~v~~~---------~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~~-gv   86 (436)
T COG2256          18 LRPKSLDEVVGQEHLLGE-GKPLRRAVEAG---------HLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTS-GV   86 (436)
T ss_pred             hCCCCHHHhcChHhhhCC-CchHHHHHhcC---------CCceeEEECCCCCCHHHHHHHHHHhhCCceEEeccccc-cH
Confidence            479999999998876532 11222222222         24579999999999999999999999999999975432 33


Q ss_pred             HHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE-Ec-C
Q 013128          283 SELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF-TT-N  354 (449)
Q Consensus       283 ~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~-tT-N  354 (449)
                      .+++..+.++      .+..|||||||+.+-.    .              ....||..++.      +.+++|+ || |
T Consensus        87 kdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK----~--------------QQD~lLp~vE~------G~iilIGATTEN  142 (436)
T COG2256          87 KDLREIIEEARKNRLLGRRTILFLDEIHRFNK----A--------------QQDALLPHVEN------GTIILIGATTEN  142 (436)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEehhhhcCh----h--------------hhhhhhhhhcC------CeEEEEeccCCC
Confidence            4566555544      3589999999999842    1              22348888863      4567776 44 4


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      ..-.|.+||++  |. ..+.+...+.++.++++++-+..
T Consensus       143 PsF~ln~ALlS--R~-~vf~lk~L~~~di~~~l~ra~~~  178 (436)
T COG2256         143 PSFELNPALLS--RA-RVFELKPLSSEDIKKLLKRALLD  178 (436)
T ss_pred             CCeeecHHHhh--hh-heeeeecCCHHHHHHHHHHHHhh
Confidence            45689999999  66 45889999999999999984443

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=1.2e-15  Score=159.16  Aligned_cols=157  Identities=19%  Similarity=0.329  Sum_probs=115.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+.    ...        .+.++|||||||||||++|+++|+.++.            
T Consensus         7 kyRP~~~~divGq~~i~~~L~~~i~----~~~--------l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c   74 (472)
T PRK14962          7 KYRPKTFSEVVGQDHVKKLIINALK----KNS--------ISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNEC   74 (472)
T ss_pred             HHCCCCHHHccCcHHHHHHHHHHHH----cCC--------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCccc
Confidence            5789999999999988776655433    221        2467999999999999999999999864            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.+.-.....++.+....      ....||+|||+|.+..                  ..+..
T Consensus        75 ~~c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~------------------~a~~~  136 (472)
T PRK14962         75 RACRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTK------------------EAFNA  136 (472)
T ss_pred             HHHHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHH------------------HHHHH
Confidence                        57777765433334444433222      2457999999998842                  23466


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      ||..++..    +..+++|++|+.+..+++++.+  |+ ..+++..++.++...+++..+..++
T Consensus       137 LLk~LE~p----~~~vv~Ilattn~~kl~~~L~S--R~-~vv~f~~l~~~el~~~L~~i~~~eg  193 (472)
T PRK14962        137 LLKTLEEP----PSHVVFVLATTNLEKVPPTIIS--RC-QVIEFRNISDELIIKRLQEVAEAEG  193 (472)
T ss_pred             HHHHHHhC----CCcEEEEEEeCChHhhhHHHhc--Cc-EEEEECCccHHHHHHHHHHHHHHcC
Confidence            88888753    3457777777788899999998  77 4699999999998888887765443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=7e-16  Score=162.88  Aligned_cols=161  Identities=19%  Similarity=0.274  Sum_probs=123.9

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++|+|.+.+++.|.+.+..    .        ..+..|||+||+|||||++++.+|+.++.            
T Consensus         9 KYRPqtFddVIGQe~vv~~L~~al~~----g--------RLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~   76 (700)
T PRK12323          9 KWRPRDFTTLVGQEHVVRALTHALEQ----Q--------RLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQ   76 (700)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHHh----C--------CCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCC
Confidence            67999999999999998877766541    1        12467999999999999999999999975            


Q ss_pred             -----------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhH
Q 013128          270 -----------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENK  326 (449)
Q Consensus       270 -----------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~  326 (449)
                                       +++.++..+-..-.+++.++...      ....|+||||+|.+..                  
T Consensus        77 PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~------------------  138 (700)
T PRK12323         77 PCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTN------------------  138 (700)
T ss_pred             CCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCH------------------
Confidence                             45666655433344555554432      2457999999998842                  


Q ss_pred             HHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          327 VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       327 ~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ...+.||..|+.-    ...+++|++||.+++|.+.+++  |+ .++.|..++.++..+.++.++..++....
T Consensus       139 ~AaNALLKTLEEP----P~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d  204 (700)
T PRK12323        139 HAFNAMLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHE  204 (700)
T ss_pred             HHHHHHHHhhccC----CCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCC
Confidence            3457788888763    4567899999999999999998  87 67999999999999988888776554443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=1.4e-15  Score=156.92  Aligned_cols=159  Identities=16%  Similarity=0.298  Sum_probs=117.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+.+.+...+.    ..        ..+..|||+||||||||++|+++|+.++.            
T Consensus        11 KyRP~~f~dvVGQe~iv~~L~~~i~----~~--------ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C   78 (484)
T PRK14956         11 KYRPQFFRDVIHQDLAIGALQNALK----SG--------KIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNEC   78 (484)
T ss_pred             HhCCCCHHHHhChHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCC
Confidence            6799999999999988887665543    11        12356999999999999999999999975            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++...-.....++.+....      ....|+||||+|.+..                  ..++.
T Consensus        79 ~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~------------------~A~NA  140 (484)
T PRK14956         79 TSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTD------------------QSFNA  140 (484)
T ss_pred             cHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCH------------------HHHHH
Confidence                        35555553322233344332221      2456999999998842                  35677


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..|+..    ...+++|++|+.++.|.+++++  |+ .++.|..++.++..+.++..+..++..
T Consensus       141 LLKtLEEP----p~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Egi~  199 (484)
T PRK14956        141 LLKTLEEP----PAHIVFILATTEFHKIPETILS--RC-QDFIFKKVPLSVLQDYSEKLCKIENVQ  199 (484)
T ss_pred             HHHHhhcC----CCceEEEeecCChhhccHHHHh--hh-heeeecCCCHHHHHHHHHHHHHHcCCC
Confidence            88888752    4578889999999999999999  88 468899999988888888877655433

>PLN03025 replication factor C subunit; Provisional

Probab=99.66  E-value=1.9e-15  Score=151.14  Aligned_cols=163  Identities=14%  Similarity=0.195  Sum_probs=116.3

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-----
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-----  268 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-----  268 (449)
                      +|..    .++|.+|++++|.+++.+.+...+.    ...         ..++|||||||||||++|+++|+++.     
T Consensus         2 ~w~~----kyrP~~l~~~~g~~~~~~~L~~~~~----~~~---------~~~lll~Gp~G~GKTtla~~la~~l~~~~~~   64 (319)
T PLN03025          2 PWVE----KYRPTKLDDIVGNEDAVSRLQVIAR----DGN---------MPNLILSGPPGTGKTTSILALAHELLGPNYK   64 (319)
T ss_pred             Chhh----hcCCCCHHHhcCcHHHHHHHHHHHh----cCC---------CceEEEECCCCCCHHHHHHHHHHHHhcccCc
Confidence            4755    8899999999999988777655432    211         23699999999999999999999982     


Q ss_pred             CcEEEEecccccChHHHHHHH---HcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          269 FDIYDLDLSAVQSNSELRFLL---LTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       269 ~~~~~l~~s~~~~~~~l~~~~---~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                      ..++.++.++......++..+   ...      ....|++|||+|.+..                  ...+.|+..|+..
T Consensus        65 ~~~~eln~sd~~~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~------------------~aq~aL~~~lE~~  126 (319)
T PLN03025         65 EAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTS------------------GAQQALRRTMEIY  126 (319)
T ss_pred             cceeeecccccccHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCH------------------HHHHHHHHHHhcc
Confidence            346677766654433444332   211      2467999999999843                  1234466666542


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                          +....+|+++|....+.++|.+  |+ ..++|+.|+.++....++..+..++..+
T Consensus       127 ----~~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~egi~i  178 (319)
T PLN03025        127 ----SNTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAEKVPY  178 (319)
T ss_pred             ----cCCceEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHcCCCC
Confidence                2334677888999999999998  76 4699999999999888888776655444

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.66  E-value=2.1e-15  Score=161.16  Aligned_cols=161  Identities=18%  Similarity=0.290  Sum_probs=122.4

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-----------
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-----------  269 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-----------  269 (449)
                      ..++|.+|++|+|.+.+++.|...+.    ..        ..+..|||+||+|||||++++++|+.+++           
T Consensus         8 rKYRPqtFdEVIGQe~Vv~~L~~aL~----~g--------RL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~   75 (830)
T PRK07003          8 RKWRPKDFASLVGQEHVVRALTHALD----GG--------RLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGV   75 (830)
T ss_pred             HHhCCCcHHHHcCcHHHHHHHHHHHh----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcc
Confidence            36799999999999998887766543    11        12467999999999999999999999864           


Q ss_pred             -------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHH
Q 013128          270 -------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS  330 (449)
Q Consensus       270 -------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls  330 (449)
                                   +++.++..+-....+++.++...      ....|+||||+|.+..                  ...+
T Consensus        76 C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~------------------~A~N  137 (830)
T PRK07003         76 CRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTN------------------HAFN  137 (830)
T ss_pred             cHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCH------------------HHHH
Confidence                         46666655433344555554432      2457999999998842                  2456


Q ss_pred             HHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       331 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      .||..|+..    ...+++|++||++++|.+.+++  |+ .++.|..++.++..+.++..++.++..+
T Consensus       138 ALLKtLEEP----P~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~i  198 (830)
T PRK07003        138 AMLKTLEEP----PPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAF  198 (830)
T ss_pred             HHHHHHHhc----CCCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCC
Confidence            788888763    3568899999999999999998  87 6799999999999999988887654433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.66  E-value=5e-15  Score=147.72  Aligned_cols=159  Identities=16%  Similarity=0.222  Sum_probs=116.0

Q ss_pred             cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          192 HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       192 ~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      ...|..    .++|.+|++++|.++.++.+...+.    .       | ..+..+||+||||+|||++++++|++++.++
T Consensus         8 ~~~w~~----kyrP~~~~~~~~~~~~~~~l~~~~~----~-------~-~~~~~lll~G~~G~GKT~la~~l~~~~~~~~   71 (316)
T PHA02544          8 EFMWEQ----KYRPSTIDECILPAADKETFKSIVK----K-------G-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEV   71 (316)
T ss_pred             CCccee----ccCCCcHHHhcCcHHHHHHHHHHHh----c-------C-CCCeEEEeeCcCCCCHHHHHHHHHHHhCccc
Confidence            346855    8899999999999999888776654    1       1 1245677799999999999999999999999


Q ss_pred             EEEecccccChHHHHH----HHHcC---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC
Q 013128          272 YDLDLSAVQSNSELRF----LLLTM---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG  344 (449)
Q Consensus       272 ~~l~~s~~~~~~~l~~----~~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  344 (449)
                      +.++++. .....++.    .....   ..+.||+|||+|.+..              ..   ....|...++..    .
T Consensus        72 ~~i~~~~-~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~--------------~~---~~~~L~~~le~~----~  129 (316)
T PHA02544         72 LFVNGSD-CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGL--------------AD---AQRHLRSFMEAY----S  129 (316)
T ss_pred             eEeccCc-ccHHHHHHHHHHHHHhhcccCCCeEEEEECcccccC--------------HH---HHHHHHHHHHhc----C
Confidence            9999887 22222222    11111   3678999999998721              01   122344455543    2


Q ss_pred             CCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          345 EGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       345 ~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      ....+|+|||.+..+++++.+  |+. .+.++.|+.+++..++..++
T Consensus       130 ~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~~  173 (316)
T PHA02544        130 KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQMI  173 (316)
T ss_pred             CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHHH
Confidence            456788899999999999998  884 68999999999887776543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.64  E-value=3.1e-15  Score=158.36  Aligned_cols=160  Identities=18%  Similarity=0.278  Sum_probs=122.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+.    ..        ..+.+|||+||||||||++|+++|+.++.            
T Consensus         8 KyRPktFddVIGQe~vv~~L~~aI~----~g--------rl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C   75 (702)
T PRK14960          8 KYRPRNFNELVGQNHVSRALSSALE----RG--------RLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVC   75 (702)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccC
Confidence            5789999999999999888776654    11        12468999999999999999999999864            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.++-..-..++.++...      .+..|++|||+|.+..                  ...+.
T Consensus        76 ~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~------------------~A~NA  137 (702)
T PRK14960         76 ATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLST------------------HSFNA  137 (702)
T ss_pred             HHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCH------------------HHHHH
Confidence                        56777766444445566555433      2456999999998742                  24566


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    ...+.+|++|+.+..+.+.+++  |+ .+++|..++.++....+...+..++...
T Consensus       138 LLKtLEEP----P~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kEgI~i  197 (702)
T PRK14960        138 LLKTLEEP----PEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKEQIAA  197 (702)
T ss_pred             HHHHHhcC----CCCcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888753    3557888888889999989887  77 5799999999998888888877655444

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.64  E-value=6.3e-15  Score=149.87  Aligned_cols=160  Identities=16%  Similarity=0.264  Sum_probs=116.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+..++.+...+..    .        ..+..|||+||||||||++|+++|+.++.            
T Consensus         9 kyrP~~~~~iiGq~~~~~~l~~~~~~----~--------~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c   76 (363)
T PRK14961          9 KWRPQYFRDIIGQKHIVTAISNGLSL----G--------RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKC   76 (363)
T ss_pred             HhCCCchhhccChHHHHHHHHHHHHc----C--------CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            57899999999999988877655431    1        12467999999999999999999999852            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.++-.....++.+....      ....|++|||+|.+..                  ...+.
T Consensus        77 ~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~------------------~a~na  138 (363)
T PRK14961         77 IICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSR------------------HSFNA  138 (363)
T ss_pred             HHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCH------------------HHHHH
Confidence                        45555544322333444444332      2356999999998742                  23456


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..++..    +..+.+|++|+.++.+.+++.+  |+ ..++++.++.++....+...+..++..+
T Consensus       139 LLk~lEe~----~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i  198 (363)
T PRK14961        139 LLKTLEEP----PQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDT  198 (363)
T ss_pred             HHHHHhcC----CCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888753    3456778888888999999987  77 6799999999999988888776554434

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=8.8e-15  Score=153.44  Aligned_cols=166  Identities=17%  Similarity=0.267  Sum_probs=122.1

Q ss_pred             cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC--
Q 013128          192 HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--  269 (449)
Q Consensus       192 ~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~--  269 (449)
                      +..|..    ..+|.+|++++|.+.+.+.+...+.   .+         ..+.++||+||||||||++|+++|+.++.  
T Consensus         8 y~~la~----kyRP~~f~dliGq~~vv~~L~~ai~---~~---------ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~   71 (507)
T PRK06645          8 YIPFAR----KYRPSNFAELQGQEVLVKVLSYTIL---ND---------RLAGGYLLTGIRGVGKTTSARIIAKAVNCSA   71 (507)
T ss_pred             ccchhh----hhCCCCHHHhcCcHHHHHHHHHHHH---cC---------CCCceEEEECCCCCCHHHHHHHHHHHhcCcc
Confidence            345654    7899999999999988876655432   11         12468999999999999999999999854  


Q ss_pred             --------------------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhh
Q 013128          270 --------------------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEV  317 (449)
Q Consensus       270 --------------------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~  317 (449)
                                                +++.++..+-.....++.++...      ....|++|||+|.+..         
T Consensus        72 ~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~---------  142 (507)
T PRK06645         72 LITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSK---------  142 (507)
T ss_pred             ccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCH---------
Confidence                                      44555544333345555554443      2467999999998732         


Q ss_pred             hhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       318 ~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                               ..++.||..|+..    +..+++|++|+.++.+++++.+  |+ ..++|..++.++....++..+..++..
T Consensus       143 ---------~a~naLLk~LEep----p~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~  206 (507)
T PRK06645        143 ---------GAFNALLKTLEEP----PPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLK  206 (507)
T ss_pred             ---------HHHHHHHHHHhhc----CCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCC
Confidence                     3456788888752    4567888888899999999988  77 578999999999999998888765443


Q ss_pred             C
Q 013128          398 L  398 (449)
Q Consensus       398 l  398 (449)
                      .
T Consensus       207 i  207 (507)
T PRK06645        207 T  207 (507)
T ss_pred             C
Confidence            3

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.62  E-value=1.2e-14  Score=147.16  Aligned_cols=161  Identities=19%  Similarity=0.325  Sum_probs=118.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------------  268 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------------  268 (449)
                      ..+|.+|++++|.+..++.+.+.+..           | ..+..+|||||||+|||++++++|+.+.             
T Consensus         7 ~~rp~~~~~iig~~~~~~~l~~~~~~-----------~-~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c   74 (355)
T TIGR02397         7 KYRPQTFEDVIGQEHIVQTLKNAIKN-----------G-RIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNEC   74 (355)
T ss_pred             HhCCCcHhhccCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            67899999999999998888776532           1 1246799999999999999999999974             


Q ss_pred             -----------CcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          269 -----------FDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       269 -----------~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                 .+++.++.........++.++...      ..+.|++|||+|.+..                  ...+.
T Consensus        75 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~------------------~~~~~  136 (355)
T TIGR02397        75 ESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK------------------SAFNA  136 (355)
T ss_pred             HHHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCH------------------HHHHH
Confidence                       235555554333333344444432      2456999999998732                  23566


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      |+..++..    +...++|++|++++.+.+++.+  |+ ..++++.|+.++...++..++...+..+.
T Consensus       137 Ll~~le~~----~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~  197 (355)
T TIGR02397       137 LLKTLEEP----PEHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIE  197 (355)
T ss_pred             HHHHHhCC----ccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            88888753    3567788888999999999988  77 56899999999999999887766554443

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.

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

Probab=99.62  E-value=3.7e-15  Score=164.32  Aligned_cols=159  Identities=17%  Similarity=0.188  Sum_probs=117.7

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEE
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYD  273 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~  273 (449)
                      +|-.+|+++|.++....+++.|.    +.         .+.++||+||||||||++++++|..+          +..++.
T Consensus       177 r~~~l~~~igr~~ei~~~~~~L~----~~---------~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~  243 (731)
T TIGR02639       177 KNGKIDPLIGREDELERTIQVLC----RR---------KKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS  243 (731)
T ss_pred             hcCCCCcccCcHHHHHHHHHHHh----cC---------CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE
Confidence            56789999999988887665542    11         25789999999999999999999998          788999


Q ss_pred             EecccccC--------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC
Q 013128          274 LDLSAVQS--------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC  343 (449)
Q Consensus       274 l~~s~~~~--------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~  343 (449)
                      ++++.+..        +..++.++...  ..++||||||||.+.+.+...+..         ....+-|+..+.      
T Consensus       244 ~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~---------~~~~~~L~~~l~------  308 (731)
T TIGR02639       244 LDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGS---------MDASNLLKPALS------  308 (731)
T ss_pred             ecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCcc---------HHHHHHHHHHHh------
Confidence            99877643        24667777654  358999999999998643211110         111223445553      


Q ss_pred             CCCeEEEEEcCCC-----CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          344 GEGRIIVFTTNHK-----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       344 ~~~~iiI~tTN~~-----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      .+.+.+|++||..     -.+|+||.|  ||. .|+++.|+.+++.+|++.....
T Consensus       309 ~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~  360 (731)
T TIGR02639       309 SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKEK  360 (731)
T ss_pred             CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHHH
Confidence            2467888888864     357999999  997 6999999999999999976653

>PRK06893 DNA replication initiation factor; Validated

Probab=99.61  E-value=1.1e-14  Score=138.87  Aligned_cols=170  Identities=14%  Similarity=0.150  Sum_probs=105.6

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +....+.+||++++.++..  ....+.....         ....+.++||||||||||+|++|+|+++   +.....+++
T Consensus         7 ~~~~~~~~fd~f~~~~~~~--~~~~~~~~~~---------~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893          7 IHQIDDETLDNFYADNNLL--LLDSLRKNFI---------DLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CCCCCcccccccccCChHH--HHHHHHHHhh---------ccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            5567788999998765431  2222221111         1113458999999999999999999997   445566655


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc-CC
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT-NH  355 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT-N~  355 (449)
                      +....  .....+....+..+|+||||+.+.+.             ......   |++.++....  .+..++|.|+ ..
T Consensus        76 ~~~~~--~~~~~~~~~~~~dlLilDDi~~~~~~-------------~~~~~~---l~~l~n~~~~--~~~~illits~~~  135 (229)
T PRK06893         76 SKSQY--FSPAVLENLEQQDLVCLDDLQAVIGN-------------EEWELA---IFDLFNRIKE--QGKTLLLISADCS  135 (229)
T ss_pred             HHhhh--hhHHHHhhcccCCEEEEeChhhhcCC-------------hHHHHH---HHHHHHHHHH--cCCcEEEEeCCCC
Confidence            43211  11234455567789999999987531             111122   4444443322  1234545554 45


Q ss_pred             CCCCC---ccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH
Q 013128          356 KEKLD---PALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE  400 (449)
Q Consensus       356 ~~~ld---~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~  400 (449)
                      |..++   |+|.++.+.+..+.++.|+.+++.+++++.....+..+.+
T Consensus       136 p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~  183 (229)
T PRK06893        136 PHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSD  183 (229)
T ss_pred             hHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            65554   8899855556889999999999999999877544444433

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=1e-14  Score=151.91  Aligned_cols=160  Identities=15%  Similarity=0.228  Sum_probs=122.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc--------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL--------------  267 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l--------------  267 (449)
                      .++|.+|++++|.+.+++.+...+.    ..        ..+.++||+||||||||++|+.+|+.+              
T Consensus         6 KyRP~~f~dliGQe~vv~~L~~a~~----~~--------ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C   73 (491)
T PRK14964          6 KYRPSSFKDLVGQDVLVRILRNAFT----LN--------KIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTC   73 (491)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCcccc
Confidence            6789999999999988876654432    11        125689999999999999999999875              


Q ss_pred             ----------CCcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          268 ----------KFDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       268 ----------~~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                +.+++.++.++-.+...++.++...      ...-|++|||+|.+..                  ..++.
T Consensus        74 ~~C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~------------------~A~Na  135 (491)
T PRK14964         74 HNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSN------------------SAFNA  135 (491)
T ss_pred             HHHHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCH------------------HHHHH
Confidence                      2467888877655555666555443      2467999999998742                  35677


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    +..+++|++|+.++++.+.+++  |+ ..++|..++.++....+...+..++..+
T Consensus       136 LLK~LEeP----p~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i  195 (491)
T PRK14964        136 LLKTLEEP----APHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEH  195 (491)
T ss_pred             HHHHHhCC----CCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHcCCCC
Confidence            89998863    4567888888999999999998  77 5689999999998888888776655444

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=8.2e-15  Score=154.46  Aligned_cols=159  Identities=17%  Similarity=0.288  Sum_probs=119.9

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..|||+||||||||++|+++|+.++.            
T Consensus         9 kyRP~~f~divGq~~v~~~L~~~~~~----~--------~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C   76 (509)
T PRK14958          9 KWRPRCFQEVIGQAPVVRALSNALDQ----Q--------YLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDC   76 (509)
T ss_pred             HHCCCCHHHhcCCHHHHHHHHHHHHh----C--------CCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCC
Confidence            67999999999999998887766632    1        12457999999999999999999999964            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++..+-..-..++.++...      .+..|++|||+|.+..                  ...+.
T Consensus        77 ~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~------------------~a~na  138 (509)
T PRK14958         77 ENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSG------------------HSFNA  138 (509)
T ss_pred             HHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCH------------------HHHHH
Confidence                        36777765544445566555432      2346999999998843                  24567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..|+..    ++.+++|++|+.+.++.+.+++  |+ ..++|..++.++....++..+..++..
T Consensus       139 LLk~LEep----p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~  197 (509)
T PRK14958        139 LLKTLEEP----PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVE  197 (509)
T ss_pred             HHHHHhcc----CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCC
Confidence            88888763    4567888888899999989988  76 568899998888777777777655443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.61  E-value=1.2e-14  Score=150.23  Aligned_cols=151  Identities=22%  Similarity=0.279  Sum_probs=110.7

Q ss_pred             cCCCCCcccccCCHHHHHH---HHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc
Q 013128          202 LKHPMTFKTLALDSELKRE---ITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~---i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~  278 (449)
                      ..+|.+|++++|.++....   +...+    ...         ...++||+||||||||++|+++|+.++.+++.++...
T Consensus         5 ~~RP~~l~d~vGq~~~v~~~~~L~~~i----~~~---------~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~   71 (413)
T PRK13342          5 RMRPKTLDEVVGQEHLLGPGKPLRRMI----EAG---------RLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT   71 (413)
T ss_pred             hhCCCCHHHhcCcHHHhCcchHHHHHH----HcC---------CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccc
Confidence            6789999999999887554   44443    221         1357999999999999999999999999999998764


Q ss_pred             ccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          279 VQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       279 ~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      .. ...++.++...      ..+.||||||+|.+..                  .....|+..++.      ..+++|++
T Consensus        72 ~~-~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~------------------~~q~~LL~~le~------~~iilI~a  126 (413)
T PRK13342         72 SG-VKDLREVIEEARQRRSAGRRTILFIDEIHRFNK------------------AQQDALLPHVED------GTITLIGA  126 (413)
T ss_pred             cc-HHHHHHHHHHHHHhhhcCCceEEEEechhhhCH------------------HHHHHHHHHhhc------CcEEEEEe
Confidence            32 23344433332      2678999999998742                  123446777653      23566655


Q ss_pred             c--CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          353 T--NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       353 T--N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      |  |....++++|++  |+ ..+.++.++.++...+++..+..
T Consensus       127 tt~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~  166 (413)
T PRK13342        127 TTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALED  166 (413)
T ss_pred             CCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHH
Confidence            4  334689999999  87 67899999999999999987754

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.60  E-value=5.3e-14  Score=130.63  Aligned_cols=174  Identities=20%  Similarity=0.302  Sum_probs=144.0

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +...+|..+.+|+|.+.+|+.+.+....|+.+..         -+++||+|..|||||||++|+-+++   +..++.|+-
T Consensus        51 v~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~p---------ANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k  121 (287)
T COG2607          51 VPDPDPIDLADLVGVDRQKEALVRNTEQFAEGLP---------ANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDK  121 (287)
T ss_pred             CCCCCCcCHHHHhCchHHHHHHHHHHHHHHcCCc---------ccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcH
Confidence            6666778899999999999999999999998653         5789999999999999999999998   678999999


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      .++.+-..+...+...+.+.|||+||+--  .               ........|-..+||--...+.+|+|.+|+|+.
T Consensus       122 ~dl~~Lp~l~~~Lr~~~~kFIlFcDDLSF--e---------------~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRR  184 (287)
T COG2607         122 EDLATLPDLVELLRARPEKFILFCDDLSF--E---------------EGDDAYKALKSALEGGVEGRPANVLFYATSNRR  184 (287)
T ss_pred             HHHhhHHHHHHHHhcCCceEEEEecCCCC--C---------------CCchHHHHHHHHhcCCcccCCCeEEEEEecCCc
Confidence            99998889999999999999999999742  1               122345567888998877778899999999987


Q ss_pred             CCCCcccc--------------------CCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          357 EKLDPALL--------------------RPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       357 ~~ld~aLl--------------------rpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ..|+....                    -..||+.-+.|+.|+.++..+|+..|....+..+.
T Consensus       185 HLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~  247 (287)
T COG2607         185 HLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDIS  247 (287)
T ss_pred             ccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCC
Confidence            65542111                    12399999999999999999999999976655553

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=1.7e-14  Score=154.08  Aligned_cols=160  Identities=17%  Similarity=0.289  Sum_probs=120.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++|+|.+.+++.+...+..    .        ..+.+|||+||||||||++|+++|+.++.            
T Consensus         9 KYRP~tFddIIGQe~vv~~L~~ai~~----~--------rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C   76 (709)
T PRK08691          9 KWRPKTFADLVGQEHVVKALQNALDE----G--------RLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVC   76 (709)
T ss_pred             HhCCCCHHHHcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCccc
Confidence            67899999999999998887776542    1        12568999999999999999999998753            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++..+-.....++.++...      ....|+||||+|.+..                  ..++.
T Consensus        77 ~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~------------------~A~NA  138 (709)
T PRK08691         77 QSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSK------------------SAFNA  138 (709)
T ss_pred             HHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCH------------------HHHHH
Confidence                        34555544433444566555432      3457999999997632                  24567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    .+.+++|++|+.+..+.+.+++  |+ ..+.|+.++.++....++..+..++..+
T Consensus       139 LLKtLEEP----p~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~i  198 (709)
T PRK08691        139 MLKTLEEP----PEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAY  198 (709)
T ss_pred             HHHHHHhC----CCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCc
Confidence            88888753    3457888888999999999886  87 6788999999999999988887665444

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.3e-14  Score=155.90  Aligned_cols=159  Identities=19%  Similarity=0.283  Sum_probs=116.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc-----------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-----------  270 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~-----------  270 (449)
                      ..+|.+|++++|.+.+++.+...+.    ..        ..+..|||+||||||||++|+++|+.++..           
T Consensus         9 KyRP~tFddIIGQe~Iv~~LknaI~----~~--------rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C   76 (944)
T PRK14949          9 KWRPATFEQMVGQSHVLHALTNALT----QQ--------RLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVC   76 (944)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----hC--------CCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCc
Confidence            5789999999999998887765543    11        125678999999999999999999999653           


Q ss_pred             -------------EEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          271 -------------IYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       271 -------------~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                   ++.++..+-.....++.+....      ....|+||||+|.+..                  ..++.
T Consensus        77 ~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~------------------eAqNA  138 (944)
T PRK14949         77 SSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSR------------------SSFNA  138 (944)
T ss_pred             hHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCH------------------HHHHH
Confidence                         2333333222223344443322      2456999999999842                  35678


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..|+..    +..+++|++|+.+..|.+.++.  |+ .+++|..++.++....+++.+..++..
T Consensus       139 LLKtLEEP----P~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~  197 (944)
T PRK14949        139 LLKTLEEP----PEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLP  197 (944)
T ss_pred             HHHHHhcc----CCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            99999863    4557778888889999999998  77 679999999999998888877654433

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.5e-14  Score=152.87  Aligned_cols=161  Identities=17%  Similarity=0.261  Sum_probs=119.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++++|.+.+++.+...+.    ..        ..+..|||+||+|||||++|+++|+.++.            
T Consensus         9 KyRP~~f~dviGQe~vv~~L~~~l~----~~--------rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~   76 (618)
T PRK14951          9 KYRPRSFSEMVGQEHVVQALTNALT----QQ--------RLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITAT   76 (618)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCC
Confidence            6789999999999888877666543    11        12467999999999999999999999864            


Q ss_pred             -----------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhH
Q 013128          270 -----------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENK  326 (449)
Q Consensus       270 -----------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~  326 (449)
                                       +++.++..+-..-..++.++...      ...-|++|||+|.+..                  
T Consensus        77 pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~------------------  138 (618)
T PRK14951         77 PCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTN------------------  138 (618)
T ss_pred             CCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCH------------------
Confidence                             35555554333334555555432      1346999999999843                  


Q ss_pred             HHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          327 VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       327 ~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ...+.||..++..    ++.+++|++|+.+.++.+.+++  |+ .+++|..++.++....++..+..++....
T Consensus       139 ~a~NaLLKtLEEP----P~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie  204 (618)
T PRK14951        139 TAFNAMLKTLEEP----PEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAE  204 (618)
T ss_pred             HHHHHHHHhcccC----CCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            2466788888753    4567888888889999989888  76 67999999999988888887766554443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=3.9e-14  Score=151.16  Aligned_cols=160  Identities=16%  Similarity=0.275  Sum_probs=120.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------------  268 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------------  268 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..++.||||||+|||||++|+.+|+.++             
T Consensus         9 k~rP~~f~~viGq~~v~~~L~~~i~~----~--------~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C   76 (559)
T PRK05563          9 KWRPQTFEDVVGQEHITKTLKNAIKQ----G--------KISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNEC   76 (559)
T ss_pred             HhCCCcHHhccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            56899999999999988877766542    1        1256799999999999999999999984             


Q ss_pred             -----------CcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          269 -----------FDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       269 -----------~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                 .+++.++.++-..-..++.+....      ...-|++|||+|.+..                  ...+.
T Consensus        77 ~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~------------------~a~na  138 (559)
T PRK05563         77 EICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLST------------------GAFNA  138 (559)
T ss_pred             HHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCH------------------HHHHH
Confidence                       466777765444444555554442      2457999999998742                  24667


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..++..    +..+++|++|+.++.+.+.+++  |+ ..+.|+.++.++....+...+..++..+
T Consensus       139 LLKtLEep----p~~~ifIlatt~~~ki~~tI~S--Rc-~~~~f~~~~~~ei~~~L~~i~~~egi~i  198 (559)
T PRK05563        139 LLKTLEEP----PAHVIFILATTEPHKIPATILS--RC-QRFDFKRISVEDIVERLKYILDKEGIEY  198 (559)
T ss_pred             HHHHhcCC----CCCeEEEEEeCChhhCcHHHHh--Hh-eEEecCCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888764    4567888888889999999988  77 4688999999998888888776554444

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.58  E-value=1.8e-14  Score=153.04  Aligned_cols=189  Identities=20%  Similarity=0.268  Sum_probs=128.7

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc------
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL------  267 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l------  267 (449)
                      +|..    ..+|.+|++++|.+...+.+...+    ..         +.+.++||+||||||||++|+++++++      
T Consensus        54 ~~~~----~~rp~~f~~iiGqs~~i~~l~~al----~~---------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s  116 (531)
T TIGR02902        54 PLSE----KTRPKSFDEIIGQEEGIKALKAAL----CG---------PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPAS  116 (531)
T ss_pred             hHHH----hhCcCCHHHeeCcHHHHHHHHHHH----hC---------CCCceEEEECCCCCCHHHHHHHHHHHhhhccCC
Confidence            5655    678999999999998887776432    11         124689999999999999999998753      


Q ss_pred             ----CCcEEEEeccccc-ChHHHH-HH--------------------------HHcCCCCceEEeeccchhhhcccccch
Q 013128          268 ----KFDIYDLDLSAVQ-SNSELR-FL--------------------------LLTMPSRSMLVIEDIDCSVKLQNRESS  315 (449)
Q Consensus       268 ----~~~~~~l~~s~~~-~~~~l~-~~--------------------------~~~~~~~~Il~iDeiD~l~~~~~~~~~  315 (449)
                          +.+++.++|+... ++..+. .+                          .......++|||||||.+..       
T Consensus       117 ~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~-------  189 (531)
T TIGR02902       117 PFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHP-------  189 (531)
T ss_pred             CcCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCH-------
Confidence                3578999986421 111110 00                          01122458999999999853       


Q ss_pred             hhhhccchhhHHHHHHHHHHhcCc--------ccc-----------------CCCCeEEEEEcCCCCCCCccccCCCccc
Q 013128          316 EVQATNQEENKVTLSGLLNFIDGL--------WSC-----------------CGEGRIIVFTTNHKEKLDPALLRPGRMD  370 (449)
Q Consensus       316 ~~~~~~~~~~~~~ls~LL~~ldg~--------~~~-----------------~~~~~iiI~tTN~~~~ld~aLlrpgR~d  370 (449)
                                 ...+.||..|+.-        ...                 .-+-++|++|||.++.|+|++++  |+ 
T Consensus       190 -----------~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrs--R~-  255 (531)
T TIGR02902       190 -----------VQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRS--RC-  255 (531)
T ss_pred             -----------HHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhh--hh-
Confidence                       2334455555321        000                 11236677788999999999999  87 


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHHHH
Q 013128          371 MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       371 ~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~~l  420 (449)
                      ..|.|+.++.+++..++++.+...+..+.++..+++....++.+++.+.+
T Consensus       256 ~~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll  305 (531)
T TIGR02902       256 VEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV  305 (531)
T ss_pred             heeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH
Confidence            57889999999999999999887666666665555555555666655544

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=4.3e-14  Score=148.74  Aligned_cols=160  Identities=20%  Similarity=0.320  Sum_probs=117.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+++++.+...+..    .        ..+..+|||||||||||++|+++|+.+..            
T Consensus         7 KyRP~~~~dvvGq~~v~~~L~~~i~~----~--------~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~   74 (504)
T PRK14963          7 RARPITFDEVVGQEHVKEVLLAALRQ----G--------RLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECE   74 (504)
T ss_pred             hhCCCCHHHhcChHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcCh
Confidence            56899999999999988877766542    1        12456899999999999999999999852            


Q ss_pred             -----------cEEEEecccccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHH
Q 013128          270 -----------DIYDLDLSAVQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGL  332 (449)
Q Consensus       270 -----------~~~~l~~s~~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~L  332 (449)
                                 +++.++.+.-.....++.+...      ...+.|+||||+|.+.                  ...++.|
T Consensus        75 sc~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls------------------~~a~naL  136 (504)
T PRK14963         75 SCLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMS------------------KSAFNAL  136 (504)
T ss_pred             hhHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccC------------------HHHHHHH
Confidence                       3666665533333334433222      1356799999999763                  1346778


Q ss_pred             HHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          333 LNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       333 L~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      +..++..    +...++|++||.+..+.+++.+  |+ .+++|+.++.++....+...+..++...
T Consensus       137 Lk~LEep----~~~t~~Il~t~~~~kl~~~I~S--Rc-~~~~f~~ls~~el~~~L~~i~~~egi~i  195 (504)
T PRK14963        137 LKTLEEP----PEHVIFILATTEPEKMPPTILS--RT-QHFRFRRLTEEEIAGKLRRLLEAEGREA  195 (504)
T ss_pred             HHHHHhC----CCCEEEEEEcCChhhCChHHhc--ce-EEEEecCCCHHHHHHHHHHHHHHcCCCC
Confidence            8888753    3457888888999999999988  76 4799999999999998888776554433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3.2e-14  Score=152.40  Aligned_cols=157  Identities=18%  Similarity=0.309  Sum_probs=118.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..|||+||+|||||++|+++|+.++.            
T Consensus         9 KyRP~~f~divGQe~vv~~L~~~l~~----~--------rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C   76 (647)
T PRK07994          9 KWRPQTFAEVVGQEHVLTALANALDL----G--------RLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGEC   76 (647)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCC
Confidence            56899999999999988877655531    1        12456999999999999999999999965            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.++-.....++.+....      ...-|+||||+|.+..                  ...+.
T Consensus        77 ~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~------------------~a~NA  138 (647)
T PRK07994         77 DNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSR------------------HSFNA  138 (647)
T ss_pred             HHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCH------------------HHHHH
Confidence                        45556654322334455444332      2456999999998842                  35677


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      ||..|+..    ++.+++|++|+.+..|.+.+++  |+ .+++|..++.++....+.+.+..++
T Consensus       139 LLKtLEEP----p~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~  195 (647)
T PRK07994        139 LLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAEQ  195 (647)
T ss_pred             HHHHHHcC----CCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcC
Confidence            99998863    4567888888899999999998  86 7899999999999988888775443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3e-14  Score=157.03  Aligned_cols=159  Identities=18%  Similarity=0.263  Sum_probs=118.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++|+|.+.+++.|...+..    .        .....|||+||+|||||++|+.+|+.|++            
T Consensus         8 KyRP~~f~eiiGqe~v~~~L~~~i~~----~--------ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C   75 (824)
T PRK07764          8 RYRPATFAEVIGQEHVTEPLSTALDS----G--------RINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGEC   75 (824)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHh----C--------CCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCccc
Confidence            67999999999999988877665531    1        12457999999999999999999999953            


Q ss_pred             --------------cEEEEecccccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          270 --------------DIYDLDLSAVQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       270 --------------~~~~l~~s~~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                                    +++.++..+......++.+...      .....|+||||+|.+..                  ...
T Consensus        76 ~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~------------------~a~  137 (824)
T PRK07764         76 DSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTP------------------QGF  137 (824)
T ss_pred             HHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCH------------------HHH
Confidence                          3555554333333444443221      13567999999999842                  345


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      +.||..|+..    ...+++|++|+.+++|-+.|+.  |+ .++.|..++.++...++...+..++..
T Consensus       138 NaLLK~LEEp----P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~  198 (824)
T PRK07764        138 NALLKIVEEP----PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVP  198 (824)
T ss_pred             HHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCC
Confidence            6789999864    4567888888999999999988  76 678999999999988888887655443

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

Probab=99.58  E-value=1.7e-14  Score=150.61  Aligned_cols=192  Identities=15%  Similarity=0.222  Sum_probs=131.7

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----CcEEEEecccccCh--
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLDLSAVQSN--  282 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----~~~~~l~~s~~~~~--  282 (449)
                      .+++..+..|+...++...+           +....++||+||+|||||.|++++++++.    +++..++|+.+...  
T Consensus       408 ~d~i~~~s~kke~~n~~~sp-----------v~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~  476 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSP-----------VFRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSL  476 (952)
T ss_pred             Cceeecchhhhhhhhhhccc-----------ccccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhH
Confidence            45566666666655433222           23346799999999999999999999985    45567888887543  


Q ss_pred             HH----HHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          283 SE----LRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       283 ~~----l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      ..    +...|...  .+|+||++||+|+++...+.++.     ........+..+|+.+-..+...+..+.+|+|.+..
T Consensus       477 e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s~~e~~-----q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~  551 (952)
T KOG0735|consen  477 EKIQKFLNNVFSEALWYAPSIIVLDDLDCLASASSNENG-----QDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQEL  551 (952)
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccCcccCC-----cchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhh
Confidence            22    23333333  48999999999999872222211     122333445556654433333334557889999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC-CCCHHHHHHHHHc-cCCCHHHH
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH-HYLFEQIEELIKE-VNVTPAEV  416 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~-~~l~~~i~~l~~~-~~~tpa~i  416 (449)
                      ..|+|-|..|++|+.++.+|.|...+|.+|++.++.... ...+++++-+..+ .++.+.|+
T Consensus       552 qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL  613 (952)
T KOG0735|consen  552 QTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDL  613 (952)
T ss_pred             hhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhH
Confidence            999999999999999999999999999999999887542 2334555554333 35666666

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

Probab=99.57  E-value=1.1e-14  Score=139.57  Aligned_cols=165  Identities=18%  Similarity=0.256  Sum_probs=117.0

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC---
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF---  269 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~---  269 (449)
                      ..|..    .++|.+|++++|++.+.+.+...+.. -.            -..||||||||||||+.|++.|.+++.   
T Consensus        24 ~swte----KYrPkt~de~~gQe~vV~~L~~a~~~-~~------------lp~~LFyGPpGTGKTStalafar~L~~~~~   86 (346)
T KOG0989|consen   24 RSWTE----KYRPKTFDELAGQEHVVQVLKNALLR-RI------------LPHYLFYGPPGTGKTSTALAFARALNCEQL   86 (346)
T ss_pred             cchHH----HhCCCcHHhhcchHHHHHHHHHHHhh-cC------------CceEEeeCCCCCcHhHHHHHHHHHhcCccc
Confidence            35654    88999999999999999988887754 11            247999999999999999999999965   


Q ss_pred             ---cEEEEecccccChHH-------HHHHHHcC----C----CCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ---DIYDLDLSAVQSNSE-------LRFLLLTM----P----SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ---~~~~l~~s~~~~~~~-------l~~~~~~~----~----~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                         .+..++.+.....+-       ...+....    .    ..-|++|||.|.+..                  ...+.
T Consensus        87 ~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmts------------------daq~a  148 (346)
T KOG0989|consen   87 FPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTS------------------DAQAA  148 (346)
T ss_pred             cccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhH------------------HHHHH
Confidence               233444444322211       11111111    1    125999999998853                  35677


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      |...||..    .....+|+.||..+.|.+.+..  |.. .+.|+....+....-++.....++....
T Consensus       149 Lrr~mE~~----s~~trFiLIcnylsrii~pi~S--RC~-KfrFk~L~d~~iv~rL~~Ia~~E~v~~d  209 (346)
T KOG0989|consen  149 LRRTMEDF----SRTTRFILICNYLSRIIRPLVS--RCQ-KFRFKKLKDEDIVDRLEKIASKEGVDID  209 (346)
T ss_pred             HHHHHhcc----ccceEEEEEcCChhhCChHHHh--hHH-HhcCCCcchHHHHHHHHHHHHHhCCCCC
Confidence            88889873    2457889999999999999998  884 4778887777666666666665555443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=3.2e-14  Score=150.51  Aligned_cols=157  Identities=18%  Similarity=0.323  Sum_probs=116.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------------  268 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------------  268 (449)
                      ..+|.+|++++|.+.+++.+...+..           | ..+++|||+||||||||++|+++|+.+.             
T Consensus         9 KyRP~~F~dIIGQe~iv~~L~~aI~~-----------~-rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C   76 (605)
T PRK05896          9 KYRPHNFKQIIGQELIKKILVNAILN-----------N-KLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSC   76 (605)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCccc
Confidence            67999999999999988777665421           1 1246899999999999999999999984             


Q ss_pred             -----------CcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          269 -----------FDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       269 -----------~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                 .+++.++.++......++.+....      ....|++|||+|.+..                  ...+.
T Consensus        77 ~sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~------------------~A~Na  138 (605)
T PRK05896         77 SVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLST------------------SAWNA  138 (605)
T ss_pred             HHHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCH------------------HHHHH
Confidence                       255666654433334455443322      2456999999998732                  13467


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      ||..|+..    +...++|++|+.+..|.+++++  |+. .++|+.++.++....+...+..++
T Consensus       139 LLKtLEEP----p~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~keg  195 (605)
T PRK05896        139 LLKTLEEP----PKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKEK  195 (605)
T ss_pred             HHHHHHhC----CCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHcC
Confidence            88888763    4567888888899999999998  774 699999999998888887765544

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=8.4e-14  Score=141.94  Aligned_cols=160  Identities=18%  Similarity=0.313  Sum_probs=115.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+..++.+.+.+..    .        ..+.++|||||||+|||++++++|+.+..            
T Consensus        10 k~rP~~~~~iig~~~~~~~l~~~i~~----~--------~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~   77 (367)
T PRK14970         10 KYRPQTFDDVVGQSHITNTLLNAIEN----N--------HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSF   77 (367)
T ss_pred             HHCCCcHHhcCCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCc
Confidence            67899999999999988777666542    1        12568999999999999999999998743            


Q ss_pred             cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC
Q 013128          270 DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC  343 (449)
Q Consensus       270 ~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~  343 (449)
                      +++.++.........++.++...      ..+.|++|||+|.+..                  ..++.|+..++..    
T Consensus        78 ~~~~l~~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~------------------~~~~~ll~~le~~----  135 (367)
T PRK14970         78 NIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS------------------AAFNAFLKTLEEP----  135 (367)
T ss_pred             ceEEeccccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCH------------------HHHHHHHHHHhCC----
Confidence            33444433323334555555432      2457999999997642                  2356688888753    


Q ss_pred             CCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          344 GEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       344 ~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      +...++|++|+.+..+.+++.+  |+ ..++++.++.++...++...+..++..+
T Consensus       136 ~~~~~~Il~~~~~~kl~~~l~s--r~-~~v~~~~~~~~~l~~~l~~~~~~~g~~i  187 (367)
T PRK14970        136 PAHAIFILATTEKHKIIPTILS--RC-QIFDFKRITIKDIKEHLAGIAVKEGIKF  187 (367)
T ss_pred             CCceEEEEEeCCcccCCHHHHh--cc-eeEecCCccHHHHHHHHHHHHHHcCCCC
Confidence            3456777788888999999988  65 3589999999998888887666554444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.56  E-value=1.8e-14  Score=160.31  Aligned_cols=158  Identities=16%  Similarity=0.217  Sum_probs=113.4

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIY  272 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~  272 (449)
                      -+|-+++.++|.++....+++.+.   ++          .+.+++|+||||||||++|+.+|..+          +..++
T Consensus       181 ~r~~~ld~~iGr~~ei~~~i~~l~---r~----------~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~  247 (852)
T TIGR03345       181 AREGKIDPVLGRDDEIRQMIDILL---RR----------RQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLL  247 (852)
T ss_pred             hcCCCCCcccCCHHHHHHHHHHHh---cC----------CcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEE
Confidence            357789999999987666665542   11          24689999999999999999999987          35688


Q ss_pred             EEecccccC--------hHHHHHHHHcC---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          273 DLDLSAVQS--------NSELRFLLLTM---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       273 ~l~~s~~~~--------~~~l~~~~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                      .++++.+..        +..++.++...   ..++|||||||+.+.+.++..++.          ..-+-|+..+.    
T Consensus       248 ~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~----------d~~n~Lkp~l~----  313 (852)
T TIGR03345       248 SLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQG----------DAANLLKPALA----  313 (852)
T ss_pred             EeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccc----------cHHHHhhHHhh----
Confidence            888876542        14566666543   468999999999998643221110          01122444443    


Q ss_pred             cCCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          342 CCGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                        .+.+.+|+||+..+     .+||||.|  ||. .|.++.|+.++...|++.+..
T Consensus       314 --~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~~  364 (852)
T TIGR03345       314 --RGELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLAP  364 (852)
T ss_pred             --CCCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHHH
Confidence              25678888887643     48999999  995 799999999999999765554

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.56  E-value=4.7e-14  Score=151.96  Aligned_cols=157  Identities=20%  Similarity=0.330  Sum_probs=115.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++++|.+.+++.+...+..    .        ..+.+||||||||||||++|+++|+.+..            
T Consensus        11 KyRP~~f~dIiGQe~~v~~L~~aI~~----~--------rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~   78 (725)
T PRK07133         11 KYRPKTFDDIVGQDHIVQTLKNIIKS----N--------KISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQE   78 (725)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhH
Confidence            78999999999999988877766642    1        12567999999999999999999998853            


Q ss_pred             ---------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          270 ---------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       270 ---------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                               +++.++...-.....++.+....      ....|++|||+|.+..                  ...+.||.
T Consensus        79 C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~------------------~A~NALLK  140 (725)
T PRK07133         79 CIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSK------------------SAFNALLK  140 (725)
T ss_pred             HHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCH------------------HHHHHHHH
Confidence                     23334332211223344443332      3467999999998742                  24677888


Q ss_pred             HhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .|+..    +..+++|++|+.++.|.+++++  |+ ..+.|..++.++....+...+..++
T Consensus       141 tLEEP----P~~tifILaTte~~KLl~TI~S--Rc-q~ieF~~L~~eeI~~~L~~il~keg  194 (725)
T PRK07133        141 TLEEP----PKHVIFILATTEVHKIPLTILS--RV-QRFNFRRISEDEIVSRLEFILEKEN  194 (725)
T ss_pred             HhhcC----CCceEEEEEcCChhhhhHHHHh--hc-eeEEccCCCHHHHHHHHHHHHHHcC
Confidence            88863    4567888888999999999998  77 4799999999998888877665443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=6.8e-14  Score=148.96  Aligned_cols=162  Identities=19%  Similarity=0.303  Sum_probs=119.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+.    ..        ..+..|||+||+|||||++|+++|+.++.            
T Consensus         6 kyRP~~f~eivGq~~i~~~L~~~i~----~~--------r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C   73 (584)
T PRK14952          6 KYRPATFAEVVGQEHVTEPLSSALD----AG--------RINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVC   73 (584)
T ss_pred             HhCCCcHHHhcCcHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCccccc
Confidence            5789999999999988887766553    11        12456999999999999999999998752            


Q ss_pred             --------------cEEEEecccccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          270 --------------DIYDLDLSAVQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       270 --------------~~~~l~~s~~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                                    +++.++.++...-..++.+...      ....-|++|||+|.+..                  ...
T Consensus        74 ~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~------------------~A~  135 (584)
T PRK14952         74 ESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTT------------------AGF  135 (584)
T ss_pred             HHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCH------------------HHH
Confidence                          3555655443333444433222      13456999999998842                  256


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE  400 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~  400 (449)
                      +.||..|+..    +..+++|++|+.+++|.+++++  |. .+++|..++.++....+..++..++..+.+
T Consensus       136 NALLK~LEEp----p~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~  199 (584)
T PRK14952        136 NALLKIVEEP----PEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDD  199 (584)
T ss_pred             HHHHHHHhcC----CCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            6788888863    4568888888999999999998  75 679999999999888888877766544433

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.56  E-value=4.9e-14  Score=133.56  Aligned_cols=168  Identities=16%  Similarity=0.207  Sum_probs=105.8

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      .....+.+||+++..  ..+.+++.+..+...         ..+++++|+||||||||++++++++++   +.+++.+++
T Consensus         6 ~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~---------~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~   74 (226)
T TIGR03420         6 VGLPDDPTFDNFYAG--GNAELLAALRQLAAG---------KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPL   74 (226)
T ss_pred             CCCCCchhhcCcCcC--CcHHHHHHHHHHHhc---------CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeH
Confidence            344566789998832  234445555554331         125689999999999999999999987   467888888


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC-C
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN-H  355 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN-~  355 (449)
                      +.+....  ...+.......+|+|||+|.+...             ..   ....|...++.....  +. .+|+|++ .
T Consensus        75 ~~~~~~~--~~~~~~~~~~~lLvIDdi~~l~~~-------------~~---~~~~L~~~l~~~~~~--~~-~iIits~~~  133 (226)
T TIGR03420        75 AELAQAD--PEVLEGLEQADLVCLDDVEAIAGQ-------------PE---WQEALFHLYNRVREA--GG-RLLIAGRAA  133 (226)
T ss_pred             HHHHHhH--HHHHhhcccCCEEEEeChhhhcCC-------------hH---HHHHHHHHHHHHHHc--CC-eEEEECCCC
Confidence            8775321  233344455679999999987420             00   112344444432221  22 3444554 4


Q ss_pred             CCCCC---ccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH
Q 013128          356 KEKLD---PALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ  401 (449)
Q Consensus       356 ~~~ld---~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~  401 (449)
                      +..++   +.|.+  |+  ..++.+|.|+.+++..+++.+....+..+.++
T Consensus       134 ~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~  182 (226)
T TIGR03420       134 PAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDE  182 (226)
T ss_pred             hHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence            44432   67776  55  57899999999999999987765444444333

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=4.4e-14  Score=149.76  Aligned_cols=159  Identities=19%  Similarity=0.308  Sum_probs=117.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..|||+||||||||++|+++|+.++.            
T Consensus         9 k~rP~~f~divGq~~v~~~L~~~i~~----~--------~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C   76 (527)
T PRK14969          9 KWRPKSFSELVGQEHVVRALTNALEQ----Q--------RLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVC   76 (527)
T ss_pred             HhCCCcHHHhcCcHHHHHHHHHHHHc----C--------CCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            56899999999999998877665542    1        12467999999999999999999999954            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.+.-.....++.++...      ....|++|||+|.+..                  ...+.
T Consensus        77 ~~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~------------------~a~na  138 (527)
T PRK14969         77 SACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSK------------------SAFNA  138 (527)
T ss_pred             HHHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCH------------------HHHHH
Confidence                        35555544333334455554432      2356999999998742                  24567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..|+..    ++.+++|++|++++.+.+.+++  |+ ..++|..++.++....+...+..++..
T Consensus       139 LLK~LEep----p~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~  197 (527)
T PRK14969        139 MLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIP  197 (527)
T ss_pred             HHHHHhCC----CCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCC
Confidence            89988863    4567888888888889888887  76 679999999999888888777554433

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=8.7e-14  Score=146.88  Aligned_cols=159  Identities=19%  Similarity=0.275  Sum_probs=115.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..|||+||||||||++|+++|+.++.            
T Consensus         9 KyRP~~f~diiGq~~~v~~L~~~i~~----~--------rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C   76 (546)
T PRK14957          9 KYRPQSFAEVAGQQHALNSLVHALET----Q--------KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKC   76 (546)
T ss_pred             HHCcCcHHHhcCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCccc
Confidence            57899999999999998877655531    1        12457999999999999999999998853            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++...-.....++.++..      ....-|++|||+|.+..                  ...+.
T Consensus        77 ~sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~------------------~a~na  138 (546)
T PRK14957         77 ENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSK------------------QSFNA  138 (546)
T ss_pred             HHHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccH------------------HHHHH
Confidence                        5556655332222333333322      13567999999998742                  24567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..|+..    ++.+++|++|+.+..+.++++.  |+ ..++|..++.++....+...+..++..
T Consensus       139 LLK~LEep----p~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~  197 (546)
T PRK14957        139 LLKTLEEP----PEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQADIKDQLKIILAKENIN  197 (546)
T ss_pred             HHHHHhcC----CCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCC
Confidence            88888863    3556777777788888888888  77 679999999999888888766654433

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

Probab=99.55  E-value=9.7e-14  Score=152.96  Aligned_cols=158  Identities=22%  Similarity=0.182  Sum_probs=117.3

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHH----
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSEL----  285 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l----  285 (449)
                      ++.|.+++|+.|++.+.......       ...+..++|+||||||||++++++|+.++.+++.++++.+.+...+    
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~~-------~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRVN-------KIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhcc-------cCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccch
Confidence            48999999999998887544321       1224469999999999999999999999999999998877554333    


Q ss_pred             -----------HHHHHcCC-CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc----c-------c
Q 013128          286 -----------RFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW----S-------C  342 (449)
Q Consensus       286 -----------~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~----~-------~  342 (449)
                                 ...+.... ...||+|||||.+....  +            ....+.|+..+|.-.    .       .
T Consensus       396 ~~~~g~~~G~~~~~l~~~~~~~~villDEidk~~~~~--~------------g~~~~aLlevld~~~~~~~~d~~~~~~~  461 (784)
T PRK10787        396 RTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDM--R------------GDPASALLEVLDPEQNVAFSDHYLEVDY  461 (784)
T ss_pred             hccCCCCCcHHHHHHHhcCCCCCEEEEEChhhccccc--C------------CCHHHHHHHHhccccEEEEecccccccc
Confidence                       22233332 45689999999986411  1            113466888887410    0       0


Q ss_pred             CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          343 CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       343 ~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .-+++++|+|+|.. .|+|+|+.  ||. .|.++.++.++..+|+++||.
T Consensus       462 dls~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~  507 (784)
T PRK10787        462 DLSDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLL  507 (784)
T ss_pred             cCCceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhh
Confidence            12568999999988 59999999  996 588999999999999999994

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.55  E-value=8.7e-14  Score=139.72  Aligned_cols=163  Identities=13%  Similarity=0.258  Sum_probs=109.8

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-----
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-----  268 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-----  268 (449)
                      .|..    .+.|.+|++++|.+++++.+...+.    .+.         ..++|||||||||||++|+++|+++.     
T Consensus         4 ~w~~----ky~P~~~~~~~g~~~~~~~L~~~~~----~~~---------~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~   66 (337)
T PRK12402          4 LWTE----KYRPALLEDILGQDEVVERLSRAVD----SPN---------LPHLLVQGPPGSGKTAAVRALARELYGDPWE   66 (337)
T ss_pred             chHH----hhCCCcHHHhcCCHHHHHHHHHHHh----CCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcccc
Confidence            5754    7899999999999988777765443    211         23699999999999999999999984     


Q ss_pred             CcEEEEecccccCh--------------------------HHHHHHHH---c----CCCCceEEeeccchhhhcccccch
Q 013128          269 FDIYDLDLSAVQSN--------------------------SELRFLLL---T----MPSRSMLVIEDIDCSVKLQNRESS  315 (449)
Q Consensus       269 ~~~~~l~~s~~~~~--------------------------~~l~~~~~---~----~~~~~Il~iDeiD~l~~~~~~~~~  315 (449)
                      .+++.++++++...                          ..++.+..   .    ...+.+|+|||+|.+..       
T Consensus        67 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~-------  139 (337)
T PRK12402         67 NNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALRE-------  139 (337)
T ss_pred             cceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCH-------
Confidence            34667776553210                          11111111   1    13456999999997732       


Q ss_pred             hhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          316 EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       316 ~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                                 .....|+..++..    .....+|++++.+..+.++|.+  |+ ..+.++.|+.++...++...+..++
T Consensus       140 -----------~~~~~L~~~le~~----~~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~  201 (337)
T PRK12402        140 -----------DAQQALRRIMEQY----SRTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEG  201 (337)
T ss_pred             -----------HHHHHHHHHHHhc----cCCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcC
Confidence                       1123355555543    1234566677777778888887  65 5689999999999999988776554


Q ss_pred             CCC
Q 013128          396 HYL  398 (449)
Q Consensus       396 ~~l  398 (449)
                      ..+
T Consensus       202 ~~~  204 (337)
T PRK12402        202 VDY  204 (337)
T ss_pred             CCC
Confidence            443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.55  E-value=6.5e-14  Score=148.86  Aligned_cols=160  Identities=16%  Similarity=0.252  Sum_probs=116.0

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++|+|.+.+++.|...+..    .        .....|||+||||||||++|+++|+.+..            
T Consensus         9 KyRP~sf~dIiGQe~v~~~L~~ai~~----~--------ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C   76 (624)
T PRK14959          9 RYRPQTFAEVAGQETVKAILSRAAQE----N--------RVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTC   76 (624)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHc----C--------CCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCccc
Confidence            67999999999999887777665531    1        11468999999999999999999999964            


Q ss_pred             ------------cEEEEecccccChHHHHHH---HHcC---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFL---LLTM---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~---~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++...-.....++.+   +...   ....||||||+|.+..                  ...+.
T Consensus        77 ~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~------------------~a~na  138 (624)
T PRK14959         77 EQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTR------------------EAFNA  138 (624)
T ss_pred             HHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCH------------------HHHHH
Confidence                        2556654322222333332   2222   3467999999998842                  23567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    ...+++|++||.+..+.+.+++  |+ .+++|+.++.++....+...+..++..+
T Consensus       139 LLk~LEEP----~~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pLs~~eL~~~L~~il~~egi~i  198 (624)
T PRK14959        139 LLKTLEEP----PARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRLSEAGLEAHLTKVLGREGVDY  198 (624)
T ss_pred             HHHHhhcc----CCCEEEEEecCChhhhhHHHHh--hh-hccccCCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888753    3457888999999999989888  77 4689999999998888887665544333

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=3.8e-13  Score=140.14  Aligned_cols=157  Identities=17%  Similarity=0.255  Sum_probs=113.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..+|||||||+|||++|+++|+.+..            
T Consensus        10 kyRP~~~~diiGq~~~v~~L~~~i~~----~--------~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~   77 (451)
T PRK06305         10 KYRPQTFSEILGQDAVVAVLKNALRF----N--------RAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQ   77 (451)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcc
Confidence            56899999999999888877665531    1        13567999999999999999999998842            


Q ss_pred             -------------cEEEEecccccChHHHHHH---HHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHH
Q 013128          270 -------------DIYDLDLSAVQSNSELRFL---LLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS  330 (449)
Q Consensus       270 -------------~~~~l~~s~~~~~~~l~~~---~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls  330 (449)
                                   +++.++.........++.+   +..   .....|++|||+|.+..                  ...+
T Consensus        78 c~~C~~i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~------------------~~~n  139 (451)
T PRK06305         78 CASCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTK------------------EAFN  139 (451)
T ss_pred             cHHHHHHhcCCCCceEEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCH------------------HHHH
Confidence                         3455553322222333322   221   24678999999998742                  1346


Q ss_pred             HHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       331 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .|+..|+..    ++.+++|++||.+..|.+++.+  |+ ..++++.++.++....+...+..++
T Consensus       140 ~LLk~lEep----~~~~~~Il~t~~~~kl~~tI~s--Rc-~~v~f~~l~~~el~~~L~~~~~~eg  197 (451)
T PRK06305        140 SLLKTLEEP----PQHVKFFLATTEIHKIPGTILS--RC-QKMHLKRIPEETIIDKLALIAKQEG  197 (451)
T ss_pred             HHHHHhhcC----CCCceEEEEeCChHhcchHHHH--hc-eEEeCCCCCHHHHHHHHHHHHHHcC
Confidence            688888763    3467788888989999999998  77 4689999999998888877665443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.54  E-value=1.4e-13  Score=133.93  Aligned_cols=144  Identities=22%  Similarity=0.244  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH-----------
Q 013128          218 KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR-----------  286 (449)
Q Consensus       218 k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~-----------  286 (449)
                      .+.+++.+..++..           .+.+||+||||||||++|+++|+.++.+++.++++.-.....+.           
T Consensus         7 ~~~l~~~~l~~l~~-----------g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~   75 (262)
T TIGR02640         7 VKRVTSRALRYLKS-----------GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKV   75 (262)
T ss_pred             HHHHHHHHHHHHhc-----------CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhH
Confidence            34455555555442           35799999999999999999999999999999886543222211           


Q ss_pred             ----------------------HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-cc-
Q 013128          287 ----------------------FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SC-  342 (449)
Q Consensus       287 ----------------------~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~-  342 (449)
                                            .++....++.+|+||||+.+-+                  .+.+.|+..|+.-. .. 
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~~------------------~~q~~Ll~~Le~~~~~i~  137 (262)
T TIGR02640        76 HDQFIHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKP------------------ETNNVLLSVFEEGVLELP  137 (262)
T ss_pred             HHHHHHHhhhhhcccceeecCchHHHHHHcCCEEEEcchhhCCH------------------HHHHHHHHHhcCCeEEcc
Confidence                                  0111223568999999998632                  24556777775321 00 


Q ss_pred             ----------CCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          343 ----------CGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       343 ----------~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                                ......||+|+|...     .++++|++  || ..+.+++|+.++..+|++...+.
T Consensus       138 ~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~~  200 (262)
T TIGR02640       138 GKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDTETAILRAKTDV  200 (262)
T ss_pred             CCCCCCceEecCCCCEEEEeeCCccccceecccHHHHh--hc-EEEECCCCCHHHHHHHHHHhhCC
Confidence                      012456899999763     56899999  98 78999999999999999987653

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).

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.54  E-value=3.7e-14  Score=158.18  Aligned_cols=159  Identities=18%  Similarity=0.176  Sum_probs=116.4

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIY  272 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~  272 (449)
                      -+|-.++.++|.++..+.+++.|..-             .+.+++|+||||||||++|+++|..+          +.+++
T Consensus       172 ~r~~~l~~vigr~~ei~~~i~iL~r~-------------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~  238 (857)
T PRK10865        172 AEQGKLDPVIGRDEEIRRTIQVLQRR-------------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL  238 (857)
T ss_pred             HhcCCCCcCCCCHHHHHHHHHHHhcC-------------CcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEE
Confidence            35678999999998877777665421             24689999999999999999999998          78899


Q ss_pred             EEecccccC--------hHHHHHHHHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          273 DLDLSAVQS--------NSELRFLLLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       273 ~l~~s~~~~--------~~~l~~~~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                      .++++.+..        +..++.++..   ...++||||||||.+.+.++..+.       .   ..-+-|+..+.    
T Consensus       239 ~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~-------~---d~~~~lkp~l~----  304 (857)
T PRK10865        239 ALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA-------M---DAGNMLKPALA----  304 (857)
T ss_pred             EEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccc-------h---hHHHHhcchhh----
Confidence            998887642        2345656544   346899999999999764322111       0   01111333332    


Q ss_pred             cCCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          342 CCGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                        .+.+.+|+||+..+     .+|+||.|  ||+ .|.++.|+.+++..+++.....
T Consensus       305 --~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~~  356 (857)
T PRK10865        305 --RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKER  356 (857)
T ss_pred             --cCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhhh
Confidence              35788899888876     48999999  997 5889999999999999876653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=8.8e-14  Score=149.08  Aligned_cols=160  Identities=16%  Similarity=0.255  Sum_probs=118.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++|+|.+++++.+...+..    .        ..+..||||||+|||||++|+++|+.++.            
T Consensus         9 k~RP~~f~~iiGq~~v~~~L~~~i~~----~--------~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c   76 (576)
T PRK14965          9 KYRPQTFSDLTGQEHVSRTLQNAIDT----G--------RVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVC   76 (576)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCcc
Confidence            57899999999999998888766542    1        12567999999999999999999999853            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++..+......++.+....      ...-|++|||+|.+..                  ...+.
T Consensus        77 ~~c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~------------------~a~na  138 (576)
T PRK14965         77 PPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLST------------------NAFNA  138 (576)
T ss_pred             HHHHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCH------------------HHHHH
Confidence                        35556544333334444443332      2356999999998742                  24577


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    .+.+++|++|+.+++|.+.+++  |+ ..++|..++.++....+...+..++..+
T Consensus       139 LLk~LEep----p~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~egi~i  198 (576)
T PRK14965        139 LLKTLEEP----PPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQKIVDRLRYIADQEGISI  198 (576)
T ss_pred             HHHHHHcC----CCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHHHHHHHHHHHHHHhCCCC
Confidence            89988863    4567888899999999999998  76 4689999999888888877776554433

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.53  E-value=4.2e-13  Score=137.18  Aligned_cols=155  Identities=17%  Similarity=0.252  Sum_probs=111.4

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc----------------
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD----------------  270 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~----------------  270 (449)
                      .|++|+|.+.+++.+...+.....   .+...+...+.+|||+||||+|||++|+++|+.+..+                
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~---~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~   79 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARA---DVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTV   79 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccc---cccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHH
Confidence            589999999999998887765433   2333445567889999999999999999999987432                


Q ss_pred             -------EEEEecccc-cChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHh
Q 013128          271 -------IYDLDLSAV-QSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFI  336 (449)
Q Consensus       271 -------~~~l~~s~~-~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~l  336 (449)
                             ++.+..... ....+++.++...      ....|++|||+|.+..                  ...+.||..|
T Consensus        80 ~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~------------------~aanaLLk~L  141 (394)
T PRK07940         80 LAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTE------------------RAANALLKAV  141 (394)
T ss_pred             hcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCH------------------HHHHHHHHHh
Confidence                   333433221 1234455544432      2356999999999843                  1346688888


Q ss_pred             cCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHH
Q 013128          337 DGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       337 dg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                      +..    +.+.++|++|++++.|.|++++  |+ ..++|+.|+.++..+.+..
T Consensus       142 Eep----~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~  187 (394)
T PRK07940        142 EEP----PPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVR  187 (394)
T ss_pred             hcC----CCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHH
Confidence            763    3456677777779999999998  77 6899999999998877764

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=2e-13  Score=143.86  Aligned_cols=170  Identities=16%  Similarity=0.226  Sum_probs=124.3

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------hHHHHHHHHcC--CCCceEEeeccchhhhccc
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQN  311 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~  311 (449)
                      +.....+||+|+||||||+++++.|.++|.+++.++|.++..      +..+...+.++  .+|+||||-++|.+.-  +
T Consensus       428 ~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~i--d  505 (953)
T KOG0736|consen  428 LTLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGI--D  505 (953)
T ss_pred             cccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeee--c
Confidence            334456999999999999999999999999999999988853      35566666665  4899999999999863  2


Q ss_pred             ccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          312 RESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       312 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      +.+.     ..-.....+..++. +|-... ....+|+|+||+..+.+++.+.+  .|-..|.+|.|+.++|.++++.|+
T Consensus       506 ~dgg-----ed~rl~~~i~~~ls-~e~~~~-~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~  576 (953)
T KOG0736|consen  506 QDGG-----EDARLLKVIRHLLS-NEDFKF-SCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYL  576 (953)
T ss_pred             CCCc-----hhHHHHHHHHHHHh-cccccC-CCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHH
Confidence            2211     11223334444444 332222 24678999999999999999998  888999999999999999999999


Q ss_pred             CcCCCCCHHHHHHHHHcc-CCCHHHHHHHH
Q 013128          392 GISHHYLFEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       392 ~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      ......-......++.+. +|+.+++..+.
T Consensus       577 ~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~  606 (953)
T KOG0736|consen  577 NHLPLNQDVNLKQLARKTSGFSFGDLEALV  606 (953)
T ss_pred             hccccchHHHHHHHHHhcCCCCHHHHHHHh
Confidence            854322223344555543 58888885443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=2.5e-13  Score=142.46  Aligned_cols=160  Identities=18%  Similarity=0.277  Sum_probs=114.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+.+.+...+..    .        ..+..||||||||+|||++|+.+|..++.            
T Consensus         9 kyRP~~f~diiGq~~i~~~L~~~i~~----~--------~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c   76 (486)
T PRK14953          9 KYRPKFFKEVIGQEIVVRILKNAVKL----Q--------RVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKC   76 (486)
T ss_pred             hhCCCcHHHccChHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCcc
Confidence            67899999999999988877665532    1        12467999999999999999999999852            


Q ss_pred             ------------cEEEEecccccChHHHHHHH---HcC---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLL---LTM---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~---~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.+.-.....++.+.   ...   ....|++|||+|.+..                  ...+.
T Consensus        77 ~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~------------------~a~na  138 (486)
T PRK14953         77 ENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTK------------------EAFNA  138 (486)
T ss_pred             HHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCH------------------HHHHH
Confidence                        34455543322223333332   222   3567999999998742                  23466


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..++..    +...++|++|+.++.+.+++.+  |+ ..+.++.++.++....+...+...+...
T Consensus       139 LLk~LEep----p~~~v~Il~tt~~~kl~~tI~S--Rc-~~i~f~~ls~~el~~~L~~i~k~egi~i  198 (486)
T PRK14953        139 LLKTLEEP----PPRTIFILCTTEYDKIPPTILS--RC-QRFIFSKPTKEQIKEYLKRICNEEKIEY  198 (486)
T ss_pred             HHHHHhcC----CCCeEEEEEECCHHHHHHHHHH--hc-eEEEcCCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888753    3456777777888889999988  76 4699999999999988888776554443

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=1.7e-13  Score=141.03  Aligned_cols=157  Identities=16%  Similarity=0.283  Sum_probs=111.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+.+||||||||||||++|+++|+.+..            
T Consensus         9 k~RP~~~~eiiGq~~~~~~L~~~~~~----~--------~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~   76 (397)
T PRK14955          9 KYRPKKFADITAQEHITRTIQNSLRM----G--------RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQE   76 (397)
T ss_pred             hcCCCcHhhccChHHHHHHHHHHHHh----C--------CcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCccccccc
Confidence            57899999999999998877665531    1        12467999999999999999999999954            


Q ss_pred             --------------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccch
Q 013128          270 --------------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQE  323 (449)
Q Consensus       270 --------------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~  323 (449)
                                          +++.++.........++.+....      ....|++|||+|.+..               
T Consensus        77 ~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~---------------  141 (397)
T PRK14955         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI---------------  141 (397)
T ss_pred             CCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH---------------
Confidence                                23334332222234444443333      2457999999998742               


Q ss_pred             hhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          324 ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       324 ~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                         ...+.|+..++..    ....++|++|+.+..+-+++.+  |.. .++++.++.++....+...+..++
T Consensus       142 ---~~~~~LLk~LEep----~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~~g  203 (397)
T PRK14955        142 ---AAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEAEG  203 (397)
T ss_pred             ---HHHHHHHHHHhcC----CCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHHcC
Confidence               2345678887643    3456777777778888888887  664 689999999888888887765443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.51  E-value=2.7e-13  Score=145.12  Aligned_cols=161  Identities=16%  Similarity=0.296  Sum_probs=118.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc-----------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-----------  270 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~-----------  270 (449)
                      .++|.+|++|+|.+.+++.+...+..           | ..+.++||+||+|+|||++|+++|+.+++.           
T Consensus        17 KyRP~~f~dliGq~~~v~~L~~~~~~-----------g-ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~   84 (598)
T PRK09111         17 KYRPQTFDDLIGQEAMVRTLTNAFET-----------G-RIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTID   84 (598)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccc
Confidence            67999999999999988887765531           1 125689999999999999999999998642           


Q ss_pred             ------------------EEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhH
Q 013128          271 ------------------IYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENK  326 (449)
Q Consensus       271 ------------------~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~  326 (449)
                                        ++.++..+...-..++.++...      ....|+||||+|.+..                  
T Consensus        85 ~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~------------------  146 (598)
T PRK09111         85 LCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLST------------------  146 (598)
T ss_pred             cCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCH------------------
Confidence                              3333333322334455443332      2467999999998742                  


Q ss_pred             HHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          327 VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       327 ~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      ...+.||..|+..    ...+++|++|+.++++.+.+++  |+ ..++|..++.++....+...+..++..+.
T Consensus       147 ~a~naLLKtLEeP----p~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~  212 (598)
T PRK09111        147 AAFNALLKTLEEP----PPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVE  212 (598)
T ss_pred             HHHHHHHHHHHhC----CCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCC
Confidence            2467788888763    4567888888888889889888  76 56999999999998888888766554443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.51  E-value=6.8e-14  Score=156.53  Aligned_cols=159  Identities=18%  Similarity=0.189  Sum_probs=113.1

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIY  272 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~  272 (449)
                      -+|-.++.++|.++..+.+++.+..             ..+++++|+||||||||++++++|..+          +.+++
T Consensus       167 ~~~~~~~~~igr~~ei~~~~~~l~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~  233 (852)
T TIGR03346       167 AREGKLDPVIGRDEEIRRTIQVLSR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLL  233 (852)
T ss_pred             hhCCCCCcCCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEE
Confidence            3667899999999877766665532             125689999999999999999999986          67888


Q ss_pred             EEecccccC--------hHHHHHHHHcC---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          273 DLDLSAVQS--------NSELRFLLLTM---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       273 ~l~~s~~~~--------~~~l~~~~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                      .++++.+..        +..+..++...   ..++||||||||.+.+.+...+.          ....+-|...+.    
T Consensus       234 ~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~----------~d~~~~Lk~~l~----  299 (852)
T TIGR03346       234 ALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGA----------MDAGNMLKPALA----  299 (852)
T ss_pred             EeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcch----------hHHHHHhchhhh----
Confidence            888776532        12455555543   46899999999999753221110          011122333331    


Q ss_pred             cCCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          342 CCGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                        .+.+.+|++|+..+     .+|+||.|  ||. .|.++.|+.+++..|++.+...
T Consensus       300 --~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~~~  351 (852)
T TIGR03346       300 --RGELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLKER  351 (852)
T ss_pred             --cCceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHHHH
Confidence              34678888887763     47999999  996 4899999999999999876543

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.51  E-value=4.8e-13  Score=140.70  Aligned_cols=160  Identities=18%  Similarity=0.267  Sum_probs=118.9

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------------  268 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------------  268 (449)
                      ..+|.+|++++|.+.+++.+...+.    ..        ..+..||||||||+|||++|+++|+.+.             
T Consensus         7 KyRP~~fdeiiGqe~v~~~L~~~I~----~g--------rl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C   74 (535)
T PRK08451          7 KYRPKHFDELIGQESVSKTLSLALD----NN--------RLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTC   74 (535)
T ss_pred             HHCCCCHHHccCcHHHHHHHHHHHH----cC--------CCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCccc
Confidence            6789999999999999887776653    11        1356799999999999999999999973             


Q ss_pred             -----------CcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          269 -----------FDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       269 -----------~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                 .+++.++.++-..-..++.+....      ...-|++|||+|.+..                  ...+.
T Consensus        75 ~~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~------------------~A~NA  136 (535)
T PRK08451         75 IQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTK------------------EAFNA  136 (535)
T ss_pred             HHHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCH------------------HHHHH
Confidence                       245666544322345566555432      2346999999998742                  34567


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      ||..|+..    +..+.+|++|+.+..|.++++.  |. .+++|..++.++....+...+..++...
T Consensus       137 LLK~LEEp----p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i  196 (535)
T PRK08451        137 LLKTLEEP----PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSY  196 (535)
T ss_pred             HHHHHhhc----CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCC
Confidence            88888764    3456777788888999999998  75 5799999999998888887776654443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.51  E-value=4.8e-13  Score=144.00  Aligned_cols=159  Identities=18%  Similarity=0.270  Sum_probs=116.0

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+++++.+...+..    .        ....+||||||||||||++|+++|+.++.            
T Consensus         9 kyRP~~f~~liGq~~i~~~L~~~l~~----~--------rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg   76 (620)
T PRK14948          9 KYRPQRFDELVGQEAIATTLKNALIS----N--------RIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCG   76 (620)
T ss_pred             HhCCCcHhhccChHHHHHHHHHHHHc----C--------CCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCc
Confidence            67899999999999988887766542    1        11357999999999999999999999864            


Q ss_pred             --------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          270 --------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       270 --------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                                    +++.++.........++.++...      ...-|+||||+|.+..                  ...
T Consensus        77 ~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~------------------~a~  138 (620)
T PRK14948         77 KCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLST------------------AAF  138 (620)
T ss_pred             ccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCH------------------HHH
Confidence                          34455543323334555554433      2356999999998732                  345


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      +.||..|+..    ...+++|++|++++.+-+++++  |+ ..++|+.++.++....+......++..
T Consensus       139 naLLK~LEeP----p~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~  199 (620)
T PRK14948        139 NALLKTLEEP----PPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAEKESIE  199 (620)
T ss_pred             HHHHHHHhcC----CcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHhCCC
Confidence            7789999853    3567888888889999999988  76 568899998888777776665544333

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.51  E-value=3.8e-13  Score=143.25  Aligned_cols=159  Identities=18%  Similarity=0.273  Sum_probs=116.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+..    .        ..+..||||||||+|||++|+++|+.++.            
T Consensus         9 kyRP~~f~diiGqe~iv~~L~~~i~~----~--------~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C   76 (563)
T PRK06647          9 KRRPRDFNSLEGQDFVVETLKHSIES----N--------KIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGEC   76 (563)
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHc----C--------CCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccc
Confidence            56899999999999998887766642    1        12567999999999999999999999853            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++...-..-..++.+...      ....-|++|||+|.+..                  ..++.
T Consensus        77 ~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~------------------~a~na  138 (563)
T PRK06647         77 SSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSN------------------SAFNA  138 (563)
T ss_pred             hHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCH------------------HHHHH
Confidence                        3444543322222344444321      23567999999998742                  24677


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ||..++..    +..+++|++|+.+..|.+++.+  |+. .+++..++.++....++..+..++..
T Consensus       139 LLK~LEep----p~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~egi~  197 (563)
T PRK06647        139 LLKTIEEP----PPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLEDQIK  197 (563)
T ss_pred             HHHhhccC----CCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHHHHHHHHHHHHHcCCC
Confidence            88888753    4567888888889999999998  774 58999999999888888777544433

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

Probab=99.51  E-value=2.4e-13  Score=139.66  Aligned_cols=177  Identities=19%  Similarity=0.213  Sum_probs=112.9

Q ss_pred             cc-cccCCHHHHHHHHHHHHHHHcChhHHhh--hcC-CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          208 FK-TLALDSELKREITEDLENFMNGKEYYTR--IGR-AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       208 f~-~l~g~~~~k~~i~~~l~~~~~~~~~~~~--~g~-~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      ++ .++|.++.|+.+...+....++-.....  -+. ....++||+||||||||++|+++|..++.+++.++++.+..  
T Consensus        69 L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~g  148 (412)
T PRK05342         69 LDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAG  148 (412)
T ss_pred             HhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccCC
Confidence            44 4799999999887666544332211000  011 13567999999999999999999999999999999887642  


Q ss_pred             ------hHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc-------
Q 013128          282 ------NSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC-------  342 (449)
Q Consensus       282 ------~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-------  342 (449)
                            ...+..++..      ...++||||||||.+.......+  ..  .+-....+.+.||..|||....       
T Consensus       149 yvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~--~~--~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~  224 (412)
T PRK05342        149 YVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPS--IT--RDVSGEGVQQALLKILEGTVASVPPQGGR  224 (412)
T ss_pred             cccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCC--cC--CCcccHHHHHHHHHHHhcCeEEeCCCCCc
Confidence                  1222333222      23689999999999975311110  00  0111234678899999875311       


Q ss_pred             --CCCCeEEEEEcCCCC----------------------------------------------------CCCccccCCCc
Q 013128          343 --CGEGRIIVFTTNHKE----------------------------------------------------KLDPALLRPGR  368 (449)
Q Consensus       343 --~~~~~iiI~tTN~~~----------------------------------------------------~ld~aLlrpgR  368 (449)
                        .....++|.|+|-..                                                    .+.|+|+  ||
T Consensus       225 ~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEfl--gR  302 (412)
T PRK05342        225 KHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFI--GR  302 (412)
T ss_pred             CcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHh--CC
Confidence              112346667766510                                                    0234444  49


Q ss_pred             cceEEEeCCCCHHHHHHHHHHH
Q 013128          369 MDMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       369 ~d~~i~l~~p~~~~r~~l~~~~  390 (449)
                      ++..+.|..++.++...|+...
T Consensus       303 ld~iv~f~~L~~~~L~~Il~~~  324 (412)
T PRK05342        303 LPVVATLEELDEEALVRILTEP  324 (412)
T ss_pred             CCeeeecCCCCHHHHHHHHHHH
Confidence            9999999999999988888743

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.50  E-value=7e-13  Score=132.07  Aligned_cols=164  Identities=16%  Similarity=0.192  Sum_probs=113.1

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      ..|..    .++|.+|++++|.+++++.+...+.    ...         ..++|||||||||||++++++++++.    
T Consensus         5 ~~w~~----kyrP~~~~~~~g~~~~~~~l~~~i~----~~~---------~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~   67 (319)
T PRK00440          5 EIWVE----KYRPRTLDEIVGQEEIVERLKSYVK----EKN---------MPHLLFAGPPGTGKTTAALALARELYGEDW   67 (319)
T ss_pred             Cccch----hhCCCcHHHhcCcHHHHHHHHHHHh----CCC---------CCeEEEECCCCCCHHHHHHHHHHHHcCCcc
Confidence            35865    8899999999999988887776553    111         23589999999999999999999973    


Q ss_pred             -CcEEEEecccccChHHHH----HHHHcC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          269 -FDIYDLDLSAVQSNSELR----FLLLTM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       269 -~~~~~l~~s~~~~~~~l~----~~~~~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                       ..++.++.+.......+.    ......    ..+.+|+|||+|.+..                  .....|+..++..
T Consensus        68 ~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~------------------~~~~~L~~~le~~  129 (319)
T PRK00440         68 RENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS------------------DAQQALRRTMEMY  129 (319)
T ss_pred             ccceEEeccccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH------------------HHHHHHHHHHhcC
Confidence             345555544433222221    111111    2356999999998742                  1123466666543


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      .    ....+|+++|.+..+.+++.+  |+. .++++.++.++...+++.++...+..+
T Consensus       130 ~----~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~~~~~~~~i  181 (319)
T PRK00440        130 S----QNTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEAVAERLRYIAENEGIEI  181 (319)
T ss_pred             C----CCCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHHHHHHHHHHHHHcCCCC
Confidence            2    335677788888888888887  765 589999999999999998887655444

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.50  E-value=2.3e-13  Score=140.48  Aligned_cols=190  Identities=16%  Similarity=0.213  Sum_probs=119.1

Q ss_pred             cCCCCCcccc-cCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEe
Q 013128          202 LKHPMTFKTL-ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLD  275 (449)
Q Consensus       202 ~~~p~~f~~l-~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~  275 (449)
                      +.+..+||+. +|....  .....+..+...+      +. ..++++||||||||||+|++++|+++     +..++.++
T Consensus       103 l~~~~tfd~fi~g~~n~--~a~~~~~~~~~~~------~~-~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       103 LNPKYTFDNFVVGKSNR--LAHAAALAVAENP------GK-AYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CCCCCcccccccCCcHH--HHHHHHHHHHhCc------Cc-cCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            4455689995 454332  2333444443332      11 13569999999999999999999998     56788888


Q ss_pred             cccccCh-------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeE
Q 013128          276 LSAVQSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI  348 (449)
Q Consensus       276 ~s~~~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  348 (449)
                      +.++...       .....+........+|+|||||.+.+..                .+...|+..++.+...  +..+
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~----------------~~~~~l~~~~n~~~~~--~~~i  235 (405)
T TIGR00362       174 SEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGKE----------------RTQEEFFHTFNALHEN--GKQI  235 (405)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCCH----------------HHHHHHHHHHHHHHHC--CCCE
Confidence            7654321       0111222223456799999999875310                1122345555444332  2345


Q ss_pred             EEEEcCCCC---CCCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHH-HHHHHccCCCHHHHHHHH
Q 013128          349 IVFTTNHKE---KLDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQI-EELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       349 iI~tTN~~~---~ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i-~~l~~~~~~tpa~i~~~l  420 (449)
                      ||.++..|.   .+++.+.+  ||.  ..++++.|+.++|..+++..+...+..+.+++ +.+++...-+..++...|
T Consensus       236 iits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l  311 (405)
T TIGR00362       236 VLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGAL  311 (405)
T ss_pred             EEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence            554444554   36788888  775  58999999999999999999987766665554 444555555666655544

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).

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.50  E-value=5.6e-13  Score=127.56  Aligned_cols=161  Identities=19%  Similarity=0.198  Sum_probs=98.5

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~  276 (449)
                      +......+||+.+-..+  +.....+..+...+.         .+.++||||||||||+|++++|+++.   ..+..+++
T Consensus        13 ~~~~~~~~fd~f~~~~n--~~a~~~l~~~~~~~~---------~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~   81 (235)
T PRK08084         13 LYLPDDETFASFYPGDN--DSLLAALQNALRQEH---------SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPL   81 (235)
T ss_pred             CCCCCcCCccccccCcc--HHHHHHHHHHHhCCC---------CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEH
Confidence            33556678999873321  224455554433221         35799999999999999999999874   44566665


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      ......  ....+....+-.+|+||||+.+.+.             ......+-.+++.+   ... +...+|+.+++.|
T Consensus        82 ~~~~~~--~~~~~~~~~~~dlliiDdi~~~~~~-------------~~~~~~lf~l~n~~---~e~-g~~~li~ts~~~p  142 (235)
T PRK08084         82 DKRAWF--VPEVLEGMEQLSLVCIDNIECIAGD-------------ELWEMAIFDLYNRI---LES-GRTRLLITGDRPP  142 (235)
T ss_pred             HHHhhh--hHHHHHHhhhCCEEEEeChhhhcCC-------------HHHHHHHHHHHHHH---HHc-CCCeEEEeCCCCh
Confidence            543221  1122223333468999999987431             11122232333332   221 2224555555566


Q ss_pred             CC---CCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhC
Q 013128          357 EK---LDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       357 ~~---ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      ..   +.|.|.+  |+.  ..+.+..|+.+++.++++....
T Consensus       143 ~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~~l~~~a~  181 (235)
T PRK08084        143 RQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQALQLRAR  181 (235)
T ss_pred             HHcCcccHHHHH--HHhCCceeeecCCCHHHHHHHHHHHHH
Confidence            55   5799998  775  7899999999999999886443

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

Probab=99.50  E-value=1.6e-13  Score=149.61  Aligned_cols=153  Identities=22%  Similarity=0.293  Sum_probs=106.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+|.+|++++|.+..... ...+...+....         ..++|||||||||||++|+++|+.++.+++.+++.... 
T Consensus        21 k~RP~tldd~vGQe~ii~~-~~~L~~~i~~~~---------~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~~~-   89 (725)
T PRK13341         21 RLRPRTLEEFVGQDHILGE-GRLLRRAIKADR---------VGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAG-   89 (725)
T ss_pred             hcCCCcHHHhcCcHHHhhh-hHHHHHHHhcCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhhhh-
Confidence            5679999999999887643 112222232211         34799999999999999999999999998888865322 


Q ss_pred             hHHHHHH-------HHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc-
Q 013128          282 NSELRFL-------LLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT-  353 (449)
Q Consensus       282 ~~~l~~~-------~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT-  353 (449)
                      ...++..       +.......||||||||.+..                  .....|+..++.      ..+++|++| 
T Consensus        90 i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~------------------~qQdaLL~~lE~------g~IiLI~aTT  145 (725)
T PRK13341         90 VKDLRAEVDRAKERLERHGKRTILFIDEVHRFNK------------------AQQDALLPWVEN------GTITLIGATT  145 (725)
T ss_pred             hHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH------------------HHHHHHHHHhcC------ceEEEEEecC
Confidence            1122221       22234578999999998742                  122346666653      335666644 


Q ss_pred             -CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          354 -NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       354 -N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                       |....+++++++  |+ ..+.++.++.++...++++++.
T Consensus       146 enp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~  182 (725)
T PRK13341        146 ENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQ  182 (725)
T ss_pred             CChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHH
Confidence             333578999998  64 4589999999999999999886

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=7.1e-13  Score=142.12  Aligned_cols=158  Identities=15%  Similarity=0.249  Sum_probs=113.0

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.+.+++.+...+.    ..        ..+.+|||+||||||||++|+++|+.+..            
T Consensus         9 kyRP~~f~eivGQe~i~~~L~~~i~----~~--------ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~   76 (620)
T PRK14954          9 KYRPSKFADITAQEHITHTIQNSLR----MD--------RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQE   76 (620)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHH----cC--------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccc
Confidence            5689999999999988887665442    11        22567999999999999999999999965            


Q ss_pred             --------------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccch
Q 013128          270 --------------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQE  323 (449)
Q Consensus       270 --------------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~  323 (449)
                                          +++.++.........++.+....      ...-|++|||+|.+..               
T Consensus        77 ~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~---------------  141 (620)
T PRK14954         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST---------------  141 (620)
T ss_pred             cCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH---------------
Confidence                                23333332222234455444333      3467999999998742               


Q ss_pred             hhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCC
Q 013128          324 ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHH  396 (449)
Q Consensus       324 ~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~  396 (449)
                         ...+.||..|+..    +...++|++|+.+..|-+++.+  |. ..++|..++.++....+...+..++.
T Consensus       142 ---~a~naLLK~LEeP----p~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi  204 (620)
T PRK14954        142 ---AAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGI  204 (620)
T ss_pred             ---HHHHHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCC
Confidence               2356788888763    3456777777888899999988  66 56999999999888777776654443

>PRK08727 hypothetical protein; Validated

Probab=99.49  E-value=7.9e-13  Score=126.37  Aligned_cols=160  Identities=19%  Similarity=0.243  Sum_probs=103.1

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +......+||+.++.+.-   ....+.....        | .+...++|+||+|||||+|++|+|+++   +..+..+++
T Consensus        10 ~~~~~~~~f~~f~~~~~n---~~~~~~~~~~--------~-~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~   77 (233)
T PRK08727         10 LRYPSDQRFDSYIAAPDG---LLAQLQALAA--------G-QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPL   77 (233)
T ss_pred             CCCCCcCChhhccCCcHH---HHHHHHHHHh--------c-cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeH
Confidence            445566789998766543   1222222211        1 123569999999999999999998886   566677776


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC-C
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN-H  355 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN-~  355 (449)
                      ....  ..+...+....+..+|+|||++.+...             ......+-.++|.+   ..   .+.-+|+|+| .
T Consensus        78 ~~~~--~~~~~~~~~l~~~dlLiIDDi~~l~~~-------------~~~~~~lf~l~n~~---~~---~~~~vI~ts~~~  136 (233)
T PRK08727         78 QAAA--GRLRDALEALEGRSLVALDGLESIAGQ-------------REDEVALFDFHNRA---RA---AGITLLYTARQM  136 (233)
T ss_pred             HHhh--hhHHHHHHHHhcCCEEEEeCcccccCC-------------hHHHHHHHHHHHHH---HH---cCCeEEEECCCC
Confidence            5543  234455666677789999999987531             11122233344443   22   1233555554 5


Q ss_pred             CCCC---CccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcC
Q 013128          356 KEKL---DPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGIS  394 (449)
Q Consensus       356 ~~~l---d~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~  394 (449)
                      |..+   +|+|.+  ||  ...+.++.|+.+++.++++......
T Consensus       137 p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~  178 (233)
T PRK08727        137 PDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQRR  178 (233)
T ss_pred             hhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHHc
Confidence            6554   799998  86  5789999999999999999765433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.49  E-value=7.9e-13  Score=125.72  Aligned_cols=163  Identities=15%  Similarity=0.189  Sum_probs=102.2

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      .....|.+||++++..+  +.+...+..+..        +....++++|+||||||||+|++++++++   +..++.+++
T Consensus         9 ~~~~~~~~~d~f~~~~~--~~~~~~l~~~~~--------~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~   78 (227)
T PRK08903          9 LGPPPPPTFDNFVAGEN--AELVARLRELAA--------GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA   78 (227)
T ss_pred             CCCCChhhhcccccCCc--HHHHHHHHHHHh--------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeh
Confidence            44567788999873322  123333443332        12235689999999999999999999986   667888887


Q ss_pred             ccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          277 SAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       277 s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      ......      +.......+|+|||+|.+..               ...   ..|+..++....  ....++|+|++.+
T Consensus        79 ~~~~~~------~~~~~~~~~liiDdi~~l~~---------------~~~---~~L~~~~~~~~~--~~~~~vl~~~~~~  132 (227)
T PRK08903         79 ASPLLA------FDFDPEAELYAVDDVERLDD---------------AQQ---IALFNLFNRVRA--HGQGALLVAGPAA  132 (227)
T ss_pred             HHhHHH------HhhcccCCEEEEeChhhcCc---------------hHH---HHHHHHHHHHHH--cCCcEEEEeCCCC
Confidence            665321      23344578999999998632               111   224444443322  1233455555543


Q ss_pred             C---CCCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH
Q 013128          357 E---KLDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFE  400 (449)
Q Consensus       357 ~---~ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~  400 (449)
                      .   .+.+.|.+  |+  ...+++|.|+.++...++..+....+..+.+
T Consensus       133 ~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~  179 (227)
T PRK08903        133 PLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAAAAERGLQLAD  179 (227)
T ss_pred             HHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            2   35567776  66  5799999999988888887665444444433

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

Probab=99.49  E-value=1.5e-13  Score=150.44  Aligned_cols=155  Identities=18%  Similarity=0.222  Sum_probs=107.8

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      .++.++|.++..+.+++.+...             .+.++||+||||||||++|+++|..+          +..++.+++
T Consensus       184 ~~~~liGR~~ei~~~i~iL~r~-------------~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~  250 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLCRR-------------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI  250 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHhcc-------------CCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccH
Confidence            3667888888878777765431             14688999999999999999999875          556777766


Q ss_pred             ccccC--------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC
Q 013128          277 SAVQS--------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG  346 (449)
Q Consensus       277 s~~~~--------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  346 (449)
                      +.+..        +..+..++..  ...++||||||||.+++.+...+.         .....+-|...+.      .++
T Consensus       251 ~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g---------~~d~~nlLkp~L~------~g~  315 (758)
T PRK11034        251 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG---------QVDAANLIKPLLS------SGK  315 (758)
T ss_pred             HHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCc---------HHHHHHHHHHHHh------CCC
Confidence            55432        2234444432  346889999999999864321111         0011122222332      356


Q ss_pred             eEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          347 RIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       347 ~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      +.+|++||.++     ..|+||.|  ||+ .|.++.|+.+++..|++.+..
T Consensus       316 i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~~  363 (758)
T PRK11034        316 IRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_pred             eEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHH
Confidence            88899988765     57999999  996 799999999999999997654

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=6.1e-13  Score=143.16  Aligned_cols=160  Identities=16%  Similarity=0.259  Sum_probs=114.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++|+|.+.+++.+...+..    .        ..+..||||||||+|||++|+++|+.++.            
T Consensus         9 kyRP~~~~eiiGq~~~~~~L~~~i~~----~--------~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~   76 (585)
T PRK14950          9 KWRSQTFAELVGQEHVVQTLRNAIAE----G--------RVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGT   76 (585)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHh----C--------CCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            57899999999999998887665542    1        12456999999999999999999998842            


Q ss_pred             -------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHH
Q 013128          270 -------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS  330 (449)
Q Consensus       270 -------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls  330 (449)
                                   +++.++.+.......++.+....      ....|+||||+|.+..                  ..++
T Consensus        77 c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~------------------~a~n  138 (585)
T PRK14950         77 CEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLST------------------AAFN  138 (585)
T ss_pred             CHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCH------------------HHHH
Confidence                         34455543333334444433221      3467999999998742                  2456


Q ss_pred             HHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       331 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      .||..++..    ....++|++++..+.+.+.+.+  |+ ..++|..++..+....+...+..++..+
T Consensus       139 aLLk~LEep----p~~tv~Il~t~~~~kll~tI~S--R~-~~i~f~~l~~~el~~~L~~~a~~egl~i  199 (585)
T PRK14950        139 ALLKTLEEP----PPHAIFILATTEVHKVPATILS--RC-QRFDFHRHSVADMAAHLRKIAAAEGINL  199 (585)
T ss_pred             HHHHHHhcC----CCCeEEEEEeCChhhhhHHHHh--cc-ceeeCCCCCHHHHHHHHHHHHHHcCCCC
Confidence            788888763    3456778888888888888887  66 4588999999988888887766554433

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

Probab=99.49  E-value=7.9e-13  Score=144.86  Aligned_cols=159  Identities=18%  Similarity=0.276  Sum_probs=113.8

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLL  289 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~  289 (449)
                      .++|.++.++.|.+.+.....+-.   ..+ .+...+||+||||||||.+|+++|..++.+++.++++..........++
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~---~~~-kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~Li  534 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLG---HEH-KPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI  534 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhcccc---CCC-CCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHc
Confidence            478999998888888765432110   001 1223599999999999999999999999999999998875432222221


Q ss_pred             ------------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-cccc-C-----C
Q 013128          290 ------------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSC-C-----G  344 (449)
Q Consensus       290 ------------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~-~-----~  344 (449)
                                        ......+||+|||||.+.+                  .+.+.||+.||. .... .     -
T Consensus       535 G~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~~------------------~v~~~LLq~ld~G~ltd~~g~~vd~  596 (758)
T PRK11034        535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHP------------------DVFNLLLQVMDNGTLTDNNGRKADF  596 (758)
T ss_pred             CCCCCcccccccchHHHHHHhCCCcEEEeccHhhhhH------------------HHHHHHHHHHhcCeeecCCCceecC
Confidence                              1123468999999998743                  356778888873 2111 1     1


Q ss_pred             CCeEEEEEcCCC-------------------------CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          345 EGRIIVFTTNHK-------------------------EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       345 ~~~iiI~tTN~~-------------------------~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .+.++|+|||.-                         ..+.|.|+.  |+|..|.|++++.++..+|+..++.
T Consensus       597 rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        597 RNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             CCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHH
Confidence            357899999932                         125577777  9999999999999999999988775

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.48  E-value=3.7e-12  Score=129.51  Aligned_cols=158  Identities=15%  Similarity=0.181  Sum_probs=109.7

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---------CcEEEEeccc
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------FDIYDLDLSA  278 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---------~~~~~l~~s~  278 (449)
                      .+.++|.++..+.|...+...+.+..         +.+++|+||||||||++++++++++.         ..++.++|..
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~---------~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~   84 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSR---------PSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQI   84 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCC---------CCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCC
Confidence            46789999999999988877665321         46799999999999999999998763         5677888765


Q ss_pred             ccChHH--------------------------HH---HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          279 VQSNSE--------------------------LR---FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       279 ~~~~~~--------------------------l~---~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                      ..+...                          +.   ..+....++.||+|||+|.+...               ....+
T Consensus        85 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~---------------~~~~L  149 (365)
T TIGR02928        85 LDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGD---------------DDDLL  149 (365)
T ss_pred             CCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccC---------------CcHHH
Confidence            433211                          01   11222345789999999998620               01133


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCC---CCCccccCCCccc-eEEEeCCCCHHHHHHHHHHHhC
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKE---KLDPALLRPGRMD-MHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~---~ld~aLlrpgR~d-~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      ..|+...+- ....+..+.+|+++|.++   .+++.+.+  ||. ..++|++++.++..++++..+.
T Consensus       150 ~~l~~~~~~-~~~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       150 YQLSRARSN-GDLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             HhHhccccc-cCCCCCeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence            344433111 111235678888998875   57888877  664 6799999999999999998875

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.48  E-value=3.4e-13  Score=141.13  Aligned_cols=191  Identities=16%  Similarity=0.231  Sum_probs=119.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEec
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDL  276 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~  276 (449)
                      +.+..+||+.+..+.-+ .....+..+...+      |.. .++++||||||||||+|++++|+++     +..++.+++
T Consensus       115 l~~~~tfd~fv~g~~n~-~a~~~~~~~~~~~------~~~-~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~  186 (450)
T PRK00149        115 LNPKYTFDNFVVGKSNR-LAHAAALAVAENP------GKA-YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS  186 (450)
T ss_pred             CCCCCcccccccCCCcH-HHHHHHHHHHhCc------Ccc-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            55667899965333222 1333344443322      111 2569999999999999999999998     566888887


Q ss_pred             ccccCh-------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEE
Q 013128          277 SAVQSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII  349 (449)
Q Consensus       277 s~~~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  349 (449)
                      .++...       .....+.....+..+|+|||||.+.+..                .+...|+..++.+...  +..+|
T Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~----------------~~~~~l~~~~n~l~~~--~~~ii  248 (450)
T PRK00149        187 EKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKE----------------RTQEEFFHTFNALHEA--GKQIV  248 (450)
T ss_pred             HHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCCH----------------HHHHHHHHHHHHHHHC--CCcEE
Confidence            665321       1112233344467899999999875311                1223345555444332  22355


Q ss_pred             EEEcCCCCC---CCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHH-HHHccCCCHHHHHHHH
Q 013128          350 VFTTNHKEK---LDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEE-LIKEVNVTPAEVAGEL  420 (449)
Q Consensus       350 I~tTN~~~~---ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~-l~~~~~~tpa~i~~~l  420 (449)
                      |.++..|..   ++++|.+  ||.  ..+++..|+.+++..+++..+...+..+.+++.. +++...-+..++...|
T Consensus       249 its~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l  323 (450)
T PRK00149        249 LTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGAL  323 (450)
T ss_pred             EECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHH
Confidence            544455544   6789988  885  6899999999999999999887666666555433 4444445555554444

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=8.4e-13  Score=142.11  Aligned_cols=161  Identities=17%  Similarity=0.293  Sum_probs=121.0

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------------  268 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------------  268 (449)
                      .++|.+|++++|.+.+++.+...+..    .        ..+..||||||+|+|||++|+++|+.+.             
T Consensus        10 kyRP~~f~~viGq~~~~~~L~~~i~~----~--------~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~   77 (614)
T PRK14971         10 KYRPSTFESVVGQEALTTTLKNAIAT----N--------KLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNE   77 (614)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHHc----C--------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCc
Confidence            67899999999999998887766541    1        1256799999999999999999999874             


Q ss_pred             ------------CcEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHH
Q 013128          269 ------------FDIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS  330 (449)
Q Consensus       269 ------------~~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls  330 (449)
                                  .+++.++..+......++.+....      ...-|++|||+|.+..                  ...+
T Consensus        78 C~sC~~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~------------------~a~n  139 (614)
T PRK14971         78 CESCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQ------------------AAFN  139 (614)
T ss_pred             chHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCH------------------HHHH
Confidence                        456666665444445566555333      2456999999998742                  2456


Q ss_pred             HHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       331 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                      .||..|+..    +...++|++|+.+..|-++|++  |+ ..++|..++.++....+...+..++....
T Consensus       140 aLLK~LEep----p~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~ls~~ei~~~L~~ia~~egi~i~  201 (614)
T PRK14971        140 AFLKTLEEP----PSYAIFILATTEKHKILPTILS--RC-QIFDFNRIQVADIVNHLQYVASKEGITAE  201 (614)
T ss_pred             HHHHHHhCC----CCCeEEEEEeCCchhchHHHHh--hh-heeecCCCCHHHHHHHHHHHHHHcCCCCC
Confidence            788888864    3456788888888899999998  76 45999999999988888877766554443

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

Probab=99.46  E-value=1.4e-12  Score=133.35  Aligned_cols=175  Identities=19%  Similarity=0.225  Sum_probs=111.5

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhh----hcCC-CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC---
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTR----IGRA-WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS---  281 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~----~g~~-~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~---  281 (449)
                      -++|.++.++.+...+....++-.....    -++. .+.++||+||||||||++|+++|..++.++..++++.+..   
T Consensus        78 ~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~gy  157 (413)
T TIGR00382        78 YVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGY  157 (413)
T ss_pred             eecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhcccccc
Confidence            3589999999887766443332110000    0111 1357999999999999999999999999999888776532   


Q ss_pred             -----hHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc--------
Q 013128          282 -----NSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC--------  342 (449)
Q Consensus       282 -----~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--------  342 (449)
                           ...+..++..      ...++||+|||||.+....+...  ..  ..-....+.+.||..|||....        
T Consensus       158 vG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s--~~--~dvsg~~vq~~LL~iLeG~~~~v~~~~gr~  233 (413)
T TIGR00382       158 VGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPS--IT--RDVSGEGVQQALLKIIEGTVANVPPQGGRK  233 (413)
T ss_pred             ccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhcccc--cc--ccccchhHHHHHHHHhhccceecccCCCcc
Confidence                 1223333322      23678999999999875322111  00  0111124667788988876421        


Q ss_pred             -CCCCeEEEEEcCCC---------------------------C-----------------------CCCccccCCCccce
Q 013128          343 -CGEGRIIVFTTNHK---------------------------E-----------------------KLDPALLRPGRMDM  371 (449)
Q Consensus       343 -~~~~~iiI~tTN~~---------------------------~-----------------------~ld~aLlrpgR~d~  371 (449)
                       ...+.++|+|+|-.                           +                       .+.|+|+.  |++.
T Consensus       234 ~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflg--Rld~  311 (413)
T TIGR00382       234 HPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIG--RLPV  311 (413)
T ss_pred             ccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhC--CCCe
Confidence             11345788888861                           0                       02244544  9999


Q ss_pred             EEEeCCCCHHHHHHHHHHH
Q 013128          372 HLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~~~  390 (449)
                      .+.|.+++.++..+|+..-
T Consensus       312 Iv~f~pL~~~~L~~Il~~~  330 (413)
T TIGR00382       312 IATLEKLDEEALIAILTKP  330 (413)
T ss_pred             EeecCCCCHHHHHHHHHHH
Confidence            9999999999988888753

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.

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

Probab=99.45  E-value=1.3e-12  Score=136.01  Aligned_cols=162  Identities=17%  Similarity=0.295  Sum_probs=124.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc-----------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-----------  270 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~-----------  270 (449)
                      .++|.+|++++|.+.+.+.+...+..=            ....+|||.||.||||||+|+.+|..+++.           
T Consensus         9 KyRP~~F~evvGQe~v~~~L~nal~~~------------ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C   76 (515)
T COG2812           9 KYRPKTFDDVVGQEHVVKTLSNALENG------------RIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKC   76 (515)
T ss_pred             HhCcccHHHhcccHHHHHHHHHHHHhC------------cchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhh
Confidence            568999999999999888887765421            114689999999999999999999999643           


Q ss_pred             -------------EEEEecccccChHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          271 -------------IYDLDLSAVQSNSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       271 -------------~~~l~~s~~~~~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                   ++.+|..+-..-.+++.+..+..      +.-|.+|||++.+.                  ...++.
T Consensus        77 ~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS------------------~~afNA  138 (515)
T COG2812          77 ISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLS------------------KQAFNA  138 (515)
T ss_pred             hhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhh------------------HHHHHH
Confidence                         23333333233455666665543      35699999999874                  356788


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE  400 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~  400 (449)
                      ||..++.-    +..+++|++|..+.++++.+++  |+ .++.|...+.++....+..++..++....+
T Consensus       139 LLKTLEEP----P~hV~FIlATTe~~Kip~TIlS--Rc-q~f~fkri~~~~I~~~L~~i~~~E~I~~e~  200 (515)
T COG2812         139 LLKTLEEP----PSHVKFILATTEPQKIPNTILS--RC-QRFDFKRLDLEEIAKHLAAILDKEGINIEE  200 (515)
T ss_pred             HhcccccC----ccCeEEEEecCCcCcCchhhhh--cc-ccccccCCCHHHHHHHHHHHHHhcCCccCH
Confidence            99888763    6789999999999999999999  87 568899999999999999999877554443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.45  E-value=6.5e-13  Score=148.26  Aligned_cols=153  Identities=17%  Similarity=0.212  Sum_probs=109.9

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      .++.++|.++..+.+++.|...             .+++++|+||||||||++|+++|..+          +..++.+++
T Consensus       177 ~~~~~igr~~ei~~~~~~L~r~-------------~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~  243 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILGRR-------------TKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDI  243 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHccc-------------ccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeH
Confidence            5778899998888888766421             25789999999999999999999987          478999998


Q ss_pred             ccccC--------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC
Q 013128          277 SAVQS--------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG  346 (449)
Q Consensus       277 s~~~~--------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  346 (449)
                      +.+..        +..+..++...  ..++||||||||.+.+.+...+.          ....+-|...+.      .++
T Consensus       244 ~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~----------~~~a~lLkp~l~------rg~  307 (821)
T CHL00095        244 GLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGA----------IDAANILKPALA------RGE  307 (821)
T ss_pred             HHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCc----------ccHHHHhHHHHh------CCC
Confidence            76532        23566666543  45899999999999864322111          011122334442      246


Q ss_pred             eEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          347 RIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       347 ~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      +.+|++|+..+     ..||+|.+  ||.. |.++.|+.++...|++...
T Consensus       308 l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~-I~v~ep~~~e~~aILr~l~  354 (821)
T CHL00095        308 LQCIGATTLDEYRKHIEKDPALER--RFQP-VYVGEPSVEETIEILFGLR  354 (821)
T ss_pred             cEEEEeCCHHHHHHHHhcCHHHHh--cceE-EecCCCCHHHHHHHHHHHH
Confidence            77888887653     47999999  9964 8999999999888887543

>PRK05642 DNA replication initiation factor; Validated

Probab=99.43  E-value=2.8e-12  Score=122.63  Aligned_cols=161  Identities=16%  Similarity=0.208  Sum_probs=102.4

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCC-CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAW-KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~-~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +...+..+||+.+...  .....+.+..+.....       .| .+.++||||+|||||+|++|+|+++   +..+++++
T Consensus        10 ~~~~~~~tfdnF~~~~--~~~a~~~~~~~~~~~~-------~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~   80 (234)
T PRK05642         10 VRLRDDATFANYYPGA--NAAALGYVERLCEADA-------GWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLP   80 (234)
T ss_pred             CCCCCcccccccCcCC--hHHHHHHHHHHhhccc-------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEee
Confidence            4556667999987332  2345555554433211       12 3678999999999999999999875   56788888


Q ss_pred             cccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          276 LSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       276 ~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                      ..++...  ...++....+.-+|+|||++.+.+.             ..   +...|+..++....  .+..+|+.++..
T Consensus        81 ~~~~~~~--~~~~~~~~~~~d~LiiDDi~~~~~~-------------~~---~~~~Lf~l~n~~~~--~g~~ilits~~~  140 (234)
T PRK05642         81 LAELLDR--GPELLDNLEQYELVCLDDLDVIAGK-------------AD---WEEALFHLFNRLRD--SGRRLLLAASKS  140 (234)
T ss_pred             HHHHHhh--hHHHHHhhhhCCEEEEechhhhcCC-------------hH---HHHHHHHHHHHHHh--cCCEEEEeCCCC
Confidence            7766432  1223333444568999999977431             11   11234444444332  234455555555


Q ss_pred             CCC---CCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHh
Q 013128          356 KEK---LDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       356 ~~~---ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      |..   ..|+|.+  |+  ...+.+..|+.+++..+++...
T Consensus       141 p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~il~~ka  179 (234)
T PRK05642        141 PRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRALQLRA  179 (234)
T ss_pred             HHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHHHHHHH
Confidence            533   3688988  77  5778899999999999998544

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.42  E-value=1.1e-12  Score=129.52  Aligned_cols=129  Identities=16%  Similarity=0.208  Sum_probs=92.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHH-------------------HHHcCCCCceEEeecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRF-------------------LLLTMPSRSMLVIEDI  303 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~-------------------~~~~~~~~~Il~iDei  303 (449)
                      .+.+||.||||||||++++++|..++.+++.++++......++..                   +......+++|++|||
T Consensus        64 ~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illlDEi  143 (327)
T TIGR01650        64 DRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCFDEY  143 (327)
T ss_pred             CCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEechh
Confidence            468999999999999999999999999999998776543221110                   0011135788999999


Q ss_pred             chhhhcccccchhhhhccchhhHHHHHHHHHHhcC--ccc--------cCCCCeEEEEEcCCCC------------CCCc
Q 013128          304 DCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG--LWS--------CCGEGRIIVFTTNHKE------------KLDP  361 (449)
Q Consensus       304 D~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg--~~~--------~~~~~~iiI~tTN~~~------------~ld~  361 (449)
                      |..-+                  .+++.|...+|.  ...        .......+|+|+|..+            .+++
T Consensus       144 n~a~p------------------~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~  205 (327)
T TIGR01650       144 DAGRP------------------DVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQ  205 (327)
T ss_pred             hccCH------------------HHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCH
Confidence            97632                  233444444431  110        0123467899999865            3689


Q ss_pred             cccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          362 ALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       362 aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      |++.  ||-+.+.++||+.+...+|+....
T Consensus       206 A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~  233 (327)
T TIGR01650       206 AQMD--RWSIVTTLNYLEHDNEAAIVLAKA  233 (327)
T ss_pred             HHHh--heeeEeeCCCCCHHHHHHHHHhhc
Confidence            9999  998889999999999999988764

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.

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

Probab=99.42  E-value=5.1e-12  Score=139.50  Aligned_cols=155  Identities=17%  Similarity=0.269  Sum_probs=110.6

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCc-ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKR-GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~r-g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~  284 (449)
                      +.++|.++.++.|.+.+....        .|..   .|. .+||+||||||||++|+++|..++.+++.++++.+.....
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~--------~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~  525 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSR--------AGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHT  525 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHh--------cCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhccc
Confidence            346777777777776654321        2221   133 4899999999999999999999999999999887643211


Q ss_pred             -------------------HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC--
Q 013128          285 -------------------LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC--  343 (449)
Q Consensus       285 -------------------l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~--  343 (449)
                                         +...+. ....+||+|||||.+.+                  ...+.||+.+|.-.-..  
T Consensus       526 ~~~lig~~~gyvg~~~~~~l~~~~~-~~p~~VvllDEieka~~------------------~~~~~Ll~~ld~g~~~d~~  586 (731)
T TIGR02639       526 VSRLIGAPPGYVGFEQGGLLTEAVR-KHPHCVLLLDEIEKAHP------------------DIYNILLQVMDYATLTDNN  586 (731)
T ss_pred             HHHHhcCCCCCcccchhhHHHHHHH-hCCCeEEEEechhhcCH------------------HHHHHHHHhhccCeeecCC
Confidence                               222222 34568999999998743                  35567888887432110  


Q ss_pred             -----CCCeEEEEEcCCCC-------------------------CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          344 -----GEGRIIVFTTNHKE-------------------------KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       344 -----~~~~iiI~tTN~~~-------------------------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                           -.+.+||+|||...                         .+.|.|+.  |||..|.|.+.+.++..+|++..+.
T Consensus       587 g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       587 GRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVD  663 (731)
T ss_pred             CcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHH
Confidence                 13468999998631                         24567766  9999999999999999999998875

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.42  E-value=1.6e-11  Score=126.15  Aligned_cols=158  Identities=18%  Similarity=0.211  Sum_probs=109.3

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEecccccC
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAVQS  281 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~~~  281 (449)
                      ..+.+++.++..+++...+...+.+..         +.+++||||||||||++++.+++++     +..++.++|....+
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~---------~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~   98 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSR---------PLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRT   98 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCC---------CCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCC
Confidence            346788888888888888776654321         4579999999999999999999988     57788888764422


Q ss_pred             h-----------------------HHH----HHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          282 N-----------------------SEL----RFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       282 ~-----------------------~~l----~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                      .                       .++    ...+.....+.||+|||+|.+..  ..            ....+..|+.
T Consensus        99 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~--~~------------~~~~l~~l~~  164 (394)
T PRK00411         99 RYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFE--KE------------GNDVLYSLLR  164 (394)
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhc--cC------------CchHHHHHHH
Confidence            1                       111    11122234568999999999862  00            1124555666


Q ss_pred             HhcCccccCCCCeEEEEEcCCC---CCCCccccCCCcc-ceEEEeCCCCHHHHHHHHHHHhC
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRM-DMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~-d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .++...   +..+.+|+++|..   +.+++.+.+  |+ ...|+|++++.++..++++..+.
T Consensus       165 ~~~~~~---~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        165 AHEEYP---GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             hhhccC---CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHH
Confidence            555432   2357788888876   357777766  55 35789999999999999988774

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.41  E-value=2.6e-12  Score=136.22  Aligned_cols=191  Identities=13%  Similarity=0.162  Sum_probs=121.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEec
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDL  276 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~  276 (449)
                      +....+||+++..+.-. .....+......+      +. +.+.++|||++|||||+|++|||+++     ++.++++++
T Consensus       281 L~~~~TFDnFvvG~sN~-~A~aaa~avae~~------~~-~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yita  352 (617)
T PRK14086        281 LNPKYTFDTFVIGASNR-FAHAAAVAVAEAP------AK-AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSS  352 (617)
T ss_pred             CCCCCCHhhhcCCCccH-HHHHHHHHHHhCc------cc-cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH
Confidence            44556899987443322 1222222222221      11 23469999999999999999999987     567888887


Q ss_pred             ccccCh-------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEE
Q 013128          277 SAVQSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII  349 (449)
Q Consensus       277 s~~~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  349 (449)
                      .++...       ..+..+.....+..+|+||||+.+.+..                .+...|++.++.+...  +. -|
T Consensus       353 eef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gke----------------~tqeeLF~l~N~l~e~--gk-~I  413 (617)
T PRK14086        353 EEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDKE----------------STQEEFFHTFNTLHNA--NK-QI  413 (617)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCCH----------------HHHHHHHHHHHHHHhc--CC-CE
Confidence            665321       1112223334567899999999875311                1122344444444332  22 34


Q ss_pred             EEEcCCC----CCCCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHH-HHccCCCHHHHHHHHh
Q 013128          350 VFTTNHK----EKLDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEEL-IKEVNVTPAEVAGELM  421 (449)
Q Consensus       350 I~tTN~~----~~ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l-~~~~~~tpa~i~~~l~  421 (449)
                      |+|+|.+    ..+++.|.+  ||  ...+++..|+.+.|..|++......+..+.+++.+. +.+..-+..++...|.
T Consensus       414 IITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL~  490 (617)
T PRK14086        414 VLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGALI  490 (617)
T ss_pred             EEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHHH
Confidence            4566654    357889998  66  778899999999999999999888777776665554 4555556666666554

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

Probab=99.41  E-value=3.4e-12  Score=120.86  Aligned_cols=185  Identities=17%  Similarity=0.227  Sum_probs=107.8

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEeccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSA  278 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~  278 (449)
                      +..|||+.+-.+.-+ .....+......+.      . ....++||||+|+|||+|++|+|+++     +..+++++...
T Consensus         3 ~~~tFdnfv~g~~N~-~a~~~~~~ia~~~~------~-~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~   74 (219)
T PF00308_consen    3 PKYTFDNFVVGESNE-LAYAAAKAIAENPG------E-RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEE   74 (219)
T ss_dssp             TT-SCCCS--TTTTH-HHHHHHHHHHHSTT------T-SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHH
T ss_pred             CCCccccCCcCCcHH-HHHHHHHHHHhcCC------C-CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHH
Confidence            446899986332221 23333334444332      1 12458999999999999999999986     56788887766


Q ss_pred             ccCh-------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          279 VQSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       279 ~~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      +...       ..+..+......--+|+|||++.+.+.                ..+...|...++.+...  +..+|+.
T Consensus        75 f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~----------------~~~q~~lf~l~n~~~~~--~k~li~t  136 (219)
T PF00308_consen   75 FIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGK----------------QRTQEELFHLFNRLIES--GKQLILT  136 (219)
T ss_dssp             HHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTH----------------HHHHHHHHHHHHHHHHT--TSEEEEE
T ss_pred             HHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCc----------------hHHHHHHHHHHHHHHhh--CCeEEEE
Confidence            5321       223344455567889999999988531                12333455555444332  3456666


Q ss_pred             EcCCCCC---CCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHH-HccCCCHHHH
Q 013128          352 TTNHKEK---LDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELI-KEVNVTPAEV  416 (449)
Q Consensus       352 tTN~~~~---ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~-~~~~~tpa~i  416 (449)
                      +...|..   +++.|..  ||  ...+.+..|+.+.|..+++......+..+.+++...+ +...-+..++
T Consensus       137 s~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L  205 (219)
T PF00308_consen  137 SDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVREL  205 (219)
T ss_dssp             ESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHH
T ss_pred             eCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHH
Confidence            6566655   4677777  66  4589999999999999999988877666665554433 3333344444

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.

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

Probab=99.40  E-value=1.4e-12  Score=127.52  Aligned_cols=152  Identities=20%  Similarity=0.308  Sum_probs=101.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc---EEEEeccc
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~  278 (449)
                      ..+|.++++.+|.+++... ...|...+....         -.+++||||||||||+||+.|++....+   ++.++...
T Consensus       131 rmRPktL~dyvGQ~hlv~q-~gllrs~ieq~~---------ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~  200 (554)
T KOG2028|consen  131 RMRPKTLDDYVGQSHLVGQ-DGLLRSLIEQNR---------IPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATN  200 (554)
T ss_pred             hcCcchHHHhcchhhhcCc-chHHHHHHHcCC---------CCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccc
Confidence            4578889988888766543 222333333221         3579999999999999999999998765   55554443


Q ss_pred             ccChHHHHHHHHcC-------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          279 VQSNSELRFLLLTM-------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       279 ~~~~~~l~~~~~~~-------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      -. -.+++.+|...       ..+.|||||||+.+..    .              ....||..++.      +.+++|+
T Consensus       201 a~-t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNk----s--------------QQD~fLP~VE~------G~I~lIG  255 (554)
T KOG2028|consen  201 AK-TNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNK----S--------------QQDTFLPHVEN------GDITLIG  255 (554)
T ss_pred             cc-hHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhh----h--------------hhhcccceecc------CceEEEe
Confidence            32 24566555544       4689999999998743    1              12236666542      4566775


Q ss_pred             -Ec-CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          352 -TT-NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       352 -tT-N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                       || |..-.|..||+.  |+ ..+.+...+.+....|+.+-+
T Consensus       256 ATTENPSFqln~aLlS--RC-~VfvLekL~~n~v~~iL~rai  294 (554)
T KOG2028|consen  256 ATTENPSFQLNAALLS--RC-RVFVLEKLPVNAVVTILMRAI  294 (554)
T ss_pred             cccCCCccchhHHHHh--cc-ceeEeccCCHHHHHHHHHHHH
Confidence             44 444689999999  65 336677788888888887733

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

Probab=99.40  E-value=4.2e-12  Score=110.10  Aligned_cols=115  Identities=30%  Similarity=0.443  Sum_probs=81.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHH-----------HHHHcCCCCceEEeeccchhhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELR-----------FLLLTMPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~-----------~~~~~~~~~~Il~iDeiD~l~~  308 (449)
                      .++++++||||||||++++.+++.+   +.+++.+++..........           ........+.+|+|||++.+..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~~   98 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSR   98 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhhH
Confidence            4689999999999999999999999   8999999988765432222           1233345789999999998621


Q ss_pred             cccccchhhhhccchhhHHHHHHHHHHhcCcccc--CCCCeEEEEEcCCCC--CCCccccCCCccceEEEeCC
Q 013128          309 LQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC--CGEGRIIVFTTNHKE--KLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--~~~~~iiI~tTN~~~--~ld~aLlrpgR~d~~i~l~~  377 (449)
                                        .....++..+......  ...+..+|+++|...  .+++.+..  |++.++.+++
T Consensus        99 ------------------~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~~  151 (151)
T cd00009          99 ------------------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIPL  151 (151)
T ss_pred             ------------------HHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecCC
Confidence                              1122344444433211  124578888888877  77888887  9988888763

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.39  E-value=3.2e-12  Score=132.85  Aligned_cols=152  Identities=18%  Similarity=0.272  Sum_probs=98.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh-------HHHHHHHHcCCCCceEEeeccchhhhccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRE  313 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~  313 (449)
                      ++++||||||+|||+|++|+|+++   +..+++++...+...       .....+.....+..+|+||||+.+.+.    
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k----  217 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGK----  217 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCC----
Confidence            579999999999999999999987   678888876554221       111122222456789999999987431    


Q ss_pred             chhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC-C---CCCCccccCCCccc--eEEEeCCCCHHHHHHHH
Q 013128          314 SSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH-K---EKLDPALLRPGRMD--MHLHMSYCNTSVFKQLA  387 (449)
Q Consensus       314 ~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~-~---~~ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~  387 (449)
                               ..   +...|+..++.+..   .+..+|+|+|. |   ..++++|.+  ||.  ..+.++.|+.+.+..++
T Consensus       218 ---------~~---~qeelf~l~N~l~~---~~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL  280 (445)
T PRK12422        218 ---------GA---TQEEFFHTFNSLHT---EGKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFL  280 (445)
T ss_pred             ---------hh---hHHHHHHHHHHHHH---CCCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHH
Confidence                     11   11223333332222   12345555554 4   356889998  884  89999999999999999


Q ss_pred             HHHhCcCCCCCHHHHHH-HHHccCCCHHHH
Q 013128          388 FNYLGISHHYLFEQIEE-LIKEVNVTPAEV  416 (449)
Q Consensus       388 ~~~l~~~~~~l~~~i~~-l~~~~~~tpa~i  416 (449)
                      +......+..+.+++.. ++....-+..++
T Consensus       281 ~~k~~~~~~~l~~evl~~la~~~~~dir~L  310 (445)
T PRK12422        281 ERKAEALSIRIEETALDFLIEALSSNVKSL  310 (445)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHhcCCCHHHH
Confidence            99887766666655544 444443333333

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.39  E-value=1.2e-11  Score=133.40  Aligned_cols=156  Identities=20%  Similarity=0.258  Sum_probs=108.3

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEeccc
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDLSA  278 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~s~  278 (449)
                      +.|.+.++..++|...|...+....        +...++|+||||||||.+++.+++++          .+.++.++|..
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsg--------pnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~  826 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSG--------SNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMN  826 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCC--------CCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCc
Confidence            7788999999999988887776322        12335799999999999999999887          25678899865


Q ss_pred             ccCh-----------------------HHHHHHHHcC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          279 VQSN-----------------------SELRFLLLTM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       279 ~~~~-----------------------~~l~~~~~~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                      +.+.                       ..+..++...    ....||+|||||.+...               .+..   
T Consensus       827 Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK---------------~QDV---  888 (1164)
T PTZ00112        827 VVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITK---------------TQKV---  888 (1164)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCcc---------------HHHH---
Confidence            4322                       1122333322    23569999999998641               1122   


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCC---CCCCCccccCCCccce-EEEeCCCCHHHHHHHHHHHhCc
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNH---KEKLDPALLRPGRMDM-HLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~---~~~ld~aLlrpgR~d~-~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      |++.++.... .+..++||+++|.   ++.|+|.+..  ||.. .|.|++++.+++..|++.-+..
T Consensus       889 LYnLFR~~~~-s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~  951 (1164)
T PTZ00112        889 LFTLFDWPTK-INSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLEN  951 (1164)
T ss_pred             HHHHHHHhhc-cCCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHh
Confidence            3333332221 2456788898886   5677888887  6543 4888999999999999987764

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.39  E-value=7.6e-12  Score=135.13  Aligned_cols=178  Identities=19%  Similarity=0.280  Sum_probs=116.6

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ..+|.+|++++|.....+.+...+.             .+.+..++|+||||||||++|+++++..          +.++
T Consensus       147 ~~rp~~~~~iiGqs~~~~~l~~~ia-------------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~f  213 (615)
T TIGR02903       147 LLRPRAFSEIVGQERAIKALLAKVA-------------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPF  213 (615)
T ss_pred             hcCcCcHHhceeCcHHHHHHHHHHh-------------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCe
Confidence            3468999999999888877655442             1124579999999999999999998776          3468


Q ss_pred             EEEecccccCh-HHH----------------HHHHHc------------CCCCceEEeeccchhhhcccccchhhhhccc
Q 013128          272 YDLDLSAVQSN-SEL----------------RFLLLT------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQ  322 (449)
Q Consensus       272 ~~l~~s~~~~~-~~l----------------~~~~~~------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~  322 (449)
                      +.+++..+... ..+                ...+..            ....++|||||++.+-.              
T Consensus       214 v~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~--------------  279 (615)
T TIGR02903       214 VEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDP--------------  279 (615)
T ss_pred             EEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCH--------------
Confidence            88887665311 111                001111            12467999999998742              


Q ss_pred             hhhHHHHHHHHHHhcCc--------c----------------ccCCCCeEEEE-EcCCCCCCCccccCCCccceEEEeCC
Q 013128          323 EENKVTLSGLLNFIDGL--------W----------------SCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       323 ~~~~~~ls~LL~~ldg~--------~----------------~~~~~~~iiI~-tTN~~~~ld~aLlrpgR~d~~i~l~~  377 (449)
                          .....|+..++.-        +                ...+..+++|+ ||+.++.++++|.+  ||. .++++.
T Consensus       280 ----~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~p  352 (615)
T TIGR02903       280 ----LLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRS--RCA-EVFFEP  352 (615)
T ss_pred             ----HHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHh--cee-EEEeCC
Confidence                1122344444210        0                00112345554 66778899999988  886 578999


Q ss_pred             CCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCH
Q 013128          378 CNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTP  413 (449)
Q Consensus       378 p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tp  413 (449)
                      ++.++...|+++++...+..+.+++..++.+..+..
T Consensus       353 ls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~g  388 (615)
T TIGR02903       353 LTPEDIALIVLNAAEKINVHLAAGVEELIARYTIEG  388 (615)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcH
Confidence            999999999999887554455566666665555533

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.37  E-value=4.8e-12  Score=131.69  Aligned_cols=190  Identities=15%  Similarity=0.247  Sum_probs=114.9

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEec
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDL  276 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~  276 (449)
                      +.+..+||+.+..+.-. .....+..+...+.        +.++++||||||||||+|++|+|+++     +..++++++
T Consensus        98 l~~~~tFdnFv~g~~n~-~a~~~~~~~~~~~~--------~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088         98 LNPDYTFENFVVGPGNS-FAYHAALEVAKNPG--------RYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CCCCCcccccccCCchH-HHHHHHHHHHhCcC--------CCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            44556899987333322 23333334433222        13569999999999999999999987     456788877


Q ss_pred             ccccCh-------HHHHHHHHcC-CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeE
Q 013128          277 SAVQSN-------SELRFLLLTM-PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI  348 (449)
Q Consensus       277 s~~~~~-------~~l~~~~~~~-~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  348 (449)
                      .++...       ..+....... .++.+|+|||++.+.+..             .   +...|+..++.+...  ...+
T Consensus       169 ~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~-------------~---~q~elf~~~n~l~~~--~k~i  230 (440)
T PRK14088        169 EKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKT-------------G---VQTELFHTFNELHDS--GKQI  230 (440)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcH-------------H---HHHHHHHHHHHHHHc--CCeE
Confidence            654321       1111122222 257899999999875410             0   112234444433332  2234


Q ss_pred             EEEEcCCCCC---CCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHH-HHccCCCHHHHHHHH
Q 013128          349 IVFTTNHKEK---LDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEEL-IKEVNVTPAEVAGEL  420 (449)
Q Consensus       349 iI~tTN~~~~---ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l-~~~~~~tpa~i~~~l  420 (449)
                      ||.+.++|..   +++.+.+  ||  ...+.+..|+.+.|..|+++.+...+..+.+++... ++...-+..++...|
T Consensus       231 Iitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l  306 (440)
T PRK14088        231 VICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAI  306 (440)
T ss_pred             EEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHH
Confidence            4444455544   5677887  65  568899999999999999999887666666655443 344444555554444

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

Probab=99.36  E-value=7.5e-13  Score=115.97  Aligned_cols=105  Identities=29%  Similarity=0.401  Sum_probs=75.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHc---------------CCCCceEEeeccchhhhc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLT---------------MPSRSMLVIEDIDCSVKL  309 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~---------------~~~~~Il~iDeiD~l~~~  309 (449)
                      ++||+||||||||++|+.+|..++.+++.+.++...+..++.....-               ..+++|++||||+..-+ 
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a~~-   79 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRAPP-   79 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG--H-
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccCCH-
Confidence            48999999999999999999999999999999987776655421110               01578999999997532 


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcCcccc----------CCC-----CeEEEEEcCCCC----CCCccccCCCcc
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSC----------CGE-----GRIIVFTTNHKE----KLDPALLRPGRM  369 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----------~~~-----~~iiI~tTN~~~----~ld~aLlrpgR~  369 (449)
                                       .++..|++.+|.-.-.          ...     +..||+|+|..+    .+++||++  ||
T Consensus        80 -----------------~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~--Rf  139 (139)
T PF07728_consen   80 -----------------EVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD--RF  139 (139)
T ss_dssp             -----------------HHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT--T-
T ss_pred             -----------------HHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh--hC
Confidence                             3455566666532110          011     379999999998    89999999  87

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.

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

Probab=99.35  E-value=1.2e-11  Score=124.17  Aligned_cols=130  Identities=25%  Similarity=0.294  Sum_probs=92.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH------HHH--H----cCCC---C---ceEEeeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR------FLL--L----TMPS---R---SMLVIEDID  304 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~------~~~--~----~~~~---~---~Il~iDeiD  304 (449)
                      .+.+||.||||||||++|+++|..++.+++.++|+.-....++.      ...  .    -.+.   .   +|+++|||+
T Consensus        43 ~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEIn  122 (329)
T COG0714          43 GGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEIN  122 (329)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccc
Confidence            56899999999999999999999999999999998664433322      110  0    0111   1   399999999


Q ss_pred             hhhhcccccchhhhhccchhhHHHHHHHHHHhcC-------cc-ccCCCCeEEEEEcCC-----CCCCCccccCCCccce
Q 013128          305 CSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-------LW-SCCGEGRIIVFTTNH-----KEKLDPALLRPGRMDM  371 (449)
Q Consensus       305 ~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-------~~-~~~~~~~iiI~tTN~-----~~~ld~aLlrpgR~d~  371 (449)
                      ...+                  .+.+.||..|+.       .. -......++|+|+|.     ...|++|+++  ||..
T Consensus       123 ra~p------------------~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~  182 (329)
T COG0714         123 RAPP------------------EVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--RFLL  182 (329)
T ss_pred             cCCH------------------HHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--hEEE
Confidence            7643                  456667777764       11 122355788888893     4568999999  9999


Q ss_pred             EEEeCCC-CHHHHHHHHHHHhC
Q 013128          372 HLHMSYC-NTSVFKQLAFNYLG  392 (449)
Q Consensus       372 ~i~l~~p-~~~~r~~l~~~~l~  392 (449)
                      .+.++|| ..++...+......
T Consensus       183 ~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         183 RIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             EEecCCCCchHHHHHHHHhCcc
Confidence            9999999 55555555555554

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.35  E-value=8.5e-12  Score=124.71  Aligned_cols=157  Identities=20%  Similarity=0.237  Sum_probs=104.1

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-------Cc--EEE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-------FD--IYD  273 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-------~~--~~~  273 (449)
                      +.|.+|+.++|.++.++.+.-.+.   .          +...++||+||||||||++++++|+.+.       .+  +..
T Consensus         2 ~~~~~f~~i~Gq~~~~~~l~~~~~---~----------~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~   68 (334)
T PRK13407          2 KKPFPFSAIVGQEEMKQAMVLTAI---D----------PGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSAR   68 (334)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHh---c----------cCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCc
Confidence            357889999999999887754221   1          1125799999999999999999999983       21  111


Q ss_pred             Ee----cc-----c-------------------ccChHHHHHHHHc-----------CCCCceEEeeccchhhhcccccc
Q 013128          274 LD----LS-----A-------------------VQSNSELRFLLLT-----------MPSRSMLVIEDIDCSVKLQNRES  314 (449)
Q Consensus       274 l~----~s-----~-------------------~~~~~~l~~~~~~-----------~~~~~Il~iDeiD~l~~~~~~~~  314 (449)
                      +.    +.     .                   +.....+...+..           .....+|+||||+.+..      
T Consensus        69 ~~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~------  142 (334)
T PRK13407         69 PEDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLED------  142 (334)
T ss_pred             ccCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCH------
Confidence            10    00     0                   0001111111111           12357999999998743      


Q ss_pred             hhhhhccchhhHHHHHHHHHHhcCc---------cccCCCCeEEEEEcCCCC-CCCccccCCCccceEEEeCCCCH-HHH
Q 013128          315 SEVQATNQEENKVTLSGLLNFIDGL---------WSCCGEGRIIVFTTNHKE-KLDPALLRPGRMDMHLHMSYCNT-SVF  383 (449)
Q Consensus       315 ~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~-~ld~aLlrpgR~d~~i~l~~p~~-~~r  383 (449)
                                  .+++.|++.|+.-         ....+..+++|+|+|..+ .++++|+.  ||.+.+.+++|.. +++
T Consensus       143 ------------~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~  208 (334)
T PRK13407        143 ------------HIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETR  208 (334)
T ss_pred             ------------HHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHH
Confidence                        4566677777532         111234567888888655 58999999  9999999999988 888


Q ss_pred             HHHHHHHhC
Q 013128          384 KQLAFNYLG  392 (449)
Q Consensus       384 ~~l~~~~l~  392 (449)
                      .+++.+...
T Consensus       209 ~~il~~~~~  217 (334)
T PRK13407        209 VEVIRRRDA  217 (334)
T ss_pred             HHHHHHhhc
Confidence            999988654

>PRK06620 hypothetical protein; Validated

Probab=99.35  E-value=2.5e-11  Score=114.49  Aligned_cols=155  Identities=19%  Similarity=0.258  Sum_probs=94.9

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCC-CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAW-KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~-~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      ...+..+||+++..+.-. .....+..+...+      +..+ .+.++||||||||||+|++++|+..+..++.  ....
T Consensus         8 ~~~~~~tfd~Fvvg~~N~-~a~~~~~~~~~~~------~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~--~~~~   78 (214)
T PRK06620          8 TTSSKYHPDEFIVSSSND-QAYNIIKNWQCGF------GVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK--DIFF   78 (214)
T ss_pred             CCCCCCCchhhEecccHH-HHHHHHHHHHHcc------ccCCCcceEEEECCCCCCHHHHHHHHHhccCCEEcc--hhhh
Confidence            344556899986544222 2344444443211      2222 3679999999999999999999998763322  1111


Q ss_pred             cChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC-
Q 013128          280 QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK-  358 (449)
Q Consensus       280 ~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~-  358 (449)
                        ..   ..   .....+|+|||||.+.                  ...+-.++|.+..     .+..++|.++..|.. 
T Consensus        79 --~~---~~---~~~~d~lliDdi~~~~------------------~~~lf~l~N~~~e-----~g~~ilits~~~p~~l  127 (214)
T PRK06620         79 --NE---EI---LEKYNAFIIEDIENWQ------------------EPALLHIFNIINE-----KQKYLLLTSSDKSRNF  127 (214)
T ss_pred             --ch---hH---HhcCCEEEEeccccch------------------HHHHHHHHHHHHh-----cCCEEEEEcCCCcccc
Confidence              11   11   1245799999999531                  1233345554432     234566666655544 


Q ss_pred             -CCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          359 -LDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       359 -ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                       + |+|+.  |+.  ..+.+..|+.+.+..++++.....+..+
T Consensus       128 ~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l  167 (214)
T PRK06620        128 TL-PDLSS--RIKSVLSILLNSPDDELIKILIFKHFSISSVTI  167 (214)
T ss_pred             ch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCC
Confidence             5 78888  774  4699999999999999987765433333

>PHA02244 ATPase-like protein

Probab=99.34  E-value=1.8e-11  Score=122.42  Aligned_cols=116  Identities=21%  Similarity=0.305  Sum_probs=80.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc----c----cChHHHH--HHHHcCCCCceEEeeccchhhhccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA----V----QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRE  313 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~----~----~~~~~l~--~~~~~~~~~~Il~iDeiD~l~~~~~~~  313 (449)
                      ..+||+||||||||++|++||..++.+++.++...    +    .....+.  .++.......+|+||||+.+.+     
T Consensus       120 ~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~p-----  194 (383)
T PHA02244        120 IPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASIP-----  194 (383)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHhhcCCEEEEeCcCcCCH-----
Confidence            57999999999999999999999999999887321    0    0001111  2333346789999999997643     


Q ss_pred             chhhhhccchhhHHHHHHHHHHhc--------CccccCCCCeEEEEEcCCC-----------CCCCccccCCCccceEEE
Q 013128          314 SSEVQATNQEENKVTLSGLLNFID--------GLWSCCGEGRIIVFTTNHK-----------EKLDPALLRPGRMDMHLH  374 (449)
Q Consensus       314 ~~~~~~~~~~~~~~~ls~LL~~ld--------g~~~~~~~~~iiI~tTN~~-----------~~ld~aLlrpgR~d~~i~  374 (449)
                                   .++..|...++        +.. .....+-+|+|+|.+           ..+++|++.  || .+|+
T Consensus       195 -------------~vq~~L~~lLd~r~l~l~g~~i-~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~I~  257 (383)
T PHA02244        195 -------------EALIIINSAIANKFFDFADERV-TAHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-APIE  257 (383)
T ss_pred             -------------HHHHHHHHHhccCeEEecCcEE-ecCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EEee
Confidence                         12333444443        111 113457889999973           568999999  99 6799


Q ss_pred             eCCCCHH
Q 013128          375 MSYCNTS  381 (449)
Q Consensus       375 l~~p~~~  381 (449)
                      ++||+..
T Consensus       258 ~dyp~~~  264 (383)
T PHA02244        258 FDYDEKI  264 (383)
T ss_pred             CCCCcHH
Confidence            9999843

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.32  E-value=3.4e-11  Score=125.59  Aligned_cols=188  Identities=13%  Similarity=0.230  Sum_probs=116.5

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEecccc
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAV  279 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~  279 (449)
                      +.+||+.+-.+.- +.....+..+...+      |.. .++++||||+|||||+|++|+++++     +..++++++.++
T Consensus       111 ~~tFdnFv~g~~n-~~A~~aa~~~a~~~------~~~-~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f  182 (450)
T PRK14087        111 ENTFENFVIGSSN-EQAFIAVQTVSKNP------GIS-YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEF  182 (450)
T ss_pred             ccchhcccCCCcH-HHHHHHHHHHHhCc------Ccc-cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHH
Confidence            4688887643332 22334444443322      211 3579999999999999999999976     467788877665


Q ss_pred             cCh---------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEE
Q 013128          280 QSN---------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIV  350 (449)
Q Consensus       280 ~~~---------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  350 (449)
                      ...         ..+........+..+|+|||++.+.+.             ......+-.++|.+   ...  + ..+|
T Consensus       183 ~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~k-------------~~~~e~lf~l~N~~---~~~--~-k~iI  243 (450)
T PRK14087        183 ARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSYK-------------EKTNEIFFTIFNNF---IEN--D-KQLF  243 (450)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccCC-------------HHHHHHHHHHHHHH---HHc--C-CcEE
Confidence            321         123333444567789999999987431             11122333344444   222  2 2456


Q ss_pred             EEcCCC-C---CCCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCC--CCHHHH-HHHHHccCCCHHHHHHHHh
Q 013128          351 FTTNHK-E---KLDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHH--YLFEQI-EELIKEVNVTPAEVAGELM  421 (449)
Q Consensus       351 ~tTN~~-~---~ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~--~l~~~i-~~l~~~~~~tpa~i~~~l~  421 (449)
                      +|+|.+ +   .+++.|..  ||  +..+.+..|+.+++.+++++.+...+.  .+.+++ +-+++...=++.++...|.
T Consensus       244 ltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~  321 (450)
T PRK14087        244 FSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVS  321 (450)
T ss_pred             EECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHH
Confidence            666543 3   46788888  77  578889999999999999998876442  354443 4444555556666655553

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

Probab=99.31  E-value=7.1e-11  Score=124.39  Aligned_cols=178  Identities=21%  Similarity=0.249  Sum_probs=121.2

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHc---C---------h-----hHH----hhhcCCCCcceEEeCCC
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMN---G---------K-----EYY----TRIGRAWKRGYLLYGPP  252 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~---~---------~-----~~~----~~~g~~~~rg~LL~GPp  252 (449)
                      .|..    ...|..|.+|.+++.+-+.++-+|+.|--   +         +     +.+    ...+.|.++-+||+|||
T Consensus       260 LWVd----ky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~Gpp  335 (877)
T KOG1969|consen  260 LWVD----KYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPP  335 (877)
T ss_pred             eeec----ccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCC
Confidence            6854    88999999999999999999999886631   1         0     011    12356777889999999


Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHc----------CCCCceEEeeccchhhhcccccchhhhhccc
Q 013128          253 GTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLT----------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQ  322 (449)
Q Consensus       253 GtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~----------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~  322 (449)
                      |-||||||+.+|++.||.+++++.++-.+...+...+..          -.+|.+|||||||-...              
T Consensus       336 GlGKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~--------------  401 (877)
T KOG1969|consen  336 GLGKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPR--------------  401 (877)
T ss_pred             CCChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcH--------------
Confidence            999999999999999999999999998876655543322          25799999999996431              


Q ss_pred             hhhHHHHHHHHHHhc-------Ccccc----------CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHH
Q 013128          323 EENKVTLSGLLNFID-------GLWSC----------CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQ  385 (449)
Q Consensus       323 ~~~~~~ls~LL~~ld-------g~~~~----------~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~  385 (449)
                          ..+..+|..+.       |-...          ..=.+-||+.+|..-.  |||..---+...|+|+.|......+
T Consensus       402 ----~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYa--PaLR~Lr~~A~ii~f~~p~~s~Lv~  475 (877)
T KOG1969|consen  402 ----AAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYA--PALRPLRPFAEIIAFVPPSQSRLVE  475 (877)
T ss_pred             ----HHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCccc--hhhhhcccceEEEEecCCChhHHHH
Confidence                11222222221       11000          0012578999998544  7775211467788999998876554


Q ss_pred             HHHHHhCcCC
Q 013128          386 LAFNYLGISH  395 (449)
Q Consensus       386 l~~~~l~~~~  395 (449)
                      =++.....++
T Consensus       476 RL~~IC~rE~  485 (877)
T KOG1969|consen  476 RLNEICHREN  485 (877)
T ss_pred             HHHHHHhhhc
Confidence            4444444443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.30  E-value=1.5e-10  Score=117.54  Aligned_cols=154  Identities=17%  Similarity=0.219  Sum_probs=110.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.++++|+|.++.++.+.+.+..           | ..+.++||+||+|+||+++|.++|+.+-.            
T Consensus        12 ~~~P~~~~~iiGq~~~~~~L~~~~~~-----------~-rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~   79 (365)
T PRK07471         12 APHPRETTALFGHAAAEAALLDAYRS-----------G-RLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPP   79 (365)
T ss_pred             CCCCCchhhccChHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccc
Confidence            36899999999999998888765532           1 12568999999999999999999998821            


Q ss_pred             ----------------------cEEEEecc--cc-------cChHHHHHHHHcC------CCCceEEeeccchhhhcccc
Q 013128          270 ----------------------DIYDLDLS--AV-------QSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNR  312 (449)
Q Consensus       270 ----------------------~~~~l~~s--~~-------~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~  312 (449)
                                            +++.+...  +-       -.-.+++.+....      ..+-|++|||+|.+-.    
T Consensus        80 ~~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~----  155 (365)
T PRK07471         80 PTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNA----  155 (365)
T ss_pred             cccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCH----
Confidence                                  22333221  10       0113344333222      2567999999998732    


Q ss_pred             cchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          313 ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       313 ~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                                    ...+.||..++..    ....++|++|+.++.+.|.+.+  |+ ..+.|+.|+.++..+++.....
T Consensus       156 --------------~aanaLLK~LEep----p~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~~  214 (365)
T PRK07471        156 --------------NAANALLKVLEEP----PARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAGP  214 (365)
T ss_pred             --------------HHHHHHHHHHhcC----CCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhcc
Confidence                          3556788888753    3456888899999999999887  76 6799999999998888877543

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.30  E-value=2.2e-10  Score=114.34  Aligned_cols=148  Identities=14%  Similarity=0.240  Sum_probs=107.5

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC--------CcEEEEecc-
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--------FDIYDLDLS-  277 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~--------~~~~~l~~s-  277 (449)
                      +|++++|.+.+++.+...+..            ...+..|||+||+|+|||++|+++|+.+.        .+++.+... 
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~------------~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~   69 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIK------------NRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN   69 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHc------------CCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc
Confidence            689999999988888766521            12256899999999999999999999872        245555431 


Q ss_pred             -cccChHHHHHHHHc---C---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEE
Q 013128          278 -AVQSNSELRFLLLT---M---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIV  350 (449)
Q Consensus       278 -~~~~~~~l~~~~~~---~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  350 (449)
                       .-.....++.+...   .   ...-|++||++|.+..                  ...+.||..++..    +.+.++|
T Consensus        70 ~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~------------------~a~naLLK~LEep----p~~t~~i  127 (313)
T PRK05564         70 KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTE------------------QAQNAFLKTIEEP----PKGVFII  127 (313)
T ss_pred             CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCH------------------HHHHHHHHHhcCC----CCCeEEE
Confidence             11123445554442   2   2467999999998732                  2456789998863    4567888


Q ss_pred             EEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          351 FTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       351 ~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      ++|++++.+-|.+.+  |+ ..++|+.|+.++....+...+
T Consensus       128 l~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~  165 (313)
T PRK05564        128 LLCENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKY  165 (313)
T ss_pred             EEeCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHh
Confidence            888889999999998  76 579999999998877776544

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.30  E-value=1.6e-11  Score=123.18  Aligned_cols=156  Identities=18%  Similarity=0.251  Sum_probs=104.0

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-------cEE----
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-------DIY----  272 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-------~~~----  272 (449)
                      ...+|..++|.++.|..+...+..    +         ...|+||.||+|||||++++++++.+..       +|.    
T Consensus        12 ~~~pf~~ivGq~~~k~al~~~~~~----p---------~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~   78 (350)
T CHL00081         12 PVFPFTAIVGQEEMKLALILNVID----P---------KIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPS   78 (350)
T ss_pred             CCCCHHHHhChHHHHHHHHHhccC----C---------CCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCC
Confidence            345899999999999988765532    1         2358999999999999999999888731       111    


Q ss_pred             ------------------------EEecccc---cChHH------HHHHHHc-----------CCCCceEEeeccchhhh
Q 013128          273 ------------------------DLDLSAV---QSNSE------LRFLLLT-----------MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       273 ------------------------~l~~s~~---~~~~~------l~~~~~~-----------~~~~~Il~iDeiD~l~~  308 (449)
                                              .+.+..+   .++..      +...+..           ....++|+||||+.+.+
T Consensus        79 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~~  158 (350)
T CHL00081         79 DPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDD  158 (350)
T ss_pred             ChhhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCCH
Confidence                                    0000000   01111      1122111           12468999999998853


Q ss_pred             cccccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCCCeEEEEEcCCCC-CCCccccCCCccceEEEeCCC
Q 013128          309 LQNRESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGRIIVFTTNHKE-KLDPALLRPGRMDMHLHMSYC  378 (449)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgR~d~~i~l~~p  378 (449)
                                        .+.+.|++.|+.         .....+..+++|+|.|..+ .+.++|+.  ||.+++.+.+|
T Consensus       159 ------------------~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~  218 (350)
T CHL00081        159 ------------------HLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTV  218 (350)
T ss_pred             ------------------HHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCCC
Confidence                              344557777743         2112233456667777655 59999999  99999999999


Q ss_pred             C-HHHHHHHHHHHhC
Q 013128          379 N-TSVFKQLAFNYLG  392 (449)
Q Consensus       379 ~-~~~r~~l~~~~l~  392 (449)
                      + .+.+.+|+++...
T Consensus       219 ~~~~~e~~il~~~~~  233 (350)
T CHL00081        219 KDPELRVKIVEQRTS  233 (350)
T ss_pred             CChHHHHHHHHhhhc
Confidence            8 5999999988654

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.29  E-value=1.6e-10  Score=116.65  Aligned_cols=151  Identities=15%  Similarity=0.230  Sum_probs=106.2

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc------------
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD------------  270 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~------------  270 (449)
                      .||..|+.|+|.++.++.+...+..    .        ..+..+||+||+|+|||++|..+|+.+...            
T Consensus        17 ~~P~~~~~l~Gh~~a~~~L~~a~~~----g--------rl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~   84 (351)
T PRK09112         17 PSPSENTRLFGHEEAEAFLAQAYRE----G--------KLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLAD   84 (351)
T ss_pred             CCCCchhhccCcHHHHHHHHHHHHc----C--------CCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCC
Confidence            6899999999999988877765431    1        124579999999999999999999998431            


Q ss_pred             ------------------EEEEecc--c-------ccChHHHHHH---HHcC---CCCceEEeeccchhhhcccccchhh
Q 013128          271 ------------------IYDLDLS--A-------VQSNSELRFL---LLTM---PSRSMLVIEDIDCSVKLQNRESSEV  317 (449)
Q Consensus       271 ------------------~~~l~~s--~-------~~~~~~l~~~---~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~  317 (449)
                                        ++.+...  .       .-.-..++.+   +...   ...-|++|||+|.+..         
T Consensus        85 ~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~---------  155 (351)
T PRK09112         85 PDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNR---------  155 (351)
T ss_pred             CCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCH---------
Confidence                              1112100  0       0001223322   2222   2456999999998842         


Q ss_pred             hhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHH
Q 013128          318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       318 ~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~  390 (449)
                               ...+.||..++..    +...++|+.|+.++.+.|.++.  |+ .+++++.++.++...++...
T Consensus       156 ---------~aanaLLk~LEEp----p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~  212 (351)
T PRK09112        156 ---------NAANAILKTLEEP----PARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHL  212 (351)
T ss_pred             ---------HHHHHHHHHHhcC----CCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHh
Confidence                     2456688888763    3456777777889999999988  87 68999999999999888873

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.28  E-value=8.5e-11  Score=131.44  Aligned_cols=161  Identities=16%  Similarity=0.244  Sum_probs=110.7

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~  284 (449)
                      ++.++|.+...+.|...+.....+-.   ..+ .+...+||+||||||||++|++||+.+   +..++.++++.+.....
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~---~~~-~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~  642 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLS---DPN-RPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHS  642 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhccc---CCC-CCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhh
Confidence            55788999988888888765432110   000 011358999999999999999999988   45788899887754322


Q ss_pred             HHHHH------------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-cc---
Q 013128          285 LRFLL------------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SC---  342 (449)
Q Consensus       285 l~~~~------------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~---  342 (449)
                      ...++                  ......+||+||||+.+.+                  ...+.|++.+|.-. ..   
T Consensus       643 ~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~~------------------~v~~~Ll~ile~g~l~d~~g  704 (857)
T PRK10865        643 VSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHP------------------DVFNILLQVLDDGRLTDGQG  704 (857)
T ss_pred             HHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCCH------------------HHHHHHHHHHhhCceecCCc
Confidence            22222                  1122348999999997642                  34566788776321 10   


Q ss_pred             ---CCCCeEEEEEcCCC-------------------------CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          343 ---CGEGRIIVFTTNHK-------------------------EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       343 ---~~~~~iiI~tTN~~-------------------------~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                         .-.+.+||+|||..                         ..+.|+|+.  |+|..+.+.+++.+...+|+..++.
T Consensus       705 r~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L~  780 (857)
T PRK10865        705 RTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQLQ  780 (857)
T ss_pred             eEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHHH
Confidence               01235889999972                         124578887  9999999999999999999998885

>PRK09087 hypothetical protein; Validated

Probab=99.27  E-value=4.1e-11  Score=113.93  Aligned_cols=174  Identities=14%  Similarity=0.209  Sum_probs=101.7

Q ss_pred             cccCCCCCcccccC-CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc
Q 013128          200 IVLKHPMTFKTLAL-DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA  278 (449)
Q Consensus       200 ~~~~~p~~f~~l~g-~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~  278 (449)
                      +......+|++++. ..+.  .....+..+.         +. ..+.++||||+|+|||+|++++|+..+..++..  ..
T Consensus        12 ~~~~~~~~~~~Fi~~~~N~--~a~~~l~~~~---------~~-~~~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~--~~   77 (226)
T PRK09087         12 FSHDPAYGRDDLLVTESNR--AAVSLVDHWP---------NW-PSPVVVLAGPVGSGKTHLASIWREKSDALLIHP--NE   77 (226)
T ss_pred             CCCCCCCChhceeecCchH--HHHHHHHhcc---------cC-CCCeEEEECCCCCCHHHHHHHHHHhcCCEEecH--HH
Confidence            34455578999875 3222  1333333221         11 123499999999999999999999877654433  22


Q ss_pred             ccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC
Q 013128          279 VQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK  358 (449)
Q Consensus       279 ~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~  358 (449)
                      +... .+    ... ...+|+|||+|.+..                ..   .+|...++.+...  +..+||.++..|..
T Consensus        78 ~~~~-~~----~~~-~~~~l~iDDi~~~~~----------------~~---~~lf~l~n~~~~~--g~~ilits~~~p~~  130 (226)
T PRK09087         78 IGSD-AA----NAA-AEGPVLIEDIDAGGF----------------DE---TGLFHLINSVRQA--GTSLLMTSRLWPSS  130 (226)
T ss_pred             cchH-HH----Hhh-hcCeEEEECCCCCCC----------------CH---HHHHHHHHHHHhC--CCeEEEECCCChHH
Confidence            2211 11    111 125899999997521                01   1234434333221  23444444444432


Q ss_pred             ---CCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHH-HHHccCCCHHHH
Q 013128          359 ---LDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEE-LIKEVNVTPAEV  416 (449)
Q Consensus       359 ---ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~-l~~~~~~tpa~i  416 (449)
                         ..|+|..  |+.  ..+++..|+.+.+.+++++.+...+..+.+++.. +++...-+.+++
T Consensus       131 ~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l  192 (226)
T PRK09087        131 WNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAA  192 (226)
T ss_pred             hccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHH
Confidence               3688888  774  8899999999999999999987766556554433 334334333333

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.26  E-value=9.2e-11  Score=130.89  Aligned_cols=157  Identities=20%  Similarity=0.265  Sum_probs=109.8

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChH-
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNS-  283 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~-  283 (449)
                      +.++|.++..+.|.+.+.....+-..     ...|.| +||+||||||||.+|+++|..+   ...++.++++.+.... 
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~-----~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~  640 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLED-----PRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHT  640 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCC-----CCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhh
Confidence            46789999988888888654321100     012344 8999999999999999999999   4578888887764321 


Q ss_pred             ------------------HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC--
Q 013128          284 ------------------ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC--  343 (449)
Q Consensus       284 ------------------~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~--  343 (449)
                                        .|...+. ....+||+|||||.+.+                  ...+.|++.+|.-.-..  
T Consensus       641 ~~~l~g~~~gyvg~~~~g~L~~~v~-~~p~svvllDEieka~~------------------~v~~~Llq~ld~g~l~d~~  701 (852)
T TIGR03345       641 VSRLKGSPPGYVGYGEGGVLTEAVR-RKPYSVVLLDEVEKAHP------------------DVLELFYQVFDKGVMEDGE  701 (852)
T ss_pred             hccccCCCCCcccccccchHHHHHH-hCCCcEEEEechhhcCH------------------HHHHHHHHHhhcceeecCC
Confidence                              1223332 25679999999997532                  34566888887432111  


Q ss_pred             C-----CCeEEEEEcCCCC-----------------------------CCCccccCCCccceEEEeCCCCHHHHHHHHHH
Q 013128          344 G-----EGRIIVFTTNHKE-----------------------------KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       344 ~-----~~~iiI~tTN~~~-----------------------------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                      |     .+.+||+|||-..                             .+.|+|+.  |++ .|.|.+++.++..+|+..
T Consensus       702 Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~  778 (852)
T TIGR03345       702 GREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRL  778 (852)
T ss_pred             CcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHH
Confidence            1     3578999999521                             14577777  997 788999999999999998


Q ss_pred             HhC
Q 013128          390 YLG  392 (449)
Q Consensus       390 ~l~  392 (449)
                      .+.
T Consensus       779 ~L~  781 (852)
T TIGR03345       779 KLD  781 (852)
T ss_pred             HHH
Confidence            775

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.25  E-value=2e-10  Score=128.82  Aligned_cols=160  Identities=18%  Similarity=0.268  Sum_probs=110.7

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSEL  285 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l  285 (449)
                      ..++|.+...+.+.+.+.....+-.   . ...+...+||+||||||||++|+++|..+   +.+++.++++.+......
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~---~-~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLS---D-PNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCC---C-CCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchH
Confidence            5688999888888887765432100   0 00112358999999999999999999988   468899998876543222


Q ss_pred             HHHH------------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-c-c---
Q 013128          286 RFLL------------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-S-C---  342 (449)
Q Consensus       286 ~~~~------------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~-~---  342 (449)
                      ..++                  ......+||+|||||.+.+                  .+.+.||+.+|.-. . .   
T Consensus       641 ~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~------------------~v~~~Ll~~l~~g~l~d~~g~  702 (852)
T TIGR03346       641 ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHP------------------DVFNVLLQVLDDGRLTDGQGR  702 (852)
T ss_pred             HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCH------------------HHHHHHHHHHhcCceecCCCe
Confidence            2211                  1123457999999997743                  35667888886321 1 0   


Q ss_pred             --CCCCeEEEEEcCCCCC-------------------------CCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          343 --CGEGRIIVFTTNHKEK-------------------------LDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       343 --~~~~~iiI~tTN~~~~-------------------------ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                        .-.+.+||+|||....                         +.|.|+.  |+|..+.|.+++.+....|+...+.
T Consensus       703 ~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       703 TVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             EEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence              0135689999997311                         3366666  9999999999999999999988775

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.

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

Probab=99.24  E-value=3.4e-11  Score=122.09  Aligned_cols=70  Identities=16%  Similarity=0.256  Sum_probs=51.4

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcC-CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGR-AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~-~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      .++|.++.|+.+...+....++...-..... -.+.++||+||||||||++|+++|..++.+++.++++.+
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f   86 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   86 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhh
Confidence            4789999999998777543322111111111 124789999999999999999999999999999987654

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

Probab=99.24  E-value=2e-10  Score=124.16  Aligned_cols=160  Identities=20%  Similarity=0.295  Sum_probs=118.0

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEecccccChHHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQSNSEL  285 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~~~~~l  285 (449)
                      +.++|+++..+.|.+.+..-..+-.   . ...|-..+||.||+|+|||-||+++|..+.   -.++.+|+|++.....+
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~---d-p~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsV  566 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLG---D-PNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSV  566 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCC---C-CCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHH
Confidence            4578888888888877765433211   0 011123588999999999999999999996   78999999999876666


Q ss_pred             HHHHHcC------------------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC---
Q 013128          286 RFLLLTM------------------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG---  344 (449)
Q Consensus       286 ~~~~~~~------------------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~---  344 (449)
                      .++.-.-                  ...|||+||||+..-+                  .+++-||+.||.-.-..+   
T Consensus       567 SrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHp------------------dV~nilLQVlDdGrLTD~~Gr  628 (786)
T COG0542         567 SRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHP------------------DVFNLLLQVLDDGRLTDGQGR  628 (786)
T ss_pred             HHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCH------------------HHHHHHHHHhcCCeeecCCCC
Confidence            5554332                  2358999999998643                  478889999984332222   


Q ss_pred             ----CCeEEEEEcCCCC----------------------------CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          345 ----EGRIIVFTTNHKE----------------------------KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       345 ----~~~iiI~tTN~~~----------------------------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                          .+.|||+|||--.                            ...|+|+.  |+|-.|.|.+.+.+...+|+...+.
T Consensus       629 ~VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~  706 (786)
T COG0542         629 TVDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLN  706 (786)
T ss_pred             EEecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHH
Confidence                2358999998420                            12467777  9999999999999999999998885

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.23  E-value=1.2e-10  Score=116.72  Aligned_cols=153  Identities=21%  Similarity=0.266  Sum_probs=101.1

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-------cE--------
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-------DI--------  271 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-------~~--------  271 (449)
                      .|..++|.++.|..+.-.+..+             ...++||.||||+|||++++++++.+..       ++        
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~-------------~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~   68 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDP-------------KIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPE   68 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCC-------------CCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCcc
Confidence            5889999999998876544321             1357999999999999999999988721       11        


Q ss_pred             -------------------------EEEecc----cccChHHHHHHHH-----------cCCCCceEEeeccchhhhccc
Q 013128          272 -------------------------YDLDLS----AVQSNSELRFLLL-----------TMPSRSMLVIEDIDCSVKLQN  311 (449)
Q Consensus       272 -------------------------~~l~~s----~~~~~~~l~~~~~-----------~~~~~~Il~iDeiD~l~~~~~  311 (449)
                                               .++..+    .+.....+...+.           ....+.+|+||||+.+..   
T Consensus        69 ~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~---  145 (337)
T TIGR02030        69 MMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLED---  145 (337)
T ss_pred             ccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCH---
Confidence                                     111100    1111112222211           123468999999998742   


Q ss_pred             ccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCCCeEEEEEcCCCC-CCCccccCCCccceEEEeCCCCH-
Q 013128          312 RESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGRIIVFTTNHKE-KLDPALLRPGRMDMHLHMSYCNT-  380 (449)
Q Consensus       312 ~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgR~d~~i~l~~p~~-  380 (449)
                                     .+.+.|++.|+.         .....+..+++|+|+|..+ .+.++|+.  ||.+++.+++|.. 
T Consensus       146 ---------------~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~  208 (337)
T TIGR02030       146 ---------------HLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDV  208 (337)
T ss_pred             ---------------HHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCH
Confidence                           345667777742         2222233467777777655 68999999  9999999999986 


Q ss_pred             HHHHHHHHHHhC
Q 013128          381 SVFKQLAFNYLG  392 (449)
Q Consensus       381 ~~r~~l~~~~l~  392 (449)
                      +++.+|+++...
T Consensus       209 eer~eIL~~~~~  220 (337)
T TIGR02030       209 ELRVEIVERRTE  220 (337)
T ss_pred             HHHHHHHHhhhh
Confidence            888899987543

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.22  E-value=6.2e-11  Score=120.19  Aligned_cols=70  Identities=14%  Similarity=0.267  Sum_probs=51.3

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhh-cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRI-GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~-g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      -++|.++.|+.+.-.+.....+...-..+ +-..|+++||+||||||||++++++|..++.+++.++.+.+
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~   83 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   83 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeeccee
Confidence            47899999998877666443322111111 11235789999999999999999999999999999986644

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.22  E-value=2.7e-10  Score=127.32  Aligned_cols=159  Identities=19%  Similarity=0.244  Sum_probs=108.5

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH-
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE-  284 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~-  284 (449)
                      +.++|.++..+.|.+.+.....+-.   ..++ +...+||+||||||||++|+++|+.+   +.+++.++++.+..... 
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~---~~~~-p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLK---NPNR-PIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhccc---CCCC-CceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccH
Confidence            5678888888888777654322100   0011 11348999999999999999999998   46788888887643222 


Q ss_pred             ------------------HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc----
Q 013128          285 ------------------LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC----  342 (449)
Q Consensus       285 ------------------l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----  342 (449)
                                        +...+. ....+||+|||||.+.+                  ...+.|++.+|.-.-.    
T Consensus       585 ~~l~g~~~gyvg~~~~~~l~~~~~-~~p~~VvllDeieka~~------------------~v~~~Llq~le~g~~~d~~g  645 (821)
T CHL00095        585 SKLIGSPPGYVGYNEGGQLTEAVR-KKPYTVVLFDEIEKAHP------------------DIFNLLLQILDDGRLTDSKG  645 (821)
T ss_pred             HHhcCCCCcccCcCccchHHHHHH-hCCCeEEEECChhhCCH------------------HHHHHHHHHhccCceecCCC
Confidence                              222221 23358999999998743                  3567788888842210    


Q ss_pred             ---CCCCeEEEEEcCCCCC-------------------------------------CCccccCCCccceEEEeCCCCHHH
Q 013128          343 ---CGEGRIIVFTTNHKEK-------------------------------------LDPALLRPGRMDMHLHMSYCNTSV  382 (449)
Q Consensus       343 ---~~~~~iiI~tTN~~~~-------------------------------------ld~aLlrpgR~d~~i~l~~p~~~~  382 (449)
                         .-.+.++|+|||....                                     +.|.|+.  |+|..|.|.+++.++
T Consensus       646 ~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~  723 (821)
T CHL00095        646 RTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKND  723 (821)
T ss_pred             cEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHH
Confidence               1145789999985311                                     2245666  999999999999999


Q ss_pred             HHHHHHHHhC
Q 013128          383 FKQLAFNYLG  392 (449)
Q Consensus       383 r~~l~~~~l~  392 (449)
                      ..+|+...+.
T Consensus       724 l~~Iv~~~l~  733 (821)
T CHL00095        724 VWEIAEIMLK  733 (821)
T ss_pred             HHHHHHHHHH
Confidence            9999988775

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.22  E-value=2.1e-10  Score=105.89  Aligned_cols=123  Identities=24%  Similarity=0.330  Sum_probs=88.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC------------------------cEEEEecccc-cChHHHHHHHHcC-----
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF------------------------DIYDLDLSAV-QSNSELRFLLLTM-----  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~------------------------~~~~l~~s~~-~~~~~l~~~~~~~-----  292 (449)
                      +..||||||||+|||++++++++.+..                        ++..+....- .....++.+....     
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~~   93 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQ   93 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCcc
Confidence            567999999999999999999999743                        2333333221 1223443333222     


Q ss_pred             -CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccce
Q 013128          293 -PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDM  371 (449)
Q Consensus       293 -~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~  371 (449)
                       ....|++|||+|.+..                  ...+.||..|+..    +...++|++||.+..+.+++.+  |+ .
T Consensus        94 ~~~~kviiide~~~l~~------------------~~~~~Ll~~le~~----~~~~~~il~~~~~~~l~~~i~s--r~-~  148 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNE------------------AAANALLKTLEEP----PPNTLFILITPSPEKLLPTIRS--RC-Q  148 (188)
T ss_pred             cCCeEEEEEechhhhCH------------------HHHHHHHHHhcCC----CCCeEEEEEECChHhChHHHHh--hc-E
Confidence             3467999999998743                  2345688888763    3456778888888999999998  66 4


Q ss_pred             EEEeCCCCHHHHHHHHHHH
Q 013128          372 HLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~~~  390 (449)
                      .++++.|+.++...++...
T Consensus       149 ~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       149 VLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             EeeCCCCCHHHHHHHHHHc
Confidence            7999999999988877765

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.

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

Probab=99.22  E-value=1.3e-10  Score=123.09  Aligned_cols=180  Identities=26%  Similarity=0.353  Sum_probs=130.4

Q ss_pred             cChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc------ChHHHHHHHHcC--CCCceEEee
Q 013128          230 NGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ------SNSELRFLLLTM--PSRSMLVIE  301 (449)
Q Consensus       230 ~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~------~~~~l~~~~~~~--~~~~Il~iD  301 (449)
                      ..++.++..+..++++++++||||||||++++++|++ +.....++.....      +...++..+...  ..|+|+++|
T Consensus         5 ~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d   83 (494)
T COG0464           5 KEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFID   83 (494)
T ss_pred             cCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeec
Confidence            4566778889999999999999999999999999999 5544444444332      234444444444  467999999


Q ss_pred             ccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHH
Q 013128          302 DIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTS  381 (449)
Q Consensus       302 eiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~  381 (449)
                      ++|.+.+.+..       .........++.++..+|++.  .+. ++++..||.+..+|+++.+||||+..+.++.|+..
T Consensus        84 ~~~~~~~~~~~-------~~~~~~~~v~~~l~~~~d~~~--~~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  153 (494)
T COG0464          84 EIDALAPKRSS-------DQGEVERRVVAQLLALMDGLK--RGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEA  153 (494)
T ss_pred             hhhhcccCccc-------cccchhhHHHHHHHHhccccc--CCc-eEEEeecCCccccChhHhCccccceeeecCCCCHH
Confidence            99999875443       123455678899999999987  456 88888999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHH
Q 013128          382 VFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGEL  420 (449)
Q Consensus       382 ~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l  420 (449)
                      .+.+++.................++.. .+++.+++...+
T Consensus       154 ~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~  193 (494)
T COG0464         154 GRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA  193 (494)
T ss_pred             HHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHH
Confidence            988887765543211112223333322 345556654444

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

Probab=99.21  E-value=5.8e-10  Score=113.12  Aligned_cols=154  Identities=16%  Similarity=0.232  Sum_probs=112.1

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc-----EEEEecccccChH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-----IYDLDLSAVQSNS  283 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~-----~~~l~~s~~~~~~  283 (449)
                      +.+.+-+++.+++...+..++.+..         |.++++|||||||||.+++-++.++.-.     ++++||....+..
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~---------p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~   87 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGER---------PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPY   87 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCC---------CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHH
Confidence            3488889999999999888877553         5569999999999999999999999543     8899988775432


Q ss_pred             H-------------------------HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC
Q 013128          284 E-------------------------LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG  338 (449)
Q Consensus       284 ~-------------------------l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  338 (449)
                      .                         +...+.......||+|||+|.+....            .   .++-.|+...+.
T Consensus        88 ~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~------------~---~~LY~L~r~~~~  152 (366)
T COG1474          88 QVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKD------------G---EVLYSLLRAPGE  152 (366)
T ss_pred             HHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcccc------------c---hHHHHHHhhccc
Confidence            2                         12223333457899999999997511            0   233334443332


Q ss_pred             ccccCCCCeEEEEEcCCC---CCCCccccCCCcc-ceEEEeCCCCHHHHHHHHHHHhC
Q 013128          339 LWSCCGEGRIIVFTTNHK---EKLDPALLRPGRM-DMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       339 ~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~-d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .    ...+++|+.+|..   +.+||.+.+  ++ ..+|.||+.+.+|...|+..-..
T Consensus       153 ~----~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~F~pY~a~el~~Il~~R~~  204 (366)
T COG1474         153 N----KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIVFPPYTAEELYDILRERVE  204 (366)
T ss_pred             c----ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceeeeCCCCHHHHHHHHHHHHH
Confidence            2    3457888988886   578888876  44 35689999999999999987665

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.21  E-value=1.1e-10  Score=125.27  Aligned_cols=205  Identities=19%  Similarity=0.237  Sum_probs=122.3

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      ..|..    ...|.++++|++.++..+.+...+.....        +....+.++|+||||||||++++.+|++++..++
T Consensus        72 ~pW~e----KyrP~~ldel~~~~~ki~~l~~~l~~~~~--------~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~  139 (637)
T TIGR00602        72 EPWVE----KYKPETQHELAVHKKKIEEVETWLKAQVL--------ENAPKRILLITGPSGCGKSTTIKILSKELGIQVQ  139 (637)
T ss_pred             CchHH----HhCCCCHHHhcCcHHHHHHHHHHHHhccc--------ccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHH
Confidence            46865    88999999999999988887766654322        2223456999999999999999999999987654


Q ss_pred             E-Ee---cc-----------------cc-cChHHHHHHHHc------------CCCCceEEeeccchhhhcccccchhhh
Q 013128          273 D-LD---LS-----------------AV-QSNSELRFLLLT------------MPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       273 ~-l~---~s-----------------~~-~~~~~l~~~~~~------------~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      . .+   +.                 .. .....+..++..            ...+.||+||||+.++..         
T Consensus       140 Ew~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r---------  210 (637)
T TIGR00602       140 EWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYR---------  210 (637)
T ss_pred             HHhhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchh---------
Confidence            3 11   10                 00 011222222222            235679999999987530         


Q ss_pred             hccchhhHHHHHHHHH-HhcCccccCCCCeEEEEEcCCCC--------------CCCccccCCCccceEEEeCCCCHHHH
Q 013128          319 ATNQEENKVTLSGLLN-FIDGLWSCCGEGRIIVFTTNHKE--------------KLDPALLRPGRMDMHLHMSYCNTSVF  383 (449)
Q Consensus       319 ~~~~~~~~~~ls~LL~-~ldg~~~~~~~~~iiI~tTN~~~--------------~ld~aLlrpgR~d~~i~l~~p~~~~r  383 (449)
                            ....+..+|. ....    .+.-.+|+++|..+.              .|.++++...|+ .+|.|.+.+....
T Consensus       211 ------~~~~lq~lLr~~~~e----~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l  279 (637)
T TIGR00602       211 ------DTRALHEILRWKYVS----IGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIM  279 (637)
T ss_pred             ------hHHHHHHHHHHHhhc----CCCceEEEEecCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHH
Confidence                  1113444554 2211    122223334442221              133677753455 4799999999998


Q ss_pred             HHHHHHHhCcCCCCCHHHHHHHHHccCC-CHHHHHHHHh-cCCCHHHHHHHHHHH
Q 013128          384 KQLAFNYLGISHHYLFEQIEELIKEVNV-TPAEVAGELM-KSTNAEVSLNGLVKF  436 (449)
Q Consensus       384 ~~l~~~~l~~~~~~l~~~i~~l~~~~~~-tpa~i~~~l~-~~~~~~~al~~l~~~  436 (449)
                      ++.+...+..+......       ...+ ++..+..++. ..+|...|+..|+-+
T Consensus       280 ~K~L~rIl~~E~~~~~~-------~~~~p~~~~l~~I~~~s~GDiRsAIn~LQf~  327 (637)
T TIGR00602       280 KKFLNRIVTIEAKKNGE-------KIKVPKKTSVELLCQGCSGDIRSAINSLQFS  327 (637)
T ss_pred             HHHHHHHHHhhhhcccc-------ccccCCHHHHHHHHHhCCChHHHHHHHHHHH
Confidence            88888888654221111       1112 2333433332 356888888888765

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

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

Probab=99.18  E-value=3.2e-10  Score=116.32  Aligned_cols=135  Identities=17%  Similarity=0.256  Sum_probs=80.2

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc-----EEEEecc-----
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-----IYDLDLS-----  277 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~-----~~~l~~s-----  277 (449)
                      ++++.+.++..+.+...+.               .+++++|+||||||||++|+++|+.++..     +-.+..+     
T Consensus       174 l~d~~i~e~~le~l~~~L~---------------~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySY  238 (459)
T PRK11331        174 LNDLFIPETTIETILKRLT---------------IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSY  238 (459)
T ss_pred             hhcccCCHHHHHHHHHHHh---------------cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccH
Confidence            4556666655555544432               14689999999999999999999998531     1111111     


Q ss_pred             -cc------c------ChHHHHHHHHc----CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC--
Q 013128          278 -AV------Q------SNSELRFLLLT----MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG--  338 (449)
Q Consensus       278 -~~------~------~~~~l~~~~~~----~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg--  338 (449)
                       ++      .      ....+..+...    ...++||+||||+..-.                 ...+..++..|+.  
T Consensus       239 eDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani-----------------~kiFGel~~lLE~~~  301 (459)
T PRK11331        239 EDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANL-----------------SKVFGEVMMLMEHDK  301 (459)
T ss_pred             HHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCH-----------------HHhhhhhhhhccccc
Confidence             00      0      01112222222    23689999999997532                 1122222332221  


Q ss_pred             ----------------ccccCCCCeEEEEEcCCCC----CCCccccCCCccceEEEeCC
Q 013128          339 ----------------LWSCCGEGRIIVFTTNHKE----KLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       339 ----------------~~~~~~~~~iiI~tTN~~~----~ld~aLlrpgR~d~~i~l~~  377 (449)
                                      -.-..+.++.||+|+|..+    .+|.||+|  ||.. |++.+
T Consensus       302 rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~~lD~AlrR--RF~f-i~i~p  357 (459)
T PRK11331        302 RGENWSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRR--RFSF-IDIEP  357 (459)
T ss_pred             cccccceeeeccccccccccCCCCeEEEEecCccccchhhccHHHHh--hhhe-EEecC
Confidence                            0012356789999999987    79999999  9954 66653

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.17  E-value=1.2e-10  Score=111.59  Aligned_cols=155  Identities=19%  Similarity=0.311  Sum_probs=94.4

Q ss_pred             HHHHHHHHhCceeEEeeeccccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCC
Q 013128          173 EKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPP  252 (449)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPp  252 (449)
                      ..+..+.++++..++++.- ..|.-  ....++.+|+++...++..+.++..+..+.....       ....+++|+|||
T Consensus        39 ~~~~~i~~~~~q~~~~~~~-~~s~i--~~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~-------~~~~~~~l~G~~  108 (244)
T PRK07952         39 IRSAALERENRAMKMQRTF-NRSGI--RPLHQNCSFENYRVECEGQMNALSKARQYVEEFD-------GNIASFIFSGKP  108 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HHcCC--CccccCCccccccCCCchHHHHHHHHHHHHHhhc-------cCCceEEEECCC
Confidence            3334455555444443321 12222  2345678999997665555556666666664321       013589999999


Q ss_pred             CCCHHHHHHHHHHHc---CCcEEEEecccccC---------hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhc
Q 013128          253 GTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQAT  320 (449)
Q Consensus       253 GtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~  320 (449)
                      |||||+|+.|||+++   +..++.++..++..         +.....++....+..+|+|||+++...            
T Consensus       109 GtGKThLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~~~------------  176 (244)
T PRK07952        109 GTGKNHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQTE------------  176 (244)
T ss_pred             CCCHHHHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCCCC------------
Confidence            999999999999999   67788887666532         112334555666889999999988531            


Q ss_pred             cchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          321 NQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       321 ~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                       .......+..+++.-   .   ....-+|+|||..
T Consensus       177 -s~~~~~~l~~Ii~~R---y---~~~~~tiitSNl~  205 (244)
T PRK07952        177 -SRYEKVIINQIVDRR---S---SSKRPTGMLTNSN  205 (244)
T ss_pred             -CHHHHHHHHHHHHHH---H---hCCCCEEEeCCCC
Confidence             112223444444432   1   1235678889875

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.16  E-value=8.9e-11  Score=106.79  Aligned_cols=109  Identities=25%  Similarity=0.377  Sum_probs=77.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC----cEEEEecccccC----hHHHHHHHHcCC------CCceEEeeccchhhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF----DIYDLDLSAVQS----NSELRFLLLTMP------SRSMLVIEDIDCSVK  308 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~----~~~~l~~s~~~~----~~~l~~~~~~~~------~~~Il~iDeiD~l~~  308 (449)
                      ...+||.||+|||||.||+++|..+..    +++.+|++.+..    ...+..++....      ...||+|||||...+
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~   82 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHP   82 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhccc
Confidence            456999999999999999999999996    999999999987    444555554443      346999999999875


Q ss_pred             cccccchhhhhccchhhHHHHHHHHHHhcCccccCC-------CCeEEEEEcCCCCC
Q 013128          309 LQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG-------EGRIIVFTTNHKEK  358 (449)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~-------~~~iiI~tTN~~~~  358 (449)
                      . ....      .+.....+.+.||+.||+-.-...       .+.++|+|+|--..
T Consensus        83 ~-~~~~------~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~~  132 (171)
T PF07724_consen   83 S-NSGG------ADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGAE  132 (171)
T ss_dssp             T-TTTC------SHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSSTH
T ss_pred             c-cccc------chhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccccc
Confidence            3 1111      122334567888998874322111       35789999997543

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 ....

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.16  E-value=6.6e-10  Score=111.14  Aligned_cols=63  Identities=24%  Similarity=0.303  Sum_probs=51.4

Q ss_pred             Ccc-cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-------cEEEEec
Q 013128          207 TFK-TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-------DIYDLDL  276 (449)
Q Consensus       207 ~f~-~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-------~~~~l~~  276 (449)
                      -|+ +++|+++.++++.+.+.....+.       ...++.++|+||||||||++|+++|+.++.       ++|.+..
T Consensus        48 ~F~~~~~G~~~~i~~lv~~l~~~a~g~-------~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       48 FFDHDFFGMEEAIERFVNYFKSAAQGL-------EERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             ccchhccCcHHHHHHHHHHHHHHHhcC-------CCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            466 89999999999998887666421       123567999999999999999999999976       8888866

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

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.16  E-value=4.2e-11  Score=102.23  Aligned_cols=106  Identities=25%  Similarity=0.298  Sum_probs=62.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHH--HHc-------CC---CCceEEeeccchhhhcccc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFL--LLT-------MP---SRSMLVIEDIDCSVKLQNR  312 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~--~~~-------~~---~~~Il~iDeiD~l~~~~~~  312 (449)
                      ++||+|+||+|||++|+++|..++.++..+.++.-...+++.-.  +..       ..   -..|+++|||....+    
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNrapp----   76 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRAPP----   76 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS-H----
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccCCH----
Confidence            48999999999999999999999999999987643222222200  000       01   136999999987643    


Q ss_pred             cchhhhhccchhhHHHHHHHHHHhc-------CccccCCCCeEEEEEcCCCC-----CCCccccCCCccc
Q 013128          313 ESSEVQATNQEENKVTLSGLLNFID-------GLWSCCGEGRIIVFTTNHKE-----KLDPALLRPGRMD  370 (449)
Q Consensus       313 ~~~~~~~~~~~~~~~~ls~LL~~ld-------g~~~~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d  370 (449)
                                    .+.+.||..|.       |.....++..+||+|.|..+     .|+.|++.  ||-
T Consensus        77 --------------ktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--RF~  130 (131)
T PF07726_consen   77 --------------KTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--RFM  130 (131)
T ss_dssp             --------------HHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--TSS
T ss_pred             --------------HHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--ccc
Confidence                          46778888875       33334456688999999876     68889988  873

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.

>PRK08116 hypothetical protein; Validated

Probab=99.14  E-value=1.9e-10  Score=112.07  Aligned_cols=149  Identities=18%  Similarity=0.293  Sum_probs=87.7

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN  282 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~  282 (449)
                      .+|++....++.. .+...+..+...-   .... ..+.|++|+||||||||+|+.|+|+++   +.+++.++..++...
T Consensus        82 ~tFdnf~~~~~~~-~a~~~a~~y~~~~---~~~~-~~~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~  156 (268)
T PRK08116         82 STFENFLFDKGSE-KAYKIARKYVKKF---EEMK-KENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNR  156 (268)
T ss_pred             cchhcccCChHHH-HHHHHHHHHHHHH---Hhhc-cCCceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH
Confidence            4777776444432 2333444444321   1111 224689999999999999999999997   678888876654221


Q ss_pred             ----------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          283 ----------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       283 ----------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                                .....++....+..+|+|||+.....                .......|.+.+|....   .+..+|+|
T Consensus       157 i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~~----------------t~~~~~~l~~iin~r~~---~~~~~IiT  217 (268)
T PRK08116        157 IKSTYKSSGKEDENEIIRSLVNADLLILDDLGAERD----------------TEWAREKVYNIIDSRYR---KGLPTIVT  217 (268)
T ss_pred             HHHHHhccccccHHHHHHHhcCCCEEEEecccCCCC----------------CHHHHHHHHHHHHHHHH---CCCCEEEE
Confidence                      11223444455677999999964211                11223445566665432   33467888


Q ss_pred             cCCC-CC----CCccccCCCcc---ceEEEeCCCCH
Q 013128          353 TNHK-EK----LDPALLRPGRM---DMHLHMSYCNT  380 (449)
Q Consensus       353 TN~~-~~----ld~aLlrpgR~---d~~i~l~~p~~  380 (449)
                      ||.+ +.    ++.++..  |+   ...|.++-++.
T Consensus       218 sN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        218 TNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             CCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence            8875 22    5667776  64   34456655553

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.13  E-value=1.8e-09  Score=107.59  Aligned_cols=148  Identities=18%  Similarity=0.233  Sum_probs=106.0

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC------------------
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK------------------  268 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~------------------  268 (449)
                      .|++|+|.+++++.+...+..-            ..+.+|||+||+|+||+++|.++|+.+-                  
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~------------rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~h   69 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQN------------RIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNH   69 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhC------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCC
Confidence            4889999999998887766421            1246899999999999999999999972                  


Q ss_pred             CcEEEEeccccc-----------------------ChHHHHHH---HHcC---CCCceEEeeccchhhhcccccchhhhh
Q 013128          269 FDIYDLDLSAVQ-----------------------SNSELRFL---LLTM---PSRSMLVIEDIDCSVKLQNRESSEVQA  319 (449)
Q Consensus       269 ~~~~~l~~s~~~-----------------------~~~~l~~~---~~~~---~~~~Il~iDeiD~l~~~~~~~~~~~~~  319 (449)
                      .+++.+......                       .-..++.+   +...   ...-|++||++|.+..           
T Consensus        70 PDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~-----------  138 (314)
T PRK07399         70 PDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNE-----------  138 (314)
T ss_pred             CCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCH-----------
Confidence            133433332100                       01123333   2222   2467999999998742           


Q ss_pred             ccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          320 TNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       320 ~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                             ...+.||..|+..    + ..++|++|+.++.|-|.+++  |+ ..++|+.++.++..+++.....
T Consensus       139 -------~aaNaLLK~LEEP----p-~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~  196 (314)
T PRK07399        139 -------AAANALLKTLEEP----G-NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGD  196 (314)
T ss_pred             -------HHHHHHHHHHhCC----C-CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhc
Confidence                   3456799999864    3 44778888899999999998  77 6799999999998888887643

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.12  E-value=2.6e-09  Score=107.33  Aligned_cols=146  Identities=18%  Similarity=0.299  Sum_probs=101.8

Q ss_pred             CcccccC-CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC----------------
Q 013128          207 TFKTLAL-DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF----------------  269 (449)
Q Consensus       207 ~f~~l~g-~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~----------------  269 (449)
                      .|++|.| .+.+++.+...+.    ..        ..+..||||||+|+||+++|+++|+.+..                
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~----~~--------~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~   70 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIA----KN--------RLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK   70 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHH----cC--------CCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHH
Confidence            4677887 6666666655442    11        12568999999999999999999999732                


Q ss_pred             --------cEEEEecccc-cChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          270 --------DIYDLDLSAV-QSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       270 --------~~~~l~~s~~-~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                              ++..+....- .....++.+....      ...-|++|||+|.+..                  ...+.||.
T Consensus        71 ~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~------------------~a~NaLLK  132 (329)
T PRK08058         71 RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTA------------------SAANSLLK  132 (329)
T ss_pred             HHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCH------------------HHHHHHHH
Confidence                    3444433211 1123444443322      2456999999998742                  34567999


Q ss_pred             HhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHH
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                      .|+..    ++..++|++|+.++.|-|++++  |+ ..++++.|+.++..+.++.
T Consensus       133 ~LEEP----p~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        133 FLEEP----SGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             HhcCC----CCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            99863    4567888899999999999998  76 5699999999887666654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.10  E-value=3.5e-09  Score=106.09  Aligned_cols=123  Identities=20%  Similarity=0.287  Sum_probs=92.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC------------------------cEEEEeccc---ccChHHHHHHHHcC---
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF------------------------DIYDLDLSA---VQSNSELRFLLLTM---  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~------------------------~~~~l~~s~---~~~~~~l~~~~~~~---  292 (449)
                      +.+|||+||+|+||+++|+++|+.+..                        +++.+....   .-.-..++.+....   
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~~  101 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQT  101 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhhc
Confidence            568999999999999999999999843                        556664432   12234455443332   


Q ss_pred             ---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          293 ---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       293 ---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                         ...-|++||++|.+..                  ...+.||..++..    +++.++|++|+.++.|.|.+++  |+
T Consensus       102 ~~~~~~kv~iI~~a~~m~~------------------~aaNaLLK~LEEP----p~~~~fiL~t~~~~~ll~TI~S--Rc  157 (328)
T PRK05707        102 AQLGGRKVVLIEPAEAMNR------------------NAANALLKSLEEP----SGDTVLLLISHQPSRLLPTIKS--RC  157 (328)
T ss_pred             cccCCCeEEEECChhhCCH------------------HHHHHHHHHHhCC----CCCeEEEEEECChhhCcHHHHh--hc
Confidence               2456889999998843                  3557799999863    4568899999999999999999  88


Q ss_pred             ceEEEeCCCCHHHHHHHHHHH
Q 013128          370 DMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       370 d~~i~l~~p~~~~r~~l~~~~  390 (449)
                      . .+.|+.|+.++..+.+...
T Consensus       158 ~-~~~~~~~~~~~~~~~L~~~  177 (328)
T PRK05707        158 Q-QQACPLPSNEESLQWLQQA  177 (328)
T ss_pred             e-eeeCCCcCHHHHHHHHHHh
Confidence            4 4999999998877776654

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.10  E-value=6.2e-09  Score=103.78  Aligned_cols=142  Identities=19%  Similarity=0.246  Sum_probs=98.3

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---------------------
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------------------  268 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---------------------  268 (449)
                      ++++.+.....+........+           .+..+||+||||||||++|.++|+++.                     
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~-----------~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~   70 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGR-----------LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPA   70 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCC-----------CCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhh
Confidence            455555555555554443221           133699999999999999999999997                     


Q ss_pred             ---CcEEEEecccccCh----HHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHH
Q 013128          269 ---FDIYDLDLSAVQSN----SELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNF  335 (449)
Q Consensus       269 ---~~~~~l~~s~~~~~----~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~  335 (449)
                         .+++.++.++....    ..++.+....      ...-|++|||+|.+..                  ...+.|+..
T Consensus        71 ~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~------------------~A~nallk~  132 (325)
T COG0470          71 GNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTE------------------DAANALLKT  132 (325)
T ss_pred             cCCCceEEecccccCCCcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhH------------------HHHHHHHHH
Confidence               68899998887652    3344333322      2457999999999853                  234557777


Q ss_pred             hcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHH
Q 013128          336 IDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLA  387 (449)
Q Consensus       336 ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~  387 (449)
                      +..-    +....+|++||.++.+-|.+.+  |+ ..+.|+.|+...+....
T Consensus       133 lEep----~~~~~~il~~n~~~~il~tI~S--Rc-~~i~f~~~~~~~~i~~~  177 (325)
T COG0470         133 LEEP----PKNTRFILITNDPSKILPTIRS--RC-QRIRFKPPSRLEAIAWL  177 (325)
T ss_pred             hccC----CCCeEEEEEcCChhhccchhhh--cc-eeeecCCchHHHHHHHh
Confidence            7643    4567889999999999998888  76 55888776554444333

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.09  E-value=6.1e-10  Score=115.12  Aligned_cols=128  Identities=19%  Similarity=0.233  Sum_probs=81.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEecc-----cccChHHHHH-----HHHc-----CCCCceEEeeccch
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLS-----AVQSNSELRF-----LLLT-----MPSRSMLVIEDIDC  305 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s-----~~~~~~~l~~-----~~~~-----~~~~~Il~iDeiD~  305 (449)
                      ..++||+||||||||++|++++..++.  ++..+.+.     ++.....+..     .+..     .....+||+|||..
T Consensus        39 g~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~r  118 (498)
T PRK13531         39 GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWK  118 (498)
T ss_pred             CCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeeccccc
Confidence            457999999999999999999998753  23322221     1111111111     1111     11234999999986


Q ss_pred             hhhcccccchhhhhccchhhHHHHHHHHHHhc-CccccCC-----CCeEEEEEcCCCCC---CCccccCCCccceEEEeC
Q 013128          306 SVKLQNRESSEVQATNQEENKVTLSGLLNFID-GLWSCCG-----EGRIIVFTTNHKEK---LDPALLRPGRMDMHLHMS  376 (449)
Q Consensus       306 l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld-g~~~~~~-----~~~iiI~tTN~~~~---ld~aLlrpgR~d~~i~l~  376 (449)
                      +.                  ..+.+.||..|. +.....+     ..+++++|||....   ..+|+..  ||-+.+.+|
T Consensus       119 as------------------p~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RFliri~vp  178 (498)
T PRK13531        119 AG------------------PAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RMLIRLWLD  178 (498)
T ss_pred             CC------------------HHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hEEEEEECC
Confidence            53                  256788998884 3222111     23577778885322   3358999  999999999


Q ss_pred             CCC-HHHHHHHHHHH
Q 013128          377 YCN-TSVFKQLAFNY  390 (449)
Q Consensus       377 ~p~-~~~r~~l~~~~  390 (449)
                      +|+ .++++.|+...
T Consensus       179 ~l~~~~~e~~lL~~~  193 (498)
T PRK13531        179 KVQDKANFRSMLTSQ  193 (498)
T ss_pred             CCCchHHHHHHHHcc
Confidence            997 57778888764

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.07  E-value=1.1e-09  Score=93.71  Aligned_cols=118  Identities=25%  Similarity=0.344  Sum_probs=71.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc---EEEEecccccC--------------------hHHHHHHHHcC--CCCce
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSAVQS--------------------NSELRFLLLTM--PSRSM  297 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~~~~--------------------~~~l~~~~~~~--~~~~I  297 (449)
                      +..++|+||||||||++++++|..+...   ++.++++....                    .......+...  ..+.|
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            4679999999999999999999999775   88887765422                    12222222222  23699


Q ss_pred             EEeeccchhhhcccccchhhhhccchhhHHHHHHH--HHHhcCccccCCCCeEEEEEcCC-CCCCCccccCCCccceEEE
Q 013128          298 LVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGL--LNFIDGLWSCCGEGRIIVFTTNH-KEKLDPALLRPGRMDMHLH  374 (449)
Q Consensus       298 l~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~L--L~~ldg~~~~~~~~~iiI~tTN~-~~~ld~aLlrpgR~d~~i~  374 (449)
                      |+|||++.+.....              .......  .......  .......+|+++|. ....+..+.+  |++.++.
T Consensus        82 iiiDei~~~~~~~~--------------~~~~~~~~~~~~~~~~--~~~~~~~~i~~~~~~~~~~~~~~~~--~~~~~~~  143 (148)
T smart00382       82 LILDEITSLLDAEQ--------------EALLLLLEELRLLLLL--KSEKNLTVILTTNDEKDLGPALLRR--RFDRRIV  143 (148)
T ss_pred             EEEECCcccCCHHH--------------HHHHHhhhhhHHHHHH--HhcCCCEEEEEeCCCccCchhhhhh--ccceEEE
Confidence            99999998864111              0000000  0000000  11245688888886 3334444444  8888888


Q ss_pred             eCCC
Q 013128          375 MSYC  378 (449)
Q Consensus       375 l~~p  378 (449)
                      ++.+
T Consensus       144 ~~~~  147 (148)
T smart00382      144 LLLI  147 (148)
T ss_pred             ecCC
Confidence            7654

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.

>PRK08181 transposase; Validated

Probab=99.06  E-value=6.3e-10  Score=108.21  Aligned_cols=124  Identities=17%  Similarity=0.299  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHHHHHHHhCceeEEeeeccccccccccccCCCCCcccccCC--HHHHHHHH---HHHHHHHcChhHHhhh
Q 013128          164 LNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALD--SELKREIT---EDLENFMNGKEYYTRI  238 (449)
Q Consensus       164 ~~~yl~~v~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~p~~f~~l~g~--~~~k~~i~---~~l~~~~~~~~~~~~~  238 (449)
                      ...||..+++.....+++++..+....         ..+..+.+|+++.-.  +.+.+...   ..+..|+.        
T Consensus        42 ~~e~L~~ll~~E~~~R~~~~~~r~lk~---------A~~p~~~tle~fd~~~~~~~~~~~~~~L~~~~~~~~--------  104 (269)
T PRK08181         42 AARFLAAIAEHELAERARRRIERHLAE---------AHLPPGKTLDSFDFEAVPMVSKAQVMAIAAGDSWLA--------  104 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---------CCCCCCCCHhhCCccCCCCCCHHHHHHHHHHHHHHh--------
Confidence            456788888877776665544322211         112233455554221  11112222   22223332        


Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-------hHHHHHHHHcCCCCceEEeeccchhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-------NSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-------~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                         ...+++|+||||||||+|+.|+|+++   |+.++.++..++..       +..+...+....+..+|+|||++...
T Consensus       105 ---~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~  180 (269)
T PRK08181        105 ---KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVT  180 (269)
T ss_pred             ---cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEecccccc
Confidence               24689999999999999999999876   67777777655432       12334456666788999999998753

>smart00350 MCM minichromosome maintenance proteins

Probab=99.06  E-value=1.3e-09  Score=115.65  Aligned_cols=160  Identities=16%  Similarity=0.193  Sum_probs=98.8

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhc--CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE----ecccccCh-
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIG--RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL----DLSAVQSN-  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g--~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l----~~s~~~~~-  282 (449)
                      .+.|.+.+|..+.-.+   +.+......-|  +....++||+|+||||||++++++++......+..    ++..+... 
T Consensus       204 ~i~G~~~~k~~l~l~l---~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~~~  280 (509)
T smart00350      204 SIYGHEDIKKAILLLL---FGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAV  280 (509)
T ss_pred             cccCcHHHHHHHHHHH---hCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccccc
Confidence            4677788777665433   22211000001  11123599999999999999999999886554432    11112110 


Q ss_pred             ------H--HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCC
Q 013128          283 ------S--ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGE  345 (449)
Q Consensus       283 ------~--~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~  345 (449)
                            .  .+..-........+++|||+|.+..                  .+.+.|+..|+.         .....+.
T Consensus       281 ~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~~------------------~~q~~L~e~me~~~i~i~k~G~~~~l~~  342 (509)
T smart00350      281 TRDPETREFTLEGGALVLADNGVCCIDEFDKMDD------------------SDRTAIHEAMEQQTISIAKAGITTTLNA  342 (509)
T ss_pred             eEccCcceEEecCccEEecCCCEEEEechhhCCH------------------HHHHHHHHHHhcCEEEEEeCCEEEEecC
Confidence                  0  0000011123578999999998743                  234556666643         2222234


Q ss_pred             CeEEEEEcCCCC-------------CCCccccCCCccceEEEe-CCCCHHHHHHHHHHHhC
Q 013128          346 GRIIVFTTNHKE-------------KLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       346 ~~iiI~tTN~~~-------------~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~~l~  392 (449)
                      ...||+|+|..+             .|++++++  |||..+.+ ++|+.+..+.|+++.+.
T Consensus       343 ~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      343 RCSVLAAANPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             CcEEEEEeCCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHHH
Confidence            567899999763             58999999  99886555 88999999999998764

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.05  E-value=7.5e-10  Score=120.34  Aligned_cols=153  Identities=19%  Similarity=0.212  Sum_probs=102.9

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-------------------
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-------------------  267 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-------------------  267 (449)
                      .|..|+|.+..|..+.-.+.    .+.         ..||||.||||||||++|+++++.+                   
T Consensus         2 pf~~ivGq~~~~~al~~~av----~~~---------~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~   68 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAV----DPR---------IGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPE   68 (633)
T ss_pred             CcchhcChHHHHHHHHHHhh----CCC---------CCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCcc
Confidence            57899999988876643322    111         2479999999999999999999998                   


Q ss_pred             ----------------CCcEEEEeccccc----ChHHHHHHHH-----------cCCCCceEEeeccchhhhcccccchh
Q 013128          268 ----------------KFDIYDLDLSAVQ----SNSELRFLLL-----------TMPSRSMLVIEDIDCSVKLQNRESSE  316 (449)
Q Consensus       268 ----------------~~~~~~l~~s~~~----~~~~l~~~~~-----------~~~~~~Il~iDeiD~l~~~~~~~~~~  316 (449)
                                      ..+++.+.++...    ....+...+.           ......|||||||+.+..        
T Consensus        69 ~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~--------  140 (633)
T TIGR02442        69 EWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDD--------  140 (633)
T ss_pred             ccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCH--------
Confidence                            2456665544321    1112222221           112457999999998843        


Q ss_pred             hhhccchhhHHHHHHHHHHhcCc---------cccCCCCeEEEEEcCCC-CCCCccccCCCccceEEEeCCCC-HHHHHH
Q 013128          317 VQATNQEENKVTLSGLLNFIDGL---------WSCCGEGRIIVFTTNHK-EKLDPALLRPGRMDMHLHMSYCN-TSVFKQ  385 (449)
Q Consensus       317 ~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~-~~ld~aLlrpgR~d~~i~l~~p~-~~~r~~  385 (449)
                                .+++.|++.|+.-         .......+++|+|+|.. ..+.++|+.  ||+++|.++++. .+++.+
T Consensus       141 ----------~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~  208 (633)
T TIGR02442       141 ----------HLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEERVE  208 (633)
T ss_pred             ----------HHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHHHHH
Confidence                      3556688887521         11112346888888864 358899999  999999999886 477788


Q ss_pred             HHHHHhC
Q 013128          386 LAFNYLG  392 (449)
Q Consensus       386 l~~~~l~  392 (449)
                      ++...+.
T Consensus       209 il~~~~~  215 (633)
T TIGR02442       209 IIRRRLA  215 (633)
T ss_pred             HHHHHHh
Confidence            8876544

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

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

Probab=99.04  E-value=1.3e-09  Score=118.10  Aligned_cols=201  Identities=19%  Similarity=0.198  Sum_probs=130.2

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEe
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLD  275 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~  275 (449)
                      -.+|.++|-++..+++++.|.+..             +++-+|.|+||+|||.++..+|...          +..++.+|
T Consensus       167 gklDPvIGRd~EI~r~iqIL~RR~-------------KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD  233 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSRRT-------------KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLD  233 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhccC-------------CCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEec
Confidence            357889999999898888875433             4678999999999999999999988          57899999


Q ss_pred             cccccC--------hHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          276 LSAVQS--------NSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       276 ~s~~~~--------~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      ++.+..        +..++.++....  .+.|||||||+.+.+.....+. .        .-.-+-|...+.     .|+
T Consensus       234 ~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~-a--------~DAaNiLKPaLA-----RGe  299 (786)
T COG0542         234 LGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGG-A--------MDAANLLKPALA-----RGE  299 (786)
T ss_pred             HHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCccccc-c--------cchhhhhHHHHh-----cCC
Confidence            888854        344555554432  3899999999999875443221 0        011122333332     233


Q ss_pred             CeEEEEEcCCC----CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC--CCC--CHHHHHHHHHccCCCHHHHH
Q 013128          346 GRIIVFTTNHK----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHY--LFEQIEELIKEVNVTPAEVA  417 (449)
Q Consensus       346 ~~iiI~tTN~~----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~--~~~--l~~~i~~l~~~~~~tpa~i~  417 (449)
                      -++|-+||-.-    =.=|+||-|  ||. .|.+..|+.++-..|++-.-...  +|.  +.++.-       ...++++
T Consensus       300 L~~IGATT~~EYRk~iEKD~AL~R--RFQ-~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al-------~aAv~LS  369 (786)
T COG0542         300 LRCIGATTLDEYRKYIEKDAALER--RFQ-KVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEAL-------VAAVTLS  369 (786)
T ss_pred             eEEEEeccHHHHHHHhhhchHHHh--cCc-eeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHH-------HHHHHHH
Confidence            34444455221    123899999  994 69999999999888887433321  222  222211       1223344


Q ss_pred             HHHhcC-CCHHHHHHHHHHHHHHHHHh
Q 013128          418 GELMKS-TNAEVSLNGLVKFLHAKMTQ  443 (449)
Q Consensus       418 ~~l~~~-~~~~~al~~l~~~l~~~~~~  443 (449)
                      ...+.+ .-|+.|++-+.++....+..
T Consensus       370 ~RYI~dR~LPDKAIDLiDeA~a~~~l~  396 (786)
T COG0542         370 DRYIPDRFLPDKAIDLLDEAGARVRLE  396 (786)
T ss_pred             HhhcccCCCCchHHHHHHHHHHHHHhc
Confidence            444433 36888888888877777664

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

Probab=99.04  E-value=1.6e-09  Score=100.64  Aligned_cols=187  Identities=16%  Similarity=0.261  Sum_probs=110.2

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-C----CcEEEE
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-K----FDIYDL  274 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~----~~~~~l  274 (449)
                      +..++|..+.+++|.++..+.+.-.    .+...         -.++++.||||||||+-+.++|++| |    --+..+
T Consensus        18 VeKYrP~~l~dIVGNe~tv~rl~vi----a~~gn---------mP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLEL   84 (333)
T KOG0991|consen   18 VEKYRPSVLQDIVGNEDTVERLSVI----AKEGN---------MPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLEL   84 (333)
T ss_pred             HHhhCchHHHHhhCCHHHHHHHHHH----HHcCC---------CCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhc
Confidence            4489999999999999887665432    22111         2469999999999999999999998 3    245677


Q ss_pred             ecccccChHHHH---HHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          275 DLSAVQSNSELR---FLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       275 ~~s~~~~~~~l~---~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      +.|+-....-.+   ..|+...      ..-||++||.|.+..               ..+..   |-..|+ +++   .
T Consensus        85 NASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~---------------gAQQA---lRRtME-iyS---~  142 (333)
T KOG0991|consen   85 NASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTA---------------GAQQA---LRRTME-IYS---N  142 (333)
T ss_pred             cCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhh---------------HHHHH---HHHHHH-HHc---c
Confidence            777765544333   2333321      345999999998753               11112   222222 222   1


Q ss_pred             CeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHHHHh-cCC
Q 013128          346 GRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELM-KST  424 (449)
Q Consensus       346 ~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~~l~-~~~  424 (449)
                      ..-+.+++|..+++=+.+.+  |+.. +.+...+.++...-+.....             .++..+|+.-+..++. ..+
T Consensus       143 ttRFalaCN~s~KIiEPIQS--RCAi-LRysklsd~qiL~Rl~~v~k-------------~Ekv~yt~dgLeaiifta~G  206 (333)
T KOG0991|consen  143 TTRFALACNQSEKIIEPIQS--RCAI-LRYSKLSDQQILKRLLEVAK-------------AEKVNYTDDGLEAIIFTAQG  206 (333)
T ss_pred             cchhhhhhcchhhhhhhHHh--hhHh-hhhcccCHHHHHHHHHHHHH-------------HhCCCCCcchHHHhhhhccc
Confidence            23456678887777666666  5532 45555565543333332222             2334455544433333 234


Q ss_pred             CHHHHHHHHHHHH
Q 013128          425 NAEVSLNGLVKFL  437 (449)
Q Consensus       425 ~~~~al~~l~~~l  437 (449)
                      |-.+||++|+.-+
T Consensus       207 DMRQalNnLQst~  219 (333)
T KOG0991|consen  207 DMRQALNNLQSTV  219 (333)
T ss_pred             hHHHHHHHHHHHh
Confidence            6666666665544

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.03  E-value=4.4e-09  Score=105.53  Aligned_cols=154  Identities=18%  Similarity=0.171  Sum_probs=105.7

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNS  283 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~  283 (449)
                      .|++++|.....+.+++.+......           ...|||.|++||||+++|++|-...   +.+++.++|..+..+ 
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~-----------~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~~-   71 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPL-----------DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN-   71 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCHH-
Confidence            4678999988888888888777643           3579999999999999999998766   368999999987532 


Q ss_pred             HHHH-HH-----------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC
Q 013128          284 ELRF-LL-----------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG  344 (449)
Q Consensus       284 ~l~~-~~-----------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~  344 (449)
                      .+.. +|                 ......+.|||||||.+..                  .....|++.++.-. ...+
T Consensus        72 ~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~------------------~~Q~~L~~~l~~~~~~~~g  133 (326)
T PRK11608         72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM------------------LVQEKLLRVIEYGELERVG  133 (326)
T ss_pred             HHHHHHccccccccCCcccccCCchhccCCCeEEeCChhhCCH------------------HHHHHHHHHHhcCcEEeCC
Confidence            2222 11                 1233568899999999853                  23345666665321 1111


Q ss_pred             ------CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          345 ------EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       345 ------~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                            ..+-||+||+..       ..+.+.|..  |+ ..+|++|+...  ++...|+..|+.
T Consensus       134 ~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl~  195 (326)
T PRK11608        134 GSQPLQVNVRLVCATNADLPAMVAEGKFRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFAI  195 (326)
T ss_pred             CCceeeccEEEEEeCchhHHHHHHcCCchHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHHH
Confidence                  135677777653       345566776  77 56888888765  566777777764

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.01  E-value=1.9e-08  Score=100.96  Aligned_cols=124  Identities=18%  Similarity=0.198  Sum_probs=90.4

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCC-------------------------cEEEEeccc------------------
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKF-------------------------DIYDLDLSA------------------  278 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~-------------------------~~~~l~~s~------------------  278 (449)
                      .+.+|||+||+|+||+++|.++|+.+..                         +++.+....                  
T Consensus        20 l~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~~   99 (342)
T PRK06964         20 LPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADAD   99 (342)
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccchhh
Confidence            3678999999999999999999998833                         233332211                  


Q ss_pred             -----------ccChHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          279 -----------VQSNSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       279 -----------~~~~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                                 .-.-.+++.+.....      ..-|++||++|.+..                  ..-+.||..++..  
T Consensus       100 ~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~------------------~AaNaLLKtLEEP--  159 (342)
T PRK06964        100 EGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNV------------------AAANALLKTLEEP--  159 (342)
T ss_pred             cccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcCH------------------HHHHHHHHHhcCC--
Confidence                       011234444433321      345888899888743                  3567799999863  


Q ss_pred             cCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHH
Q 013128          342 CCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~  390 (449)
                        +.++++|++|++++.|.|.+++  |+ ..+.|+.|+.++..+.+...
T Consensus       160 --p~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        160 --PPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             --CcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence              5678999999999999999999  88 68999999998888777653

>PRK12377 putative replication protein; Provisional

Probab=99.01  E-value=2.2e-09  Score=103.24  Aligned_cols=136  Identities=19%  Similarity=0.249  Sum_probs=82.3

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ...+|++....++..+.+...+..+...-.   .    ...+++|+||||||||+|+.|||+++   +..++.+...++.
T Consensus        69 ~~~tFdnf~~~~~~~~~a~~~a~~~a~~~~---~----~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~  141 (248)
T PRK12377         69 RKCSFANYQVQNDGQRYALSQAKSIADELM---T----GCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVM  141 (248)
T ss_pred             ccCCcCCcccCChhHHHHHHHHHHHHHHHH---h----cCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHH
Confidence            344788876543333334444444433211   1    13689999999999999999999998   5677777665553


Q ss_pred             Ch--------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 SN--------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~~--------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      ..        ......+....+..+|+|||++....             .....   ..|.+.+|.-..   ...-+|+|
T Consensus       142 ~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~~~-------------s~~~~---~~l~~ii~~R~~---~~~ptiit  202 (248)
T PRK12377        142 SRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQRE-------------TKNEQ---VVLNQIIDRRTA---SMRSVGML  202 (248)
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCCC-------------CHHHH---HHHHHHHHHHHh---cCCCEEEE
Confidence            21        12334566677889999999976421             11122   234455554322   23457889


Q ss_pred             cCCC-----CCCCccccC
Q 013128          353 TNHK-----EKLDPALLR  365 (449)
Q Consensus       353 TN~~-----~~ld~aLlr  365 (449)
                      ||..     +.++.+++.
T Consensus       203 SNl~~~~l~~~~~~ri~d  220 (248)
T PRK12377        203 TNLNHEAMSTLLGERVMD  220 (248)
T ss_pred             cCCCHHHHHHHhhHHHHH
Confidence            9975     234455555

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.99  E-value=9.2e-09  Score=110.07  Aligned_cols=157  Identities=17%  Similarity=0.184  Sum_probs=105.9

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ...+|+.++|.....+.+++.+......           ...+||+|++||||+++|++|....   +.+++.++|..+.
T Consensus       191 ~~~~~~~liG~s~~~~~~~~~~~~~a~~-----------~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~  259 (534)
T TIGR01817       191 RSGKEDGIIGKSPAMRQVVDQARVVARS-----------NSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALS  259 (534)
T ss_pred             ccCccCceEECCHHHHHHHHHHHHHhCc-----------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCC
Confidence            3457999999999999998888776542           3579999999999999999999886   5699999999885


Q ss_pred             ChHHHHH-HHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc-cc
Q 013128          281 SNSELRF-LLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL-WS  341 (449)
Q Consensus       281 ~~~~l~~-~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-~~  341 (449)
                      .. .+.. +|.                 .....++|||||||.+..                  .....|+..++.- ..
T Consensus       260 ~~-~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~------------------~~Q~~Ll~~l~~~~~~  320 (534)
T TIGR01817       260 ET-LLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISP------------------AFQAKLLRVLQEGEFE  320 (534)
T ss_pred             HH-HHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCH------------------HHHHHHHHHHhcCcEE
Confidence            42 2222 211                 123568999999999853                  2334567777532 11


Q ss_pred             cCCC------CeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCC--HHHHHHHHHHHhC
Q 013128          342 CCGE------GRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCN--TSVFKQLAFNYLG  392 (449)
Q Consensus       342 ~~~~------~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~--~~~r~~l~~~~l~  392 (449)
                      ..++      .+-+|+||+..       ..+.+.|..  |+ ...|.+|+..  .++...|+..|+.
T Consensus       321 ~~~~~~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLreR~eDi~~L~~~~l~  385 (534)
T TIGR01817       321 RVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYY--RINVVPIFLPPLRERREDIPLLAEAFLE  385 (534)
T ss_pred             ECCCCceEeecEEEEEeCCCCHHHHHHcCCCCHHHHH--HhcCCeeeCCCcccccccHHHHHHHHHH
Confidence            1111      35567776653       123334433  44 3578888876  4667777777775

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.

>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=98.98  E-value=8.7e-09  Score=92.95  Aligned_cols=111  Identities=20%  Similarity=0.300  Sum_probs=80.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC-----------------------CcEEEEecccc---cChHHHHHHHHcCC---
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK-----------------------FDIYDLDLSAV---QSNSELRFLLLTMP---  293 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~-----------------------~~~~~l~~s~~---~~~~~l~~~~~~~~---  293 (449)
                      +..+||+||+|+||+++|.++|+.+-                       .+++.++....   .....++.+.....   
T Consensus        19 ~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~   98 (162)
T PF13177_consen   19 PHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSP   98 (162)
T ss_dssp             -SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHHH
Confidence            56799999999999999999999881                       35666665543   23455665555442   


Q ss_pred             ---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccc
Q 013128          294 ---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD  370 (449)
Q Consensus       294 ---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d  370 (449)
                         ..-|++|||+|.+..                  ...+.||..|+..    +...++|++|+.++.|-|.+++  |+ 
T Consensus        99 ~~~~~KviiI~~ad~l~~------------------~a~NaLLK~LEep----p~~~~fiL~t~~~~~il~TI~S--Rc-  153 (162)
T PF13177_consen   99 SEGKYKVIIIDEADKLTE------------------EAQNALLKTLEEP----PENTYFILITNNPSKILPTIRS--RC-  153 (162)
T ss_dssp             TTSSSEEEEEETGGGS-H------------------HHHHHHHHHHHST----TTTEEEEEEES-GGGS-HHHHT--TS-
T ss_pred             hcCCceEEEeehHhhhhH------------------HHHHHHHHHhcCC----CCCEEEEEEECChHHChHHHHh--hc-
Confidence               356999999998843                  4567899999874    4678999999999999999998  77 


Q ss_pred             eEEEeCCC
Q 013128          371 MHLHMSYC  378 (449)
Q Consensus       371 ~~i~l~~p  378 (449)
                      ..+.|+..
T Consensus       154 ~~i~~~~l  161 (162)
T PF13177_consen  154 QVIRFRPL  161 (162)
T ss_dssp             EEEEE---
T ss_pred             eEEecCCC
Confidence            55777654

...

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.98  E-value=1.4e-08  Score=101.93  Aligned_cols=168  Identities=18%  Similarity=0.137  Sum_probs=106.0

Q ss_pred             cCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHH-H
Q 013128          212 ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELR-F  287 (449)
Q Consensus       212 ~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~-~  287 (449)
                      +|.....+.+++.+......           ...+||.|++||||+++|++|....   +.+++.++|..+... .+. .
T Consensus         2 iG~S~~m~~~~~~~~~~a~~-----------~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~-~l~~~   69 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPL-----------DRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSEN-LLDSE   69 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChH-HHHHH
Confidence            45555666677766655432           3579999999999999999998776   469999999987532 222 2


Q ss_pred             HH-----------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-cc------C
Q 013128          288 LL-----------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SC------C  343 (449)
Q Consensus       288 ~~-----------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~------~  343 (449)
                      +|                 ......+.|||||||.+..                  .....|+..++.-. ..      .
T Consensus        70 lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~------------------~~Q~~Ll~~l~~~~~~~~g~~~~~  131 (329)
T TIGR02974        70 LFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASL------------------LVQEKLLRVIEYGEFERVGGSQTL  131 (329)
T ss_pred             HhccccccccCcccccCCchhhCCCCEEEeCChHhCCH------------------HHHHHHHHHHHcCcEEecCCCcee
Confidence            22                 1233578999999998843                  23344666664211 11      1


Q ss_pred             CCCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCC--HHHHHHHHHHHhCcC------C--CCCHHHHHHH
Q 013128          344 GEGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCN--TSVFKQLAFNYLGIS------H--HYLFEQIEEL  405 (449)
Q Consensus       344 ~~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~--~~~r~~l~~~~l~~~------~--~~l~~~i~~l  405 (449)
                      ...+-||++||..       ..+.+.|..  |+ ...|++|+..  .++...|+..|+...      .  ..+.++..+.
T Consensus       132 ~~~~RiI~at~~~l~~~~~~g~fr~dL~~--rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~  209 (329)
T TIGR02974       132 QVDVRLVCATNADLPALAAEGRFRADLLD--RLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQ  209 (329)
T ss_pred             ccceEEEEechhhHHHHhhcCchHHHHHH--HhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHH
Confidence            1235677777653       234566666  67 4578888877  467777777776531      1  2355555555


Q ss_pred             HHccCC
Q 013128          406 IKEVNV  411 (449)
Q Consensus       406 ~~~~~~  411 (449)
                      +....|
T Consensus       210 L~~y~W  215 (329)
T TIGR02974       210 LLEYHW  215 (329)
T ss_pred             HHhCCC
Confidence            555544

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.98  E-value=2.7e-09  Score=105.84  Aligned_cols=97  Identities=23%  Similarity=0.357  Sum_probs=67.7

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~  281 (449)
                      ..+|+++...+..+..+......|+...   .. + +..+|++||||||||||+|+.|||+++   |..+..+....+..
T Consensus       123 ~atf~~~~~~~~~~~~~~~~~~~fi~~~---~~-~-~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~  197 (306)
T PRK08939        123 QASLADIDLDDRDRLDALMAALDFLEAY---PP-G-EKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIR  197 (306)
T ss_pred             cCcHHHhcCCChHHHHHHHHHHHHHHHh---hc-c-CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHH
Confidence            4678888766545555555555555422   11 1 235799999999999999999999999   67777776555421


Q ss_pred             -------hHHHHHHHHcCCCCceEEeeccchh
Q 013128          282 -------NSELRFLLLTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       282 -------~~~l~~~~~~~~~~~Il~iDeiD~l  306 (449)
                             ...+...+....+..+|+||||..-
T Consensus       198 ~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e  229 (306)
T PRK08939        198 ELKNSISDGSVKEKIDAVKEAPVLMLDDIGAE  229 (306)
T ss_pred             HHHHHHhcCcHHHHHHHhcCCCEEEEecCCCc
Confidence                   1234456666778999999999864

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.97  E-value=9.1e-09  Score=108.68  Aligned_cols=210  Identities=16%  Similarity=0.239  Sum_probs=123.3

Q ss_pred             ccccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          191 MHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       191 ~~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      +...|..    ...|.+.++|+......++|..++...+.        +....+-+||+||||||||++++.+|+++++.
T Consensus         5 ~~~~W~~----ky~P~~~~eLavhkkKv~eV~~wl~~~~~--------~~~~~~iLlLtGP~G~GKtttv~~La~elg~~   72 (519)
T PF03215_consen    5 ESEPWVE----KYAPKTLDELAVHKKKVEEVRSWLEEMFS--------GSSPKRILLLTGPSGCGKTTTVKVLAKELGFE   72 (519)
T ss_pred             ccCccch----hcCCCCHHHhhccHHHHHHHHHHHHHHhc--------cCCCcceEEEECCCCCCHHHHHHHHHHHhCCe
Confidence            4567865    88999999999998888888888876443        22334568899999999999999999999988


Q ss_pred             EEEEe-cccc----------cC----h----H---HHHHH-HHc-------------CCCCceEEeeccchhhhcccccc
Q 013128          271 IYDLD-LSAV----------QS----N----S---ELRFL-LLT-------------MPSRSMLVIEDIDCSVKLQNRES  314 (449)
Q Consensus       271 ~~~l~-~s~~----------~~----~----~---~l~~~-~~~-------------~~~~~Il~iDeiD~l~~~~~~~~  314 (449)
                      +.+-. ...+          .+    .    +   .+..+ +..             ..++.||+|||+-.++.      
T Consensus        73 v~Ew~np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~------  146 (519)
T PF03215_consen   73 VQEWINPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFH------  146 (519)
T ss_pred             eEEecCCCCccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccc------
Confidence            87642 2221          00    0    0   11111 111             12467999999986653      


Q ss_pred             hhhhhccchhhHHHHHHHHHHhcCccccCCC-CeEEEEEc-------CCCC--------CCCccccCCCccceEEEeCCC
Q 013128          315 SEVQATNQEENKVTLSGLLNFIDGLWSCCGE-GRIIVFTT-------NHKE--------KLDPALLRPGRMDMHLHMSYC  378 (449)
Q Consensus       315 ~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~-~~iiI~tT-------N~~~--------~ld~aLlrpgR~d~~i~l~~p  378 (449)
                              ......-..|..++..-    .. .+|||.|-       |...        .+++.++.-.++ .+|.|-+.
T Consensus       147 --------~~~~~f~~~L~~~l~~~----~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i-~~I~FNpI  213 (519)
T PF03215_consen  147 --------RDTSRFREALRQYLRSS----RCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI-TRIKFNPI  213 (519)
T ss_pred             --------hhHHHHHHHHHHHHHcC----CCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc-eEEEecCC
Confidence                    11112222233444321    22 56666661       1111        346666654444 56888888


Q ss_pred             CHHHHHHHHHHHhCcCCCCCHHHHHHHHHccC-CCHHHHHHHHhc--CCCHHHHHHHHHHHHH
Q 013128          379 NTSVFKQLAFNYLGISHHYLFEQIEELIKEVN-VTPAEVAGELMK--STNAEVSLNGLVKFLH  438 (449)
Q Consensus       379 ~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~-~tpa~i~~~l~~--~~~~~~al~~l~~~l~  438 (449)
                      .....+..+++.+..+       ......... -.+.++.+.+..  .+|...|+..|+=+..
T Consensus       214 a~T~mkKaL~rI~~~E-------~~~~~~~~~~p~~~~~l~~I~~~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  214 APTFMKKALKRILKKE-------ARSSSGKNKVPDKQSVLDSIAESSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             CHHHHHHHHHHHHHHH-------hhhhcCCccCCChHHHHHHHHHhcCchHHHHHHHHHHHhc
Confidence            8877777777665433       111111111 122443344432  3688888887775554

>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=98.97  E-value=5.3e-09  Score=94.88  Aligned_cols=116  Identities=18%  Similarity=0.185  Sum_probs=75.4

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHHH
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELRF  287 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~~  287 (449)
                      |+|.....+++++.+......+           ..|||+|++||||+.+|++|-+..   +.+|+.++|+.+..+.--..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~-----------~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~~~e~~   69 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSD-----------LPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEELLESE   69 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTST-----------S-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HHHHHHH
T ss_pred             CEeCCHHHHHHHHHHHHHhCCC-----------CCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcchhhhh
Confidence            4566667777777776665533           589999999999999999999977   46899999998855433334


Q ss_pred             HHHcC-----------------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-ccccCC-----
Q 013128          288 LLLTM-----------------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSCCG-----  344 (449)
Q Consensus       288 ~~~~~-----------------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~~~-----  344 (449)
                      +|-..                 ....+||||||+.+..                  .....|+++|+. -....+     
T Consensus        70 LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~------------------~~Q~~Ll~~l~~~~~~~~g~~~~~  131 (168)
T PF00158_consen   70 LFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPP------------------ELQAKLLRVLEEGKFTRLGSDKPV  131 (168)
T ss_dssp             HHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-H------------------HHHHHHHHHHHHSEEECCTSSSEE
T ss_pred             hhccccccccccccccCCceeeccceEEeecchhhhHH------------------HHHHHHHHHHhhchhccccccccc
Confidence            44321                 2578999999999854                  244557777762 111111     


Q ss_pred             -CCeEEEEEcCC
Q 013128          345 -EGRIIVFTTNH  355 (449)
Q Consensus       345 -~~~iiI~tTN~  355 (449)
                       -.+-||+||+.
T Consensus       132 ~~~~RiI~st~~  143 (168)
T PF00158_consen  132 PVDVRIIASTSK  143 (168)
T ss_dssp             E--EEEEEEESS
T ss_pred             cccceEEeecCc
Confidence             24567777775

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 ....

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=98.97  E-value=6.9e-09  Score=105.50  Aligned_cols=190  Identities=15%  Similarity=0.212  Sum_probs=114.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEec
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDL  276 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~  276 (449)
                      ..+..|||+++..+.-.. .......+...+.      . ..+.++||||.|.|||+|++|++++.     +..++++..
T Consensus        80 l~~~ytFdnFv~g~~N~~-A~aa~~~va~~~g------~-~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~s  151 (408)
T COG0593          80 LNPKYTFDNFVVGPSNRL-AYAAAKAVAENPG------G-AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTS  151 (408)
T ss_pred             CCCCCchhheeeCCchHH-HHHHHHHHHhccC------C-cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccH
Confidence            445568999865544332 2222233333221      1 24679999999999999999999998     234555554


Q ss_pred             ccccC-------hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEE
Q 013128          277 SAVQS-------NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII  349 (449)
Q Consensus       277 s~~~~-------~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  349 (449)
                      .....       +.....+-... +--+++||||+.+.+..                .+..+|...+..+...  ++.||
T Consensus       152 e~f~~~~v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~gk~----------------~~qeefFh~FN~l~~~--~kqIv  212 (408)
T COG0593         152 EDFTNDFVKALRDNEMEKFKEKY-SLDLLLIDDIQFLAGKE----------------RTQEEFFHTFNALLEN--GKQIV  212 (408)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHhh-ccCeeeechHhHhcCCh----------------hHHHHHHHHHHHHHhc--CCEEE
Confidence            44321       11122222223 55699999999986511                1223344444443332  23455


Q ss_pred             EEEcCCCCC---CCccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHH-HccCCCHHHHHHHH
Q 013128          350 VFTTNHKEK---LDPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELI-KEVNVTPAEVAGEL  420 (449)
Q Consensus       350 I~tTN~~~~---ld~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~-~~~~~tpa~i~~~l  420 (449)
                      +.+...|..   ++|.|.+  ||  ...+.+..|+.+.+..++.......+..+.+++...+ ....-+..++...|
T Consensus       213 ltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nvReLegaL  287 (408)
T COG0593         213 LTSDRPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGAL  287 (408)
T ss_pred             EEcCCCchhhccccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccHHHHHHHH
Confidence            544455554   4688888  76  4678889999999999999988777777776655443 33334444444443

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=98.96  E-value=2.7e-09  Score=98.87  Aligned_cols=139  Identities=22%  Similarity=0.316  Sum_probs=65.8

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-cEE-EEeccccc-----
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-DIY-DLDLSAVQ-----  280 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-~~~-~l~~s~~~-----  280 (449)
                      |.+|.|++..|..+.-...            |   ..++||+||||||||++|+++...|.- ..- .++.+.+.     
T Consensus         2 f~dI~GQe~aKrAL~iAAa------------G---~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e~le~~~i~s~~~~   66 (206)
T PF01078_consen    2 FSDIVGQEEAKRALEIAAA------------G---GHHLLLIGPPGTGKTMLARRLPSLLPPLTEEEALEVSKIYSVAGL   66 (206)
T ss_dssp             TCCSSSTHHHHHHHHHHHH------------C---C--EEEES-CCCTHHHHHHHHHHCS--CCEECCESS--S-TT---
T ss_pred             hhhhcCcHHHHHHHHHHHc------------C---CCCeEEECCCCCCHHHHHHHHHHhCCCCchHHHhhhccccccccC
Confidence            7899999999988754332            2   468999999999999999999998831 000 01111111     


Q ss_pred             ----------------ChHHHHHHHHc----------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          281 ----------------SNSELRFLLLT----------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       281 ----------------~~~~l~~~~~~----------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                                      .......++..          .....|||+||+-.+-                  ..++..|+.
T Consensus        67 ~~~~~~~~~~Pfr~phhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef~------------------~~vld~Lr~  128 (206)
T PF01078_consen   67 GPDEGLIRQRPFRAPHHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEFD------------------RSVLDALRQ  128 (206)
T ss_dssp             S---EEEE---EEEE-TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS-------------------HHHHHHHHH
T ss_pred             CCCCceecCCCcccCCCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhcC------------------HHHHHHHHH
Confidence                            01111222222          1357899999997652                  357777888


Q ss_pred             HhcCcc---------ccCCCCeEEEEEcCCC-----------------------CCCCccccCCCccceEEEeCCCCHH
Q 013128          335 FIDGLW---------SCCGEGRIIVFTTNHK-----------------------EKLDPALLRPGRMDMHLHMSYCNTS  381 (449)
Q Consensus       335 ~ldg~~---------~~~~~~~iiI~tTN~~-----------------------~~ld~aLlrpgR~d~~i~l~~p~~~  381 (449)
                      .++.-.         -.-+-..++|+|+|.=                       .+|...|+.  |||.++.++..+.+
T Consensus       129 ple~g~v~i~R~~~~~~~Pa~f~lv~a~NPcpCG~~~~~~~~C~Cs~~~~~~Y~~rlsgpllD--RiDi~v~~~~~~~~  205 (206)
T PF01078_consen  129 PLEDGEVTISRAGGSVTYPARFLLVAAMNPCPCGYYGDPDNRCRCSPRQIRRYQSRLSGPLLD--RIDIHVEVPRVSYE  205 (206)
T ss_dssp             HHHHSBEEEEETTEEEEEB--EEEEEEE-S-------------------------------------------------
T ss_pred             HHHCCeEEEEECCceEEEecccEEEEEeccccccccccccccccccccccccccccccccccc--cccccccccccccC
Confidence            775211         0112346788888851                       235566667  88888877776554

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK06526 transposase; Provisional

Probab=98.96  E-value=1.4e-09  Score=105.07  Aligned_cols=126  Identities=17%  Similarity=0.285  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHHHHHhCceeEEeeeccccccccccccCCCCCcccccCC--HHHHHHHHHHHHHHHcChhHHhhhcCC
Q 013128          164 LNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALD--SELKREITEDLENFMNGKEYYTRIGRA  241 (449)
Q Consensus       164 ~~~yl~~v~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~p~~f~~l~g~--~~~k~~i~~~l~~~~~~~~~~~~~g~~  241 (449)
                      ...||..+++.....+++++..+.....+.+         .+.+|+++--.  +...+..+..+    ..-+|..     
T Consensus        35 ~~e~l~~ll~~E~~~R~~~~~~~~lk~a~~p---------~~~~le~fd~~~~~~~~~~~~~~l----~~~~fi~-----   96 (254)
T PRK06526         35 HEEFLAACLQREVAARESHGGEGRIRAARFP---------ARKSLEEFDFDHQRSLKRDTIAHL----GTLDFVT-----   96 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC---------CCCChhhccCccCCCcchHHHHHH----hcCchhh-----
Confidence            3567888888887777766544333222222         22333333111  11122222221    1122222     


Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-------hHHHHHHHHcCCCCceEEeeccchhh
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-------NSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-------~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      .+.+++|+||||||||+|+.+|+.++   |..++.+....+..       ...+...+.....+.+|+|||++...
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~  172 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIP  172 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCC
Confidence            14689999999999999999999987   56666555544321       12233445556678899999999753

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.96  E-value=1.2e-08  Score=111.39  Aligned_cols=154  Identities=18%  Similarity=0.154  Sum_probs=101.7

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEecccccChH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQSNS  283 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~~~~  283 (449)
                      +|++++|.....+++++.+......           ...+||+|++||||+++|++|.+...   .+++.+||..+..+.
T Consensus       323 ~~~~l~g~s~~~~~~~~~~~~~a~~-----------~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~~  391 (638)
T PRK11388        323 TFDHMPQDSPQMRRLIHFGRQAAKS-----------SFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEA  391 (638)
T ss_pred             cccceEECCHHHHHHHHHHHHHhCc-----------CCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChHH
Confidence            5888999888888888877766543           34699999999999999999998764   699999999886432


Q ss_pred             HHHHHHH--------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCCC---
Q 013128          284 ELRFLLL--------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCGE---  345 (449)
Q Consensus       284 ~l~~~~~--------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~~---  345 (449)
                      -...+|.              .....+.||||||+.+..                  .....|+..++.-. ...+.   
T Consensus       392 ~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~------------------~~Q~~Ll~~l~~~~~~~~~~~~~  453 (638)
T PRK11388        392 LAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSP------------------ELQSALLQVLKTGVITRLDSRRL  453 (638)
T ss_pred             HHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCH------------------HHHHHHHHHHhcCcEEeCCCCce
Confidence            2222332              123568999999998853                  23344666665321 11111   


Q ss_pred             ---CeEEEEEcCCCCCCCccccCCCcc---------ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          346 ---GRIIVFTTNHKEKLDPALLRPGRM---------DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       346 ---~~iiI~tTN~~~~ld~aLlrpgR~---------d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                         .+-||+||+..-   ..+...|+|         ...|.+|+...  ++...|+..|+.
T Consensus       454 ~~~~~riI~~t~~~l---~~~~~~~~f~~dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~  511 (638)
T PRK11388        454 IPVDVRVIATTTADL---AMLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVNNKLR  511 (638)
T ss_pred             EEeeEEEEEeccCCH---HHHHhcCCChHHHhhhhceeEEeCCChhhhhhHHHHHHHHHHH
Confidence               345777777531   122223344         56777877755  456677777765

>PRK04132 replication factor C small subunit; Provisional

Probab=98.94  E-value=1.3e-08  Score=112.24  Aligned_cols=127  Identities=12%  Similarity=0.133  Sum_probs=98.4

Q ss_pred             eEEeC--CCCCCHHHHHHHHHHHc-----CCcEEEEecccccChHHHHHHHHcC----C----CCceEEeeccchhhhcc
Q 013128          246 YLLYG--PPGTGKSSLIAAMANQL-----KFDIYDLDLSAVQSNSELRFLLLTM----P----SRSMLVIEDIDCSVKLQ  310 (449)
Q Consensus       246 ~LL~G--PpGtGKT~la~aiA~~l-----~~~~~~l~~s~~~~~~~l~~~~~~~----~----~~~Il~iDeiD~l~~~~  310 (449)
                      .+..|  |++.||||+|.|+|+++     +.+++.+|.++..+...++..+...    +    +.-|++|||+|.+..  
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~--  644 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ--  644 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH--
Confidence            45568  99999999999999998     5689999999876666666554321    1    236999999999842  


Q ss_pred             cccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHH
Q 013128          311 NRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~  390 (449)
                                      ...+.|+..|+..    +..+.+|++||+++.+.+++++  |+ ..+.|+.|+.++....+...
T Consensus       645 ----------------~AQnALLk~lEep----~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L~~I  701 (846)
T PRK04132        645 ----------------DAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYI  701 (846)
T ss_pred             ----------------HHHHHHHHHhhCC----CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHHHHH
Confidence                            2346688888753    3457899999999999999998  87 67999999998888888776


Q ss_pred             hCcCCCC
Q 013128          391 LGISHHY  397 (449)
Q Consensus       391 l~~~~~~  397 (449)
                      ...++..
T Consensus       702 ~~~Egi~  708 (846)
T PRK04132        702 AENEGLE  708 (846)
T ss_pred             HHhcCCC
Confidence            6554433

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.94  E-value=9.5e-09  Score=105.11  Aligned_cols=136  Identities=21%  Similarity=0.289  Sum_probs=95.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE-eccccc------ChHHHHHHHHcCC--CCceEEeeccchhhhccccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL-DLSAVQ------SNSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRE  313 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l-~~s~~~------~~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~  313 (449)
                      -.++||+||||+|||.||..+|...+++|+.+ +..++.      .-..+...|..+.  .-+||++|||+.++.--   
T Consensus       538 lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~v---  614 (744)
T KOG0741|consen  538 LVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYV---  614 (744)
T ss_pred             ceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhccc---
Confidence            35699999999999999999999999999965 333332      2245666777664  46899999999987411   


Q ss_pred             chhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCC-ccccCCCccceEEEeCCCCH-HHHHHHHHH
Q 013128          314 SSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLD-PALLRPGRMDMHLHMSYCNT-SVFKQLAFN  389 (449)
Q Consensus       314 ~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld-~aLlrpgR~d~~i~l~~p~~-~~r~~l~~~  389 (449)
                           ...+..+..++..|+-.+...-. .|...+|++||...+-|. -.++.  +|+..+++|..+. ++...++..
T Consensus       615 -----pIGPRfSN~vlQaL~VllK~~pp-kg~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~~~vl~~  684 (744)
T KOG0741|consen  615 -----PIGPRFSNLVLQALLVLLKKQPP-KGRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQLLEVLEE  684 (744)
T ss_pred             -----ccCchhhHHHHHHHHHHhccCCC-CCceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHHHHHHHH
Confidence                 11345667788888888876432 233445556776655442 34556  8999999999877 555555553

>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=98.92  E-value=3.4e-08  Score=98.32  Aligned_cols=64  Identities=25%  Similarity=0.400  Sum_probs=44.0

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC--CcEEEEecccc
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--FDIYDLDLSAV  279 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~--~~~~~l~~s~~  279 (449)
                      .+.++|+.+.++..--.++ .++.       |+-.++++||.||||||||.||-+||++||  .||..++.+++
T Consensus        23 ~~GlVGQ~~AReAagiiv~-mIk~-------~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEi   88 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVD-MIKE-------GKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEI   88 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHH-HHHT-------T--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG
T ss_pred             cccccChHHHHHHHHHHHH-HHhc-------ccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEccccee
Confidence            4789999999887654443 2322       223368999999999999999999999996  66666665555

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=5.7e-09  Score=100.99  Aligned_cols=95  Identities=25%  Similarity=0.348  Sum_probs=68.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--------hHHHHHHHHcC------CCCceEEeeccchhhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--------NSELRFLLLTM------PSRSMLVIEDIDCSVK  308 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--------~~~l~~~~~~~------~~~~Il~iDeiD~l~~  308 (449)
                      +.++||.||.|||||.||+.+|..++.+|-.-|++.+..        +.-+.+++...      .+++||+|||||.+..
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIar  176 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIAR  176 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhc
Confidence            457999999999999999999999999999999888853        23445566554      3689999999999976


Q ss_pred             cccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          309 LQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                      .....+-..    +-...-+...||..|+|.-.
T Consensus       177 kSeN~SITR----DVSGEGVQQALLKiiEGTva  205 (408)
T COG1219         177 KSENPSITR----DVSGEGVQQALLKIIEGTVA  205 (408)
T ss_pred             cCCCCCccc----ccCchHHHHHHHHHHcCcee
Confidence            433221111    11122345668888887643

>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=98.91  E-value=4.9e-09  Score=102.44  Aligned_cols=134  Identities=25%  Similarity=0.407  Sum_probs=80.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc---EEEEecccccChHHHHHHHHcC-------------CCCceEEeeccchh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSAVQSNSELRFLLLTM-------------PSRSMLVIEDIDCS  306 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~~~~~~~l~~~~~~~-------------~~~~Il~iDeiD~l  306 (449)
                      ++.+||.||+|||||++++.+-..+.-+   ...++++...+...+...+...             .++.|+||||+...
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p  112 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMP  112 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCC
Confidence            4689999999999999999988777533   3456666655544454433221             24679999999875


Q ss_pred             hhcccccchhhhhccchhhHHHHHHHH-HHhc--CccccCC------CCeEEEEEcCCCC---CCCccccCCCccceEEE
Q 013128          307 VKLQNRESSEVQATNQEENKVTLSGLL-NFID--GLWSCCG------EGRIIVFTTNHKE---KLDPALLRPGRMDMHLH  374 (449)
Q Consensus       307 ~~~~~~~~~~~~~~~~~~~~~~ls~LL-~~ld--g~~~~~~------~~~iiI~tTN~~~---~ld~aLlrpgR~d~~i~  374 (449)
                      ..  +.          ..... ..+|| +.||  |.+....      ..+.+|+++|...   .+++.|+|  .| ..+.
T Consensus       113 ~~--d~----------ygtq~-~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~f-~i~~  176 (272)
T PF12775_consen  113 QP--DK----------YGTQP-PIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--HF-NILN  176 (272)
T ss_dssp             -----T----------TS--H-HHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--TE-EEEE
T ss_pred             CC--CC----------CCCcC-HHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--he-EEEE
Confidence            43  11          11112 22344 3343  3333211      3467788887642   47888888  77 5689


Q ss_pred             eCCCCHHHHHHHHHHHhC
Q 013128          375 MSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       375 l~~p~~~~r~~l~~~~l~  392 (449)
                      +++|+.++...|+..++.
T Consensus       177 ~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  177 IPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             ----TCCHHHHHHHHHHH
T ss_pred             ecCCChHHHHHHHHHHHh
Confidence            999999988888777665

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.90  E-value=1e-08  Score=110.52  Aligned_cols=128  Identities=19%  Similarity=0.191  Sum_probs=90.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEeccccc----ChHHHHHHHH-----------cCCCCceEEeeccchh
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLSAVQ----SNSELRFLLL-----------TMPSRSMLVIEDIDCS  306 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s~~~----~~~~l~~~~~-----------~~~~~~Il~iDeiD~l  306 (449)
                      .++||.|+||||||++++++++.+..  +++.++++...    ....+...+.           .....++|+||||+.+
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~rl   96 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANLL   96 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhhC
Confidence            47999999999999999999999864  47777653211    1111111111           1134579999999988


Q ss_pred             hhcccccchhhhhccchhhHHHHHHHHHHhcCc---------cccCCCCeEEEEEcCCCC---CCCccccCCCccceEEE
Q 013128          307 VKLQNRESSEVQATNQEENKVTLSGLLNFIDGL---------WSCCGEGRIIVFTTNHKE---KLDPALLRPGRMDMHLH  374 (449)
Q Consensus       307 ~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~---~ld~aLlrpgR~d~~i~  374 (449)
                      ..                  .+.+.|++.|+.-         .......+.||+|+|..+   .+.++|+.  ||++++.
T Consensus        97 ~~------------------~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~  156 (589)
T TIGR02031        97 DD------------------GLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLALHVS  156 (589)
T ss_pred             CH------------------HHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hccCeee
Confidence            53                  4566788888621         111223467888999875   78999999  9999999


Q ss_pred             eCCC-CHHHHHHHHHHHh
Q 013128          375 MSYC-NTSVFKQLAFNYL  391 (449)
Q Consensus       375 l~~p-~~~~r~~l~~~~l  391 (449)
                      +.++ ..++|.+|+++++
T Consensus       157 ~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031       157 LEDVASQDLRVEIVRRER  174 (589)
T ss_pred             cCCCCCHHHHHHHHHHHH
Confidence            9775 5566899998876

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.86  E-value=4.5e-08  Score=103.88  Aligned_cols=156  Identities=16%  Similarity=0.193  Sum_probs=102.1

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHH-----------cCCcEEEE
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ-----------LKFDIYDL  274 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~-----------l~~~~~~l  274 (449)
                      .+|++++|.....+.+.+.+..+...           ...+||+|++||||+++|++|-+.           .+.+|+.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s-----------~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARS-----------SAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            46899999998888888887766543           357999999999999999999887           36799999


Q ss_pred             ecccccChHHHH-HHHH------------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHH
Q 013128          275 DLSAVQSNSELR-FLLL------------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNF  335 (449)
Q Consensus       275 ~~s~~~~~~~l~-~~~~------------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~  335 (449)
                      ||+.+..+ .+. .+|.                  +....+.||||||+.+..                  .....|+..
T Consensus       285 nCaal~e~-lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~------------------~~Q~kLl~~  345 (538)
T PRK15424        285 NCGAIAES-LLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPL------------------PLQTRLLRV  345 (538)
T ss_pred             ecccCChh-hHHHHhcCCccccccCccccccCCchhccCCCEEEEcChHhCCH------------------HHHHHHHhh
Confidence            99988542 222 1221                  123567999999999853                  233456777


Q ss_pred             hcCcc-ccCC------CCeEEEEEcCCC-CC------CCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhCc
Q 013128          336 IDGLW-SCCG------EGRIIVFTTNHK-EK------LDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLGI  393 (449)
Q Consensus       336 ldg~~-~~~~------~~~iiI~tTN~~-~~------ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~~  393 (449)
                      ++.-. ...|      -.+-||++||.. +.      +.+.|.-  |+ ...|++|+...  ++...|+..|+..
T Consensus       346 L~e~~~~r~G~~~~~~~dvRiIaat~~~L~~~v~~g~Fr~dL~y--rL~~~~I~lPPLReR~eDI~~L~~~fl~~  418 (538)
T PRK15424        346 LEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFY--RLSILRLQLPPLRERVADILPLAESFLKQ  418 (538)
T ss_pred             hhcCeEEecCCCceeccceEEEEecCCCHHHHHhcccchHHHHH--HhcCCeecCCChhhchhHHHHHHHHHHHH
Confidence            65311 1111      123567776653 21      2222322  33 25677777654  5677777777754

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

Probab=98.86  E-value=1.2e-07  Score=93.33  Aligned_cols=64  Identities=27%  Similarity=0.410  Sum_probs=46.8

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC--CcEEEEecccc
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--FDIYDLDLSAV  279 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~--~~~~~l~~s~~  279 (449)
                      =+-++|+.+.++..-=.++ .++       -|+-.++|+|+.||||||||.||-+||.+||  .||..++.+.+
T Consensus        38 ~dG~VGQ~~AReAaGvIv~-mik-------~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEi  103 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVK-MIK-------QGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEI  103 (450)
T ss_pred             CCcccchHHHHHhhhHHHH-HHH-------hCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeecccee
Confidence            3678898888776432222 121       2444578999999999999999999999996  56666666665

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.84  E-value=1.2e-07  Score=94.30  Aligned_cols=122  Identities=17%  Similarity=0.190  Sum_probs=91.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC-----------------------CcEEEEeccc---ccChHHHHHHHHc---CC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK-----------------------FDIYDLDLSA---VQSNSELRFLLLT---MP  293 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~-----------------------~~~~~l~~s~---~~~~~~l~~~~~~---~~  293 (449)
                      +.++||+||.|+||+++|.++|..+-                       .+++.+....   .-....++.+...   .+
T Consensus        25 ~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~~~  104 (319)
T PRK06090         25 PGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQESS  104 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhhCc
Confidence            56899999999999999999999872                       2566665432   1223444443222   22


Q ss_pred             ---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccc
Q 013128          294 ---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD  370 (449)
Q Consensus       294 ---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d  370 (449)
                         ..-|++||++|.+..                  ..-+.||..++.-    +.+.++|++|+.++.|-|.+++  |+ 
T Consensus       105 ~~~~~kV~iI~~ae~m~~------------------~AaNaLLKtLEEP----p~~t~fiL~t~~~~~lLpTI~S--RC-  159 (319)
T PRK06090        105 QLNGYRLFVIEPADAMNE------------------SASNALLKTLEEP----APNCLFLLVTHNQKRLLPTIVS--RC-  159 (319)
T ss_pred             ccCCceEEEecchhhhCH------------------HHHHHHHHHhcCC----CCCeEEEEEECChhhChHHHHh--cc-
Confidence               356999999998843                  3557799999873    5678999999999999999998  87 


Q ss_pred             eEEEeCCCCHHHHHHHHHH
Q 013128          371 MHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       371 ~~i~l~~p~~~~r~~l~~~  389 (449)
                      ..+.|+.|+.++..+.+..
T Consensus       160 q~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        160 QQWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             eeEeCCCCCHHHHHHHHHH
Confidence            5799999999887776654

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.84  E-value=1.2e-07  Score=101.13  Aligned_cols=177  Identities=15%  Similarity=0.174  Sum_probs=108.9

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ...+|++++|.....+.+++.+......           ...+||+|++||||+++|+++-...   +.+++.++|..+.
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~A~~-----------~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~  267 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKLAML-----------DAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIP  267 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCC
Confidence            3457999999888878888877655442           3569999999999999999987665   3689999999876


Q ss_pred             ChHHHHHHHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-cccc
Q 013128          281 SNSELRFLLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSC  342 (449)
Q Consensus       281 ~~~~l~~~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~  342 (449)
                      ...--..+|.                 .....+.|||||||.+..                  .....|++++.. ....
T Consensus       268 ~~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~------------------~~Q~~Ll~~l~~~~~~~  329 (520)
T PRK10820        268 DDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSP------------------RMQAKLLRFLNDGTFRR  329 (520)
T ss_pred             HHHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCH------------------HHHHHHHHHHhcCCccc
Confidence            4211112221                 123467899999999853                  122446666642 2211


Q ss_pred             CC------CCeEEEEEcCCC-C------CCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhCcC-------CCCCH
Q 013128          343 CG------EGRIIVFTTNHK-E------KLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLGIS-------HHYLF  399 (449)
Q Consensus       343 ~~------~~~iiI~tTN~~-~------~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~~~-------~~~l~  399 (449)
                      .|      ..+-||+||+.. .      .+.+.|..  |+ ...|++|++..  ++...|+..|+...       ...+.
T Consensus       330 ~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~--rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls  407 (520)
T PRK10820        330 VGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYY--RLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLA  407 (520)
T ss_pred             CCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHh--hcCeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcC
Confidence            11      124566666553 2      23445555  54 35677777755  45666666665421       12345


Q ss_pred             HHHHHHHHccCC
Q 013128          400 EQIEELIKEVNV  411 (449)
Q Consensus       400 ~~i~~l~~~~~~  411 (449)
                      ++..+.+....|
T Consensus       408 ~~a~~~L~~y~W  419 (520)
T PRK10820        408 ADLNTVLTRYGW  419 (520)
T ss_pred             HHHHHHHhcCCC
Confidence            555555544443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.84  E-value=1.8e-07  Score=93.36  Aligned_cols=123  Identities=14%  Similarity=0.123  Sum_probs=91.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------------------------CcEEEEecc--cccChHHHHHHHHcC----
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------------------------FDIYDLDLS--AVQSNSELRFLLLTM----  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------------------------~~~~~l~~s--~~~~~~~l~~~~~~~----  292 (449)
                      +.++||+||+|+||+++|.++|..+-                        .+++.+...  .--.-..++.+....    
T Consensus        24 ~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~~  103 (325)
T PRK06871         24 HHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQHA  103 (325)
T ss_pred             ceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhcc
Confidence            56899999999999999999999982                        235545431  111234455443332    


Q ss_pred             --CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccc
Q 013128          293 --PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD  370 (449)
Q Consensus       293 --~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d  370 (449)
                        ...-|++||++|.+..                  ...+.||..++.-    +..+++|++|++++.|.|.+++  |+ 
T Consensus       104 ~~g~~KV~iI~~a~~m~~------------------~AaNaLLKtLEEP----p~~~~fiL~t~~~~~llpTI~S--RC-  158 (325)
T PRK06871        104 QQGGNKVVYIQGAERLTE------------------AAANALLKTLEEP----RPNTYFLLQADLSAALLPTIYS--RC-  158 (325)
T ss_pred             ccCCceEEEEechhhhCH------------------HHHHHHHHHhcCC----CCCeEEEEEECChHhCchHHHh--hc-
Confidence              2346999999998843                  3557799999863    5678999999999999999998  87 


Q ss_pred             eEEEeCCCCHHHHHHHHHHH
Q 013128          371 MHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       371 ~~i~l~~p~~~~r~~l~~~~  390 (449)
                      ..+.|+.|+.++..+.+...
T Consensus       159 ~~~~~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        159 QTWLIHPPEEQQALDWLQAQ  178 (325)
T ss_pred             eEEeCCCCCHHHHHHHHHHH
Confidence            56899999998877766653

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.83  E-value=5.5e-08  Score=103.20  Aligned_cols=158  Identities=17%  Similarity=0.188  Sum_probs=103.9

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ...+|++++|.....+.+.+.+..+...           ...+||.|++||||+++|++|.+..   +.+++.+||..+.
T Consensus       207 ~~~~f~~iiG~S~~m~~~~~~i~~~A~~-----------~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~  275 (526)
T TIGR02329       207 TRYRLDDLLGASAPMEQVRALVRLYARS-----------DATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIA  275 (526)
T ss_pred             cccchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCC
Confidence            3467999999998888888888766553           3579999999999999999999875   5799999999885


Q ss_pred             ChHHHHH-HHH------------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-
Q 013128          281 SNSELRF-LLL------------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-  340 (449)
Q Consensus       281 ~~~~l~~-~~~------------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-  340 (449)
                      .. .+.. +|.                  +....+.||||||+.+..                  .....|+..++.-. 
T Consensus       276 e~-lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~------------------~~Q~~Ll~~L~~~~~  336 (526)
T TIGR02329       276 ES-LLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPL------------------PLQTRLLRVLEEREV  336 (526)
T ss_pred             hh-HHHHHhcCCcccccccccccccccchhhcCCceEEecChHhCCH------------------HHHHHHHHHHhcCcE
Confidence            42 2221 221                  123467899999999853                  23344666664211 


Q ss_pred             ccCC------CCeEEEEEcCCC-C-CC-----CccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhCc
Q 013128          341 SCCG------EGRIIVFTTNHK-E-KL-----DPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLGI  393 (449)
Q Consensus       341 ~~~~------~~~iiI~tTN~~-~-~l-----d~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~~  393 (449)
                      ...|      -.+-+|++||.. . .+     .+.|..  |+ ...|++|+...  ++...|+..|+..
T Consensus       337 ~r~g~~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~--rL~~~~I~lPPLReR~eDI~~L~~~fl~~  403 (526)
T TIGR02329       337 VRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFY--RLSILRIALPPLRERPGDILPLAAEYLVQ  403 (526)
T ss_pred             EecCCCceeeecceEEeccCCCHHHHhhhcchhHHHHH--hcCCcEEeCCCchhchhHHHHHHHHHHHH
Confidence            1111      123466666553 2 12     223333  44 36788888765  5677777777754

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.82  E-value=8.9e-08  Score=96.24  Aligned_cols=122  Identities=16%  Similarity=0.154  Sum_probs=91.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------------------------CcEEEEeccc---ccChHHHHHHHHcC---
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------------------------FDIYDLDLSA---VQSNSELRFLLLTM---  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------------------------~~~~~l~~s~---~~~~~~l~~~~~~~---  292 (449)
                      +.++||+||+|+||+++|.++|..+-                        .+++.+....   .-.-..++.+....   
T Consensus        24 ~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~  103 (334)
T PRK07993         24 HHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLYEH  103 (334)
T ss_pred             ceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHhhc
Confidence            56899999999999999999999982                        2455554321   12234444443332   


Q ss_pred             C---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          293 P---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       293 ~---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                      +   ..-|++||++|.+..                  ..-+.||..|+.-    +...++|.+|++++.|.|.+++  |+
T Consensus       104 ~~~g~~kV~iI~~ae~m~~------------------~AaNaLLKtLEEP----p~~t~fiL~t~~~~~lLpTIrS--RC  159 (334)
T PRK07993        104 ARLGGAKVVWLPDAALLTD------------------AAANALLKTLEEP----PENTWFFLACREPARLLATLRS--RC  159 (334)
T ss_pred             cccCCceEEEEcchHhhCH------------------HHHHHHHHHhcCC----CCCeEEEEEECChhhChHHHHh--cc
Confidence            2   456999999999843                  3557799999873    5678999999999999999998  87


Q ss_pred             ceEEEeCCCCHHHHHHHHHH
Q 013128          370 DMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       370 d~~i~l~~p~~~~r~~l~~~  389 (449)
                      . .+.|+.|+.++..+.+..
T Consensus       160 q-~~~~~~~~~~~~~~~L~~  178 (334)
T PRK07993        160 R-LHYLAPPPEQYALTWLSR  178 (334)
T ss_pred             c-cccCCCCCHHHHHHHHHH
Confidence            5 589999998887776654

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

Probab=98.82  E-value=1.9e-08  Score=97.37  Aligned_cols=95  Identities=23%  Similarity=0.459  Sum_probs=65.4

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ....+.++-+.+...+.....+..+..   +|.     .+.+++||||||||||+|+.|||+++   |..++.+...++.
T Consensus        74 k~~~~~d~~~~~~~~~~~l~~~~~~~~---~~~-----~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~  145 (254)
T COG1484          74 KTFEEFDFEFQPGIDKKALEDLASLVE---FFE-----RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLL  145 (254)
T ss_pred             CCcccccccCCcchhHHHHHHHHHHHH---Hhc-----cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHH
Confidence            334455566666666666655555443   222     26799999999999999999999998   6778888777663


Q ss_pred             Ch-------HHHH-HHHHcCCCCceEEeeccchh
Q 013128          281 SN-------SELR-FLLLTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       281 ~~-------~~l~-~~~~~~~~~~Il~iDeiD~l  306 (449)
                      .+       .... .+.....+.-+|+|||+...
T Consensus       146 ~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~  179 (254)
T COG1484         146 SKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYE  179 (254)
T ss_pred             HHHHHHHhcCchHHHHHHHhhcCCEEEEecccCc
Confidence            22       1222 23333678899999999875

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.79  E-value=4.8e-08  Score=99.15  Aligned_cols=203  Identities=13%  Similarity=0.078  Sum_probs=131.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhCceeEEeeeccccccc-------cc--cccCCCCCcccccCCHHHHHHHHHHHHHHHcC
Q 013128          161 DVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDA-------NN--IVLKHPMTFKTLALDSELKREITEDLENFMNG  231 (449)
Q Consensus       161 ~~v~~~yl~~v~~~~~~~~~~~~~~~~~~~~~~~w~~-------~~--~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~  231 (449)
                      ...++.++..+...++..+...+++.....+...-..       .+  -.......+++|+|....-+++++.+..+-  
T Consensus        21 r~~vs~~l~~l~~~~~~~~~~~~pv~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~LIG~~~~~~~~~eqik~~a--   98 (403)
T COG1221          21 RANVSHELNGLGREGDLAKINGRPVIFLPSEAFSMSELTELQALLPQARPYLKSEALDDLIGESPSLQELREQIKAYA--   98 (403)
T ss_pred             HHHhHHHHHhhhhhhhHHHhcCCCchhHHHHHhhhhhhhhhhhcccchhhhccchhhhhhhccCHHHHHHHHHHHhhC--
Confidence            3566788888888888888888877332221111000       00  011233468999999998888888887622  


Q ss_pred             hhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEecccccChHHHHHHHHc----------------
Q 013128          232 KEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAVQSNSELRFLLLT----------------  291 (449)
Q Consensus       232 ~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~~~~~~l~~~~~~----------------  291 (449)
                               +....+|++|++||||+.+|++|....    +.+++.+||..+..+.....+|--                
T Consensus        99 ---------p~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~~k~Glf  169 (403)
T COG1221          99 ---------PSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGGKAGLF  169 (403)
T ss_pred             ---------CCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHHHhccccceeecccCCcCchh
Confidence                     124579999999999999999998544    568999999999877665554431                


Q ss_pred             -CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-cccc------CCCCeEEEEEcCC-C-CCCCc
Q 013128          292 -MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSC------CGEGRIIVFTTNH-K-EKLDP  361 (449)
Q Consensus       292 -~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~------~~~~~iiI~tTN~-~-~~ld~  361 (449)
                       ....++||+|||..+..                  .....|+.+||. .+..      ....+-+|++||. + +.+-.
T Consensus       170 e~A~GGtLfLDEI~~LP~------------------~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~~  231 (403)
T COG1221         170 EQANGGTLFLDEIHRLPP------------------EGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVLA  231 (403)
T ss_pred             eecCCCEEehhhhhhCCH------------------hHHHHHHHHHHcCceEecCCCCCcCCCceeeeccccCHHHHHHh
Confidence             12568999999998854                  122337777873 2221      1234566666654 2 22222


Q ss_pred             --cccCCCccceEEEeCCCCH--HHHHHHHHHHhCc
Q 013128          362 --ALLRPGRMDMHLHMSYCNT--SVFKQLAFNYLGI  393 (449)
Q Consensus       362 --aLlrpgR~d~~i~l~~p~~--~~r~~l~~~~l~~  393 (449)
                        .|.+ -|+.+.|++|+..+  +++..|+..|+..
T Consensus       232 g~dl~~-rl~~~~I~LPpLrER~~Di~~L~e~Fl~~  266 (403)
T COG1221         232 GADLTR-RLNILTITLPPLRERKEDILLLAEHFLKS  266 (403)
T ss_pred             hcchhh-hhcCceecCCChhhchhhHHHHHHHHHHH
Confidence              3332 16778888888765  6677788888764

>PRK09183 transposase/IS protein; Provisional

Probab=98.79  E-value=1.5e-08  Score=98.45  Aligned_cols=64  Identities=19%  Similarity=0.328  Sum_probs=46.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh-------HHHHHHHHc-CCCCceEEeeccchh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN-------SELRFLLLT-MPSRSMLVIEDIDCS  306 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~-------~~l~~~~~~-~~~~~Il~iDeiD~l  306 (449)
                      ..+++|+||||||||+|+.++|+.+   |..+..++..++...       ..+...+.. ...+.+++|||++..
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~  176 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYL  176 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccC
Confidence            4579999999999999999998775   677777765544311       123334433 457789999999864

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.77  E-value=2.8e-07  Score=91.83  Aligned_cols=122  Identities=16%  Similarity=0.276  Sum_probs=87.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC---------------------CcEEEEe--cccc-------cChHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK---------------------FDIYDLD--LSAV-------QSNSELRFLLLTM  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~---------------------~~~~~l~--~s~~-------~~~~~l~~~~~~~  292 (449)
                      +.++||+||+|+||+++|.++|+.+-                     .|++.+.  ...-       -.-..++.+....
T Consensus        26 ~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~~  105 (319)
T PRK08769         26 GHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKL  105 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHHH
Confidence            56899999999999999999998872                     2345442  2111       0123344433322


Q ss_pred             ---C---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCC
Q 013128          293 ---P---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRP  366 (449)
Q Consensus       293 ---~---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrp  366 (449)
                         +   ..-|++||++|.+..                  ...+.||..|+.-    +...++|.+|+.++.|-|.+++ 
T Consensus       106 ~~~p~~g~~kV~iI~~ae~m~~------------------~AaNaLLKtLEEP----p~~~~fiL~~~~~~~lLpTIrS-  162 (319)
T PRK08769        106 ALTPQYGIAQVVIVDPADAINR------------------AACNALLKTLEEP----SPGRYLWLISAQPARLPATIRS-  162 (319)
T ss_pred             hhCcccCCcEEEEeccHhhhCH------------------HHHHHHHHHhhCC----CCCCeEEEEECChhhCchHHHh-
Confidence               2   346999999998842                  3557799998863    4567899999999999999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHH
Q 013128          367 GRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       367 gR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                       |+ ..+.|+.|+.++-.+.+..
T Consensus       163 -RC-q~i~~~~~~~~~~~~~L~~  183 (319)
T PRK08769        163 -RC-QRLEFKLPPAHEALAWLLA  183 (319)
T ss_pred             -hh-eEeeCCCcCHHHHHHHHHH
Confidence             87 5689999998877666654

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

Probab=98.77  E-value=4.4e-09  Score=96.37  Aligned_cols=64  Identities=30%  Similarity=0.565  Sum_probs=46.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc-------ChHHHHHHHHcCCCCceEEeeccchh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ-------SNSELRFLLLTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~-------~~~~l~~~~~~~~~~~Il~iDeiD~l  306 (449)
                      +.|++|+||||||||+||.|||+++   |+.+..++..++.       ........+.......+|+|||+...
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~  120 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYE  120 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEeccccccee
Confidence            5789999999999999999999987   7888888766652       12223344555567889999999753

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.76  E-value=3.5e-08  Score=98.80  Aligned_cols=103  Identities=21%  Similarity=0.305  Sum_probs=66.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh---------HHHHHHHHcCCCCceEEeeccchhhhccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN---------SELRFLLLTMPSRSMLVIEDIDCSVKLQN  311 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~---------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~  311 (449)
                      .+++||||||||||+|+.|||+++   +..++.++...+...         ......+......-+|+|||+.....   
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~~---  260 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEKI---  260 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCCC---
Confidence            689999999999999999999998   778888876655321         11122245556778999999986532   


Q ss_pred             ccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC-CC----CCccccC
Q 013128          312 RESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK-EK----LDPALLR  365 (449)
Q Consensus       312 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~----ld~aLlr  365 (449)
                                   .....+.|.+.++....   .+.-+|+|||.+ +.    +++++..
T Consensus       261 -------------t~~~~~~Lf~iin~R~~---~~k~tIiTSNl~~~el~~~~~eri~S  303 (329)
T PRK06835        261 -------------TEFSKSELFNLINKRLL---RQKKMIISTNLSLEELLKTYSERISS  303 (329)
T ss_pred             -------------CHHHHHHHHHHHHHHHH---CCCCEEEECCCCHHHHHHHHhHHHHH
Confidence                         11223445555554332   123577788864 22    4555555

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.76  E-value=1.4e-07  Score=104.07  Aligned_cols=157  Identities=16%  Similarity=0.178  Sum_probs=101.0

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~  281 (449)
                      ..+|++++|.....+.+.+.+......           ...+||.|++|||||++|++|....   +.+++.++|..+..
T Consensus       372 n~~~~~liG~S~~~~~~~~~~~~~a~~-----------~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~  440 (686)
T PRK15429        372 DSEFGEIIGRSEAMYSVLKQVEMVAQS-----------DSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA  440 (686)
T ss_pred             cccccceeecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh
Confidence            357889999999999998888776542           3579999999999999999999876   57999999988743


Q ss_pred             hHHHHHH-----------------HHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccC
Q 013128          282 NSELRFL-----------------LLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCC  343 (449)
Q Consensus       282 ~~~l~~~-----------------~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~  343 (449)
                      ..--..+                 ......+++||||||+.+..                  .....|++.++.-. ...
T Consensus       441 ~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~------------------~~Q~~L~~~l~~~~~~~~  502 (686)
T PRK15429        441 GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPL------------------ELQPKLLRVLQEQEFERL  502 (686)
T ss_pred             hHhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhCCH------------------HHHHHHHHHHHhCCEEeC
Confidence            2100011                 11234578999999998743                  23345666665321 110


Q ss_pred             C------CCeEEEEEcCCC-C------CCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          344 G------EGRIIVFTTNHK-E------KLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       344 ~------~~~iiI~tTN~~-~------~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                      +      ..+-+|+||+.. +      .+.+.|..  |+ ...|++|+...  ++...|+..|+.
T Consensus       503 g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~~L~~--~l~~~~i~lPpLreR~~Di~~L~~~~l~  565 (686)
T PRK15429        503 GSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYY--RLNVFPIHLPPLRERPEDIPLLVKAFTF  565 (686)
T ss_pred             CCCCcccceEEEEEeCCCCHHHHHHcCcccHHHHh--ccCeeEEeCCChhhhHhHHHHHHHHHHH
Confidence            1      234577777653 1      12222332  33 24577777654  456667777764

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.75  E-value=2.2e-07  Score=98.81  Aligned_cols=154  Identities=16%  Similarity=0.155  Sum_probs=101.6

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNS  283 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~  283 (449)
                      .+++++|.....+.+.+.+......           ...+||+|++||||+++|++|....   +.+++.++|..+... 
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~-----------~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~-  252 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAAS-----------DLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPES-  252 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChH-
Confidence            5788999999888898888765543           3589999999999999999999886   478999999988542 


Q ss_pred             HHH-HHHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC
Q 013128          284 ELR-FLLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG  344 (449)
Q Consensus       284 ~l~-~~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~  344 (449)
                      .+. .+|.                 .....+.|||||||.+..                  .....|++.++.-. ...+
T Consensus       253 ~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~------------------~~Q~~Ll~~l~~~~~~~~g  314 (509)
T PRK05022        253 LAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELPL------------------ALQAKLLRVLQYGEIQRVG  314 (509)
T ss_pred             HHHHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhCCH------------------HHHHHHHHHHhcCCEeeCC
Confidence            111 1211                 223567899999999853                  23344666664321 1101


Q ss_pred             ------CCeEEEEEcCCC-------CCCCccccCCCccc-eEEEeCCCCH--HHHHHHHHHHhC
Q 013128          345 ------EGRIIVFTTNHK-------EKLDPALLRPGRMD-MHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       345 ------~~~iiI~tTN~~-------~~ld~aLlrpgR~d-~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                            ..+-||+|||..       ..+.+.|..  |+. ..|++|+...  ++...|+..|+.
T Consensus       315 ~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~dL~~--rl~~~~i~lPpLreR~eDI~~L~~~fl~  376 (509)
T PRK05022        315 SDRSLRVDVRVIAATNRDLREEVRAGRFRADLYH--RLSVFPLSVPPLRERGDDVLLLAGYFLE  376 (509)
T ss_pred             CCcceecceEEEEecCCCHHHHHHcCCccHHHHh--cccccEeeCCCchhchhhHHHHHHHHHH
Confidence                  134567777653       224444444  443 4577887754  456666666664

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.75  E-value=3.1e-08  Score=99.35  Aligned_cols=130  Identities=22%  Similarity=0.282  Sum_probs=85.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--------hHHHHHHHHcCC------CCceEEeeccchhhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--------NSELRFLLLTMP------SRSMLVIEDIDCSVK  308 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--------~~~l~~~~~~~~------~~~Il~iDeiD~l~~  308 (449)
                      +.++||.||+|+|||.|++.+|.-++.+|...||+.+..        ++-+..++..+.      +..|+||||+|.+..
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~  305 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITK  305 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcc
Confidence            568999999999999999999999999999999999854        344566666653      689999999999874


Q ss_pred             cccccchhhhhccchhhHHHHHHHHHHhcCccccC---------CCCeEEEEEc-------CCCCCCCccccCCCcc-ce
Q 013128          309 LQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC---------GEGRIIVFTT-------NHKEKLDPALLRPGRM-DM  371 (449)
Q Consensus       309 ~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~---------~~~~iiI~tT-------N~~~~ld~aLlrpgR~-d~  371 (449)
                      ....-....    +-...-+...||..++|.--..         .+..+.|=||       .---.||.-+.|  |+ +.
T Consensus       306 ~~~~i~~~R----DVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~r--R~~d~  379 (564)
T KOG0745|consen  306 KAESIHTSR----DVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIISR--RLDDK  379 (564)
T ss_pred             cCccccccc----cccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHHH--hhcch
Confidence            222111110    0112335566888888653221         1223333333       334556666666  55 34


Q ss_pred             EEEeCCC
Q 013128          372 HLHMSYC  378 (449)
Q Consensus       372 ~i~l~~p  378 (449)
                      .+-|+.|
T Consensus       380 slGFg~~  386 (564)
T KOG0745|consen  380 SLGFGAP  386 (564)
T ss_pred             hcccCCC
Confidence            5556666

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.74  E-value=5.6e-08  Score=97.32  Aligned_cols=121  Identities=13%  Similarity=0.176  Sum_probs=86.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC-------------------------CcEEEEecccc----------cChHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK-------------------------FDIYDLDLSAV----------QSNSELRF  287 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~-------------------------~~~~~l~~s~~----------~~~~~l~~  287 (449)
                      +.++||+||+|+|||++|+++|+.+.                         .+++.++...-          -.-..++.
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~iR~  100 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAVRE  100 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHHHH
Confidence            56899999999999999999999972                         35666765321          12334444


Q ss_pred             HHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCc
Q 013128          288 LLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDP  361 (449)
Q Consensus       288 ~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~  361 (449)
                      +....      ...-|++||+++.+-.                  ...+.|+..++...    .+..+|++|++++.+.+
T Consensus       101 l~~~~~~~p~~~~~kV~iiEp~~~Ld~------------------~a~naLLk~LEep~----~~~~~Ilvth~~~~ll~  158 (325)
T PRK08699        101 IIDNVYLTSVRGGLRVILIHPAESMNL------------------QAANSLLKVLEEPP----PQVVFLLVSHAADKVLP  158 (325)
T ss_pred             HHHHHhhCcccCCceEEEEechhhCCH------------------HHHHHHHHHHHhCc----CCCEEEEEeCChHhChH
Confidence            43332      2456899999998742                  23455777777642    34678889999999999


Q ss_pred             cccCCCccceEEEeCCCCHHHHHHHHH
Q 013128          362 ALLRPGRMDMHLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       362 aLlrpgR~d~~i~l~~p~~~~r~~l~~  388 (449)
                      .+.+  |+ ..+.|+.|+.++..+.+.
T Consensus       159 ti~S--Rc-~~~~~~~~~~~~~~~~L~  182 (325)
T PRK08699        159 TIKS--RC-RKMVLPAPSHEEALAYLR  182 (325)
T ss_pred             HHHH--Hh-hhhcCCCCCHHHHHHHHH
Confidence            9988  76 568899999888766554

>PRK06921 hypothetical protein; Provisional

Probab=98.74  E-value=4.3e-08  Score=95.53  Aligned_cols=63  Identities=29%  Similarity=0.376  Sum_probs=46.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEecccccCh-----HHHHHHHHcCCCCceEEeeccch
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAVQSN-----SELRFLLLTMPSRSMLVIEDIDC  305 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~~~~-----~~l~~~~~~~~~~~Il~iDeiD~  305 (449)
                      ..+++|+||||||||+|+.|||+++    +..++.+...++...     ..+...+....+..+|+|||++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl~~  188 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDLFK  188 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEecccc
Confidence            4689999999999999999999987    566777765443211     11223344556788999999954

>PF13173 AAA_14: AAA domain

Probab=98.73  E-value=5e-08  Score=84.34  Aligned_cols=63  Identities=24%  Similarity=0.486  Sum_probs=48.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC--CcEEEEecccccChH----HHHHHHHcC--CCCceEEeeccchh
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK--FDIYDLDLSAVQSNS----ELRFLLLTM--PSRSMLVIEDIDCS  306 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~--~~~~~l~~s~~~~~~----~l~~~~~~~--~~~~Il~iDeiD~l  306 (449)
                      +.++|+||+|||||++++.+++.+.  .+++.+++.+.....    .+...+.+.  ..+.+||||||+.+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~   73 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYL   73 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhh
Confidence            5689999999999999999999887  888888887764321    122333333  36799999999986

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

Probab=98.71  E-value=3.2e-08  Score=86.69  Aligned_cols=126  Identities=23%  Similarity=0.303  Sum_probs=74.9

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC---cEEEEecccccChHHHHHHH
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF---DIYDLDLSAVQSNSELRFLL  289 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~---~~~~l~~s~~~~~~~l~~~~  289 (449)
                      |.....+++.+.+......           ...+||+|+|||||+++|++|....+.   +++.++|....     ..++
T Consensus         2 G~S~~~~~l~~~l~~~a~~-----------~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l   65 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKS-----------SSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELL   65 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCS-----------SS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHH
T ss_pred             CCCHHHHHHHHHHHHHhCC-----------CCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHH
Confidence            3445556677777666543           357999999999999999999998864   45555666543     2334


Q ss_pred             HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC------CCccc
Q 013128          290 LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK------LDPAL  363 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~------ld~aL  363 (449)
                      ... .+..|+|+|||.+..                  .....|++.++...  ...-++|..++..++.      +++.|
T Consensus        66 ~~a-~~gtL~l~~i~~L~~------------------~~Q~~L~~~l~~~~--~~~~RlI~ss~~~l~~l~~~~~~~~~L  124 (138)
T PF14532_consen   66 EQA-KGGTLYLKNIDRLSP------------------EAQRRLLDLLKRQE--RSNVRLIASSSQDLEELVEEGRFSPDL  124 (138)
T ss_dssp             HHC-TTSEEEEECGCCS-H------------------HHHHHHHHHHHHCT--TTTSEEEEEECC-CCCHHHHSTHHHHH
T ss_pred             HHc-CCCEEEECChHHCCH------------------HHHHHHHHHHHhcC--CCCeEEEEEeCCCHHHHhhccchhHHH
Confidence            443 888999999999853                  22333555554321  1233555555555544      44555


Q ss_pred             cCCCccc-eEEEeCC
Q 013128          364 LRPGRMD-MHLHMSY  377 (449)
Q Consensus       364 lrpgR~d-~~i~l~~  377 (449)
                      ..  |+. ..|++|+
T Consensus       125 ~~--~l~~~~i~lPp  137 (138)
T PF14532_consen  125 YY--RLSQLEIHLPP  137 (138)
T ss_dssp             HH--HCSTCEEEE--
T ss_pred             HH--HhCCCEEeCCC
Confidence            54  443 5666664

>TIGR00368 Mg chelatase-related protein

Probab=98.65  E-value=1.3e-07  Score=99.76  Aligned_cols=143  Identities=18%  Similarity=0.214  Sum_probs=87.9

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc--EEEEecccccC-
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD--IYDLDLSAVQS-  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~--~~~l~~s~~~~-  281 (449)
                      +..|+++.|....++.+.-.+               .....++|.||||||||+++++++..+...  -..++.+.+.+ 
T Consensus       188 ~~d~~dv~Gq~~~~~al~~aa---------------~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~  252 (499)
T TIGR00368       188 DLDLKDIKGQQHAKRALEIAA---------------AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSL  252 (499)
T ss_pred             CCCHHHhcCcHHHHhhhhhhc---------------cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccc
Confidence            347899999887766543221               123579999999999999999999865210  00111111100 


Q ss_pred             -----------------------hHH-------HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          282 -----------------------NSE-------LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       282 -----------------------~~~-------l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                             ...       .+.-.......++|||||++.+..                  ..+..
T Consensus       253 ~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~~------------------~~~~~  314 (499)
T TIGR00368       253 VGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKR------------------SVLDA  314 (499)
T ss_pred             hhhhccccccccCCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhCCH------------------HHHHH
Confidence                                   000       000012234568999999997632                  34455


Q ss_pred             HHHHhcCcc---------ccCCCCeEEEEEcCCC------C-----------------CCCccccCCCccceEEEeCCCC
Q 013128          332 LLNFIDGLW---------SCCGEGRIIVFTTNHK------E-----------------KLDPALLRPGRMDMHLHMSYCN  379 (449)
Q Consensus       332 LL~~ldg~~---------~~~~~~~iiI~tTN~~------~-----------------~ld~aLlrpgR~d~~i~l~~p~  379 (449)
                      |++.|+.-.         ..-...+.+|+++|.-      +                 +|...|+.  |||.++.++.++
T Consensus       315 L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllD--R~dl~~~~~~~~  392 (499)
T TIGR00368       315 LREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLD--RIDLSVEVPLLP  392 (499)
T ss_pred             HHHHHHcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHh--hCCEEEEEcCCC
Confidence            666664211         0112356788888852      1                 57888999  999999999987


Q ss_pred             HHH
Q 013128          380 TSV  382 (449)
Q Consensus       380 ~~~  382 (449)
                      .++
T Consensus       393 ~~~  395 (499)
T TIGR00368       393 PEK  395 (499)
T ss_pred             HHH
Confidence            654

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.64  E-value=2.9e-07  Score=89.94  Aligned_cols=70  Identities=16%  Similarity=0.253  Sum_probs=50.2

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhh-cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRI-GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~-g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      -++|.++.|+.+-=.|..-.++...-..+ .---|+++|..||.|+|||-+|+-+|+..+.||+.+..+.+
T Consensus        16 yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATKf   86 (444)
T COG1220          16 YIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKF   86 (444)
T ss_pred             HhcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeeee
Confidence            36788888888765555443332111111 11236899999999999999999999999999998876554

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.62  E-value=1.4e-07  Score=91.60  Aligned_cols=164  Identities=16%  Similarity=0.201  Sum_probs=104.2

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc--
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD--  270 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~--  270 (449)
                      .+|..    .++|..++++++.++....+.+    |...         +.-.+.|+|||||||||+.+.+.|..+-.+  
T Consensus        29 ~pwve----kyrP~~l~dv~~~~ei~st~~~----~~~~---------~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~   91 (360)
T KOG0990|consen   29 QPWVE----KYRPPFLGIVIKQEPIWSTENR----YSGM---------PGLPHLLFYGPPGTGKTSTILANARDFYSPHP   91 (360)
T ss_pred             CCCcc----CCCCchhhhHhcCCchhhHHHH----hccC---------CCCCcccccCCCCCCCCCchhhhhhhhcCCCC
Confidence            46865    8899999999998766554433    3221         112389999999999999999999998432  


Q ss_pred             ----EEEEecccccCh---HHHHHHHHcCC---------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          271 ----IYDLDLSAVQSN---SELRFLLLTMP---------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       271 ----~~~l~~s~~~~~---~~l~~~~~~~~---------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                          +..++.++-..-   ..-...|+.+.         ..-.+++||.|++..                  ...+.|-.
T Consensus        92 ~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~------------------~AQnALRR  153 (360)
T KOG0990|consen   92 TTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTR------------------DAQNALRR  153 (360)
T ss_pred             chhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhH------------------HHHHHHHH
Confidence                223444433221   11112333332         567899999999753                  12222334


Q ss_pred             HhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      .+...    ..+.-++.-+|++..+.|++..  |+.. +.+...+..+-.....+....+....
T Consensus       154 viek~----t~n~rF~ii~n~~~ki~pa~qs--Rctr-frf~pl~~~~~~~r~shi~e~e~~~~  210 (360)
T KOG0990|consen  154 VIEKY----TANTRFATISNPPQKIHPAQQS--RCTR-FRFAPLTMAQQTERQSHIRESEQKET  210 (360)
T ss_pred             HHHHh----ccceEEEEeccChhhcCchhhc--cccc-CCCCCCChhhhhhHHHHHHhcchhhc
Confidence            44433    2334556788999999999998  7743 56666776666666676666554333

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.62  E-value=6.1e-08  Score=81.22  Aligned_cols=62  Identities=24%  Similarity=0.367  Sum_probs=40.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhh
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      |.||||||+|||++++.+|..+...+-.-....+-....-...+.......++++||+....
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~~   62 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQDN   62 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCccc
Confidence            57999999999999999998885333111111211111122345566678899999998754

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

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

Probab=98.61  E-value=1.9e-06  Score=83.63  Aligned_cols=176  Identities=18%  Similarity=0.167  Sum_probs=93.3

Q ss_pred             CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-cEEEEe--ccccc----------
Q 013128          214 DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-DIYDLD--LSAVQ----------  280 (449)
Q Consensus       214 ~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-~~~~l~--~s~~~----------  280 (449)
                      .....+++...+...+...          +..++|+||+|+|||++++.+++.+.. .+....  .....          
T Consensus        24 ~~~~~~~~~~~l~~~~~~~----------~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~   93 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQR----------EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAA   93 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcC----------CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHH
Confidence            3344455666555444311          234889999999999999999999863 222111  01110          


Q ss_pred             -------C--h----HHHHHHH---HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC
Q 013128          281 -------S--N----SELRFLL---LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG  344 (449)
Q Consensus       281 -------~--~----~~l~~~~---~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  344 (449)
                             .  .    ..+...+   .....+.+|+|||++.+..               .....+..|.+....    .+
T Consensus        94 ~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~---------------~~~~~l~~l~~~~~~----~~  154 (269)
T TIGR03015        94 DFGLETEGRDKAALLRELEDFLIEQFAAGKRALLVVDEAQNLTP---------------ELLEELRMLSNFQTD----NA  154 (269)
T ss_pred             HcCCCCCCCCHHHHHHHHHHHHHHHHhCCCCeEEEEECcccCCH---------------HHHHHHHHHhCcccC----CC
Confidence                   0  0    0111111   1234678999999998632               011122223332211    11


Q ss_pred             CCeEEEEEcCC--CCCCC----ccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC----CCC-HHHHHHHHHccCCCH
Q 013128          345 EGRIIVFTTNH--KEKLD----PALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH----HYL-FEQIEELIKEVNVTP  413 (449)
Q Consensus       345 ~~~iiI~tTN~--~~~ld----~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~----~~l-~~~i~~l~~~~~~tp  413 (449)
                      ..+.||++...  .+.+.    ..+.+  |+...++++..+.++...++...+...+    ..+ .+.++.+.+..+=.|
T Consensus       155 ~~~~vvl~g~~~~~~~l~~~~~~~l~~--r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p  232 (269)
T TIGR03015       155 KLLQIFLVGQPEFRETLQSPQLQQLRQ--RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIP  232 (269)
T ss_pred             CeEEEEEcCCHHHHHHHcCchhHHHHh--heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcc
Confidence            22233333321  11221    23445  7888999999999999999888775321    223 344555555555445


Q ss_pred             HHHHHHH
Q 013128          414 AEVAGEL  420 (449)
Q Consensus       414 a~i~~~l  420 (449)
                      ..|...+
T Consensus       233 ~~i~~l~  239 (269)
T TIGR03015       233 RLINILC  239 (269)
T ss_pred             cHHHHHH
Confidence            5554433

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.

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

Probab=98.60  E-value=6.3e-07  Score=84.32  Aligned_cols=156  Identities=24%  Similarity=0.303  Sum_probs=81.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc---EEEEecccccCh-------------------------------------
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSAVQSN-------------------------------------  282 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~~~~~-------------------------------------  282 (449)
                      ...++|+||+|+|||+|++.+.+.+.-.   .+.++.......                                     
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLS   99 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcch
Confidence            4679999999999999999999999421   111111110000                                     


Q ss_pred             -------HHHHHHHHcCCCCceEEeeccchhh-hcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          283 -------SELRFLLLTMPSRSMLVIEDIDCSV-KLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       283 -------~~l~~~~~~~~~~~Il~iDeiD~l~-~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                             ..+...+.....+.||+|||++.+. ..             ......+..|.+.++....  ...+.+|+++.
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~-------------~~~~~~~~~l~~~~~~~~~--~~~~~~v~~~S  164 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIAS-------------EEDKDFLKSLRSLLDSLLS--QQNVSIVITGS  164 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCT-------------TTTHHHHHHHHHHHHH------TTEEEEEEES
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcc-------------cchHHHHHHHHHHHhhccc--cCCceEEEECC
Confidence                   1111222222345999999999986 21             1123345556666665333  23344444333


Q ss_pred             CC----C--CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC---CHHHHHHHHHccCCCHHHHH
Q 013128          355 HK----E--KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY---LFEQIEELIKEVNVTPAEVA  417 (449)
Q Consensus       355 ~~----~--~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~---l~~~i~~l~~~~~~tpa~i~  417 (449)
                      ..    +  .-...+..  |+.. +.+++.+.++.++++...+... ..   -.++++.+..-.+=.|.-|.
T Consensus       165 ~~~~~~~~~~~~~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~gG~P~~l~  232 (234)
T PF01637_consen  165 SDSLMEEFLDDKSPLFG--RFSH-IELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLTGGNPRYLQ  232 (234)
T ss_dssp             SHHHHHHTT-TTSTTTT-----E-EEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHH
T ss_pred             chHHHHHhhcccCcccc--ccce-EEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHhCCCHHHHh
Confidence            21    1  12233444  7877 9999999999999999865443 32   24455666555555665554

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

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.58  E-value=1.8e-07  Score=98.33  Aligned_cols=119  Identities=24%  Similarity=0.333  Sum_probs=77.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcE--EEEecccccC---------------------hHHHHHH----------H
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDI--YDLDLSAVQS---------------------NSELRFL----------L  289 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~--~~l~~s~~~~---------------------~~~l~~~----------~  289 (449)
                      ...++|.||||||||++++.++..+...-  ..++.+.+.+                     ......+          .
T Consensus       210 G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~  289 (506)
T PRK09862        210 GHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGE  289 (506)
T ss_pred             CcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCccCCCccchHHHHhCCCceehhhH
Confidence            45799999999999999999998874210  1111111110                     0011111          2


Q ss_pred             HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc-Ccc--cc------CCCCeEEEEEcCCCC---
Q 013128          290 LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID-GLW--SC------CGEGRIIVFTTNHKE---  357 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld-g~~--~~------~~~~~iiI~tTN~~~---  357 (449)
                      .......+|||||++.+-                  ..++..|++.|+ |..  ..      ....+.+|+|+|...   
T Consensus       290 l~~A~gGvLfLDEi~e~~------------------~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~  351 (506)
T PRK09862        290 ISLAHNGVLFLDELPEFE------------------RRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGH  351 (506)
T ss_pred             hhhccCCEEecCCchhCC------------------HHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCcccee
Confidence            223457899999998753                  245666777774 221  11      123568899999753   


Q ss_pred             ------------------CCCccccCCCccceEEEeCCCCHH
Q 013128          358 ------------------KLDPALLRPGRMDMHLHMSYCNTS  381 (449)
Q Consensus       358 ------------------~ld~aLlrpgR~d~~i~l~~p~~~  381 (449)
                                        +|..+++.  |||+++.+++++.+
T Consensus       352 ~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        352 YQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             cCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence                              47778999  99999999999866

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=98.58  E-value=6.3e-07  Score=85.39  Aligned_cols=173  Identities=19%  Similarity=0.205  Sum_probs=94.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCC-CCceEEeeccchhhhcccccchhhhhcc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATN  321 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~  321 (449)
                      ..|-.++||+|||||.+++++|..+|..++.++|+.-.+-..+.+++.... ..+-+++||++++-.             
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl~~-------------   98 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRLSE-------------   98 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCSSH-------------
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhhhH-------------
Confidence            356789999999999999999999999999999999998888888887764 689999999998742             


Q ss_pred             chhhHH---HHHHHHHHhcCcc---------ccCCCCeEEEEEcCC----CCCCCccccCCCccceEEEeCCCCHHHHHH
Q 013128          322 QEENKV---TLSGLLNFIDGLW---------SCCGEGRIIVFTTNH----KEKLDPALLRPGRMDMHLHMSYCNTSVFKQ  385 (449)
Q Consensus       322 ~~~~~~---~ls~LL~~ldg~~---------~~~~~~~iiI~tTN~----~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~  385 (449)
                       +....   .+..+.+.+..-.         -......-++.|.|.    ...||+.|..  -| +-+.|..||.....+
T Consensus        99 -~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~--lF-Rpvam~~PD~~~I~e  174 (231)
T PF12774_consen   99 -EVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKA--LF-RPVAMMVPDLSLIAE  174 (231)
T ss_dssp             -HHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCT--TE-EEEE--S--HHHHHH
T ss_pred             -HHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHH--Hh-heeEEeCCCHHHHHH
Confidence             11111   1112222221100         000112335556663    3578888876  33 778999999887666


Q ss_pred             HHHHHhCcCC-CCCHHHHHHHHHccCCCHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 013128          386 LAFNYLGISH-HYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFLHA  439 (449)
Q Consensus       386 l~~~~l~~~~-~~l~~~i~~l~~~~~~tpa~i~~~l~~~~~~~~al~~l~~~l~~  439 (449)
                      +.-.-.+..+ ..+...+..+.+.       ..+.|-+....+-.|+.+...|..
T Consensus       175 i~L~s~GF~~a~~La~kl~~l~~l-------~~~~lS~q~hydfgLRalk~vl~~  222 (231)
T PF12774_consen  175 ILLLSQGFKDAKSLAKKLVSLFQL-------CKEQLSKQDHYDFGLRALKSVLRM  222 (231)
T ss_dssp             HHHHCCCTSSHHHHHHHHHHHHHH-------HHHCS-SSTT---SHHHHHHHHHH
T ss_pred             HHHHHcCchhHHHHHHHHHHHHHH-------HHHhhccCccccccHHHHHHHHHH
Confidence            6655555432 2334444433321       122222334555555555544443

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.56  E-value=3.8e-07  Score=92.01  Aligned_cols=156  Identities=21%  Similarity=0.255  Sum_probs=104.1

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE-------------
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-------------  271 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~-------------  271 (449)
                      ...|.-++|.+..|..+.-...             .|.-.|+|+-|+.|||||++++|+|.-|.--.             
T Consensus        13 ~~pf~aivGqd~lk~aL~l~av-------------~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~   79 (423)
T COG1239          13 NLPFTAIVGQDPLKLALGLNAV-------------DPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDD   79 (423)
T ss_pred             ccchhhhcCchHHHHHHhhhhc-------------ccccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCC
Confidence            4568889999999987754322             12246899999999999999999999993211             


Q ss_pred             ---------------------------EEEecccccC----hHHHHHHHH-----------cCCCCceEEeeccchhhhc
Q 013128          272 ---------------------------YDLDLSAVQS----NSELRFLLL-----------TMPSRSMLVIEDIDCSVKL  309 (449)
Q Consensus       272 ---------------------------~~l~~s~~~~----~~~l~~~~~-----------~~~~~~Il~iDeiD~l~~~  309 (449)
                                                 +.+.++...+    .-.+.+.+.           ...++.||++||+..+-. 
T Consensus        80 P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d-  158 (423)
T COG1239          80 PEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDD-  158 (423)
T ss_pred             hhhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccccH-
Confidence                                       1111111100    011122222           123678999999987742 


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhc---------CccccCCCCeEEEEEcCCC-CCCCccccCCCccceEEEeCCC-
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFID---------GLWSCCGEGRIIVFTTNHK-EKLDPALLRPGRMDMHLHMSYC-  378 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~~~~~iiI~tTN~~-~~ld~aLlrpgR~d~~i~l~~p-  378 (449)
                                       .....||+.+.         |+.-..+-.+++|+|+|.- ..|-|-|+.  ||+.+|...+| 
T Consensus       159 -----------------~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlD--Rfg~~v~~~~~~  219 (423)
T COG1239         159 -----------------HLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLD--RFGLEVDTHYPL  219 (423)
T ss_pred             -----------------HHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHh--hhcceeeccCCC
Confidence                             35566776664         3333334567899999986 468888999  99999999776 


Q ss_pred             CHHHHHHHHHHHhCc
Q 013128          379 NTSVFKQLAFNYLGI  393 (449)
Q Consensus       379 ~~~~r~~l~~~~l~~  393 (449)
                      +.+++.++..+-+..
T Consensus       220 ~~~~rv~Ii~r~~~f  234 (423)
T COG1239         220 DLEERVEIIRRRLAF  234 (423)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            457788888776654

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.56  E-value=2.2e-06  Score=82.42  Aligned_cols=113  Identities=15%  Similarity=0.127  Sum_probs=79.8

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcC----------------------CcEEEEeccc-ccChHHHHHH---HHcCC-
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLK----------------------FDIYDLDLSA-VQSNSELRFL---LLTMP-  293 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~----------------------~~~~~l~~s~-~~~~~~l~~~---~~~~~-  293 (449)
                      ..+.++||+||+|+||..+|.++|..+-                      .|++.+.... .-...+.+.+   +...+ 
T Consensus         5 ~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~   84 (261)
T PRK05818          5 NKTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSV   84 (261)
T ss_pred             CCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCch
Confidence            3467899999999999999999998872                      2344432211 1122333333   32222 


Q ss_pred             ---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccc
Q 013128          294 ---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD  370 (449)
Q Consensus       294 ---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d  370 (449)
                         ..-|++|+++|.+..                  ...+.||..++.-    +...++|++|+.++.+.|.+++  |..
T Consensus        85 e~~~~KV~II~~ae~m~~------------------~AaNaLLK~LEEP----p~~t~fiLit~~~~~lLpTI~S--RCq  140 (261)
T PRK05818         85 ESNGKKIYIIYGIEKLNK------------------QSANSLLKLIEEP----PKNTYGIFTTRNENNILNTILS--RCV  140 (261)
T ss_pred             hcCCCEEEEeccHhhhCH------------------HHHHHHHHhhcCC----CCCeEEEEEECChHhCchHhhh--hee
Confidence               357999999998743                  3567799999863    5678999999999999999999  874


Q ss_pred             eEEEeCCC
Q 013128          371 MHLHMSYC  378 (449)
Q Consensus       371 ~~i~l~~p  378 (449)
                       .+.++.+
T Consensus       141 -~~~~~~~  147 (261)
T PRK05818        141 -QYVVLSK  147 (261)
T ss_pred             -eeecCCh
Confidence             4667666

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.55  E-value=2.3e-06  Score=90.19  Aligned_cols=153  Identities=16%  Similarity=0.207  Sum_probs=97.7

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~  284 (449)
                      +.+++|.....+.+.+.+.....           ....+|+.|++||||+++|+++....   +.+++.++|..+... .
T Consensus       137 ~~~lig~s~~~~~l~~~~~~~~~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~~-~  204 (469)
T PRK10923        137 TTDIIGEAPAMQDVFRIIGRLSR-----------SSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKD-L  204 (469)
T ss_pred             cccceecCHHHHHHHHHHHHHhc-----------cCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCHH-H
Confidence            55677777666666665544332           13579999999999999999999987   468999999988432 2


Q ss_pred             HHH-HHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC-
Q 013128          285 LRF-LLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG-  344 (449)
Q Consensus       285 l~~-~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~-  344 (449)
                      +.. +|.                 ....++.|||||||.+..                  .....|+.+++.-. ...+ 
T Consensus       205 ~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~------------------~~q~~L~~~l~~~~~~~~~~  266 (469)
T PRK10923        205 IESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPL------------------DVQTRLLRVLADGQFYRVGG  266 (469)
T ss_pred             HHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCH------------------HHHHHHHHHHhcCcEEeCCC
Confidence            222 221                 123467899999998853                  12344666665321 1001 


Q ss_pred             -----CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          345 -----EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       345 -----~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                           ..+-||+||+..       ..+.+.|..  |+ ...|++|+...  ++...|+..|+.
T Consensus       267 ~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~~~~i~~PpLreR~~Di~~l~~~~l~  327 (469)
T PRK10923        267 YAPVKVDVRIIAATHQNLEQRVQEGKFREDLFH--RLNVIRVHLPPLRERREDIPRLARHFLQ  327 (469)
T ss_pred             CCeEEeeEEEEEeCCCCHHHHHHcCCchHHHHH--HhcceeecCCCcccchhhHHHHHHHHHH
Confidence                 123566666542       234556665  66 57788887654  566677777765

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.52  E-value=3.4e-06  Score=81.08  Aligned_cols=52  Identities=27%  Similarity=0.441  Sum_probs=37.4

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.++|..+.++..- .+...++.+.       -.+|++||.||||||||.||-+|+++||
T Consensus        38 ~g~vGQ~~AReAag-iivdlik~Kk-------maGravLlaGppgtGKTAlAlaisqELG   89 (456)
T KOG1942|consen   38 AGFVGQENAREAAG-IIVDLIKSKK-------MAGRAVLLAGPPGTGKTALALAISQELG   89 (456)
T ss_pred             cccccchhhhhhhh-HHHHHHHhhh-------ccCcEEEEecCCCCchhHHHHHHHHHhC
Confidence            45678877766532 2233333332       2368999999999999999999999995

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.52  E-value=6.1e-07  Score=98.95  Aligned_cols=129  Identities=16%  Similarity=0.205  Sum_probs=81.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC-------cEEEEecccccC-hHHH-HHH-----HHcCCCCceEEeeccchhhhc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF-------DIYDLDLSAVQS-NSEL-RFL-----LLTMPSRSMLVIEDIDCSVKL  309 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~-------~~~~l~~s~~~~-~~~l-~~~-----~~~~~~~~Il~iDeiD~l~~~  309 (449)
                      -.+||.|+||||||.+++++++....       +...++++.... .... ...     .......++++|||+|.+.. 
T Consensus       493 ihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms~-  571 (915)
T PTZ00111        493 INVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCHN-  571 (915)
T ss_pred             ceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccchhhhcccccCcccccCCcEEEcCCCeEEecchhhCCH-
Confidence            35999999999999999999987643       333344433211 0000 000     01123568999999998742 


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCCCeEEEEEcCCCC-------------CCCccccCCC
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGRIIVFTTNHKE-------------KLDPALLRPG  367 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~~-------------~ld~aLlrpg  367 (449)
                                       ...+.|+..|+.         .....+...-||+|+|...             .|+++|+.  
T Consensus       572 -----------------~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLS--  632 (915)
T PTZ00111        572 -----------------ESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFT--  632 (915)
T ss_pred             -----------------HHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhh--
Confidence                             233456666642         2222234568899999852             36799999  


Q ss_pred             ccceEE-EeCCCCHHHHHHHHHHHhC
Q 013128          368 RMDMHL-HMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       368 R~d~~i-~l~~p~~~~r~~l~~~~l~  392 (449)
                      |||... .++.|+.+.=+.|+.+.+.
T Consensus       633 RFDLIf~l~D~~d~~~D~~lA~hI~~  658 (915)
T PTZ00111        633 RFDLIYLVLDHIDQDTDQLISLSIAK  658 (915)
T ss_pred             hhcEEEEecCCCChHHHHHHHHHHHH
Confidence            998764 4588888777777666553

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.51  E-value=4e-06  Score=88.98  Aligned_cols=195  Identities=17%  Similarity=0.210  Sum_probs=114.3

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~s~~  279 (449)
                      .|...+.....|...+..++...        .....+++.|-||||||.+++.+-+.|          .++++.+|.-.+
T Consensus       397 sLpcRe~E~~~I~~f~~~~i~~~--------~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l  468 (767)
T KOG1514|consen  397 SLPCRENEFSEIEDFLRSFISDQ--------GLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRL  468 (767)
T ss_pred             cccchhHHHHHHHHHHHhhcCCC--------CCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceee
Confidence            34445555555555555555431        113468899999999999999999977          366777776555


Q ss_pred             cCh----------------------HHHHHHHH---cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          280 QSN----------------------SELRFLLL---TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       280 ~~~----------------------~~l~~~~~---~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                      .+.                      ..|.+-|.   ....++||+|||+|.+...                  ...-|.|
T Consensus       469 ~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr------------------~QdVlYn  530 (767)
T KOG1514|consen  469 ASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTR------------------SQDVLYN  530 (767)
T ss_pred             cCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcc------------------cHHHHHH
Confidence            432                      12223333   1236799999999999741                  1122667


Q ss_pred             HhcCccccCCCCeEEEEEcCCCCCC----CccccCCCccc-eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHKEKL----DPALLRPGRMD-MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV  409 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~~~l----d~aLlrpgR~d-~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~  409 (449)
                      ++|-.... +...+||+..|+.+..    ....-.  |++ ..|.|.+.+.+|.++|+..-|....+-..+.++-..+.+
T Consensus       531 ~fdWpt~~-~sKLvvi~IaNTmdlPEr~l~nrvsS--Rlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkV  607 (767)
T KOG1514|consen  531 IFDWPTLK-NSKLVVIAIANTMDLPERLLMNRVSS--RLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKV  607 (767)
T ss_pred             HhcCCcCC-CCceEEEEecccccCHHHHhccchhh--hccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHH
Confidence            77754432 4556777767765432    222222  443 357778888999999998877755333233333222222


Q ss_pred             CCCHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHh
Q 013128          410 NVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQ  443 (449)
Q Consensus       410 ~~tpa~i~~~l~~~~~~~~al~~l~~~l~~~~~~  443 (449)
                      +          .-++|...|++-...+.+.....
T Consensus       608 A----------avSGDaRraldic~RA~Eia~~~  631 (767)
T KOG1514|consen  608 A----------AVSGDARRALDICRRAAEIAEER  631 (767)
T ss_pred             H----------hccccHHHHHHHHHHHHHHhhhh
Confidence            1          11345566665555555544433

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.50  E-value=1.6e-06  Score=82.85  Aligned_cols=163  Identities=15%  Similarity=0.203  Sum_probs=110.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CCc----------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KFD----------  270 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~~----------  270 (449)
                      ..+|.+++.+.+..+....+.....    ..+         -.++|+|||+|+||-|.+.++-+++ |..          
T Consensus         6 kyrpksl~~l~~~~e~~~~Lksl~~----~~d---------~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t   72 (351)
T KOG2035|consen    6 KYRPKSLDELIYHEELANLLKSLSS----TGD---------FPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRT   72 (351)
T ss_pred             hcCcchhhhcccHHHHHHHHHHhcc----cCC---------CCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEE
Confidence            7889999999888887776654332    111         1479999999999999999999998 211          


Q ss_pred             ------------------EEEEecccccChHH--HHHHHHcCC-----------CCceEEeeccchhhhcccccchhhhh
Q 013128          271 ------------------IYDLDLSAVQSNSE--LRFLLLTMP-----------SRSMLVIEDIDCSVKLQNRESSEVQA  319 (449)
Q Consensus       271 ------------------~~~l~~s~~~~~~~--l~~~~~~~~-----------~~~Il~iDeiD~l~~~~~~~~~~~~~  319 (449)
                                        -+.++.|+....++  +..++....           .--+++|-|.|.+..           
T Consensus        73 ~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~-----------  141 (351)
T KOG2035|consen   73 FTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTR-----------  141 (351)
T ss_pred             EecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhH-----------
Confidence                              11223333322111  122222221           224899999998843           


Q ss_pred             ccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH
Q 013128          320 TNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF  399 (449)
Q Consensus       320 ~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~  399 (449)
                             ....+|-..|+...+.    .-+|..+|....+=+++.+  |. ..|.+|.|+.++.-.++...+..++..+.
T Consensus       142 -------dAQ~aLRRTMEkYs~~----~RlIl~cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp  207 (351)
T KOG2035|consen  142 -------DAQHALRRTMEKYSSN----CRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGLQLP  207 (351)
T ss_pred             -------HHHHHHHHHHHHHhcC----ceEEEEecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcccCc
Confidence                   1223455556554333    3567788888888889988  76 56999999999999999999998887776


Q ss_pred             HHH
Q 013128          400 EQI  402 (449)
Q Consensus       400 ~~i  402 (449)
                      .++
T Consensus       208 ~~~  210 (351)
T KOG2035|consen  208 KEL  210 (351)
T ss_pred             HHH
Confidence            554

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.49  E-value=3.4e-06  Score=88.16  Aligned_cols=154  Identities=20%  Similarity=0.213  Sum_probs=92.8

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNS  283 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~  283 (449)
                      .+..+++.....+.+.+.+.....           ....++|+|++||||+++|+++....   +.+++.++|..+... 
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~~-  204 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAP-----------SDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPEN-  204 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCChH-
Confidence            345566666666666665543322           13579999999999999999998876   468999999988542 


Q ss_pred             HHHHH-HH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC
Q 013128          284 ELRFL-LL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG  344 (449)
Q Consensus       284 ~l~~~-~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~  344 (449)
                      .+... |.                 ....+++||||||+.+..                  .....|+..++.-. ...+
T Consensus       205 ~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~------------------~~q~~l~~~l~~~~~~~~~  266 (445)
T TIGR02915       205 LLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPL------------------NLQAKLLRFLQERVIERLG  266 (445)
T ss_pred             HHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCH------------------HHHHHHHHHHhhCeEEeCC
Confidence            22222 11                 113568999999999853                  23344666664211 1111


Q ss_pred             ------CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          345 ------EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       345 ------~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                            ..+-+|+||+..       ..+.+.|..  |+ ...|++|+...  ++...|+..|+.
T Consensus       267 ~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~~~~i~lPpLr~R~~Di~~l~~~~l~  328 (445)
T TIGR02915       267 GREEIPVDVRIVCATNQDLKRMIAEGTFREDLFY--RIAEISITIPPLRSRDGDAVLLANAFLE  328 (445)
T ss_pred             CCceeeeceEEEEecCCCHHHHHHcCCccHHHHH--HhccceecCCCchhchhhHHHHHHHHHH
Confidence                  134566666553       234444443  44 35667776643  344556666654

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.47  E-value=6.3e-06  Score=89.27  Aligned_cols=50  Identities=34%  Similarity=0.369  Sum_probs=40.3

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      .-+++++|.++.++.+...+.               .+++++|+||||||||++++++|+.++.+
T Consensus        15 ~~~~~viG~~~a~~~l~~a~~---------------~~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        15 RLIDQVIGQEEAVEIIKKAAK---------------QKRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             hhHhhccCHHHHHHHHHHHHH---------------cCCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            457889999888876655443               13589999999999999999999999654

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

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=98.46  E-value=4.1e-06  Score=86.97  Aligned_cols=126  Identities=20%  Similarity=0.191  Sum_probs=86.6

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      .....+|++|+|......++++.+..+...           ...+||.|.+||||..+|++|-+..   +-+|+.+||..
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~t-----------dstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaA  306 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAKT-----------DSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAA  306 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhcCC-----------CCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEeccc
Confidence            345668999999988887777766554432           3579999999999999999999887   57999999998


Q ss_pred             ccCh---HHHH----HHHH-----------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC--
Q 013128          279 VQSN---SELR----FLLL-----------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG--  338 (449)
Q Consensus       279 ~~~~---~~l~----~~~~-----------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg--  338 (449)
                      +-..   ++|.    -.|.           +..+.+-||||||..+..                  .....||..+..  
T Consensus       307 iPe~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl------------------~LQaKLLRVLQEke  368 (560)
T COG3829         307 IPETLLESELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPL------------------PLQAKLLRVLQEKE  368 (560)
T ss_pred             CCHHHHHHHHhCcCCccccccccCCCCcceeeccCCeEEehhhccCCH------------------HHHHHHHHHHhhce
Confidence            8432   2221    1111           223567899999987742                  234556766641  


Q ss_pred             ---c--cccCCCCeEEEEEcCCC
Q 013128          339 ---L--WSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       339 ---~--~~~~~~~~iiI~tTN~~  356 (449)
                         +  ...-.-.+-||+|||..
T Consensus       369 i~rvG~t~~~~vDVRIIAATN~n  391 (560)
T COG3829         369 IERVGGTKPIPVDVRIIAATNRN  391 (560)
T ss_pred             EEecCCCCceeeEEEEEeccCcC
Confidence               1  11112236789999973

>PF05729 NACHT: NACHT domain

Probab=98.45  E-value=1.3e-06  Score=77.83  Aligned_cols=134  Identities=21%  Similarity=0.247  Sum_probs=73.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC---------cEEEEecccccChH---HHH------------------HHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF---------DIYDLDLSAVQSNS---ELR------------------FLLLTMP  293 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~---------~~~~l~~s~~~~~~---~l~------------------~~~~~~~  293 (449)
                      |-++|+|+||+|||++++.++..+..         -++.+.+.......   .+.                  ..+....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            35789999999999999999988821         12334443332211   111                  1233345


Q ss_pred             CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC-CCCccccCCCccceE
Q 013128          294 SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE-KLDPALLRPGRMDMH  372 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgR~d~~  372 (449)
                      .+.+|+||.+|.+......  .     ........+..+   +...  ....-.++|.+..+.. .+...+..    ...
T Consensus        81 ~~~llilDglDE~~~~~~~--~-----~~~~~~~~l~~l---~~~~--~~~~~~liit~r~~~~~~~~~~~~~----~~~  144 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQDQS--Q-----ERQRLLDLLSQL---LPQA--LPPGVKLIITSRPRAFPDLRRRLKQ----AQI  144 (166)
T ss_pred             CceEEEEechHhcccchhh--h-----HHHHHHHHHHHH---hhhc--cCCCCeEEEEEcCChHHHHHHhcCC----CcE
Confidence            6789999999998641111  0     001111223333   3321  1122234443332221 22222322    156


Q ss_pred             EEeCCCCHHHHHHHHHHHhCc
Q 013128          373 LHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       373 i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +++...+.++.++++++|+..
T Consensus       145 ~~l~~~~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  145 LELEPFSEEDIKQYLRKYFSN  165 (166)
T ss_pred             EEECCCCHHHHHHHHHHHhhc
Confidence            899999999999999998863

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.44  E-value=2.2e-06  Score=89.81  Aligned_cols=154  Identities=19%  Similarity=0.201  Sum_probs=90.5

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~  284 (449)
                      +..+++.......+.+.+......           ...+|++|++||||+++|+++....   +.+++.++|..+....-
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~~-----------~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~~  210 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIALS-----------QASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLL  210 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcCC-----------CcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCHHHH
Confidence            345666555555555555444332           3579999999999999999998875   47899999998854321


Q ss_pred             HHHHHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC--
Q 013128          285 LRFLLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG--  344 (449)
Q Consensus       285 l~~~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~--  344 (449)
                      -..+|.                 .....++|||||||.+..                  .....|++.++.-. ...+  
T Consensus       211 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~------------------~~q~~L~~~l~~~~~~~~~~~  272 (457)
T PRK11361        211 ESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPL------------------VLQAKLLRILQEREFERIGGH  272 (457)
T ss_pred             HHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCH------------------HHHHHHHHHHhcCcEEeCCCC
Confidence            112221                 113467999999999853                  23345666665321 1101  


Q ss_pred             ----CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          345 ----EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       345 ----~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                          ..+-||+|||..       ..+.+.|..  |+ ...|.+|+...  ++...|+..|+.
T Consensus       273 ~~~~~~~rii~~t~~~l~~~~~~g~~~~~l~~--~l~~~~i~~ppLreR~~di~~l~~~~l~  332 (457)
T PRK11361        273 QTIKVDIRIIAATNRDLQAMVKEGTFREDLFY--RLNVIHLILPPLRDRREDISLLANHFLQ  332 (457)
T ss_pred             ceeeeceEEEEeCCCCHHHHHHcCCchHHHHH--HhccceecCCChhhchhhHHHHHHHHHH
Confidence                235677777753       123333333  33 34555655542  444556666654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.42  E-value=1e-05  Score=79.38  Aligned_cols=111  Identities=17%  Similarity=0.270  Sum_probs=79.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC----------------CcEEEEecccc---cChHHHHHHHHcC---C---CCce
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK----------------FDIYDLDLSAV---QSNSELRFLLLTM---P---SRSM  297 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~----------------~~~~~l~~s~~---~~~~~l~~~~~~~---~---~~~I  297 (449)
                      +.+|||+||+|+||+.+|.++|..+-                .+++.+....-   -.-..++.+....   +   ..-|
T Consensus        19 ~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~kv   98 (290)
T PRK05917         19 PSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKI   98 (290)
T ss_pred             CeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCceE
Confidence            56899999999999999999999882                34555533211   1233444433332   2   3469


Q ss_pred             EEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCC
Q 013128          298 LVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       298 l~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~  377 (449)
                      ++||++|.+..                  ...+.||..++..    ++.+++|..|+.++.|.|.+++  |+ ..+.|+.
T Consensus        99 ~ii~~ad~mt~------------------~AaNaLLK~LEEP----p~~~~fiL~~~~~~~ll~TI~S--Rc-q~~~~~~  153 (290)
T PRK05917         99 YIIHEADRMTL------------------DAISAFLKVLEDP----PQHGVIILTSAKPQRLPPTIRS--RS-LSIHIPM  153 (290)
T ss_pred             EEEechhhcCH------------------HHHHHHHHHhhcC----CCCeEEEEEeCChhhCcHHHHh--cc-eEEEccc
Confidence            99999998853                  3457799999863    5678999999999999999998  77 4567765


Q ss_pred             C
Q 013128          378 C  378 (449)
Q Consensus       378 p  378 (449)
                      +
T Consensus       154 ~  154 (290)
T PRK05917        154 E  154 (290)
T ss_pred             h
Confidence            4

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.42  E-value=6.9e-06  Score=85.08  Aligned_cols=74  Identities=23%  Similarity=0.379  Sum_probs=56.9

Q ss_pred             cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          192 HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       192 ~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      +..|..    ...|.+.++|+-......+|.+++..+.....      ....+-+||.||+|||||+.++-||.++|+.+
T Consensus        69 ~elW~e----Ky~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~------~l~~~iLLltGPsGcGKSTtvkvLskelg~~~  138 (634)
T KOG1970|consen   69 FELWVE----KYKPRTLEELAVHKKKISEVKQWLKQVAEFTP------KLGSRILLLTGPSGCGKSTTVKVLSKELGYQL  138 (634)
T ss_pred             cchhHH----hcCcccHHHHhhhHHhHHHHHHHHHHHHHhcc------CCCceEEEEeCCCCCCchhHHHHHHHhhCcee
Confidence            456855    88999999999988888888777773222111      11245688999999999999999999999988


Q ss_pred             EEEe
Q 013128          272 YDLD  275 (449)
Q Consensus       272 ~~l~  275 (449)
                      ..-.
T Consensus       139 ~Ew~  142 (634)
T KOG1970|consen  139 IEWS  142 (634)
T ss_pred             eeec
Confidence            8654

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.41  E-value=5.5e-06  Score=87.05  Aligned_cols=153  Identities=18%  Similarity=0.245  Sum_probs=97.0

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSEL  285 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l  285 (449)
                      ..+++......++...+......           ...+++.|.+||||+++++++....   +.+++.++|..+..+ .+
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~-----------~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~~-~~  201 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRS-----------DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKD-LI  201 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCc-----------CCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCHH-HH
Confidence            45677766666777666543321           3579999999999999999998876   468999999987432 22


Q ss_pred             HHHH-H-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc-cccCC--
Q 013128          286 RFLL-L-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL-WSCCG--  344 (449)
Q Consensus       286 ~~~~-~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-~~~~~--  344 (449)
                      ...+ .                 ....++.|||||||.+..                  .....|++.++.- ....+  
T Consensus       202 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~------------------~~q~~ll~~l~~~~~~~~~~~  263 (463)
T TIGR01818       202 ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPL------------------DAQTRLLRVLADGEFYRVGGR  263 (463)
T ss_pred             HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCH------------------HHHHHHHHHHhcCcEEECCCC
Confidence            2222 1                 123468899999998853                  1234466666521 11111  


Q ss_pred             ----CCeEEEEEcCCC-------CCCCccccCCCccc-eEEEeCCCC--HHHHHHHHHHHhCc
Q 013128          345 ----EGRIIVFTTNHK-------EKLDPALLRPGRMD-MHLHMSYCN--TSVFKQLAFNYLGI  393 (449)
Q Consensus       345 ----~~~iiI~tTN~~-------~~ld~aLlrpgR~d-~~i~l~~p~--~~~r~~l~~~~l~~  393 (449)
                          ..+-||+||+..       ..+.+.|..  |+. .+|++|+..  .++...|+..|+..
T Consensus       264 ~~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~~l~~  324 (463)
T TIGR01818       264 TPIKVDVRIVAATHQNLEALVRQGKFREDLFH--RLNVIRIHLPPLRERREDIPRLARHFLAL  324 (463)
T ss_pred             ceeeeeeEEEEeCCCCHHHHHHcCCcHHHHHH--HhCcceecCCCcccchhhHHHHHHHHHHH
Confidence                134566666543       233444444  454 588899887  57788888877653

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.

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.41  E-value=1.6e-06  Score=96.09  Aligned_cols=188  Identities=22%  Similarity=0.288  Sum_probs=122.0

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcC-hhHHhhhcCCC-Cc-ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNG-KEYYTRIGRAW-KR-GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~-~~~~~~~g~~~-~r-g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      ..|..    .+.|.....+.+....-..+.+.+..+-+. +..|...+... .. ..|++||||+|||+.+.++|.++++
T Consensus       308 ~~~~~----k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~  383 (871)
T KOG1968|consen  308 AGWTE----KYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGF  383 (871)
T ss_pred             ccccc----ccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhccc
Confidence            35655    667777788888877777888887776322 12222222111 12 3699999999999999999999999


Q ss_pred             cEEEEecccccChHHHHHHHHcCC--------------------CCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          270 DIYDLDLSAVQSNSELRFLLLTMP--------------------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       270 ~~~~l~~s~~~~~~~l~~~~~~~~--------------------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                      .++..|.+...++..+...+....                    ...||++||+|.+.. .+|+.           -..+
T Consensus       384 ~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~-~dRg~-----------v~~l  451 (871)
T KOG1968|consen  384 KVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG-EDRGG-----------VSKL  451 (871)
T ss_pred             ceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc-hhhhh-----------HHHH
Confidence            999999998877655554333321                    134999999998865 22221           1123


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHH
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIK  407 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~  407 (449)
                      +.+...         ..+-||+|+|...-.....+.  |-..-++|+.|+.++...-+..++..+...+ .+.++++..
T Consensus       452 ~~l~~k---------s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~  519 (871)
T KOG1968|consen  452 SSLCKK---------SSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISK  519 (871)
T ss_pred             HHHHHh---------ccCCeEEEecCCCCccccchh--hhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHH
Confidence            333331         235688888887765553333  4446789999999988877777776654444 234444443

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

Probab=98.39  E-value=8e-07  Score=76.40  Aligned_cols=38  Identities=34%  Similarity=0.631  Sum_probs=29.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc--------CCcEEEEeccccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL--------KFDIYDLDLSAVQ  280 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l--------~~~~~~l~~s~~~  280 (449)
                      ++.++++||||+|||++++.++..+        +.+++.+++....
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   49 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR   49 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC
Confidence            4578999999999999999999998        7788888766554

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.37  E-value=1.7e-05  Score=78.40  Aligned_cols=121  Identities=17%  Similarity=0.227  Sum_probs=87.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC-------------cEEEEe--cccccChHHHHHHHHcC-------CCCceEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF-------------DIYDLD--LSAVQSNSELRFLLLTM-------PSRSMLVI  300 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~-------------~~~~l~--~s~~~~~~~l~~~~~~~-------~~~~Il~i  300 (449)
                      +..|||+|+.|+||+.++.++|+.+-.             ++..++  ... ....+++.+....       ...-|++|
T Consensus        18 ~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~-i~vd~Ir~l~~~~~~~~~~~~~~KvvII   96 (299)
T PRK07132         18 SHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKD-LSKSEFLSAINKLYFSSFVQSQKKILII   96 (299)
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCc-CCHHHHHHHHHHhccCCcccCCceEEEE
Confidence            567999999999999999999999711             344444  221 2234455444433       25679999


Q ss_pred             eccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCH
Q 013128          301 EDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT  380 (449)
Q Consensus       301 DeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~  380 (449)
                      |++|.+..                  ...+.||..|+..    ++..++|++|+.++.|-|.+.+  |+ ..++++.++.
T Consensus        97 ~~~e~m~~------------------~a~NaLLK~LEEP----p~~t~~il~~~~~~kll~TI~S--Rc-~~~~f~~l~~  151 (299)
T PRK07132         97 KNIEKTSN------------------SLLNALLKTIEEP----PKDTYFLLTTKNINKVLPTIVS--RC-QVFNVKEPDQ  151 (299)
T ss_pred             ecccccCH------------------HHHHHHHHHhhCC----CCCeEEEEEeCChHhChHHHHh--Ce-EEEECCCCCH
Confidence            99988732                  3456799999874    5667888888888999999988  66 5699999998


Q ss_pred             HHHHHHHHH
Q 013128          381 SVFKQLAFN  389 (449)
Q Consensus       381 ~~r~~l~~~  389 (449)
                      ++..+.+..
T Consensus       152 ~~l~~~l~~  160 (299)
T PRK07132        152 QKILAKLLS  160 (299)
T ss_pred             HHHHHHHHH
Confidence            887766554

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.37  E-value=3.4e-05  Score=75.81  Aligned_cols=118  Identities=21%  Similarity=0.265  Sum_probs=82.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------------------------CcEEEEeccc-ccChHHHHHHHHcC---C-
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------------------------FDIYDLDLSA-VQSNSELRFLLLTM---P-  293 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------------------------~~~~~l~~s~-~~~~~~l~~~~~~~---~-  293 (449)
                      +.+|||+||  +||+++|.++|..+-                        .+++.+.... .-....++.+....   + 
T Consensus        24 ~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p~  101 (290)
T PRK07276         24 NHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSGY  101 (290)
T ss_pred             ceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCcc
Confidence            568999996  689999999998772                        2444444322 11234455443332   2 


Q ss_pred             --CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccce
Q 013128          294 --SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDM  371 (449)
Q Consensus       294 --~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~  371 (449)
                        ..-|++||++|.+..                  ...+.||..++..    +...++|.+|+.++.|-|.+++  |+ .
T Consensus       102 ~~~~kV~II~~ad~m~~------------------~AaNaLLKtLEEP----p~~t~~iL~t~~~~~lLpTI~S--Rc-q  156 (290)
T PRK07276        102 EGKQQVFIIKDADKMHV------------------NAANSLLKVIEEP----QSEIYIFLLTNDENKVLPTIKS--RT-Q  156 (290)
T ss_pred             cCCcEEEEeehhhhcCH------------------HHHHHHHHHhcCC----CCCeEEEEEECChhhCchHHHH--cc-e
Confidence              356999999999853                  3567799999873    4568999999999999999998  77 5


Q ss_pred             EEEeCCCCHHHHHHHHH
Q 013128          372 HLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~  388 (449)
                      +|+|+. +.+...+++.
T Consensus       157 ~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        157 IFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             eeeCCC-cHHHHHHHHH
Confidence            688876 5555444443

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.36  E-value=8.8e-07  Score=89.86  Aligned_cols=96  Identities=20%  Similarity=0.389  Sum_probs=61.7

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHcCC------cEEEE--e----ccccc-ChHHHHHHHHcCCCC-ceEEeeccch
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKF------DIYDL--D----LSAVQ-SNSELRFLLLTMPSR-SMLVIEDIDC  305 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------~~~~l--~----~s~~~-~~~~l~~~~~~~~~~-~Il~iDeiD~  305 (449)
                      .+.++|++||||+|+|||+|.-+..+.+..      ++...  +    +..+. ....+........+. .||+|||++.
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~V  138 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQV  138 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeeec
Confidence            456899999999999999999999998854      11111  0    00111 112233333333344 4999999986


Q ss_pred             hhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          306 SVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       306 l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      -               +-.....+..|+..+=      ..++++|+|+|.+
T Consensus       139 ~---------------DiaDAmil~rLf~~l~------~~gvvlVaTSN~~  168 (362)
T PF03969_consen  139 T---------------DIADAMILKRLFEALF------KRGVVLVATSNRP  168 (362)
T ss_pred             c---------------chhHHHHHHHHHHHHH------HCCCEEEecCCCC
Confidence            3               2233567777777662      2578999999985

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

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

Probab=98.34  E-value=9.4e-06  Score=82.74  Aligned_cols=160  Identities=14%  Similarity=0.083  Sum_probs=109.5

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC-----CcEEEEecccccCh
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-----FDIYDLDLSAVQSN  282 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~-----~~~~~l~~s~~~~~  282 (449)
                      =.++.|.+.....+.+.+...+....         ++++++.|-||||||.+..-+-..+.     ...++++|.++...
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~~t---------~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~  219 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLELNT---------SGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEA  219 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhccc---------CcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccch
Confidence            36788888888888888777776543         56799999999999999887776663     35578888876432


Q ss_pred             HHH---------------------HHHHHc----CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc
Q 013128          283 SEL---------------------RFLLLT----MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID  337 (449)
Q Consensus       283 ~~l---------------------~~~~~~----~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld  337 (449)
                      ..+                     ...|..    ...+-|+++||+|.++. +++                  +.|-.++
T Consensus       220 ~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~t-r~~------------------~vLy~lF  280 (529)
T KOG2227|consen  220 SAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLIT-RSQ------------------TVLYTLF  280 (529)
T ss_pred             HHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhh-ccc------------------ceeeeeh
Confidence            111                     112222    12467999999999973 111                  1223333


Q ss_pred             CccccCCCCeEEEEEcCCCCCCCccccC----CCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          338 GLWSCCGEGRIIVFTTNHKEKLDPALLR----PGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       338 g~~~~~~~~~iiI~tTN~~~~ld~aLlr----pgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .+....+..+++|+..|..+.-|..|.|    -+.-...+.|++.+.++..+|++.-+....
T Consensus       281 ewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~  342 (529)
T KOG2227|consen  281 EWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEES  342 (529)
T ss_pred             hcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhccc
Confidence            3333335678888999998766655432    344567799999999999999998887653

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=1.3e-06  Score=89.57  Aligned_cols=48  Identities=33%  Similarity=0.478  Sum_probs=39.7

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...|.|+.|.+..|+.+.-..               ....++|++||||||||++|+-|..-|
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAA---------------AGgHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAA---------------AGGHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHH---------------hcCCcEEEecCCCCchHHhhhhhcccC
Confidence            457999999999998775332               225789999999999999999988877

>PRK15115 response regulator GlrR; Provisional

Probab=98.32  E-value=8.9e-06  Score=85.02  Aligned_cols=127  Identities=20%  Similarity=0.183  Sum_probs=78.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHHH-HHH-----------------cCCCCceEEeec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELRF-LLL-----------------TMPSRSMLVIED  302 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~~-~~~-----------------~~~~~~Il~iDe  302 (449)
                      ..++|+|++||||+++|+++....   +.+++.++|..+... .+.. +|.                 .....+.|||||
T Consensus       158 ~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~~-~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~  236 (444)
T PRK15115        158 VSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQ-LLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDE  236 (444)
T ss_pred             CeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCHH-HHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEc
Confidence            569999999999999999998886   478999999987432 2222 221                 123467999999


Q ss_pred             cchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC------CCeEEEEEcCCCCCCCccccCCCcc------
Q 013128          303 IDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG------EGRIIVFTTNHKEKLDPALLRPGRM------  369 (449)
Q Consensus       303 iD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~------~~~iiI~tTN~~~~ld~aLlrpgR~------  369 (449)
                      ||.+..                  .....|+.+++.-. ...|      ..+.+|+||+..  ++. +...|+|      
T Consensus       237 i~~l~~------------------~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~--l~~-~~~~~~f~~~l~~  295 (444)
T PRK15115        237 IGDMPA------------------PLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRD--LPK-AMARGEFREDLYY  295 (444)
T ss_pred             cccCCH------------------HHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCC--HHH-HHHcCCccHHHHH
Confidence            999853                  12344666665321 1111      135677777752  322 2233444      


Q ss_pred             ---ceEEEeCCCCH--HHHHHHHHHHhC
Q 013128          370 ---DMHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       370 ---d~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                         ...|++|+...  +....|+..|+.
T Consensus       296 ~l~~~~i~lPpLr~R~eDi~~l~~~~l~  323 (444)
T PRK15115        296 RLNVVSLKIPALAERTEDIPLLANHLLR  323 (444)
T ss_pred             hhceeeecCCChHhccccHHHHHHHHHH
Confidence               45666666543  345556666654

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=3.1e-06  Score=93.37  Aligned_cols=124  Identities=23%  Similarity=0.248  Sum_probs=83.1

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcC-CCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh--
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGR-AWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN--  282 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~-~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~--  282 (449)
                      +.++|+++....|-+.+.....+-      +. .+.-.+||.||.|+|||-||+|+|..+   .-.++.+|++++...  
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl------~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evsk  635 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGL------KDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSK  635 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhccc------CCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhh
Confidence            356788888888877776554321      11 234459999999999999999999998   457889999874321  


Q ss_pred             -----------HHHHHHHH--cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC-----
Q 013128          283 -----------SELRFLLL--TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG-----  344 (449)
Q Consensus       283 -----------~~l~~~~~--~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~-----  344 (449)
                                 .....+..  +....+||+|||||..-.                  ..++.|++.+|.-.-..+     
T Consensus       636 ligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkAh~------------------~v~n~llq~lD~GrltDs~Gr~V  697 (898)
T KOG1051|consen  636 LIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHP------------------DVLNILLQLLDRGRLTDSHGREV  697 (898)
T ss_pred             ccCCCcccccchhHHHHHHHHhcCCceEEEEechhhcCH------------------HHHHHHHHHHhcCccccCCCcEe
Confidence                       11112222  224569999999997532                  466778888874322222     


Q ss_pred             --CCeEEEEEcCCC
Q 013128          345 --EGRIIVFTTNHK  356 (449)
Q Consensus       345 --~~~iiI~tTN~~  356 (449)
                        .+.|||+|+|.-
T Consensus       698 d~kN~I~IMTsn~~  711 (898)
T KOG1051|consen  698 DFKNAIFIMTSNVG  711 (898)
T ss_pred             eccceEEEEecccc
Confidence              346999998863

>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=98.30  E-value=7.9e-06  Score=80.00  Aligned_cols=143  Identities=23%  Similarity=0.263  Sum_probs=76.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH--c--CCc-EEEEecccccChH------------------------HHHHHHHc--
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ--L--KFD-IYDLDLSAVQSNS------------------------ELRFLLLT--  291 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~--l--~~~-~~~l~~s~~~~~~------------------------~l~~~~~~--  291 (449)
                      .+-+.|+|++|+|||+||..+++.  .  .++ ++-++++...+..                        .+...+.+  
T Consensus        19 ~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L   98 (287)
T PF00931_consen   19 VRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELL   98 (287)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHH
T ss_pred             eEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhh
Confidence            456899999999999999999988  3  233 2334433322111                        11111111  


Q ss_pred             CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccce
Q 013128          292 MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDM  371 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~  371 (449)
                      ...+++|||||++...                    .+..+...+-.    ...+.-||.||....-. ...   +.-..
T Consensus        99 ~~~~~LlVlDdv~~~~--------------------~~~~l~~~~~~----~~~~~kilvTTR~~~v~-~~~---~~~~~  150 (287)
T PF00931_consen   99 KDKRCLLVLDDVWDEE--------------------DLEELREPLPS----FSSGSKILVTTRDRSVA-GSL---GGTDK  150 (287)
T ss_dssp             CCTSEEEEEEEE-SHH--------------------HH-------HC----HHSS-EEEEEESCGGGG-TTH---HSCEE
T ss_pred             ccccceeeeeeecccc--------------------ccccccccccc----ccccccccccccccccc-ccc---ccccc
Confidence            1348999999998642                    12222222211    11234566677653211 111   11157


Q ss_pred             EEEeCCCCHHHHHHHHHHHhCcCC----CCCHHHHHHHHHccCCCH
Q 013128          372 HLHMSYCNTSVFKQLAFNYLGISH----HYLFEQIEELIKEVNVTP  413 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~~~l~~~~----~~l~~~i~~l~~~~~~tp  413 (449)
                      .++++..+.++-.+++..+.+...    ..+.+...++++..+-.|
T Consensus       151 ~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glP  196 (287)
T PF00931_consen  151 VIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLP  196 (287)
T ss_dssp             EEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-H
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccc
Confidence            899999999999999999987644    233444455555555555

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.

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

Probab=98.27  E-value=8.8e-06  Score=79.59  Aligned_cols=179  Identities=15%  Similarity=0.165  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---------CcEEEEecccccChHHHH---
Q 013128          219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------FDIYDLDLSAVQSNSELR---  286 (449)
Q Consensus       219 ~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---------~~~~~l~~s~~~~~~~l~---  286 (449)
                      +++.+.+...+..|..      .-..++||+|++|.|||++++..+....         .+++.+.+-.--+...+-   
T Consensus        43 ~~~L~~L~~Ll~~P~~------~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~I  116 (302)
T PF05621_consen   43 KEALDRLEELLEYPKR------HRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAI  116 (302)
T ss_pred             HHHHHHHHHHHhCCcc------cCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHH
Confidence            3466777777776641      2246899999999999999999997662         356666543332222211   


Q ss_pred             ---------------------HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          287 ---------------------FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       287 ---------------------~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                                           .-+.+.-+.-+|+|||++.++..+.           .. +   ..+||.+-.+.+...=
T Consensus       117 L~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~-----------~~-q---r~~Ln~LK~L~NeL~i  181 (302)
T PF05621_consen  117 LEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSY-----------RK-Q---REFLNALKFLGNELQI  181 (302)
T ss_pred             HHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccH-----------HH-H---HHHHHHHHHHhhccCC
Confidence                                 1122334677999999999764111           11 1   2233333333222122


Q ss_pred             CeEEEEEcCCCC--CCCccccCCCccceEEEeCC-CCHHHHHHHHHHHhCc---C-CCCC-HHHH-HHHHHccCCCHHHH
Q 013128          346 GRIIVFTTNHKE--KLDPALLRPGRMDMHLHMSY-CNTSVFKQLAFNYLGI---S-HHYL-FEQI-EELIKEVNVTPAEV  416 (449)
Q Consensus       346 ~~iiI~tTN~~~--~ld~aLlrpgR~d~~i~l~~-p~~~~r~~l~~~~l~~---~-~~~l-~~~i-~~l~~~~~~tpa~i  416 (449)
                      .++.++|..-..  .-|+-+.+  ||+. +.+|. -..+++..|+..|-..   . ...+ ..++ ..+....+=+..++
T Consensus       182 piV~vGt~~A~~al~~D~QLa~--RF~~-~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l  258 (302)
T PF05621_consen  182 PIVGVGTREAYRALRTDPQLAS--RFEP-FELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGEL  258 (302)
T ss_pred             CeEEeccHHHHHHhccCHHHHh--ccCC-ccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHH
Confidence            234444433222  23777877  9965 45554 2335667777665442   1 1112 2233 44555555455566


Q ss_pred             HHHHh
Q 013128          417 AGELM  421 (449)
Q Consensus       417 ~~~l~  421 (449)
                      ..++.
T Consensus       259 ~~ll~  263 (302)
T PF05621_consen  259 SRLLN  263 (302)
T ss_pred             HHHHH
Confidence            55554

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

>PLN03210 Resistant to P

Probab=98.27  E-value=2.7e-05  Score=90.84  Aligned_cols=154  Identities=18%  Similarity=0.239  Sum_probs=90.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE---EEEeccc
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI---YDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~---~~l~~s~  278 (449)
                      ...+..+++++|.++..+++...+.           .+....+-+-|+||+|+||||||+++++.+...+   +.++...
T Consensus       177 ~~~~~~~~~~vG~~~~l~~l~~lL~-----------l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~  245 (1153)
T PLN03210        177 LTPSNDFEDFVGIEDHIAKMSSLLH-----------LESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAF  245 (1153)
T ss_pred             cccCcccccccchHHHHHHHHHHHc-----------cccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeeccc
Confidence            3445678899999888877766542           1122246688999999999999999999874321   1111100


Q ss_pred             cc------------C-h--HHH-----HHHHH--------------c-CCCCceEEeeccchhhhcccccchhhhhccch
Q 013128          279 VQ------------S-N--SEL-----RFLLL--------------T-MPSRSMLVIEDIDCSVKLQNRESSEVQATNQE  323 (449)
Q Consensus       279 ~~------------~-~--~~l-----~~~~~--------------~-~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~  323 (449)
                      +.            . +  ..+     ..++.              . ..++.+|+|||+|...                
T Consensus       246 v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~~----------------  309 (1153)
T PLN03210        246 ISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQD----------------  309 (1153)
T ss_pred             cccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCHH----------------
Confidence            00            0 0  000     01111              0 1357799999987531                


Q ss_pred             hhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          324 ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       324 ~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                          .+..|....+  |.  +.+.-||.||.+.     .+++....+..++++.|+.++..+|+..+.....
T Consensus       310 ----~l~~L~~~~~--~~--~~GsrIIiTTrd~-----~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~  368 (1153)
T PLN03210        310 ----VLDALAGQTQ--WF--GSGSRIIVITKDK-----HFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKN  368 (1153)
T ss_pred             ----HHHHHHhhCc--cC--CCCcEEEEEeCcH-----HHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCC
Confidence                1222332222  11  2334456667653     3333234677899999999999999998875443

syringae 6; Provisional

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.24  E-value=8.7e-06  Score=92.42  Aligned_cols=130  Identities=22%  Similarity=0.318  Sum_probs=94.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHH-----------------HHHHHcCCCCceEEeeccch
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSEL-----------------RFLLLTMPSRSMLVIEDIDC  305 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l-----------------~~~~~~~~~~~Il~iDeiD~  305 (449)
                      .+++||.|.||+|||+|+.|+|+..|-.++.+++++-.+--.|                 ..++..+....-+++||+..
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLDEiNL 1622 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLDEINL 1622 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEeehhhh
Confidence            4689999999999999999999999999999998876432111                 13455556788899999975


Q ss_pred             hhhcccccchhhhhccchhhHHHHHHHHHHhcC-----------ccccCCCCeEEEEEcCCC------CCCCccccCCCc
Q 013128          306 SVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-----------LWSCCGEGRIIVFTTNHK------EKLDPALLRPGR  368 (449)
Q Consensus       306 l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-----------~~~~~~~~~iiI~tTN~~------~~ld~aLlrpgR  368 (449)
                      ..                  +.++.||-..+|.           ..+ +.....|++|-|.-      ..|+..++.  |
T Consensus      1623 aS------------------QSVlEGLNacLDhR~eayIPEld~~f~-~HpnfrVFAaqNPq~qggGRKgLPkSF~n--R 1681 (4600)
T COG5271        1623 AS------------------QSVLEGLNACLDHRREAYIPELDKTFD-VHPNFRVFAAQNPQDQGGGRKGLPKSFLN--R 1681 (4600)
T ss_pred             hH------------------HHHHHHHHHHHhhccccccccccceee-ccCCeeeeeecCchhcCCCcccCCHHHhh--h
Confidence            32                  2455566555552           222 33455666676654      358999999  9


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhCcC
Q 013128          369 MDMHLHMSYCNTSVFKQLAFNYLGIS  394 (449)
Q Consensus       369 ~d~~i~l~~p~~~~r~~l~~~~l~~~  394 (449)
                      |. .|.|...+.+....|+.+.+..-
T Consensus      1682 Fs-vV~~d~lt~dDi~~Ia~~~yp~v 1706 (4600)
T COG5271        1682 FS-VVKMDGLTTDDITHIANKMYPQV 1706 (4600)
T ss_pred             hh-eEEecccccchHHHHHHhhCCcc
Confidence            94 58888888888888888777643

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=98.24  E-value=3e-05  Score=80.32  Aligned_cols=155  Identities=17%  Similarity=0.165  Sum_probs=99.7

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEecccccChH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQSNS  283 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~~~~  283 (449)
                      .+..++|.....+++.+.+......           ...||++|++||||-.+|++|-....   .+|+.+||..+-.+.
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s-----------~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l  207 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPS-----------DASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENL  207 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHHH
Confidence            4567888888888888877655443           35799999999999999999998884   599999999986442


Q ss_pred             HHHHHHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc-CccccCC-
Q 013128          284 ELRFLLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID-GLWSCCG-  344 (449)
Q Consensus       284 ~l~~~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld-g~~~~~~-  344 (449)
                      --..+|-                 +....+.||||||..+..                  .....||..+. +-....| 
T Consensus       208 ~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl------------------~~Q~kLLRvLqe~~~~rvG~  269 (464)
T COG2204         208 LESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPL------------------ELQVKLLRVLQEREFERVGG  269 (464)
T ss_pred             HHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCCH------------------HHHHHHHHHHHcCeeEecCC
Confidence            2222222                 123578999999998742                  23344666664 2111112 


Q ss_pred             -----CCeEEEEEcCCCCCCCccccCCCccc---------eEEEeCCCCH--HHHHHHHHHHhCc
Q 013128          345 -----EGRIIVFTTNHKEKLDPALLRPGRMD---------MHLHMSYCNT--SVFKQLAFNYLGI  393 (449)
Q Consensus       345 -----~~~iiI~tTN~~~~ld~aLlrpgR~d---------~~i~l~~p~~--~~r~~l~~~~l~~  393 (449)
                           -.+=||++||..  |. .....|+|-         ..|++|++-+  ++.--|+.+|+..
T Consensus       270 ~~~i~vdvRiIaaT~~d--L~-~~v~~G~FReDLyyRLnV~~i~iPpLRER~EDIp~L~~hfl~~  331 (464)
T COG2204         270 NKPIKVDVRIIAATNRD--LE-EEVAAGRFREDLYYRLNVVPLRLPPLRERKEDIPLLAEHFLKR  331 (464)
T ss_pred             CcccceeeEEEeecCcC--HH-HHHHcCCcHHHHHhhhccceecCCcccccchhHHHHHHHHHHH
Confidence                 235588888873  11 122223332         3566666644  5566677777653

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.23  E-value=8.1e-06  Score=86.32  Aligned_cols=161  Identities=21%  Similarity=0.272  Sum_probs=94.9

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhc-CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec-------ccc-c
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIG-RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL-------SAV-Q  280 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g-~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~-------s~~-~  280 (449)
                      ++.+.+++|+.++-.|  |-.....+...| ....-+|||+|.||||||.|.+.+++-+..-.|.=--       +.. .
T Consensus       430 sIye~edvKkglLLqL--fGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVt  507 (804)
T KOG0478|consen  430 SIYELEDVKKGLLLQL--FGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVT  507 (804)
T ss_pred             hhhcccchhhhHHHHH--hcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEE
Confidence            4667888888775332  222222233333 1112359999999999999999999998666553211       100 1


Q ss_pred             ChHHHHHHHHcC-----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc---------CccccCCCC
Q 013128          281 SNSELRFLLLTM-----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID---------GLWSCCGEG  346 (449)
Q Consensus       281 ~~~~l~~~~~~~-----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~~~~  346 (449)
                      .+.+-++++.+.     +..+|-+|||+|.+..                  .+-+.|+..|+         |+-.+.+-.
T Consensus       508 rd~dtkqlVLesGALVLSD~GiCCIDEFDKM~d------------------StrSvLhEvMEQQTvSIAKAGII~sLNAR  569 (804)
T KOG0478|consen  508 KDPDTRQLVLESGALVLSDNGICCIDEFDKMSD------------------STRSVLHEVMEQQTLSIAKAGIIASLNAR  569 (804)
T ss_pred             ecCccceeeeecCcEEEcCCceEEchhhhhhhH------------------HHHHHHHHHHHHhhhhHhhcceeeecccc
Confidence            111222222222     4688999999999843                  12233444443         443333344


Q ss_pred             eEEEEEcCCCC-------------CCCccccCCCccceEEEe-CCCCHHHHHHHHHHHhC
Q 013128          347 RIIVFTTNHKE-------------KLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       347 ~iiI~tTN~~~-------------~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~~l~  392 (449)
                      .=|+++.|..+             .|+|.|++  |||...-+ ..|++..=+.|..+...
T Consensus       570 ~SVLAaANP~~skynp~k~i~eNI~LpptLLS--RFDLIylllD~~DE~~Dr~La~Hivs  627 (804)
T KOG0478|consen  570 CSVLAAANPIRSKYNPNKSIIENINLPPTLLS--RFDLIFLLLDKPDERSDRRLADHIVA  627 (804)
T ss_pred             ceeeeeeccccccCCCCCchhhccCCChhhhh--hhcEEEEEecCcchhHHHHHHHHHHH
Confidence            56788888532             37899999  99976544 66776644555555444

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.20  E-value=1.8e-05  Score=82.60  Aligned_cols=150  Identities=17%  Similarity=0.153  Sum_probs=89.0

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHHH
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELRF  287 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~~  287 (449)
                      +++.......+.+.+..+..           ....++++|.+||||+++++++....   +.+++.++|+.+.. ..+..
T Consensus       141 lig~s~~~~~~~~~i~~~~~-----------~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~-~~~~~  208 (441)
T PRK10365        141 MVGKSPAMQHLLSEIALVAP-----------SEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNE-SLLES  208 (441)
T ss_pred             eEecCHHHHHHHHHHhhccC-----------CCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCH-HHHHH
Confidence            45555555555555532221           13579999999999999999998765   47899999998753 22332


Q ss_pred             HH-H-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-ccCC----
Q 013128          288 LL-L-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-SCCG----  344 (449)
Q Consensus       288 ~~-~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~----  344 (449)
                      .+ .                 ....+++|||||||.+..                  .....|+..++.-. ...+    
T Consensus       209 ~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~------------------~~q~~l~~~l~~~~~~~~~~~~~  270 (441)
T PRK10365        209 ELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP------------------MMQVRLLRAIQEREVQRVGSNQT  270 (441)
T ss_pred             HhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCH------------------HHHHHHHHHHccCcEEeCCCCce
Confidence            22 1                 123478899999999853                  12344666665321 1111    


Q ss_pred             --CCeEEEEEcCCCCCCCccccCCCcc---------ceEEEeCCCCH--HHHHHHHHHHhCc
Q 013128          345 --EGRIIVFTTNHKEKLDPALLRPGRM---------DMHLHMSYCNT--SVFKQLAFNYLGI  393 (449)
Q Consensus       345 --~~~iiI~tTN~~~~ld~aLlrpgR~---------d~~i~l~~p~~--~~r~~l~~~~l~~  393 (449)
                        ..+-+|+||+..-   ..+..+|+|         ...|.+|+...  ++...|+..|+..
T Consensus       271 ~~~~~rii~~t~~~~---~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~Di~~l~~~~l~~  329 (441)
T PRK10365        271 ISVDVRLIAATHRDL---AAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQR  329 (441)
T ss_pred             eeeceEEEEeCCCCH---HHHHHcCCchHHHHHHhccceecCCChhhcchhHHHHHHHHHHH
Confidence              1234566665421   122334444         35667776654  4566677777653

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.19  E-value=1.5e-05  Score=85.67  Aligned_cols=120  Identities=18%  Similarity=0.113  Sum_probs=85.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEeccc----ccChHHHHHHHHc-----------CCCCceEEeeccchh
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLSA----VQSNSELRFLLLT-----------MPSRSMLVIEDIDCS  306 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s~----~~~~~~l~~~~~~-----------~~~~~Il~iDeiD~l  306 (449)
                      .|+||-|++|||||+++++++..+..  ++..+..+.    +.....+...+..           .....||||||+..+
T Consensus        26 gGv~i~g~~G~~ks~~~r~l~~llp~~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~Ah~GvL~lDe~n~~  105 (584)
T PRK13406         26 GGVVLRARAGPVRDRWLAALRALLPAGTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAEADGGVLVLAMAERL  105 (584)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhcCCCCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceeeccCCEEEecCcccC
Confidence            68999999999999999999999854  776654432    1222333333322           234689999999876


Q ss_pred             hhcccccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCCCeEEEEEcCCC---CCCCccccCCCccceEEE
Q 013128          307 VKLQNRESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMDMHLH  374 (449)
Q Consensus       307 ~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d~~i~  374 (449)
                      -                  ..+++.|++.|+.         .....+...++|+|.|..   ..|.++++.  ||+++|.
T Consensus       106 ~------------------~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD--Rf~l~v~  165 (584)
T PRK13406        106 E------------------PGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD--RLAFHLD  165 (584)
T ss_pred             C------------------HHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh--heEEEEE
Confidence            4                  3578889988862         222233456778875433   458999999  9999999


Q ss_pred             eCCCCHHHH
Q 013128          375 MSYCNTSVF  383 (449)
Q Consensus       375 l~~p~~~~r  383 (449)
                      +++++..+.
T Consensus       166 v~~~~~~~~  174 (584)
T PRK13406        166 LDGLALRDA  174 (584)
T ss_pred             cCCCChHHh
Confidence            999987653

>PHA02774 E1; Provisional

Probab=98.17  E-value=9.5e-06  Score=85.61  Aligned_cols=58  Identities=26%  Similarity=0.489  Sum_probs=43.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEE-EecccccChHHHHHHHHcCCCCceEEeecc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD-LDLSAVQSNSELRFLLLTMPSRSMLVIEDI  303 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~-l~~s~~~~~~~l~~~~~~~~~~~Il~iDei  303 (449)
                      |+|.+++++||||||||||+++.+|++.++..++. ++..+       ...+......-|++|||+
T Consensus       430 ~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s-------~FwLqpl~d~ki~vlDD~  488 (613)
T PHA02774        430 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS-------HFWLQPLADAKIALLDDA  488 (613)
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc-------ccccchhccCCEEEEecC
Confidence            45556789999999999999999999999755543 55321       122444456679999999

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.16  E-value=1.6e-05  Score=70.21  Aligned_cols=63  Identities=17%  Similarity=0.346  Sum_probs=42.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-----------------------------hHH---HHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-----------------------------NSE---LRFLLL  290 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-----------------------------~~~---l~~~~~  290 (449)
                      ++|+||||+|||+++..++..+   +.+++.++......                             ...   ......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLR   81 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            6899999999999999999987   44555554322110                             011   112344


Q ss_pred             cCCCCceEEeeccchhhh
Q 013128          291 TMPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       291 ~~~~~~Il~iDeiD~l~~  308 (449)
                      ....+.+|+|||+..+..
T Consensus        82 ~~~~~~~lviDe~~~~~~   99 (165)
T cd01120          82 ERGGDDLIILDELTRLVR   99 (165)
T ss_pred             hCCCCEEEEEEcHHHHHH
Confidence            456788999999998864

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.

>PHA02624 large T antigen; Provisional

Probab=98.15  E-value=6.4e-06  Score=87.20  Aligned_cols=125  Identities=20%  Similarity=0.217  Sum_probs=80.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      |+|.++.+|||||||||||+++.+|++.++-.++.++...    +.+.+.+.-+...-+.+|||+-.-.-....-..   
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt----~ks~FwL~pl~D~~~~l~dD~t~~~~~~~~Lp~---  499 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPADNKDLPS---  499 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc----chhHHHhhhhhhceEEEeeeccccccccccCCc---
Confidence            6677889999999999999999999999966666665322    334456666667789999998643210000000   


Q ss_pred             hccchhhHHHHHHHHHHhcCccccC-----CCC-----eEEEEEcCCCCCCCccccCCCccceEEEeCC
Q 013128          319 ATNQEENKVTLSGLLNFIDGLWSCC-----GEG-----RIIVFTTNHKEKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       319 ~~~~~~~~~~ls~LL~~ldg~~~~~-----~~~-----~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~  377 (449)
                          +..-.-+.-|-+.+||--.-+     ...     --.|.|||+. .|+..+.-  ||-.++.|..
T Consensus       500 ----G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ney-~iP~T~~~--Rf~~~~~F~~  561 (647)
T PHA02624        500 ----GQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNEY-LIPQTVKA--RFAKVLDFKP  561 (647)
T ss_pred             ----ccccchhhHHHhhcCCCCccccchhccCchhccCCCeEEeecCc-ccchhHHH--HHHHhccccc
Confidence                000112345778888851100     011     1356788874 46778877  8988888764

>PHA00729 NTP-binding motif containing protein

Probab=98.06  E-value=6.1e-06  Score=77.90  Aligned_cols=133  Identities=16%  Similarity=0.214  Sum_probs=68.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE----------------ecccccChHHHHHHHHcCCCCceEEeeccchhh
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL----------------DLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l----------------~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      ..++|+|+||||||++|.++|+.++..+..+                +...+.  ..+...+.......+|+|||+..-.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll--~~L~~a~~~~~~~dlLIIDd~G~~~   95 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDAL--EKIQDAIDNDYRIPLIIFDDAGIWL   95 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHH--HHHHHHHhcCCCCCEEEEeCCchhh
Confidence            3799999999999999999999986433332                222211  1222223333334689999976433


Q ss_pred             hcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeC-CCCHHHHHHH
Q 013128          308 KLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMS-YCNTSVFKQL  386 (449)
Q Consensus       308 ~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~-~p~~~~r~~l  386 (449)
                      ..-...         .......-.+.+.+.   +   .-.++++++..++.|-..|...|=....|.=- .-....++.+
T Consensus        96 ~~~~wh---------~~~~~~yf~L~~aLr---S---R~~l~il~~ls~edL~~~Lr~Rg~~~~kI~en~~~~~~~~~~~  160 (226)
T PHA00729         96 SKYVWY---------EDYMKTFYKIYALIR---T---RVSAVIFTTPSPEDLAFYLREKGWYQIRVTMVNRKTMTARATL  160 (226)
T ss_pred             cccchh---------hhccchHHHHHHHHH---h---hCcEEEEecCCHHHHHHHHHhCCCcHHHhhhcccCcccchhhH
Confidence            200000         000011112333331   1   12367788888887777776644433333211 1111334555


Q ss_pred             HHHHhCc
Q 013128          387 AFNYLGI  393 (449)
Q Consensus       387 ~~~~l~~  393 (449)
                      .+.+...
T Consensus       161 ~~~~~~~  167 (226)
T PHA00729        161 YSKDFGR  167 (226)
T ss_pred             HHHHHhh
Confidence            5544443

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.04  E-value=1.8e-06  Score=86.95  Aligned_cols=163  Identities=19%  Similarity=0.204  Sum_probs=85.5

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc----c-----c
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA----V-----Q  280 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~----~-----~  280 (449)
                      ++.|.+.+|..|.-.|..-...... ........-++||.|.||||||.|.+.+++.....+|.--.+.    +     .
T Consensus        25 ~i~g~~~iK~aill~L~~~~~~~~~-~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~  103 (331)
T PF00493_consen   25 SIYGHEDIKKAILLQLFGGVEKNDP-DGTRIRGNIHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSR  103 (331)
T ss_dssp             TTTT-HHHHHHHCCCCTT--SCCCC-T-TEE--S--EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECC
T ss_pred             cCcCcHHHHHHHHHHHHhccccccc-cccccccccceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceecc
Confidence            4678888888775433222111000 0000111235999999999999999988877766655432111    1     0


Q ss_pred             Ch--H--HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC---------ccccCCCCe
Q 013128          281 SN--S--ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGR  347 (449)
Q Consensus       281 ~~--~--~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~  347 (449)
                      +.  .  .+..-..-....+|++|||+|.+-.                  .....|+..|+.         +....+-..
T Consensus       104 d~~~~~~~leaGalvlad~GiccIDe~dk~~~------------------~~~~~l~eaMEqq~isi~kagi~~~l~ar~  165 (331)
T PF00493_consen  104 DPVTGEWVLEAGALVLADGGICCIDEFDKMKE------------------DDRDALHEAMEQQTISIAKAGIVTTLNARC  165 (331)
T ss_dssp             CGGTSSECEEE-HHHHCTTSEEEECTTTT--C------------------HHHHHHHHHHHCSCEEECTSSSEEEEE---
T ss_pred             ccccceeEEeCCchhcccCceeeecccccccc------------------hHHHHHHHHHHcCeeccchhhhcccccchh
Confidence            10  0  0000001123679999999998742                  123456777763         211122335


Q ss_pred             EEEEEcCCCC-------------CCCccccCCCccceEEEe-CCCCHHHHHHHHHHHhCc
Q 013128          348 IIVFTTNHKE-------------KLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       348 iiI~tTN~~~-------------~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~~l~~  393 (449)
                      -|++++|...             .+++.|+.  |||..+.+ ..++.+.=+.+.++.+..
T Consensus       166 svlaa~NP~~g~~~~~~~~~~ni~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~  223 (331)
T PF00493_consen  166 SVLAAANPKFGRYDPNKSLSENINLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDS  223 (331)
T ss_dssp             EEEEEE--TT--S-TTS-CGCCT-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTT
T ss_pred             hhHHHHhhhhhhcchhhhhHHhcccchhhHh--hcCEEEEeccccccccccccceEEEec
Confidence            6888988765             47889999  99988776 667767667777766664

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=98.01  E-value=1.5e-05  Score=73.91  Aligned_cols=114  Identities=18%  Similarity=0.300  Sum_probs=61.6

Q ss_pred             eEEeCCCCCCHHHHHHHH-HHHc---CCcEEEEeccccc-----C---------------------hHHHHHHHHcCCCC
Q 013128          246 YLLYGPPGTGKSSLIAAM-ANQL---KFDIYDLDLSAVQ-----S---------------------NSELRFLLLTMPSR  295 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~ai-A~~l---~~~~~~l~~s~~~-----~---------------------~~~l~~~~~~~~~~  295 (449)
                      ++++|.||+|||+.|-.. ....   |.+++. +...+.     .                     ...+ ......+..
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t-ni~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT-NIPGLNIEKIQPVLGYDIPTRLIDLSDPDFEEDWDDP-DDWRKLPKG   80 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE---TTB-S--EEEE--TTT-S-----S--SSSEEGGGH-HHHTTSGTT
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE-ccCCcchhhhhhhccccccccccccccccchhhhhhh-hhhcccCCC
Confidence            688999999999988665 4332   666654 433221     1                     0111 222233478


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEe
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHM  375 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l  375 (449)
                      +||||||+...++.+.....            .....++.+...   ...+.-||++|.++..||+.+++  ..+.++++
T Consensus        81 ~liviDEa~~~~~~r~~~~~------------~~~~~~~~l~~h---Rh~g~diiliTQ~~~~id~~ir~--lve~~~~~  143 (193)
T PF05707_consen   81 SLIVIDEAQNFFPSRSWKGK------------KVPEIIEFLAQH---RHYGWDIILITQSPSQIDKFIRD--LVEYHYHC  143 (193)
T ss_dssp             -EEEETTGGGTSB---T-T----------------HHHHGGGGC---CCTT-EEEEEES-GGGB-HHHHC--CEEEEEEE
T ss_pred             cEEEEECChhhcCCCccccc------------cchHHHHHHHHh---CcCCcEEEEEeCCHHHHhHHHHH--HHheEEEE
Confidence            99999999998874433111            112234555432   23567899999999999999987  88888877


Q ss_pred             CCC
Q 013128          376 SYC  378 (449)
Q Consensus       376 ~~p  378 (449)
                      -.+
T Consensus       144 ~k~  146 (193)
T PF05707_consen  144 RKL  146 (193)
T ss_dssp             EE-
T ss_pred             Eee
Confidence            554

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.00  E-value=8.6e-06  Score=85.92  Aligned_cols=66  Identities=27%  Similarity=0.324  Sum_probs=51.8

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEec
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDL  276 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~  276 (449)
                      +-.-|+++.|.++.+++|++.+......-+       ..++.++|.||||+|||+|+++||+.+ .+++|.+..
T Consensus        71 ry~fF~d~yGlee~ieriv~~l~~Aa~gl~-------~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         71 RYPAFEEFYGMEEAIEQIVSYFRHAAQGLE-------EKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             cccchhcccCcHHHHHHHHHHHHHHHHhcC-------CCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            334589999999999999988865544321       124578899999999999999999998 467887654

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.99  E-value=1.7e-05  Score=74.91  Aligned_cols=23  Identities=48%  Similarity=0.846  Sum_probs=20.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      +.-+|+||+||+|||++|+.+++
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCC
Confidence            34599999999999999999974

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>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=97.98  E-value=5.3e-06  Score=70.38  Aligned_cols=31  Identities=39%  Similarity=0.778  Sum_probs=27.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      |+|.||||+||||+++.+|+.+++.++.++-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            7899999999999999999999988776653

...

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.95  E-value=5.1e-05  Score=74.58  Aligned_cols=155  Identities=19%  Similarity=0.242  Sum_probs=100.9

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHH---HcCCcEEEEeccccc-Ch---
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN---QLKFDIYDLDLSAVQ-SN---  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~---~l~~~~~~l~~s~~~-~~---  282 (449)
                      .+.|..+..+.+.+.+.+-.-..+         ...+++.||.|+|||.++...-.   +.|-+++.+-+.... ++   
T Consensus        25 ~l~g~~~~~~~l~~~lkqt~~~gE---------snsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~a   95 (408)
T KOG2228|consen   25 NLFGVQDEQKHLSELLKQTILHGE---------SNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIA   95 (408)
T ss_pred             ceeehHHHHHHHHHHHHHHHHhcC---------CCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHH
Confidence            467777888888888877665554         57899999999999998765544   456677666544321 10   


Q ss_pred             -----------------------HHHHHHHHcC-------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHH
Q 013128          283 -----------------------SELRFLLLTM-------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGL  332 (449)
Q Consensus       283 -----------------------~~l~~~~~~~-------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~L  332 (449)
                                             ..+.+++...       ..+.|.++||||...+.               .+.++  |
T Consensus        96 l~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h---------------~rQtl--l  158 (408)
T KOG2228|consen   96 LKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPH---------------SRQTL--L  158 (408)
T ss_pred             HHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccc---------------hhhHH--H
Confidence                                   1112222211       12456778899987641               12233  6


Q ss_pred             HHHhcCccccCCCCeEEEEEcCCCC---CCCccccCCCccceE-EEeC-CCCHHHHHHHHHHHhCc
Q 013128          333 LNFIDGLWSCCGEGRIIVFTTNHKE---KLDPALLRPGRMDMH-LHMS-YCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       333 L~~ldg~~~~~~~~~iiI~tTN~~~---~ld~aLlrpgR~d~~-i~l~-~p~~~~r~~l~~~~l~~  393 (449)
                      .|.+|-..+. .-.+.||+.|.+.+   .|...+..  ||... |+|+ ....++...+++..+..
T Consensus       159 YnlfDisqs~-r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~v  221 (408)
T KOG2228|consen  159 YNLFDISQSA-RAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLSV  221 (408)
T ss_pred             HHHHHHHhhc-CCCeEEEEeeccccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhcC
Confidence            6888865543 45678888776654   45567777  88655 6664 45678999999998854

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.93  E-value=6.6e-05  Score=70.23  Aligned_cols=40  Identities=25%  Similarity=0.429  Sum_probs=32.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      |++...-++++||||||||+++..+|...   +..++.++...
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            66777779999999999999999988654   56777777754

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

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.93  E-value=3.6e-05  Score=74.60  Aligned_cols=92  Identities=16%  Similarity=0.128  Sum_probs=60.6

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-----cEEE--EecccccCh
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-----DIYD--LDLSAVQSN  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-----~~~~--l~~s~~~~~  282 (449)
                      .|.|++-+++.|...+..++.++.-      ..|-.+=|||+|||||+..++.||+.+-.     +++.  +.....-.+
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p------~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~  156 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNP------RKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHA  156 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCC------CCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCCh
Confidence            5789999999999999999987641      11223448999999999999999998822     1111  111111111


Q ss_pred             -------HHHHHHHH---cCCCCceEEeeccchhh
Q 013128          283 -------SELRFLLL---TMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       283 -------~~l~~~~~---~~~~~~Il~iDeiD~l~  307 (449)
                             .+|...+.   ..-+.+|+++||+|.+-
T Consensus       157 ~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp  191 (344)
T KOG2170|consen  157 SKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLP  191 (344)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcC
Confidence                   22222222   23578999999999984

>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=97.88  E-value=0.00056  Score=69.94  Aligned_cols=82  Identities=16%  Similarity=0.210  Sum_probs=56.5

Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC---------------------CCCHHHHHHHHHccCCCHHH
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH---------------------HYLFEQIEELIKEVNVTPAE  415 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~---------------------~~l~~~i~~l~~~~~~tpa~  415 (449)
                      ..|..||  |.|.-..|.++.++++.-+..+...|....                     .....++...++..+=-..|
T Consensus       197 k~LskaL--Pn~vf~tI~L~Das~~~Ak~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltD  274 (431)
T PF10443_consen  197 KPLSKAL--PNRVFKTISLSDASPESAKQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTD  274 (431)
T ss_pred             hhHHHhC--CCCceeEEeecCCCHHHHHHHHHHHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHH
Confidence            4566777  448889999999999999999998887531                     13556777777765533334


Q ss_pred             H--HHHHhc-CCCHHHHHHHHHHHHHHH
Q 013128          416 V--AGELMK-STNAEVSLNGLVKFLHAK  440 (449)
Q Consensus       416 i--~~~l~~-~~~~~~al~~l~~~l~~~  440 (449)
                      +  --.-++ ..+|+.|++.+++.-...
T Consensus       275 Le~lvrRiksGe~p~~Av~~iI~qsa~e  302 (431)
T PF10443_consen  275 LEFLVRRIKSGESPEEAVEEIISQSASE  302 (431)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            4  222233 469999999998765543

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 [].

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.86  E-value=0.00013  Score=70.59  Aligned_cols=58  Identities=17%  Similarity=0.158  Sum_probs=41.1

Q ss_pred             eEEEEEcCC------------CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHH
Q 013128          347 RIIVFTTNH------------KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIK  407 (449)
Q Consensus       347 ~iiI~tTN~------------~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~  407 (449)
                      .++|++||+            |..++-.|+.  |+ ..|..-+.+.++.++|++.-...++..+.++...++.
T Consensus       318 PiiimaTNrgit~iRGTn~~SphGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt  387 (454)
T KOG2680|consen  318 PIIIMATNRGITRIRGTNYRSPHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLT  387 (454)
T ss_pred             cEEEEEcCCceEEeecCCCCCCCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHH
Confidence            377778875            5678888988  88 4566666667788888888777777777665555443

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

Probab=97.84  E-value=0.00014  Score=74.97  Aligned_cols=125  Identities=17%  Similarity=0.171  Sum_probs=76.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe-cccccChHHH---HHHHHcCC--CCceEEeeccchhhhcccccchhhh
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD-LSAVQSNSEL---RFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~-~s~~~~~~~l---~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      .++|+||.+||||++++.+...+.-.++.++ +.......++   ...+....  .+..||||||+++-+          
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v~~----------  108 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNVPD----------  108 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCchh----------
Confidence            7999999999999999888888865444443 3333333333   22222222  458999999998732          


Q ss_pred             hccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCC-CccccCCCccceEEEeCCCCHHHHHH------------
Q 013128          319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL-DPALLRPGRMDMHLHMSYCNTSVFKQ------------  385 (449)
Q Consensus       319 ~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l-d~aLlrpgR~d~~i~l~~p~~~~r~~------------  385 (449)
                               ....+-...|..     ..-++|.++|..-.+ ..+-.=+|| ...+++.+.++.++..            
T Consensus       109 ---------W~~~lk~l~d~~-----~~~v~itgsss~ll~~~~~~~L~GR-~~~~~l~PlSF~Efl~~~~~~~~~~~~~  173 (398)
T COG1373         109 ---------WERALKYLYDRG-----NLDVLITGSSSSLLSKEISESLAGR-GKDLELYPLSFREFLKLKGEEIEPSKLE  173 (398)
T ss_pred             ---------HHHHHHHHHccc-----cceEEEECCchhhhccchhhhcCCC-ceeEEECCCCHHHHHhhcccccchhHHH
Confidence                     222233334431     113555555544222 223334679 4789999999999854            


Q ss_pred             -HHHHHhCcC
Q 013128          386 -LAFNYLGIS  394 (449)
Q Consensus       386 -l~~~~l~~~  394 (449)
                       ++..|+...
T Consensus       174 ~~f~~Yl~~G  183 (398)
T COG1373         174 LLFEKYLETG  183 (398)
T ss_pred             HHHHHHHHhC
Confidence             678888653

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.83  E-value=1.7e-05  Score=71.42  Aligned_cols=34  Identities=32%  Similarity=0.447  Sum_probs=30.6

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .+..++|+||||||||++++++|..+++++++.+
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            3568999999999999999999999999988654

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.83  E-value=0.00024  Score=72.70  Aligned_cols=64  Identities=13%  Similarity=0.161  Sum_probs=40.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      ..++++.||||||||+++.+++.+. -..-.......+..+... ..+.......+|+|||+..+.
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG~f~T~a~Lf~~L~~-~~lg~v~~~DlLI~DEvgylp  273 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISGGTITVAKLFYNIST-RQIGLVGRWDVVAFDEVATLK  273 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcCCcCcHHHHHHHHHH-HHHhhhccCCEEEEEcCCCCc
Confidence            3589999999999999999998872 100011122222211111 344455678999999998753

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.80  E-value=0.0001  Score=65.32  Aligned_cols=24  Identities=33%  Similarity=0.679  Sum_probs=22.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      --+.+.||||+|||+++.-+|+.|
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHH
Confidence            458999999999999999999988

>PF14516 AAA_35: AAA-like domain

Probab=97.79  E-value=0.0005  Score=69.25  Aligned_cols=134  Identities=16%  Similarity=0.191  Sum_probs=80.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-----hH-------------------------------
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-----NS-------------------------------  283 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-----~~-------------------------------  283 (449)
                      +.-+.++||..+||||+...+.+.+   ++..+.+++..+..     ..                               
T Consensus        31 G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~  110 (331)
T PF14516_consen   31 GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSK  110 (331)
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCCh
Confidence            3558899999999999999988777   78888888776532     00                               


Q ss_pred             -H----HHH-HHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC-----CC-eEEEE
Q 013128          284 -E----LRF-LLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG-----EG-RIIVF  351 (449)
Q Consensus       284 -~----l~~-~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~-----~~-~iiI~  351 (449)
                       .    +.. ++....+|-||+|||||+++...                .....|+..+-.......     .. +++++
T Consensus       111 ~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~----------------~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~  174 (331)
T PF14516_consen  111 ISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYP----------------QIADDFFGLLRSWYEQRKNNPIWQKLRLILA  174 (331)
T ss_pred             hhHHHHHHHHHHhcCCCCEEEEEechhhhccCc----------------chHHHHHHHHHHHHHhcccCcccceEEEEEe
Confidence             0    001 23334578999999999987411                011223333322111100     11 23333


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      -+..+......-..|--+...|.++..+.++-..|++.|-.
T Consensus       175 ~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~  215 (331)
T PF14516_consen  175 GSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGL  215 (331)
T ss_pred             cCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhc
Confidence            22222222222245666777899999999999999987743

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.76  E-value=6.8e-05  Score=76.20  Aligned_cols=103  Identities=20%  Similarity=0.340  Sum_probs=62.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc----C-CcEEEEecccc----------------------cChHHHHHHHHcCCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL----K-FDIYDLDLSAV----------------------QSNSELRFLLLTMPSR  295 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l----~-~~~~~l~~s~~----------------------~~~~~l~~~~~~~~~~  295 (449)
                      +..++|.||+|+|||+++..||..+    + ..+..+.....                      .+...+...+......
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~  216 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNK  216 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCC
Confidence            4568999999999999999999874    3 23443433322                      1223455556666778


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccc
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPAL  363 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aL  363 (449)
                      .+|+||......                 ....+...+..+.+.... -+.++|+-+|+..+.++..+
T Consensus       217 DlVLIDTaG~~~-----------------~d~~l~e~La~L~~~~~~-~~~lLVLsAts~~~~l~evi  266 (374)
T PRK14722        217 HMVLIDTIGMSQ-----------------RDRTVSDQIAMLHGADTP-VQRLLLLNATSHGDTLNEVV  266 (374)
T ss_pred             CEEEEcCCCCCc-----------------ccHHHHHHHHHHhccCCC-CeEEEEecCccChHHHHHHH
Confidence            899999986432                 112344555656543221 12345556777777665443

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.73  E-value=0.00023  Score=75.08  Aligned_cols=163  Identities=17%  Similarity=0.254  Sum_probs=101.3

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCC--CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc-c---c--
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAW--KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS-A---V--  279 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~--~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s-~---~--  279 (449)
                      |-.+.|.+.+|.-|.-.   .+.+-..+..-|.+.  --++++.|.||||||.+.++.++.+...+|.---. +   +  
T Consensus       344 ~PsIyGhe~VK~GilL~---LfGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTa  420 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLS---LFGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTA  420 (764)
T ss_pred             CccccchHHHHhhHHHH---HhCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceE
Confidence            55678888888887533   333333222222222  23499999999999999999999998888754211 1   1  


Q ss_pred             --cChHHHHHHHHcC-----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc---------CccccC
Q 013128          280 --QSNSELRFLLLTM-----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID---------GLWSCC  343 (449)
Q Consensus       280 --~~~~~l~~~~~~~-----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~  343 (449)
                        ..+.+-.....++     ...+|-+|||+|.+-.              .    -...++..|+         |+..+.
T Consensus       421 aVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~--------------~----dqvAihEAMEQQtISIaKAGv~aTL  482 (764)
T KOG0480|consen  421 AVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDV--------------K----DQVAIHEAMEQQTISIAKAGVVATL  482 (764)
T ss_pred             EEEecCCCCceeeecCcEEEccCceEEechhcccCh--------------H----hHHHHHHHHHhheehheecceEEee
Confidence              0011111111222     3688999999998732              0    0122445554         332222


Q ss_pred             CCCeEEEEEcCCCC-------------CCCccccCCCccceE-EEeCCCCHHHHHHHHHHHhCc
Q 013128          344 GEGRIIVFTTNHKE-------------KLDPALLRPGRMDMH-LHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       344 ~~~~iiI~tTN~~~-------------~ld~aLlrpgR~d~~-i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +-..-|++++|+..             .+++++++  |||.. |-+..|++..=..|.++.+..
T Consensus       483 nARtSIlAAANPv~GhYdR~ktl~eNi~msApimS--RFDL~FiLlD~~nE~~D~~ia~hIld~  544 (764)
T KOG0480|consen  483 NARTSILAAANPVGGHYDRKKTLRENINMSAPIMS--RFDLFFILLDDCNEVVDYAIARHILDL  544 (764)
T ss_pred             cchhhhhhhcCCcCCccccccchhhhcCCCchhhh--hhcEEEEEecCCchHHHHHHHHHHHHH
Confidence            23335778888752             36889999  99964 456889998888888888765

>PRK08118 topology modulation protein; Reviewed

Probab=97.72  E-value=2.7e-05  Score=70.60  Aligned_cols=32  Identities=31%  Similarity=0.556  Sum_probs=29.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      -|++.||||+||||+|+.|++.++.+++.+|.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecch
Confidence            48999999999999999999999999988763

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

Probab=97.72  E-value=6.1e-05  Score=64.43  Aligned_cols=53  Identities=15%  Similarity=0.126  Sum_probs=42.4

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..|.|++-+++.|.+.+..++..+.      -..|--+-|+||||||||.+++.||+.+
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~------p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPN------PRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCC------CCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            4688999999999999999987652      1112235589999999999999999986

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=97.71  E-value=0.00021  Score=73.65  Aligned_cols=91  Identities=19%  Similarity=0.225  Sum_probs=68.2

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-  281 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-  281 (449)
                      ..+..++|.......+.+.++--..+           ...|||.|.+||||..+|++|-+..   +.+++.+||..+-. 
T Consensus       220 ~~~~~iIG~S~am~~ll~~i~~VA~S-----------d~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPes  288 (550)
T COG3604         220 LEVGGIIGRSPAMRQLLKEIEVVAKS-----------DSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPES  288 (550)
T ss_pred             cccccceecCHHHHHHHHHHHHHhcC-----------CCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchH
Confidence            35788999988888888877644432           3579999999999999999999887   57999999998843 


Q ss_pred             --hHHHH----HHHHc----------CCCCceEEeeccchhh
Q 013128          282 --NSELR----FLLLT----------MPSRSMLVIEDIDCSV  307 (449)
Q Consensus       282 --~~~l~----~~~~~----------~~~~~Il~iDeiD~l~  307 (449)
                        +++|.    -.|..          ....+-||+|||..+.
T Consensus       289 LlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGelP  330 (550)
T COG3604         289 LLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGELP  330 (550)
T ss_pred             HHHHHHhcccccccccchhccCcceeecCCCeEechhhccCC
Confidence              23332    11221          1357899999998764

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.70  E-value=0.00013  Score=67.34  Aligned_cols=27  Identities=22%  Similarity=0.394  Sum_probs=23.7

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .++-++|.||+|+|||+|++.+.....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~~   29 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEHP   29 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcCC
Confidence            356799999999999999999998763

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=97.69  E-value=8.3e-05  Score=80.42  Aligned_cols=156  Identities=19%  Similarity=0.219  Sum_probs=87.6

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCc---ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe-ccccc-----
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKR---GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD-LSAVQ-----  280 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~r---g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~-~s~~~-----  280 (449)
                      ++.|.+++|+.|.-.|   +.+......-| .+-|   ++||.|.||||||.|.+.+++.+...+|.-- .++-.     
T Consensus       287 sIyG~e~VKkAilLqL---fgGv~k~~~~g-~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~~GLTAa  362 (682)
T COG1241         287 SIYGHEDVKKAILLQL---FGGVKKNLPDG-TRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTAA  362 (682)
T ss_pred             cccCcHHHHHHHHHHh---cCCCcccCCCC-cccccceeEEEcCCCchhHHHHHHHHHhhCCceEEEccccccccCceeE
Confidence            5677788887775332   22211000001 1123   4999999999999999999999987777432 11110     


Q ss_pred             --ChHHHHHHHHcC-----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc---------CccccCC
Q 013128          281 --SNSELRFLLLTM-----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID---------GLWSCCG  344 (449)
Q Consensus       281 --~~~~l~~~~~~~-----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~~  344 (449)
                        .+........+.     ..++|.+|||+|.+-.                  ...+.+...|+         |+....+
T Consensus       363 v~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~~------------------~dr~aihEaMEQQtIsIaKAGI~atLn  424 (682)
T COG1241         363 VVRDKVTGEWVLEAGALVLADGGVCCIDEFDKMNE------------------EDRVAIHEAMEQQTISIAKAGITATLN  424 (682)
T ss_pred             EEEccCCCeEEEeCCEEEEecCCEEEEEeccCCCh------------------HHHHHHHHHHHhcEeeecccceeeecc
Confidence              000001111122     3689999999998732                  11233444444         2222222


Q ss_pred             CCeEEEEEcCCCC-------------CCCccccCCCccceEEEe-CCCCHHHHHHHHHH
Q 013128          345 EGRIIVFTTNHKE-------------KLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFN  389 (449)
Q Consensus       345 ~~~iiI~tTN~~~-------------~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~  389 (449)
                      -..-|++++|.+.             .|+++|++  |||..+-+ ..|+.+.=+.++.+
T Consensus       425 ARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLS--RFDLifvl~D~~d~~~D~~ia~h  481 (682)
T COG1241         425 ARCSVLAAANPKFGRYDPKKTVAENINLPAPLLS--RFDLIFVLKDDPDEEKDEEIAEH  481 (682)
T ss_pred             hhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHh--hCCeeEEecCCCCccchHHHHHH
Confidence            2335677888764             36789999  99987766 44665443333333

>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.68  E-value=0.0028  Score=58.30  Aligned_cols=137  Identities=12%  Similarity=0.156  Sum_probs=93.1

Q ss_pred             eEEEEcccCCCCcchHHHHHHHhhccCCCcccchheeccccC----------------------CCCceEEeccCCCeEE
Q 013128           52 LTIVVEEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSE----------------------KEKTFEIALDRNEETF  109 (449)
Q Consensus        52 ~ti~i~e~~~~~~n~~y~a~~~YL~t~~~~~~~~rl~~~~~~----------------------~~~~~~~~~~~~~~v~  109 (449)
                      .||.|+..     +++|+.+-.+|+.......++++.+....                      +...+.+.+..| ...
T Consensus        27 ~sv~I~~~-----D~~Y~~lm~Wls~q~~~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~G-~h~  100 (187)
T PF08740_consen   27 SSVEIPSD-----DEAYDWLMRWLSSQPFSKRSRHLSATTRSNSSWDDDESDDEDSWDTNTSDDKKKPIRFTPSPG-THW  100 (187)
T ss_pred             EEEEECCC-----CHHHHHHHHHHhhCCcccccceeEEEeecccccccccccccchhccccccCCcCCeEEEeCCC-CEE
Confidence            35566653     58999999999988765356776665522                      356788999999 667


Q ss_pred             eeecCeeeEEEEEEeecCCCCccCCCCCCCCcccCCCcceEEEEEEcCCchhHHHHHHHHHHHHHHHHHHHhCceeEEee
Q 013128          110 DVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHT  189 (449)
Q Consensus       110 D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~~~yl~~v~~~~~~~~~~~~~~~~~~  189 (449)
                      ..|+|   +|..+.++.+ +...+        .....+.+.++|++-.++.. ++.++|.+..+...  +.....+.+|.
T Consensus       101 F~y~G---~~~~~~R~~~-~~~~~--------~~~~~~~e~l~l~~lg~s~~-~l~~ll~ear~~~~--~~~~~~t~Iy~  165 (187)
T PF08740_consen  101 FWYKG---RWFWFSRQRE-SNSYN--------SWTGAPDETLTLSCLGRSPK-PLKDLLEEAREYYL--KKQKGKTTIYR  165 (187)
T ss_pred             EEECC---EEEEEEEEec-ccccc--------ccCCCCceEEEEEEecCCHH-HHHHHHHHHHHHHH--HhcCCcEEEEe
Confidence            79999   7999988875 33211        01134578999999998754 55555554444332  23334466998


Q ss_pred             ecccc--ccccccccCCCCCcccc
Q 013128          190 VMHMR--WDANNIVLKHPMTFKTL  211 (449)
Q Consensus       190 ~~~~~--w~~~~~~~~~p~~f~~l  211 (449)
                      ..+..  |..  +...++..+++|
T Consensus       166 ~~~~~~~W~~--~~~r~~RplsTV  187 (187)
T PF08740_consen  166 ADGSEYRWRR--VASRPKRPLSTV  187 (187)
T ss_pred             CCCCCCCCcC--CCCcCCCCCCCC
Confidence            87766  998  777777778775

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) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].

>PRK07261 topology modulation protein; Provisional

Probab=97.67  E-value=0.00017  Score=65.55  Aligned_cols=31  Identities=26%  Similarity=0.473  Sum_probs=27.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      +++.|+||+||||+++.++..++.+++.+|.
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~   33 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDT   33 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCC
Confidence            7899999999999999999999988776653

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.66  E-value=0.00021  Score=67.63  Aligned_cols=39  Identities=26%  Similarity=0.438  Sum_probs=32.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      |++.+.-++++||||+|||+++..+|.+.   +..++.++..
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            56666779999999999999999999755   6777777766

>cd01394 radB RadB

Probab=97.66  E-value=0.00036  Score=65.66  Aligned_cols=38  Identities=29%  Similarity=0.461  Sum_probs=30.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |++.+.-++++||||||||+++..+|.++   +.+++.++.
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~   55 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDT   55 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEC
Confidence            56666779999999999999999999776   456666654

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

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.65  E-value=0.00065  Score=69.62  Aligned_cols=65  Identities=26%  Similarity=0.398  Sum_probs=43.1

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcC-------CcEE--EEeccccc--------------------ChHHHHHHHHcC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLK-------FDIY--DLDLSAVQ--------------------SNSELRFLLLTM  292 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~-------~~~~--~l~~s~~~--------------------~~~~l~~~~~~~  292 (449)
                      .++.++|+||+|+||||++..+|..+.       ..+.  .+|+-...                    ....+...+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~  252 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQS  252 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHh
Confidence            356799999999999999999998762       3333  44432221                    123344444555


Q ss_pred             CCCceEEeeccchh
Q 013128          293 PSRSMLVIEDIDCS  306 (449)
Q Consensus       293 ~~~~Il~iDeiD~l  306 (449)
                      ....+|+||.+..+
T Consensus       253 ~~~DlVLIDTaGr~  266 (388)
T PRK12723        253 KDFDLVLVDTIGKS  266 (388)
T ss_pred             CCCCEEEEcCCCCC
Confidence            56778999988765

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.64  E-value=0.00053  Score=68.06  Aligned_cols=128  Identities=17%  Similarity=0.237  Sum_probs=88.0

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +.+.+...|+.+++.....+.+.+....+.-           ....+|+.|..||||-.+|+|.-...   +.+|+.++|
T Consensus       195 ~~~~~~~~F~~~v~~S~~mk~~v~qA~k~Am-----------lDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNC  263 (511)
T COG3283         195 VAAQDVSGFEQIVAVSPKMKHVVEQAQKLAM-----------LDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNC  263 (511)
T ss_pred             cccccccchHHHhhccHHHHHHHHHHHHhhc-----------cCCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeec
Confidence            3455667899999888777777665544332           12468999999999999999876655   579999999


Q ss_pred             ccccChHHHHHHHHc------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHh-cCccccC
Q 013128          277 SAVQSNSELRFLLLT------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFI-DGLWSCC  343 (449)
Q Consensus       277 s~~~~~~~l~~~~~~------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~l-dg~~~~~  343 (449)
                      ..+-.+..-..+|-.            ..+..-+++|||..+.+                  .....||.++ ||.....
T Consensus       264 A~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEmSp------------------~lQaKLLRFL~DGtFRRV  325 (511)
T COG3283         264 ASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEMSP------------------RLQAKLLRFLNDGTFRRV  325 (511)
T ss_pred             CCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhcCH------------------HHHHHHHHHhcCCceeec
Confidence            998654333333333            34567889999987643                  2334466666 5665555


Q ss_pred             CCC------eEEEEEcCCC
Q 013128          344 GEG------RIIVFTTNHK  356 (449)
Q Consensus       344 ~~~------~iiI~tTN~~  356 (449)
                      |++      +-||+||..+
T Consensus       326 Gee~Ev~vdVRVIcatq~n  344 (511)
T COG3283         326 GEDHEVHVDVRVICATQVN  344 (511)
T ss_pred             CCcceEEEEEEEEeccccc
Confidence            543      5688888764

>TIGR02012 tigrfam_recA protein RecA

Probab=97.64  E-value=0.00025  Score=70.74  Aligned_cols=70  Identities=19%  Similarity=0.249  Sum_probs=45.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc---------------------ChH---HHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ---------------------SNS---ELRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~---------------------~~~---~l~~~~~~  291 (449)
                      |.+..+.++++||||||||+|+..++...   +..+..++.....                     +..   .+...+.+
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~  130 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVR  130 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            56667779999999999999988766554   4455555432210                     111   11122233


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+||||-+.++.+
T Consensus       131 ~~~~~lIVIDSv~al~~  147 (321)
T TIGR02012       131 SGAVDIIVVDSVAALVP  147 (321)
T ss_pred             ccCCcEEEEcchhhhcc
Confidence            45788999999998865

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.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.63  E-value=0.00033  Score=63.94  Aligned_cols=30  Identities=27%  Similarity=0.243  Sum_probs=23.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +|++||||||||+++..++.+.   |..++.++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            7899999999999999887765   45555544

A related protein is found in archaea.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.63  E-value=0.00028  Score=65.74  Aligned_cols=110  Identities=20%  Similarity=0.312  Sum_probs=63.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      |......++|.|+.|+|||++++.|+.+.    +.-+.....+..    ....+...-|+.|||++.+..          
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~~----~~d~~~~~~~kd----~~~~l~~~~iveldEl~~~~k----------  109 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPEY----FSDSINDFDDKD----FLEQLQGKWIVELDELDGLSK----------  109 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHHh----ccCccccCCCcH----HHHHHHHhHheeHHHHhhcch----------
Confidence            44444568899999999999999997762    211122222222    223344568899999998642          


Q ss_pred             hccchhhHHHHHHHHHHhc----Ccc-------ccCCCCeEEEEEcCCCCCC-CccccCCCccceEEEeCC
Q 013128          319 ATNQEENKVTLSGLLNFID----GLW-------SCCGEGRIIVFTTNHKEKL-DPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       319 ~~~~~~~~~~ls~LL~~ld----g~~-------~~~~~~~iiI~tTN~~~~l-d~aLlrpgR~d~~i~l~~  377 (449)
                              .....|-+++.    ...       ...+...++|+|||..+-| |+.=-|  || ..|+++.
T Consensus       110 --------~~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~  169 (198)
T PF05272_consen  110 --------KDVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSK  169 (198)
T ss_pred             --------hhHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCe--EE-EEEEEcC
Confidence                    11122333322    111       1112335788999998755 555667  77 4455554

>PRK13947 shikimate kinase; Provisional

Probab=97.62  E-value=5.3e-05  Score=68.43  Aligned_cols=32  Identities=34%  Similarity=0.474  Sum_probs=29.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .++|.|+||||||++++.+|+.+++++++.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d~   34 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDK   34 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECch
Confidence            58999999999999999999999999988763

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.61  E-value=0.00043  Score=66.05  Aligned_cols=38  Identities=26%  Similarity=0.323  Sum_probs=29.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |++.+..++++||||||||+++.+++...   +..++.++.
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            67777889999999999999999997653   555555543

>PRK03839 putative kinase; Provisional

Probab=97.61  E-value=5e-05  Score=69.37  Aligned_cols=30  Identities=30%  Similarity=0.626  Sum_probs=27.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++|.|+||+||||+++.+|+.+++++++++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            789999999999999999999999987764

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

Probab=97.61  E-value=3.8e-05  Score=69.81  Aligned_cols=59  Identities=22%  Similarity=0.320  Sum_probs=36.1

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc---EEEEecccc
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSAV  279 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~~  279 (449)
                      ++|-++..+++...+. .....         .++.++|+||+|+|||+++++++..+...   ++.+++...
T Consensus         2 fvgR~~e~~~l~~~l~-~~~~~---------~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLD-AAQSG---------SPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTG-GTSS--------------EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHH-HHHcC---------CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            4566666666666554 22222         25789999999999999999998888443   677766655

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=97.60  E-value=6e-05  Score=66.58  Aligned_cols=31  Identities=32%  Similarity=0.489  Sum_probs=28.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .++|+||||+|||++++.+|..+++++++.+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3789999999999999999999999988765

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.

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=97.59  E-value=0.00021  Score=81.11  Aligned_cols=140  Identities=18%  Similarity=0.250  Sum_probs=90.3

Q ss_pred             CCCcceEEeCCCCCCHHH-HHHHHHHHcCCcEEEEecccccChH-HHHHHHHcC------------C----CCceEEeec
Q 013128          241 AWKRGYLLYGPPGTGKSS-LIAAMANQLKFDIYDLDLSAVQSNS-ELRFLLLTM------------P----SRSMLVIED  302 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~-la~aiA~~l~~~~~~l~~s~~~~~~-~l~~~~~~~------------~----~~~Il~iDe  302 (449)
                      ...|+|+++||||+|||+ +.-++-+++-++++.++.+.-.... .+..+-..+            +    +..||+.||
T Consensus      1492 nt~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcDe 1571 (3164)
T COG5245        1492 NTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCDE 1571 (3164)
T ss_pred             hccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEeec
Confidence            346899999999999998 4778899999999999988776444 444333332            1    235899999


Q ss_pred             cchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC------CCeEEEEEcCCCCCC-----CccccCCCccce
Q 013128          303 IDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG------EGRIIVFTTNHKEKL-----DPALLRPGRMDM  371 (449)
Q Consensus       303 iD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~~l-----d~aLlrpgR~d~  371 (449)
                      |. +.....-..         .....+-.-|-.-.|+|++..      .++++++++|.+...     ...++|  | .+
T Consensus      1572 In-Lp~~~~y~~---------~~vI~FlR~l~e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv~~~eRf~r--~-~v 1638 (3164)
T COG5245        1572 IN-LPYGFEYYP---------PTVIVFLRPLVERQGFWSSIAVSWVTICGIILYGACNPGTDEGRVKYYERFIR--K-PV 1638 (3164)
T ss_pred             cC-CccccccCC---------CceEEeeHHHHHhcccccchhhhHhhhcceEEEccCCCCCCcccCccHHHHhc--C-ce
Confidence            98 322111111         111111111122246776422      346788899987543     244554  2 46


Q ss_pred             EEEeCCCCHHHHHHHHHHHhCc
Q 013128          372 HLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      .+++.||.-....+|...+|..
T Consensus      1639 ~vf~~ype~~SL~~Iyea~l~~ 1660 (3164)
T COG5245        1639 FVFCCYPELASLRNIYEAVLMG 1660 (3164)
T ss_pred             EEEecCcchhhHHHHHHHHHHH
Confidence            7889999999999998877753

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

Probab=97.59  E-value=0.0003  Score=70.22  Aligned_cols=70  Identities=17%  Similarity=0.227  Sum_probs=46.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc---------------------ChHHH---HHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ---------------------SNSEL---RFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~---------------------~~~~l---~~~~~~  291 (449)
                      |++..+-+++|||||||||+|+..+|...   +.....++...-.                     +..++   ...+.+
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~  130 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVR  130 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHh
Confidence            56666779999999999999999877554   5556666542210                     11111   122333


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      .....+||||-+-++.+
T Consensus       131 s~~~~lIVIDSvaal~~  147 (325)
T cd00983         131 SGAVDLIVVDSVAALVP  147 (325)
T ss_pred             ccCCCEEEEcchHhhcc
Confidence            45788999999998875

RecA couples ATP hydrolysis to DNA strand exchange.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.59  E-value=0.00091  Score=62.20  Aligned_cols=64  Identities=25%  Similarity=0.477  Sum_probs=40.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh----------HHHHHHHHc-----------CCCCceEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN----------SELRFLLLT-----------MPSRSMLV  299 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~----------~~l~~~~~~-----------~~~~~Il~  299 (449)
                      +..+|.||||||||++++.++..+   +..++.+..+.-...          ..+..++..           .....+|+
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vli   98 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPELPKKDVLI   98 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC-TSTSEEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCcccccccccCCcccEEE
Confidence            568889999999999999988776   567777765543211          111222221           12347999


Q ss_pred             eeccchhh
Q 013128          300 IEDIDCSV  307 (449)
Q Consensus       300 iDeiD~l~  307 (449)
                      |||+..+.
T Consensus        99 VDEasmv~  106 (196)
T PF13604_consen   99 VDEASMVD  106 (196)
T ss_dssp             ESSGGG-B
T ss_pred             EecccccC
Confidence            99998763

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

Probab=97.59  E-value=0.0004  Score=65.62  Aligned_cols=40  Identities=23%  Similarity=0.256  Sum_probs=30.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---C------CcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---K------FDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~------~~~~~l~~s~  278 (449)
                      |++...-+.|+||||+|||+++..+|...   +      ..++.++...
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            56666779999999999999999998764   2      4556665543

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.

>PRK00625 shikimate kinase; Provisional

Probab=97.57  E-value=6.4e-05  Score=68.51  Aligned_cols=31  Identities=35%  Similarity=0.545  Sum_probs=29.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .++|.|+||+|||++++.+|+.++++++++|
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            4899999999999999999999999999876

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.56  E-value=0.00066  Score=61.67  Aligned_cols=64  Identities=17%  Similarity=0.212  Sum_probs=47.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChH-----------------------HHHHHHHc-CCCCceEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNS-----------------------ELRFLLLT-MPSRSMLVI  300 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~-----------------------~l~~~~~~-~~~~~Il~i  300 (449)
                      -+|+.||||+|||++|..++..++.+++.+.........                       ++..++.. ..++.+++|
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~~~VlI   82 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQPFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPGRCVLV   82 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCCCChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCCCEEEe
Confidence            479999999999999999999998887777665543321                       23344444 345678999


Q ss_pred             eccchhhh
Q 013128          301 EDIDCSVK  308 (449)
Q Consensus       301 DeiD~l~~  308 (449)
                      |-+..+..
T Consensus        83 D~Lt~~~~   90 (170)
T PRK05800         83 DCLTTWVT   90 (170)
T ss_pred             hhHHHHHH
Confidence            98887753

>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=97.56  E-value=4.3e-05  Score=66.66  Aligned_cols=28  Identities=39%  Similarity=0.706  Sum_probs=24.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      +++.||||+||||+|+.++..++..++.
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~i~   29 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVVIS   29 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEEEe
Confidence            6899999999999999999999944443

...

>PRK04040 adenylate kinase; Provisional

Probab=97.55  E-value=0.00045  Score=63.84  Aligned_cols=29  Identities=24%  Similarity=0.566  Sum_probs=25.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc--CCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL--KFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l--~~~~~  272 (449)
                      .-++++|+||||||++++.++..+  ++.++
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~   33 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeEE
Confidence            468999999999999999999999  55553

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.55  E-value=0.00029  Score=69.95  Aligned_cols=96  Identities=21%  Similarity=0.312  Sum_probs=59.9

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE-EEEecccccC--hHHHHHH----------HHc-CCCCceEEeeccch
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI-YDLDLSAVQS--NSELRFL----------LLT-MPSRSMLVIEDIDC  305 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~-~~l~~s~~~~--~~~l~~~----------~~~-~~~~~Il~iDeiD~  305 (449)
                      ...++|++||||-|+|||.|.-.....+...- ..+-...+..  -.++..+          -.+ ..+--||+|||+..
T Consensus        62 ~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF~V  141 (367)
T COG1485          62 HGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEFEV  141 (367)
T ss_pred             CCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeeeee
Confidence            34678999999999999999999888774422 1111111100  0111111          111 12456999999985


Q ss_pred             hhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          306 SVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       306 l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      -               +-.....++.|++.+=      ..++++|+|+|.+
T Consensus       142 t---------------DI~DAMiL~rL~~~Lf------~~GV~lvaTSN~~  171 (367)
T COG1485         142 T---------------DIADAMILGRLLEALF------ARGVVLVATSNTA  171 (367)
T ss_pred             c---------------ChHHHHHHHHHHHHHH------HCCcEEEEeCCCC
Confidence            2               2334567888888773      2578999999974

>PRK13949 shikimate kinase; Provisional

Probab=97.55  E-value=6.9e-05  Score=68.03  Aligned_cols=31  Identities=39%  Similarity=0.561  Sum_probs=29.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .++|.||||+|||++++.+|+.+++++++.|
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            5899999999999999999999999998876

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.54  E-value=0.00047  Score=65.58  Aligned_cols=40  Identities=20%  Similarity=0.214  Sum_probs=30.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~  278 (449)
                      |++...-+.|+||||||||+++..+|...         +..++.++...
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            56666679999999999999999998553         24666666543

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 .

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.51  E-value=0.0054  Score=69.83  Aligned_cols=151  Identities=17%  Similarity=0.115  Sum_probs=84.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh--------------------------------H----HHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN--------------------------------S----ELR  286 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~--------------------------------~----~l~  286 (449)
                      .+-+++.||+|.|||+++...+...+ ++.-+++..-.++                                .    -+.
T Consensus        32 ~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (903)
T PRK04841         32 YRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFA  110 (903)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHH
Confidence            35699999999999999999888776 5555544321100                                0    011


Q ss_pred             HHH---HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCc-c
Q 013128          287 FLL---LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDP-A  362 (449)
Q Consensus       287 ~~~---~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~-a  362 (449)
                      .++   .....|.+|||||++.+-.              ......+..|+..+       +..+.+|.|+.....++- .
T Consensus       111 ~~~~~l~~~~~~~~lvlDD~h~~~~--------------~~~~~~l~~l~~~~-------~~~~~lv~~sR~~~~~~~~~  169 (903)
T PRK04841        111 QLFIELADWHQPLYLVIDDYHLITN--------------PEIHEAMRFFLRHQ-------PENLTLVVLSRNLPPLGIAN  169 (903)
T ss_pred             HHHHHHhcCCCCEEEEEeCcCcCCC--------------hHHHHHHHHHHHhC-------CCCeEEEEEeCCCCCCchHh
Confidence            112   2235789999999998631              11122333444432       334455556654222221 1


Q ss_pred             ccCCCccceEEEeC----CCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHHHH
Q 013128          363 LLRPGRMDMHLHMS----YCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       363 LlrpgR~d~~i~l~----~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~~l  420 (449)
                      +.-.|.   .+++.    ..+.++-..++...++..  .-.++++.+.+.++=-|.-+....
T Consensus       170 l~~~~~---~~~l~~~~l~f~~~e~~~ll~~~~~~~--~~~~~~~~l~~~t~Gwp~~l~l~~  226 (903)
T PRK04841        170 LRVRDQ---LLEIGSQQLAFDHQEAQQFFDQRLSSP--IEAAESSRLCDDVEGWATALQLIA  226 (903)
T ss_pred             HHhcCc---ceecCHHhCCCCHHHHHHHHHhccCCC--CCHHHHHHHHHHhCChHHHHHHHH
Confidence            111112   23444    678888888888766642  234566777776666665554433

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.49  E-value=8.1e-05  Score=67.19  Aligned_cols=32  Identities=34%  Similarity=0.465  Sum_probs=30.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.+.|.|++|+||||+.+++|+.|+++|++.|
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccch
Confidence            56899999999999999999999999999887

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.49  E-value=0.0012  Score=60.04  Aligned_cols=63  Identities=17%  Similarity=0.216  Sum_probs=45.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh-----------------------HHHHHHHHcCCCCceEEeec
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN-----------------------SELRFLLLTMPSRSMLVIED  302 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~-----------------------~~l~~~~~~~~~~~Il~iDe  302 (449)
                      +|+.||||+|||++|..++...+.+.+++......+.                       .++...+...+.+.+++||-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLIDc   81 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLIDC   81 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEEc
Confidence            6899999999999999999987777877765543221                       23334444444567899999


Q ss_pred             cchhhh
Q 013128          303 IDCSVK  308 (449)
Q Consensus       303 iD~l~~  308 (449)
                      +..+..
T Consensus        82 lt~~~~   87 (169)
T cd00544          82 LTLWVT   87 (169)
T ss_pred             HhHHHH
Confidence            887654

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.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.47  E-value=0.00074  Score=62.98  Aligned_cols=63  Identities=14%  Similarity=0.305  Sum_probs=41.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CCcEE-------------EEec-cccc--------ChHHHHHHHHcCC--
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KFDIY-------------DLDL-SAVQ--------SNSELRFLLLTMP--  293 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~-------------~l~~-s~~~--------~~~~l~~~~~~~~--  293 (449)
                      .+.++|.||.|+|||+++++++...     |.++-             .+.. ..+.        .-.++..++....  
T Consensus        25 g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~~  104 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKG  104 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccCC
Confidence            4678999999999999999999543     43320             1100 0000        0134556677777  


Q ss_pred             CCceEEeeccch
Q 013128          294 SRSMLVIEDIDC  305 (449)
Q Consensus       294 ~~~Il~iDeiD~  305 (449)
                      .|.++++||.-.
T Consensus       105 ~p~llllDEp~~  116 (199)
T cd03283         105 EPVLFLLDEIFK  116 (199)
T ss_pred             CCeEEEEecccC
Confidence            899999999754

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

>PRK13948 shikimate kinase; Provisional

Probab=97.47  E-value=0.00013  Score=67.03  Aligned_cols=34  Identities=29%  Similarity=0.217  Sum_probs=31.6

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .++.++|.|++|||||++++.+|+.+++++++.|
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            3578999999999999999999999999999887

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.45  E-value=0.00063  Score=64.12  Aligned_cols=104  Identities=17%  Similarity=0.210  Sum_probs=58.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHH-----HcCCcE---------EEEecccccC--------------hHHHHHHHHcCCCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMAN-----QLKFDI---------YDLDLSAVQS--------------NSELRFLLLTMPSR  295 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~-----~l~~~~---------~~l~~s~~~~--------------~~~l~~~~~~~~~~  295 (449)
                      +.++|.||.|+|||++.+.++.     ..|..+         ++-....+..              -..+...+.....+
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~~~~si~~~~S~f~~el~~l~~~l~~~~~~  109 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRR  109 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeCCccChhhccchHHHHHHHHHHHHHhCCCC
Confidence            6799999999999999999983     233221         1111111111              12334445556789


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccc
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPAL  363 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aL  363 (449)
                      ++++|||+..-..             .......+..++..+-.   .......+|++|...+.+....
T Consensus       110 slvllDE~~~gtd-------------~~~~~~~~~ail~~l~~---~~~~~~~vli~TH~~~l~~~~~  161 (213)
T cd03281         110 SLVLIDEFGKGTD-------------TEDGAGLLIATIEHLLK---RGPECPRVIVSTHFHELFNRSL  161 (213)
T ss_pred             cEEEeccccCCCC-------------HHHHHHHHHHHHHHHHh---cCCCCcEEEEEcChHHHHHhhh
Confidence            9999999976431             11122333334444411   1012347888888876554443

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

>PRK05973 replicative DNA helicase; Provisional

Probab=97.44  E-value=0.00075  Score=64.53  Aligned_cols=37  Identities=22%  Similarity=0.008  Sum_probs=27.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |.+++.-+|+.|+||+|||+++..+|.+.   |.+++.++
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            55556679999999999999998877655   55554443

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.43  E-value=0.00012  Score=66.74  Aligned_cols=29  Identities=24%  Similarity=0.502  Sum_probs=25.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +++.||||+|||++++.+|..+++..+..
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            68999999999999999999998755543

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.

>PTZ00202 tuzin; Provisional

Probab=97.43  E-value=0.014  Score=60.30  Aligned_cols=63  Identities=19%  Similarity=0.219  Sum_probs=48.4

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS  277 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s  277 (449)
                      |....+.+|-+.....+...+..          .....++-+.|.||+|||||++++.++..++...+.+|+.
T Consensus       258 Pa~~~~FVGReaEla~Lr~VL~~----------~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNpr  320 (550)
T PTZ00202        258 PAVIRQFVSREAEESWVRQVLRR----------LDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVR  320 (550)
T ss_pred             CCCccCCCCcHHHHHHHHHHHhc----------cCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCC
Confidence            44566788888887777666542          1122245788999999999999999999999888888877

>PRK06217 hypothetical protein; Validated

Probab=97.43  E-value=0.00014  Score=66.84  Aligned_cols=31  Identities=32%  Similarity=0.485  Sum_probs=28.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -|+|.|+||+||||++++++..++.+++++|
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            3899999999999999999999999887765

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.41  E-value=0.00013  Score=64.30  Aligned_cols=28  Identities=32%  Similarity=0.492  Sum_probs=25.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ++|.||||+|||++++.++..++..+++
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            6899999999999999999998876654

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.41  E-value=0.00027  Score=70.54  Aligned_cols=58  Identities=22%  Similarity=0.330  Sum_probs=43.5

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..++.++.+.+.++..+....     -..++..+.|.|+||||||++++.+|..+|+++++++
T Consensus       108 l~~~~~~~~~~~l~~~~~~~~-----~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D  165 (309)
T PRK08154        108 ASPAQLARVRDALSGMLGAGR-----RAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVELN  165 (309)
T ss_pred             CCHHHHHHHHHHHHHHHhhhh-----hccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHH
Confidence            455666666666666554332     1334567999999999999999999999999999665

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.41  E-value=0.0015  Score=68.06  Aligned_cols=63  Identities=14%  Similarity=0.191  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      .+.+.+.+.+...+.......... ..|..++++||+|+|||+++..+|..+   +..+..+++...
T Consensus        69 ~~~~~v~~~L~~~l~~~~~~~~~~-~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~  134 (437)
T PRK00771         69 HVIKIVYEELVKLLGEETEPLVLP-LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTY  134 (437)
T ss_pred             HHHHHHHHHHHHHhCCCccccccC-CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCC
Confidence            445566666666555332111111 236679999999999999999999888   455665655443

>PRK14532 adenylate kinase; Provisional

Probab=97.40  E-value=0.00014  Score=66.84  Aligned_cols=30  Identities=20%  Similarity=0.464  Sum_probs=26.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .++|.||||+||||+++.+|..+++..++.
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            388999999999999999999999877654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.40  E-value=0.00088  Score=65.93  Aligned_cols=36  Identities=22%  Similarity=0.342  Sum_probs=28.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc----C-CcEEEEeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL----K-FDIYDLDLSA  278 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l----~-~~~~~l~~s~  278 (449)
                      ++.++|.||+|+||||++..+|..+    + ..+..+++..
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~  234 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDT  234 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCc
Confidence            4468899999999999999999877    3 5566565544

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.39  E-value=0.0013  Score=66.55  Aligned_cols=24  Identities=29%  Similarity=0.535  Sum_probs=21.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -.||.||||||||+|++.+|+.+.
T Consensus       135 R~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            379999999999999999999873

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=97.39  E-value=0.00048  Score=68.88  Aligned_cols=65  Identities=31%  Similarity=0.420  Sum_probs=50.9

Q ss_pred             cc-cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEecccc
Q 013128          208 FK-TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAV  279 (449)
Q Consensus       208 f~-~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~  279 (449)
                      |+ ++.|.++...++++.+.....+-+       ..++-+||.||+|+|||++++.+.+-+ .+++|.+..+-+
T Consensus        59 f~~~~~G~~~~i~~lV~~fk~AA~g~~-------~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~~~Pm  125 (358)
T PF08298_consen   59 FEDEFYGMEETIERLVNYFKSAAQGLE-------ERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLKGCPM  125 (358)
T ss_pred             ccccccCcHHHHHHHHHHHHHHHhccC-------ccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEecCCcc
Confidence            55 899999999999988776655332       225679999999999999999999998 467777754444

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

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.39  E-value=0.00015  Score=63.44  Aligned_cols=42  Identities=29%  Similarity=0.525  Sum_probs=33.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELR  286 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~  286 (449)
                      ..++|+.|-||||||+++..+|..+++..+.+  +++..+.++.
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~i--sd~vkEn~l~   48 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEI--SDLVKENNLY   48 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEeh--hhHHhhhcch
Confidence            45799999999999999999999999887655  5555444443

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=97.39  E-value=0.00078  Score=67.19  Aligned_cols=138  Identities=22%  Similarity=0.250  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCce
Q 013128          218 KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSM  297 (449)
Q Consensus       218 k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~I  297 (449)
                      .+.|.+.|+....        ++|.+|.+|+-||-.|||||+|+|+-+.++-....+++..    ..|.+-+.-+-..-.
T Consensus       138 ~~~i~~iL~~lv~--------N~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQfm  205 (417)
T PF06431_consen  138 DDVILEILKCLVE--------NIPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFM  205 (417)
T ss_dssp             HHHHHHHHHHHHH--------TBTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-SE
T ss_pred             HHHHHHHHHHHhc--------CCCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeeceEE
Confidence            3455555655554        3466889999999999999999999999988777776643    456666666677888


Q ss_pred             EEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC-----CCe-----EEEEEcCCCCCCCccccCCC
Q 013128          298 LVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG-----EGR-----IIVFTTNHKEKLDPALLRPG  367 (449)
Q Consensus       298 l~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~-----~~~-----iiI~tTN~~~~ld~aLlrpg  367 (449)
                      +++||+---... ++.      -..+..-.-|..|-.++||.-.-+-     ..+     --|.|+|+. .|+..+.-  
T Consensus       206 VvFEDVKGq~~~-~~~------Lp~G~G~~NLDNLRD~LDG~V~VNLErKH~NK~sQiFPPgIvTmNeY-~iP~Tv~v--  275 (417)
T PF06431_consen  206 VVFEDVKGQPSD-NKD------LPPGQGMNNLDNLRDYLDGAVKVNLERKHQNKRSQIFPPGIVTMNEY-KIPQTVKV--  275 (417)
T ss_dssp             EEEEEE--SSTT-TTT----------SHHHHHHTTHHHHH-SS-EEEECSSSEEEEE----EEEEESS--B--HHHHT--
T ss_pred             EEEEecCCCcCC-CCC------CCCCCCcccchhhhhhccCceeechhhhhcccccccCCCceEeeccc-cCCcceee--
Confidence            999998532110 000      0112223345667778887532100     011     246788875 47888887  


Q ss_pred             ccceEEEeCC
Q 013128          368 RMDMHLHMSY  377 (449)
Q Consensus       368 R~d~~i~l~~  377 (449)
                      ||...+.|..
T Consensus       276 Rf~~~~~F~~  285 (417)
T PF06431_consen  276 RFCKVLDFRP  285 (417)
T ss_dssp             TEEEEEE---
T ss_pred             eeEeeEeccc
Confidence            9988888764

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.37  E-value=0.00016  Score=64.89  Aligned_cols=32  Identities=28%  Similarity=0.548  Sum_probs=26.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      |+|.||||||||++++.+++.++..++  +...+
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v--~~D~~   32 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFI--EGDDL   32 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEE--eCccc
Confidence            578999999999999999999986654  44444

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.37  E-value=0.001  Score=63.48  Aligned_cols=37  Identities=24%  Similarity=0.258  Sum_probs=26.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |++....+++.||||||||+++..++..+   +...+.++
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            45666779999999999999975554433   44555444

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.36  E-value=0.00017  Score=63.03  Aligned_cols=30  Identities=30%  Similarity=0.535  Sum_probs=28.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.+.|+||||||++++.+|..++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            678999999999999999999999998877

>PRK14531 adenylate kinase; Provisional

Probab=97.36  E-value=0.00019  Score=65.95  Aligned_cols=31  Identities=26%  Similarity=0.486  Sum_probs=27.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +-+++.||||+|||++++.+|..+|+..+..
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4589999999999999999999999876654

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=97.35  E-value=0.00061  Score=66.43  Aligned_cols=91  Identities=22%  Similarity=0.425  Sum_probs=56.5

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC---cEEEEec-ccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF---DIYDLDL-SAV  279 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~---~~~~l~~-s~~  279 (449)
                      .+.+++++...+...+.+.+.+....+.           ...+++.||+|+|||+++++++.++..   .++.+.- .++
T Consensus        99 ~~~sle~l~~~~~~~~~~~~~l~~~v~~-----------~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen   99 KPFSLEDLGESGSIPEEIAEFLRSAVRG-----------RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             S--CHCCCCHTHHCHHHHHHHHHHCHHT-----------TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             ccccHhhccCchhhHHHHHHHHhhcccc-----------ceEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            4557889988777766666666544332           357999999999999999999999843   3444321 111


Q ss_pred             -------------cChHHHHHHHHcC--CCCceEEeeccch
Q 013128          280 -------------QSNSELRFLLLTM--PSRSMLVIEDIDC  305 (449)
Q Consensus       280 -------------~~~~~l~~~~~~~--~~~~Il~iDeiD~  305 (449)
                                   .....+..++...  ..|.+|++.||..
T Consensus       168 ~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~  208 (270)
T PF00437_consen  168 RLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIRD  208 (270)
T ss_dssp             --SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-S
T ss_pred             eecccceEEEEeecCcccHHHHHHHHhcCCCCcccccccCC
Confidence                         1122333333332  4789999999964

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 ....

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.35  E-value=0.0004  Score=75.40  Aligned_cols=52  Identities=27%  Similarity=0.322  Sum_probs=42.4

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -+|..|++++|.++.++.+...+..               ++.++|+||||||||+++++++..+..
T Consensus        25 ~~~~~~~~vigq~~a~~~L~~~~~~---------------~~~~l~~G~~G~GKttla~~l~~~l~~   76 (637)
T PRK13765         25 VPERLIDQVIGQEHAVEVIKKAAKQ---------------RRHVMMIGSPGTGKSMLAKAMAELLPK   76 (637)
T ss_pred             cCcccHHHcCChHHHHHHHHHHHHh---------------CCeEEEECCCCCcHHHHHHHHHHHcCh
Confidence            3578899999999888876554431               247999999999999999999999863

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=97.35  E-value=0.00018  Score=66.17  Aligned_cols=29  Identities=31%  Similarity=0.574  Sum_probs=26.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+|||++++.||..+++..+.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            78999999999999999999998876654

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.34  E-value=0.00021  Score=65.08  Aligned_cols=34  Identities=44%  Similarity=0.732  Sum_probs=30.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      +..++|.||+|+|||++++.+|+.+++++++.|.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            4569999999999999999999999999988764

>PRK13946 shikimate kinase; Provisional

Probab=97.34  E-value=0.00018  Score=66.12  Aligned_cols=33  Identities=36%  Similarity=0.478  Sum_probs=30.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++.|+|.|+||||||++++.+|+.+|+++++.|
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D   42 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDAD   42 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcC
Confidence            467999999999999999999999999999877

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.34  E-value=0.0046  Score=58.82  Aligned_cols=126  Identities=10%  Similarity=0.078  Sum_probs=92.2

Q ss_pred             CcceEEeCCCC-CCHHHHHHHHHHHc---------CCcEEEEeccc-------ccChHHHHHHHH---cCC---CCceEE
Q 013128          243 KRGYLLYGPPG-TGKSSLIAAMANQL---------KFDIYDLDLSA-------VQSNSELRFLLL---TMP---SRSMLV  299 (449)
Q Consensus       243 ~rg~LL~GPpG-tGKT~la~aiA~~l---------~~~~~~l~~s~-------~~~~~~l~~~~~---~~~---~~~Il~  299 (449)
                      ...||+.|..+ +||.-++.-++..+         +.+++.+....       .-.-.+++.+..   ..+   ..-|++
T Consensus        15 shAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KViI   94 (263)
T PRK06581         15 YNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVAI   94 (263)
T ss_pred             hheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEEE
Confidence            46799999998 99999988887776         34677665432       123344444333   222   456999


Q ss_pred             eeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCC
Q 013128          300 IEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN  379 (449)
Q Consensus       300 iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~  379 (449)
                      |+++|.+..                  ...+.||..++..    +...++|.+|..++.|.|.+++  |+ ..+.++.|.
T Consensus        95 I~~ae~mt~------------------~AANALLKtLEEP----P~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p~  149 (263)
T PRK06581         95 IYSAELMNL------------------NAANSCLKILEDA----PKNSYIFLITSRAASIISTIRS--RC-FKINVRSSI  149 (263)
T ss_pred             EechHHhCH------------------HHHHHHHHhhcCC----CCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCCC
Confidence            999999853                  3557799999863    5678888899999999999998  77 668899999


Q ss_pred             HHHHHHHHHHHhCc
Q 013128          380 TSVFKQLAFNYLGI  393 (449)
Q Consensus       380 ~~~r~~l~~~~l~~  393 (449)
                      ...-.+++..++..
T Consensus       150 ~~~~~e~~~~~~~p  163 (263)
T PRK06581        150 LHAYNELYSQFIQP  163 (263)
T ss_pred             HHHHHHHHHHhccc
Confidence            87777777766653

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.31  E-value=0.0013  Score=66.99  Aligned_cols=23  Identities=35%  Similarity=0.657  Sum_probs=21.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .||.||||||||+|++.|++...
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHH
Confidence            88999999999999999999874

>PRK08233 hypothetical protein; Provisional

Probab=97.31  E-value=0.0033  Score=57.04  Aligned_cols=33  Identities=21%  Similarity=0.293  Sum_probs=25.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC-CcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK-FDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~-~~~~~l~~  276 (449)
                      .-+.+.|+||+||||+++.++..++ ..++..+.
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~~~~~~~~d~   37 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKNSKALYFDR   37 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCCCCceEEECC
Confidence            3467889999999999999999985 44444443

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.31  E-value=0.0002  Score=67.15  Aligned_cols=22  Identities=50%  Similarity=0.908  Sum_probs=18.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .++.||||||||+++.+++..+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            8899999999998888777776

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=0.0015  Score=72.64  Aligned_cols=149  Identities=19%  Similarity=0.258  Sum_probs=93.9

Q ss_pred             cccccCC-HHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          208 FKTLALD-SELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       208 f~~l~g~-~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      ++.++|. ++..+.+++.|..             .-+++-+|.|.||+|||.++.-+|+..          +..++.+++
T Consensus       185 ldPvigr~deeirRvi~iL~R-------------rtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~  251 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILSR-------------KTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDF  251 (898)
T ss_pred             CCCccCCchHHHHHHHHHHhc-------------cCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEh
Confidence            5777776 5555666665531             114788999999999999999999988          345677777


Q ss_pred             ccccC--------hHHHHHHHHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          277 SAVQS--------NSELRFLLLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       277 s~~~~--------~~~l~~~~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      ..+..        +..+..+...   ...+.||+|||++.+.+.....           ...-...+|..+-+     .+
T Consensus       252 g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~~~-----------~~~d~~nlLkp~L~-----rg  315 (898)
T KOG1051|consen  252 GSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGSNY-----------GAIDAANLLKPLLA-----RG  315 (898)
T ss_pred             hhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCCcc-----------hHHHHHHhhHHHHh-----cC
Confidence            65532        2334444443   4577899999999997633221           01222333333321     13


Q ss_pred             CeEEEEEcCCC-----CCCCccccCCCccceEEEeCCCCHHHHHHHHH
Q 013128          346 GRIIVFTTNHK-----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       346 ~~iiI~tTN~~-----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~  388 (449)
                      +.-+|+||..-     -.=||+|-|  ||+. +.++.|+.+....++.
T Consensus       316 ~l~~IGatT~e~Y~k~iekdPalEr--rw~l-~~v~~pS~~~~~~iL~  360 (898)
T KOG1051|consen  316 GLWCIGATTLETYRKCIEKDPALER--RWQL-VLVPIPSVENLSLILP  360 (898)
T ss_pred             CeEEEecccHHHHHHHHhhCcchhh--Ccce-eEeccCcccchhhhhh
Confidence            36677655432     124899999  9975 5688888765444443

>smart00072 GuKc Guanylate kinase homologues

Probab=97.28  E-value=0.00071  Score=62.12  Aligned_cols=25  Identities=36%  Similarity=0.777  Sum_probs=22.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++-++|.||+|+||+++++.|+.+.
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            3578999999999999999999987

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.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.27  E-value=0.0019  Score=56.13  Aligned_cols=27  Identities=30%  Similarity=0.450  Sum_probs=24.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-++|.|+.|+|||++++++++.++.
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            346889999999999999999999975

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.27  E-value=0.0022  Score=61.07  Aligned_cols=24  Identities=38%  Similarity=0.537  Sum_probs=21.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -+-|.||+|||||||.+.+|....
T Consensus        31 fvsilGpSGcGKSTLLriiAGL~~   54 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGLEK   54 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            488999999999999999999883

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.26  E-value=0.0017  Score=66.41  Aligned_cols=70  Identities=21%  Similarity=0.280  Sum_probs=45.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc--------------------ChHHHHHHHH--cCC
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ--------------------SNSELRFLLL--TMP  293 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~--------------------~~~~l~~~~~--~~~  293 (449)
                      |+.+..-+||+||||+|||+|+..+|..+   +..+++++...-.                    ....+..++.  ...
T Consensus        78 Gi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~  157 (372)
T cd01121          78 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIEEL  157 (372)
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhc
Confidence            45556679999999999999999998776   3456666543210                    0111111111  224


Q ss_pred             CCceEEeeccchhhh
Q 013128          294 SRSMLVIEDIDCSVK  308 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~  308 (449)
                      ++.+|+||+|..+..
T Consensus       158 ~~~lVVIDSIq~l~~  172 (372)
T cd01121         158 KPDLVIIDSIQTVYS  172 (372)
T ss_pred             CCcEEEEcchHHhhc
Confidence            789999999998753

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.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.26  E-value=0.00029  Score=63.62  Aligned_cols=32  Identities=31%  Similarity=0.523  Sum_probs=29.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..++|.|+||||||++++.+|..+++++++.|
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~D   34 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDTD   34 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEcc
Confidence            35889999999999999999999999998775

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.25  E-value=0.0014  Score=68.65  Aligned_cols=70  Identities=26%  Similarity=0.314  Sum_probs=47.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC--------------------hHHHHHHHHc--CC
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS--------------------NSELRFLLLT--MP  293 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~--------------------~~~l~~~~~~--~~  293 (449)
                      |++....+||+||||+|||+|+..+|...   +..+++++..+-..                    ...+..++..  ..
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~  155 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEE  155 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhh
Confidence            56666679999999999999999998876   56667666432110                    0111122221  23


Q ss_pred             CCceEEeeccchhhh
Q 013128          294 SRSMLVIEDIDCSVK  308 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~  308 (449)
                      ++.+|+||.|..+..
T Consensus       156 ~~~lVVIDSIq~l~~  170 (446)
T PRK11823        156 KPDLVVIDSIQTMYS  170 (446)
T ss_pred             CCCEEEEechhhhcc
Confidence            688999999998754

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.24  E-value=0.00086  Score=60.11  Aligned_cols=24  Identities=33%  Similarity=0.558  Sum_probs=22.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.||+|||||+|.+++|+..
T Consensus        30 e~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhcc
Confidence            458999999999999999999987

>PRK14530 adenylate kinase; Provisional

Probab=97.24  E-value=0.00029  Score=66.37  Aligned_cols=31  Identities=26%  Similarity=0.464  Sum_probs=27.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||||+++.+|..++++++..
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            3589999999999999999999999877754

>PRK13808 adenylate kinase; Provisional

Probab=97.24  E-value=0.002  Score=64.45  Aligned_cols=29  Identities=28%  Similarity=0.517  Sum_probs=25.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      |+|+||||+|||++++.||..+++..+++
T Consensus         3 Iiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          3 LILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            78999999999999999999998765544

>PRK09354 recA recombinase A; Provisional

Probab=97.24  E-value=0.0012  Score=66.39  Aligned_cols=70  Identities=19%  Similarity=0.246  Sum_probs=45.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc---------------------ChH---HHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ---------------------SNS---ELRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~---------------------~~~---~l~~~~~~  291 (449)
                      |++..+-+++|||||||||+|+..++...   +...+.++...-.                     +..   .+...+.+
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~  135 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVR  135 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            46666779999999999999998776544   4455555433210                     011   11122333


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+||||-+-++.+
T Consensus       136 s~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        136 SGAVDLIVVDSVAALVP  152 (349)
T ss_pred             cCCCCEEEEeChhhhcc
Confidence            45788999999998864

>PRK06547 hypothetical protein; Provisional

Probab=97.23  E-value=0.00044  Score=62.95  Aligned_cols=33  Identities=33%  Similarity=0.544  Sum_probs=28.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-|++.||+|||||++++.+++.++..++.++
T Consensus        15 ~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         15 MITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            456889999999999999999999988777554

>PRK06762 hypothetical protein; Provisional

Probab=97.23  E-value=0.00028  Score=63.45  Aligned_cols=33  Identities=15%  Similarity=0.299  Sum_probs=27.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-++|.|+||+||||+|+.+++.++..++.++
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~   34 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLGRGTLLVS   34 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEec
Confidence            356889999999999999999999966666665

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.23  E-value=0.00028  Score=62.62  Aligned_cols=28  Identities=25%  Similarity=0.560  Sum_probs=25.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      +-+.|||||||||+++-+|.++|++++.
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceee
Confidence            5678999999999999999999999885

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

Probab=97.22  E-value=0.0025  Score=61.47  Aligned_cols=27  Identities=30%  Similarity=0.555  Sum_probs=23.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-++|.||+|||||+|++.+++.+..
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            345999999999999999999998854

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.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.19  E-value=0.0013  Score=58.05  Aligned_cols=62  Identities=24%  Similarity=0.318  Sum_probs=40.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc-----------EEEEecccccChHHHHH---HHHcCCCCceEEeeccchhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD-----------IYDLDLSAVQSNSELRF---LLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~-----------~~~l~~s~~~~~~~l~~---~~~~~~~~~Il~iDeiD~l~  307 (449)
                      +..+.|.||+|+|||+|+++++..+...           +..+.  ++ +..+.++   ...-..+|.++++||-..-+
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~--~l-S~G~~~rv~laral~~~p~illlDEP~~~L  101 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFE--QL-SGGEKMRLALAKLLLENPNLLLLDEPTNHL  101 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEc--cC-CHHHHHHHHHHHHHhcCCCEEEEeCCccCC
Confidence            4568899999999999999999987321           11111  12 2222222   22234689999999987654

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.

>PLN02674 adenylate kinase

Probab=97.19  E-value=0.00077  Score=64.73  Aligned_cols=31  Identities=23%  Similarity=0.471  Sum_probs=26.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||+|+++.||..+++..+..
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~~~~his~   62 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEYCLCHLAT   62 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcCCcEEch
Confidence            4599999999999999999999998765543

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.18  E-value=0.0003  Score=63.99  Aligned_cols=34  Identities=26%  Similarity=0.312  Sum_probs=28.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      ++-++|.||||+||||++++++..++..++.++.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~   35 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVLAEPWLHFGV   35 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhCCCccccCc
Confidence            3568999999999999999999998877665443

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK13764 ATPase; Provisional

Probab=97.18  E-value=0.0011  Score=71.38  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=40.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe------cc----ccc----ChHHHHHHHHcCCCCceEEeeccch
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLD------LS----AVQ----SNSELRFLLLTMPSRSMLVIEDIDC  305 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~------~s----~~~----~~~~l~~~~~~~~~~~Il~iDeiD~  305 (449)
                      ..++|+.||||+||||+++|+++++.   ..+..+.      +.    .+.    +...+...+ -...|-+|++||+-.
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~~~~riV~TiEDp~El~~~~~i~q~~~~~~~~~~~~~~l-LR~rPD~IivGEiRd  335 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQVPPEITQYSKLEGSMEETADIL-LLVRPDYTIYDEMRK  335 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhCCCEEEEECCCccccCCCcceEEeeccccHHHHHHHH-HhhCCCEEEECCCCC
Confidence            46899999999999999999999985   3332331      11    110    011122222 235799999999864

>TIGR00767 rho transcription termination factor Rho

Probab=97.17  E-value=0.0025  Score=65.17  Aligned_cols=25  Identities=28%  Similarity=0.563  Sum_probs=22.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-++|.||||||||++++.+++.+.
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhc
Confidence            3499999999999999999999864

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

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.17  E-value=0.0063  Score=63.34  Aligned_cols=63  Identities=22%  Similarity=0.311  Sum_probs=40.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEeccccc----------------------ChHHHHHHHHcCCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAVQ----------------------SNSELRFLLLTMPSR  295 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~~----------------------~~~~l~~~~~~~~~~  295 (449)
                      ++.++|.||+|+||||++..+|..+     +..+..+++....                      +..++...+......
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~~  300 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRDC  300 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCCC
Confidence            4568899999999999999998765     3455555554321                      122333444444556


Q ss_pred             ceEEeeccch
Q 013128          296 SMLVIEDIDC  305 (449)
Q Consensus       296 ~Il~iDeiD~  305 (449)
                      -+|+||..-.
T Consensus       301 DlVlIDt~G~  310 (424)
T PRK05703        301 DVILIDTAGR  310 (424)
T ss_pred             CEEEEeCCCC
Confidence            7888887643

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=97.16  E-value=0.0023  Score=59.63  Aligned_cols=64  Identities=20%  Similarity=0.288  Sum_probs=40.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH-----cCCc--------------EEEEecccc-c--------ChHHHHHHHHcCCCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ-----LKFD--------------IYDLDLSAV-Q--------SNSELRFLLLTMPSR  295 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~-----l~~~--------------~~~l~~s~~-~--------~~~~l~~~~~~~~~~  295 (449)
                      .-++|.||.|+|||++.++++.-     .|..              +..+...+. .        ....+..++.....|
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~d~i~~~~s~~~~e~~~l~~i~~~~~~~  109 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPR  109 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCcccccCCceeHHHHHHHHHHHHHhccCC
Confidence            46999999999999999999932     2321              111111111 0        013344555566789


Q ss_pred             ceEEeeccchhh
Q 013128          296 SMLVIEDIDCSV  307 (449)
Q Consensus       296 ~Il~iDeiD~l~  307 (449)
                      .++++||.-.-.
T Consensus       110 ~llllDEp~~gl  121 (202)
T cd03243         110 SLVLIDELGRGT  121 (202)
T ss_pred             eEEEEecCCCCC
Confidence            999999997643

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

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.16  E-value=0.0004  Score=63.45  Aligned_cols=31  Identities=19%  Similarity=0.414  Sum_probs=26.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .-+++.||||+||||+++.+|..+|+..+..
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            3588999999999999999999998765543

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.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.14  E-value=0.0015  Score=58.09  Aligned_cols=98  Identities=23%  Similarity=0.325  Sum_probs=55.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc--EEEEecccc-----------------cChHHHH---HHHHcCCCCceEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD--IYDLDLSAV-----------------QSNSELR---FLLLTMPSRSMLVI  300 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~--~~~l~~s~~-----------------~~~~~l~---~~~~~~~~~~Il~i  300 (449)
                      ...+.|.||.|+|||+|+++++..+...  -+.++...+                 .+..+.+   -...-..+|.++++
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~~~~~i~il  104 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDLLLL  104 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHhcCCCEEEE
Confidence            4568999999999999999999987432  112221111                 1111111   12222357999999


Q ss_pred             eccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCC
Q 013128          301 EDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLD  360 (449)
Q Consensus       301 DeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld  360 (449)
                      ||...-++              ......+..++..+   ..   .+..+|++|++.+.+.
T Consensus       105 DEp~~~lD--------------~~~~~~l~~~l~~~---~~---~~~tii~~sh~~~~~~  144 (157)
T cd00267         105 DEPTSGLD--------------PASRERLLELLREL---AE---EGRTVIIVTHDPELAE  144 (157)
T ss_pred             eCCCcCCC--------------HHHHHHHHHHHHHH---HH---CCCEEEEEeCCHHHHH
Confidence            99886543              12223333444433   11   1356778887765543

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.

>PRK02496 adk adenylate kinase; Provisional

Probab=97.14  E-value=0.00038  Score=63.80  Aligned_cols=29  Identities=28%  Similarity=0.596  Sum_probs=26.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +++.||||+|||++++.+|..+++..+..
T Consensus         4 i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            78999999999999999999999877654

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

Probab=97.14  E-value=0.0017  Score=58.48  Aligned_cols=26  Identities=31%  Similarity=0.433  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +..+.|.||.|+|||+|++.|+....
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~~   51 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLYK   51 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45688999999999999999998873

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.

>PF13245 AAA_19: Part of AAA domain

Probab=97.13  E-value=0.00069  Score=53.02  Aligned_cols=33  Identities=36%  Similarity=0.585  Sum_probs=21.2

Q ss_pred             ceEEeCCCCCCHH-HHHHHHHHHc------CCcEEEEecc
Q 013128          245 GYLLYGPPGTGKS-SLIAAMANQL------KFDIYDLDLS  277 (449)
Q Consensus       245 g~LL~GPpGtGKT-~la~aiA~~l------~~~~~~l~~s  277 (449)
                      -+++.|||||||| ++++.++..+      +..+..+..+
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            3556999999999 5555555555      3445555443

>PRK14528 adenylate kinase; Provisional

Probab=97.13  E-value=0.00043  Score=63.76  Aligned_cols=30  Identities=23%  Similarity=0.535  Sum_probs=26.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .+++.||||+|||++++.+|..++++.+.+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            489999999999999999999999877654

>PLN02199 shikimate kinase

Probab=97.12  E-value=0.00095  Score=65.48  Aligned_cols=33  Identities=30%  Similarity=0.524  Sum_probs=31.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++.++|.|++|+|||++++.+|+.+++++++.|
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD  134 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCD  134 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehH
Confidence            468999999999999999999999999999876

>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=97.11  E-value=0.015  Score=55.58  Aligned_cols=126  Identities=17%  Similarity=0.249  Sum_probs=76.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC---cEEEEeccc---------------ccChHHHH-----------HHHHcC-
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF---DIYDLDLSA---------------VQSNSELR-----------FLLLTM-  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~---~~~~l~~s~---------------~~~~~~l~-----------~~~~~~-  292 (449)
                      +-.+.+.||+|||||+++..+...+..   +++.+....               +.....+.           ...... 
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~~   92 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKSP   92 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhhc
Confidence            446899999999999999999988743   222221100               00011111           111111 


Q ss_pred             ----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCc
Q 013128          293 ----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGR  368 (449)
Q Consensus       293 ----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR  368 (449)
                          ..+++|+|||+-.-                ......+..+++.  |    ..-.+-+|+.+...-.|||.++.  =
T Consensus        93 ~~k~~~~~LiIlDD~~~~----------------~~k~~~l~~~~~~--g----RH~~is~i~l~Q~~~~lp~~iR~--n  148 (241)
T PF04665_consen   93 QKKNNPRFLIILDDLGDK----------------KLKSKILRQFFNN--G----RHYNISIIFLSQSYFHLPPNIRS--N  148 (241)
T ss_pred             ccCCCCCeEEEEeCCCCc----------------hhhhHHHHHHHhc--c----cccceEEEEEeeecccCCHHHhh--c
Confidence                23789999997421                0112234455541  1    12346788888888999999866  6


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          369 MDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       369 ~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      ++..+-+. -+....+.|++++...
T Consensus       149 ~~y~i~~~-~s~~dl~~i~~~~~~~  172 (241)
T PF04665_consen  149 IDYFIIFN-NSKRDLENIYRNMNIK  172 (241)
T ss_pred             ceEEEEec-CcHHHHHHHHHhcccc
Confidence            77777776 5778888888877643

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

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=97.10  E-value=0.00055  Score=69.74  Aligned_cols=98  Identities=24%  Similarity=0.417  Sum_probs=62.9

Q ss_pred             cceEEEEEEcCCchhHHHHHHHHHHHHHHHHHHHhCceeEEee---------------e---ccccccccccccCCC---
Q 013128          147 EVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHT---------------V---MHMRWDANNIVLKHP---  205 (449)
Q Consensus       147 ~~~~~~l~~~~~~~~~v~~~yl~~v~~~~~~~~~~~~~~~~~~---------------~---~~~~w~~~~~~~~~p---  205 (449)
                      +.+...|+=..- .+.-++.+-.++++.|+...  ...+.+-.               .   -...|.-   .--+|   
T Consensus       170 ~~k~v~l~d~pl-~~~ele~ia~eIi~~a~~~~--~sfIEi~r~GatVvQlrn~RIvIarPPfSd~~EI---TavRPvvk  243 (604)
T COG1855         170 EWKLVRLSDKPL-TREELEEIAREIIERAKRDP--DSFIEIDRPGATVVQLRNYRIVIARPPFSDRWEI---TAVRPVVK  243 (604)
T ss_pred             cEEEEEcCCccC-CHHHHHHHHHHHHHHHhhCc--CceEEEccCCceEEEeccEEEEEecCCCCCceEE---EEEeeeEE
Confidence            455555543332 33457778888888876532  11111110               0   0224543   22233   


Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .++++..+.+.+++++.+.                  .+|+|+.||||.||||+|+|+|..+.
T Consensus       244 ~~ledY~L~dkl~eRL~er------------------aeGILIAG~PGaGKsTFaqAlAefy~  288 (604)
T COG1855         244 LSLEDYGLSDKLKERLEER------------------AEGILIAGAPGAGKSTFAQALAEFYA  288 (604)
T ss_pred             echhhcCCCHHHHHHHHhh------------------hcceEEecCCCCChhHHHHHHHHHHH
Confidence            3688889999888888653                  36999999999999999999999983

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.10  E-value=0.00036  Score=62.66  Aligned_cols=29  Identities=24%  Similarity=0.638  Sum_probs=26.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +++.|.|||||||+++.++ ++|++++.++
T Consensus         3 I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            7899999999999999999 9999888764

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.10  E-value=0.00046  Score=65.79  Aligned_cols=31  Identities=19%  Similarity=0.551  Sum_probs=27.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -++|.||||+||||+++.+|+.++++.+.++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~g   38 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINMG   38 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEECC
Confidence            3899999999999999999999998777653

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.09  E-value=0.00053  Score=69.04  Aligned_cols=113  Identities=23%  Similarity=0.282  Sum_probs=66.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      |+|.++.++|||||+||||+++-++.+.++-.++..--      +.-...+.-...--|-+|||+-...=          
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf~N------s~ShFWLqPL~d~Ki~llDDAT~~cW----------  321 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVN------SKSHFWLQPLADAKIALLDDATYPCW----------  321 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-GGG------TTSCGGGGGGCT-SSEEEEEE-HHHH----------
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEecC------CCCcccccchhcCcEEEEcCCcccHH----------
Confidence            67888999999999999999999999999888776411      11123444455667889999864321          


Q ss_pred             hccchhhHHHH-HHHHHHhcCccccCC--C-------CeEEEEEcCCCCCCCcc---ccCCCccceEEEeCCC
Q 013128          319 ATNQEENKVTL-SGLLNFIDGLWSCCG--E-------GRIIVFTTNHKEKLDPA---LLRPGRMDMHLHMSYC  378 (449)
Q Consensus       319 ~~~~~~~~~~l-s~LL~~ldg~~~~~~--~-------~~iiI~tTN~~~~ld~a---LlrpgR~d~~i~l~~p  378 (449)
                              .-+ .-|-|.+||-.-+..  .       -.-++.|||.-=.-++.   |.+  |+ ..++||.+
T Consensus       322 --------~Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~~~~~~YLhS--Ri-~~f~F~n~  383 (432)
T PF00519_consen  322 --------DYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKKDDRWKYLHS--RI-TCFEFPNP  383 (432)
T ss_dssp             --------HHHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTTSCCCHHHCT--TE-EEEE--S-
T ss_pred             --------HHHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCcchhhhhhhh--eE-EEEEcCCc
Confidence                    111 224588887421100  0       01466788864333443   345  77 55777654

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>PRK04296 thymidine kinase; Provisional

Probab=97.08  E-value=0.004  Score=57.56  Aligned_cols=30  Identities=20%  Similarity=0.304  Sum_probs=24.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l  274 (449)
                      -++++||||+|||+++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            47899999999999998888876   4555544

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=97.08  E-value=0.0026  Score=59.18  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=19.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMA  264 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA  264 (449)
                      +.++|.||.|+|||++.+.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            469999999999999999998

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

>TIGR01351 adk adenylate kinases

Probab=97.07  E-value=0.00049  Score=64.56  Aligned_cols=29  Identities=28%  Similarity=0.550  Sum_probs=26.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +++.||||+|||++++.+|..+++..+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            78999999999999999999999877654

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.07  E-value=0.007  Score=61.82  Aligned_cols=58  Identities=28%  Similarity=0.366  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          215 SELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      .++++.+.+.+...+..+..+    ...++-++|.||+|+||||++..||..+   +..+..+++
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~----~~~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~a  277 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVF----EKEVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT  277 (436)
T ss_pred             HHHHHHHHHHHHHHhcccccc----ccCCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEec
Confidence            455666666666555543211    1224679999999999999999999887   344444444

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.07  E-value=0.0019  Score=63.07  Aligned_cols=26  Identities=31%  Similarity=0.523  Sum_probs=23.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .++++.||||+|||++.++++..+..
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            57999999999999999999999843

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.

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

Probab=97.06  E-value=0.0043  Score=62.32  Aligned_cols=131  Identities=18%  Similarity=0.278  Sum_probs=77.7

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh----------------------------HHHHHHHHc--
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN----------------------------SELRFLLLT--  291 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~----------------------------~~l~~~~~~--  291 (449)
                      .|..+.|||-.|||||.+++++-++++.+.+.+++-+..+-                            ..+..++..  
T Consensus        29 ~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~  108 (438)
T KOG2543|consen   29 IPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWP  108 (438)
T ss_pred             cceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhH
Confidence            35678999999999999999999999888777765443210                            111122222  


Q ss_pred             -C---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCC
Q 013128          292 -M---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPG  367 (449)
Q Consensus       292 -~---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpg  367 (449)
                       +   .+...|++|.+|.+-+               .....++.|+..-.-+    +...+.|...-++. .+.-+.+-|
T Consensus       109 ~~t~~d~~~~liLDnad~lrD---------------~~a~ll~~l~~L~el~----~~~~i~iils~~~~-e~~y~~n~g  168 (438)
T KOG2543|consen  109 AATNRDQKVFLILDNADALRD---------------MDAILLQCLFRLYELL----NEPTIVIILSAPSC-EKQYLINTG  168 (438)
T ss_pred             HhhccCceEEEEEcCHHhhhc---------------cchHHHHHHHHHHHHh----CCCceEEEEecccc-HHHhhcccC
Confidence             1   2356899999998842               1224455555433322    12233333332211 011222334


Q ss_pred             ccc-eEEEeCCCCHHHHHHHHHHHhC
Q 013128          368 RMD-MHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       368 R~d-~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .++ ..++||.++.++.++|+.+--.
T Consensus       169 ~~~i~~l~fP~Ys~~e~~~Il~~~~p  194 (438)
T KOG2543|consen  169 TLEIVVLHFPQYSVEETQVILSRDNP  194 (438)
T ss_pred             CCCceEEecCCCCHHHHHHHHhcCCc
Confidence            443 5789999999998888875443

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.06  E-value=0.035  Score=55.38  Aligned_cols=100  Identities=8%  Similarity=0.069  Sum_probs=55.1

Q ss_pred             CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEE-EEEcC---CCC--CCCccccCCC
Q 013128          294 SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRII-VFTTN---HKE--KLDPALLRPG  367 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii-I~tTN---~~~--~ld~aLlrpg  367 (449)
                      -|.++.||++..++....-...+- .......-.....|++.+.|-..-.++.+++ +.+|.   .+.  .++.+|....
T Consensus       156 ~PVL~avD~~n~l~~~S~Y~~~~~-~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~~~~~~l~~~L~~~~  234 (309)
T PF10236_consen  156 PPVLVAVDGFNALFGPSAYRDPDF-KPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNAPKSPTLPVALGGKE  234 (309)
T ss_pred             CceEEEehhhHHhhCCccccCCCC-ccccHHHhhHHHHHHHHhcCccccCCCeEEEEEeccccccccCCccchhhhcccc
Confidence            477888999999987432221111 1112223344555667655444332333332 44432   222  4566665311


Q ss_pred             c------cc-------------eEEEeCCCCHHHHHHHHHHHhCcC
Q 013128          368 R------MD-------------MHLHMSYCNTSVFKQLAFNYLGIS  394 (449)
Q Consensus       368 R------~d-------------~~i~l~~p~~~~r~~l~~~~l~~~  394 (449)
                      -      |.             ..|+++..+.++.+.+++.|....
T Consensus       235 ~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~~  280 (309)
T PF10236_consen  235 GFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADSG  280 (309)
T ss_pred             CCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHCC
Confidence            1      11             168899999999999999888653

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).

>PLN02200 adenylate kinase family protein

Probab=97.05  E-value=0.00064  Score=65.05  Aligned_cols=35  Identities=20%  Similarity=0.361  Sum_probs=28.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +.-+++.||||||||++++.+|.++|+..  ++.+++
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~g~~h--is~gdl   77 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETFGFKH--LSAGDL   77 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCeE--EEccHH
Confidence            34588999999999999999999998754  444443

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.05  E-value=0.00056  Score=64.43  Aligned_cols=29  Identities=28%  Similarity=0.520  Sum_probs=26.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      |+++||||+|||++++.+|..+++..+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            78999999999999999999999877764

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.04  E-value=0.0034  Score=62.82  Aligned_cols=40  Identities=20%  Similarity=0.247  Sum_probs=30.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~  278 (449)
                      |++.+.-++++||||||||+++..+|-..         +..+++++...
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            56666779999999999999999998663         23566666543

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

Probab=97.03  E-value=0.00097  Score=51.02  Aligned_cols=29  Identities=31%  Similarity=0.441  Sum_probs=23.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc-CCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL-KFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l-~~~~~~l  274 (449)
                      +.+.|+||+|||++++++++.+ +.++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l~~~~~~~i   31 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVL   31 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCEEEE
Confidence            5788999999999999999996 2444444

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.

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.03  E-value=0.0027  Score=63.17  Aligned_cols=82  Identities=22%  Similarity=0.355  Sum_probs=51.5

Q ss_pred             CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEE----EecccccChHHHHHHH
Q 013128          214 DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD----LDLSAVQSNSELRFLL  289 (449)
Q Consensus       214 ~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~----l~~s~~~~~~~l~~~~  289 (449)
                      ++++++-+.+.+-..+...       ......++|+|+.|+|||+++..+..-+|-....    +.+.++.+.   +..+
T Consensus        54 d~~~~~~l~~~lg~~L~~~-------~~~~~~~~l~G~g~nGKStl~~~l~~l~G~~~~~~~~~~~~~~~~~~---~f~~  123 (304)
T TIGR01613        54 DNELIEYLQRVIGYSLTGN-------YTEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAVASLKMNEFQEH---RFGL  123 (304)
T ss_pred             CHHHHHHHHHHHhHHhcCC-------CCceEEEEEECCCCCcHHHHHHHHHHHhChhhccCCcchhhhhccCC---Cchh
Confidence            4455555555554444332       2345679999999999999999999988854422    222222111   1234


Q ss_pred             HcCCCCceEEeeccch
Q 013128          290 LTMPSRSMLVIEDIDC  305 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~  305 (449)
                      .......+++.+|++.
T Consensus       124 a~l~gk~l~~~~E~~~  139 (304)
T TIGR01613       124 ARLEGKRAVIGDEVQK  139 (304)
T ss_pred             hhhcCCEEEEecCCCC
Confidence            4456778899999874

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.03  E-value=0.0038  Score=59.22  Aligned_cols=63  Identities=27%  Similarity=0.394  Sum_probs=41.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH-Hc----CC---------cEE-----EEecc-cccC--------hHHHHHHHHcCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN-QL----KF---------DIY-----DLDLS-AVQS--------NSELRFLLLTMPS  294 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~-~l----~~---------~~~-----~l~~s-~~~~--------~~~l~~~~~~~~~  294 (449)
                      .+.++|.||.|+|||++.+.++. .+    |.         +++     .+... ++..        -.++..++.....
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  110 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTS  110 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCC
Confidence            45689999999999999999988 32    21         111     11111 1111        1345566777889


Q ss_pred             CceEEeeccch
Q 013128          295 RSMLVIEDIDC  305 (449)
Q Consensus       295 ~~Il~iDeiD~  305 (449)
                      +++++|||+..
T Consensus       111 ~sLvllDE~~~  121 (222)
T cd03287         111 RSLVILDELGR  121 (222)
T ss_pred             CeEEEEccCCC
Confidence            99999999864

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

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.03  E-value=0.0033  Score=62.73  Aligned_cols=27  Identities=19%  Similarity=0.155  Sum_probs=23.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      |++...-++++||||||||+++..+|-
T Consensus        92 Gi~~G~iteI~G~~GsGKTql~lqla~  118 (313)
T TIGR02238        92 GIESMSITEVFGEFRCGKTQLSHTLCV  118 (313)
T ss_pred             CCcCCeEEEEECCCCCCcCHHHHHHHH
Confidence            566667799999999999999988774

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.

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.02  E-value=0.0025  Score=61.83  Aligned_cols=65  Identities=22%  Similarity=0.342  Sum_probs=51.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH------HcCCcEEEEecccccChHHHHHHHHc-----------------CCCCceEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN------QLKFDIYDLDLSAVQSNSELRFLLLT-----------------MPSRSMLV  299 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~------~l~~~~~~l~~s~~~~~~~l~~~~~~-----------------~~~~~Il~  299 (449)
                      ...+||.||.|.|||.|++-|..      .+.-.++.++|..+..+..+..+|..                 .....+||
T Consensus       208 r~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlf  287 (531)
T COG4650         208 RAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLF  287 (531)
T ss_pred             cCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEe
Confidence            45799999999999999998864      34678999999999876665554433                 23578999


Q ss_pred             eeccchhh
Q 013128          300 IEDIDCSV  307 (449)
Q Consensus       300 iDeiD~l~  307 (449)
                      +|||..+.
T Consensus       288 ldeigelg  295 (531)
T COG4650         288 LDEIGELG  295 (531)
T ss_pred             hHhhhhcC
Confidence            99998764

>PF13479 AAA_24: AAA domain

Probab=97.02  E-value=0.0031  Score=59.38  Aligned_cols=59  Identities=27%  Similarity=0.411  Sum_probs=36.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCc-EEEEeccc--c-----------cChHHHHHHHH----cCCCCceEEeeccch
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFD-IYDLDLSA--V-----------QSNSELRFLLL----TMPSRSMLVIEDIDC  305 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~-~~~l~~s~--~-----------~~~~~l~~~~~----~~~~~~Il~iDeiD~  305 (449)
                      -.++||||||+|||+++..+    +-+ +++++.+.  +           .+-..+...+.    ....--.||||-++.
T Consensus         4 ~~~lIyG~~G~GKTt~a~~~----~k~l~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~   79 (213)
T PF13479_consen    4 IKILIYGPPGSGKTTLAASL----PKPLFIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSISW   79 (213)
T ss_pred             eEEEEECCCCCCHHHHHHhC----CCeEEEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHH
Confidence            35899999999999999888    222 22333331  1           12233444332    224557999998887


Q ss_pred             h
Q 013128          306 S  306 (449)
Q Consensus       306 l  306 (449)
                      +
T Consensus        80 ~   80 (213)
T PF13479_consen   80 L   80 (213)
T ss_pred             H
Confidence            6

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.00  E-value=0.0017  Score=60.99  Aligned_cols=63  Identities=21%  Similarity=0.385  Sum_probs=41.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC--------cEEEEeccc-ccC---------------------hHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF--------DIYDLDLSA-VQS---------------------NSELRFLLLTMP  293 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~--------~~~~l~~s~-~~~---------------------~~~l~~~~~~~~  293 (449)
                      -+.|+.||||||||++.+-+|.-+..        .+..+|-++ +..                     ..+-.-...+..
T Consensus       138 lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrsm  217 (308)
T COG3854         138 LNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRSM  217 (308)
T ss_pred             eeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHHhc
Confidence            45899999999999999999988733        344444322 110                     011112233445


Q ss_pred             CCceEEeeccchh
Q 013128          294 SRSMLVIEDIDCS  306 (449)
Q Consensus       294 ~~~Il~iDeiD~l  306 (449)
                      .|-||++|||...
T Consensus       218 ~PEViIvDEIGt~  230 (308)
T COG3854         218 SPEVIIVDEIGTE  230 (308)
T ss_pred             CCcEEEEeccccH
Confidence            7999999999764

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.99  E-value=0.0038  Score=57.36  Aligned_cols=62  Identities=15%  Similarity=0.217  Sum_probs=39.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH-----cCCcE--------------EEEeccccc---------ChHHHHHHHHcCCCCce
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ-----LKFDI--------------YDLDLSAVQ---------SNSELRFLLLTMPSRSM  297 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~-----l~~~~--------------~~l~~s~~~---------~~~~l~~~~~~~~~~~I  297 (449)
                      ++|.||.|+|||++.++++-.     .|..+              ..+...+-.         .-.++..++.....|.+
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~l   81 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSL   81 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeE
Confidence            689999999999999999832     23211              112211111         01334455666678999


Q ss_pred             EEeeccchhh
Q 013128          298 LVIEDIDCSV  307 (449)
Q Consensus       298 l~iDeiD~l~  307 (449)
                      +++||...-.
T Consensus        82 lllDEp~~g~   91 (185)
T smart00534       82 VLLDELGRGT   91 (185)
T ss_pred             EEEecCCCCC
Confidence            9999997643

>PRK14527 adenylate kinase; Provisional

Probab=96.99  E-value=0.00057  Score=63.10  Aligned_cols=32  Identities=25%  Similarity=0.539  Sum_probs=27.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.-+++.||||+|||++++.+|..++...+..
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~~~~~~~is~   37 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQELGLKKLST   37 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCCCCCc
Confidence            45699999999999999999999998765543

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

Probab=96.97  E-value=0.0042  Score=60.54  Aligned_cols=87  Identities=16%  Similarity=0.266  Sum_probs=52.1

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe------
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLD------  275 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~------  275 (449)
                      +.+++++...++..+.+.+.+    ..+          ...+++.||+|+||||+++++..++.   ..++.++      
T Consensus        56 ~~~l~~lg~~~~~~~~l~~~~----~~~----------~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~  121 (264)
T cd01129          56 ILDLEKLGLKPENLEIFRKLL----EKP----------HGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ  121 (264)
T ss_pred             CCCHHHcCCCHHHHHHHHHHH----hcC----------CCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec
Confidence            346778887777666553332    111          23488999999999999999988874   2344442      


Q ss_pred             cccc-----cC--hHHHHHHHHc--CCCCceEEeeccch
Q 013128          276 LSAV-----QS--NSELRFLLLT--MPSRSMLVIEDIDC  305 (449)
Q Consensus       276 ~s~~-----~~--~~~l~~~~~~--~~~~~Il~iDeiD~  305 (449)
                      ...+     ..  ...+...+..  ...|.+|+++||..
T Consensus       122 ~~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~  160 (264)
T cd01129         122 IPGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIRD  160 (264)
T ss_pred             CCCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCCC
Confidence            1111     00  0112222222  24799999999964

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.

>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=96.97  E-value=0.0005  Score=58.37  Aligned_cols=22  Identities=32%  Similarity=0.629  Sum_probs=21.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |+|.|+|||||||+++.++..+
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            6899999999999999999998

...

>PRK04182 cytidylate kinase; Provisional

Probab=96.96  E-value=0.00074  Score=61.14  Aligned_cols=30  Identities=27%  Similarity=0.504  Sum_probs=27.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .|+|.|+||||||++++.+|..+++++++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            378999999999999999999999988763

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.96  E-value=0.0027  Score=59.40  Aligned_cols=63  Identities=21%  Similarity=0.311  Sum_probs=39.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CCcE---------E-----EEeccc-ccC--------hHHHHHHHHcCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KFDI---------Y-----DLDLSA-VQS--------NSELRFLLLTMPS  294 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~---------~-----~l~~s~-~~~--------~~~l~~~~~~~~~  294 (449)
                      ++-++|.||.|+|||++++.++...     |..+         +     .+...+ +..        -.++..++....+
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~il~~~~~  108 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADG  108 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCCccccchhhhHHHHHHHHHHHHHHhcCC
Confidence            3569999999999999999987333     3221         1     111110 110        1234455555678


Q ss_pred             CceEEeeccch
Q 013128          295 RSMLVIEDIDC  305 (449)
Q Consensus       295 ~~Il~iDeiD~  305 (449)
                      ++++++||+..
T Consensus       109 ~~lvllDE~~~  119 (204)
T cd03282         109 DSLVLIDELGR  119 (204)
T ss_pred             CcEEEeccccC
Confidence            99999999865

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

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.95  E-value=0.059  Score=59.37  Aligned_cols=173  Identities=23%  Similarity=0.224  Sum_probs=93.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc--CCcEEEEecccccCh------------------------------------HH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL--KFDIYDLDLSAVQSN------------------------------------SE  284 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l--~~~~~~l~~s~~~~~------------------------------------~~  284 (449)
                      .|-+||.-|.|.|||+++...+..+  +..+--+++++-.++                                    .-
T Consensus        37 ~RL~li~APAGfGKttl~aq~~~~~~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l  116 (894)
T COG2909          37 YRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESL  116 (894)
T ss_pred             ceEEEEeCCCCCcHHHHHHHHHHhcCcccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHH
Confidence            4679999999999999999998643  444544444332211                                    00


Q ss_pred             HHHHHH---cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCc
Q 013128          285 LRFLLL---TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDP  361 (449)
Q Consensus       285 l~~~~~---~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~  361 (449)
                      +..++.   ....|.++||||.+.+..              ......+..|++..       ++++.+|+||...-.+.-
T Consensus       117 ~~~L~~Ela~~~~pl~LVlDDyHli~~--------------~~l~~~l~fLl~~~-------P~~l~lvv~SR~rP~l~l  175 (894)
T COG2909         117 LSSLLNELASYEGPLYLVLDDYHLISD--------------PALHEALRFLLKHA-------PENLTLVVTSRSRPQLGL  175 (894)
T ss_pred             HHHHHHHHHhhcCceEEEeccccccCc--------------ccHHHHHHHHHHhC-------CCCeEEEEEeccCCCCcc
Confidence            112222   334699999999998742              33344555566643       567778887765444433


Q ss_pred             cccCCCccceEEEeCC----CCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHccC--CCHHHHHHHHhc-CCCHHHHHH--
Q 013128          362 ALLRPGRMDMHLHMSY----CNTSVFKQLAFNYLGISHHYL-FEQIEELIKEVN--VTPAEVAGELMK-STNAEVSLN--  431 (449)
Q Consensus       362 aLlrpgR~d~~i~l~~----p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~~--~tpa~i~~~l~~-~~~~~~al~--  431 (449)
                      |=+|  -=+..++++.    .+.++-.+++..-.+   .++ ..++..+.+.++  ++.-++...-.+ +.+.+.++.  
T Consensus       176 a~lR--lr~~llEi~~~~Lrf~~eE~~~fl~~~~~---l~Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~L  250 (894)
T COG2909         176 ARLR--LRDELLEIGSEELRFDTEEAAAFLNDRGS---LPLDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGL  250 (894)
T ss_pred             ccee--ehhhHHhcChHhhcCChHHHHHHHHHcCC---CCCChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhc
Confidence            3222  1123333332    455666666665443   223 345555655543  333333222223 345555555  


Q ss_pred             -----HHHHHHHHHH
Q 013128          432 -----GLVKFLHAKM  441 (449)
Q Consensus       432 -----~l~~~l~~~~  441 (449)
                           .+.+||.+..
T Consensus       251 sG~~~~l~dYL~eeV  265 (894)
T COG2909         251 SGAASHLSDYLVEEV  265 (894)
T ss_pred             cchHHHHHHHHHHHH
Confidence                 5555655543

>PRK06696 uridine kinase; Validated

Probab=96.95  E-value=0.0024  Score=60.47  Aligned_cols=40  Identities=10%  Similarity=0.210  Sum_probs=32.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN  282 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~  282 (449)
                      +.-|.+.|+||+||||+|+.|+..+   +..++.+.+.++...
T Consensus        22 ~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~~~   64 (223)
T PRK06696         22 PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFHNP   64 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeccccccCC
Confidence            4458889999999999999999999   667777777776543

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=96.95  E-value=0.00065  Score=70.03  Aligned_cols=170  Identities=17%  Similarity=0.196  Sum_probs=93.7

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhc--CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc--cc-ChHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIG--RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA--VQ-SNSE  284 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g--~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~--~~-~~~~  284 (449)
                      +|.|.+++|+.++-.|.   ...+.-..-|  +...-+++|-|.||+.||.|.+.+.+-.-..+|.-.-++  +. +..-
T Consensus       343 EIyGheDVKKaLLLlLV---Ggvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGSSGVGLTAAV  419 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLV---GGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGSSGVGLTAAV  419 (721)
T ss_pred             hhccchHHHHHHHHHhh---CCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCCCccccchhh
Confidence            56788888887765443   2221100011  111123999999999999999999998877777543221  11 1000


Q ss_pred             HHH-----HHH-----cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          285 LRF-----LLL-----TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       285 l~~-----~~~-----~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                      ++.     +..     -....+|-+|||+|.+... +|..-.. ...++.....-.       |+....+-..-|+++.|
T Consensus       420 mkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~-DRtAIHE-VMEQQTISIaKA-------GI~TtLNAR~sILaAAN  490 (721)
T KOG0482|consen  420 MKDPVTGEMVLEGGALVLADGGICCIDEFDKMDES-DRTAIHE-VMEQQTISIAKA-------GINTTLNARTSILAAAN  490 (721)
T ss_pred             hcCCCCCeeEeccceEEEccCceEeehhhhhhhhh-hhHHHHH-HHHhhhhhhhhh-------ccccchhhhHHhhhhcC
Confidence            000     000     0135789999999998641 1111000 000011111111       22222222345677777


Q ss_pred             CCC-------------CCCccccCCCccceEEEe-CCCCHHHHHHHHHHHhCc
Q 013128          355 HKE-------------KLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       355 ~~~-------------~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~~l~~  393 (449)
                      ...             .|++||++  |||..+-+ ..|+.+.=+.|+++..-.
T Consensus       491 PayGRYnprrs~e~NI~LPaALLS--RFDll~Li~D~pdrd~D~~LA~HiTyV  541 (721)
T KOG0482|consen  491 PAYGRYNPRRSPEQNINLPAALLS--RFDLLWLIQDRPDRDNDLRLAQHITYV  541 (721)
T ss_pred             ccccccCcccChhHhcCCcHHHHH--hhhhhhhhccCCcccchHHHHHHhHhh
Confidence            532             47899999  99987665 668888778888876544

>PLN02459 probable adenylate kinase

Probab=96.95  E-value=0.0046  Score=59.88  Aligned_cols=30  Identities=20%  Similarity=0.427  Sum_probs=26.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .++|.||||+|||++++.+|..+++..+..
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~is~   60 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPHIAT   60 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeC
Confidence            488899999999999999999998766543

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=96.93  E-value=0.002  Score=62.79  Aligned_cols=84  Identities=19%  Similarity=0.277  Sum_probs=53.6

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh----HHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN----SEL  285 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~----~~l  285 (449)
                      +|+.-++..+.|.... +-+..+          ....||.|.+|+||+++++..|.-.++.++.+..+.-.+.    ..|
T Consensus         9 ~lVlf~~ai~hi~ri~-RvL~~~----------~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~dL   77 (268)
T PF12780_consen    9 NLVLFDEAIEHIARIS-RVLSQP----------RGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKEDL   77 (268)
T ss_dssp             -----HHHHHHHHHHH-HHHCST----------TEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHHH
T ss_pred             ceeeHHHHHHHHHHHH-HHHcCC----------CCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHHH
Confidence            4566677766665433 333322          3458999999999999999999999999999987764433    334


Q ss_pred             HHHHHcC---CCCceEEeeccc
Q 013128          286 RFLLLTM---PSRSMLVIEDID  304 (449)
Q Consensus       286 ~~~~~~~---~~~~Il~iDeiD  304 (449)
                      +.++..+   .++.+++|+|-+
T Consensus        78 k~~~~~ag~~~~~~vfll~d~q   99 (268)
T PF12780_consen   78 KKALQKAGIKGKPTVFLLTDSQ   99 (268)
T ss_dssp             HHHHHHHHCS-S-EEEEEECCC
T ss_pred             HHHHHHHhccCCCeEEEecCcc
Confidence            4444433   468888888754

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>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=96.93  E-value=0.0032  Score=57.59  Aligned_cols=65  Identities=18%  Similarity=0.264  Sum_probs=39.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc--EEEEe-------cccc-cChHH---HHHHHHcCCCCceEEeeccchhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD--IYDLD-------LSAV-QSNSE---LRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~--~~~l~-------~s~~-~~~~~---l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      ..-+.|.||.|+|||||++.|+..+..+  -+.++       .... .+..+   +.-...-..+|.++++||--.-+
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~L  102 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYL  102 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccC
Confidence            4458899999999999999999987321  11111       1111 11111   11222234589999999987654

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.92  E-value=0.0016  Score=55.07  Aligned_cols=24  Identities=33%  Similarity=0.419  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++++++||+|+|||.++...+..+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHH
Confidence            368999999999999988887776

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

>TIGR01069 mutS2 MutS2 family protein

Probab=96.92  E-value=0.0062  Score=67.96  Aligned_cols=23  Identities=22%  Similarity=0.333  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +.++|.||.|+|||++.+.++..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHH
Confidence            56899999999999999999877

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.91  E-value=0.0051  Score=56.01  Aligned_cols=26  Identities=35%  Similarity=0.581  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +..+.|.||+|+|||+|+++|+....
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC
Confidence            45689999999999999999999873

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.

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=96.91  E-value=0.0039  Score=62.95  Aligned_cols=26  Identities=35%  Similarity=0.604  Sum_probs=22.0

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +|+|++|||.-|||||+|.-..-..+
T Consensus       113 ~PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  113 PPKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CCceEEEecccCcchhHHHHHHhhcC
Confidence            48999999999999999987766444

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.91  E-value=0.0042  Score=62.71  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=23.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      |++...-+.|+||||||||+|+..+|-
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav  148 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCV  148 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHH
Confidence            566666789999999999999998874

>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=96.90  E-value=0.00059  Score=60.44  Aligned_cols=27  Identities=26%  Similarity=0.567  Sum_probs=23.3

Q ss_pred             EeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          248 LYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       248 L~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      |.||||+|||++++.||..+++..+.+
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is~   27 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHISV   27 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEEH
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceech
Confidence            579999999999999999998765543

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 ....

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.90  E-value=0.00091  Score=61.23  Aligned_cols=29  Identities=45%  Similarity=0.786  Sum_probs=24.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -++|.||||+||||+|+.||+.++.  ..++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i--~hls   30 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGL--PHLD   30 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC--cEEc
Confidence            3789999999999999999999554  4444

>PRK01184 hypothetical protein; Provisional

Probab=96.89  E-value=0.0009  Score=61.22  Aligned_cols=29  Identities=21%  Similarity=0.369  Sum_probs=25.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      -++|.||||+||||+++ ++.++|++++..
T Consensus         3 ~i~l~G~~GsGKsT~a~-~~~~~g~~~i~~   31 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK-IAREMGIPVVVM   31 (184)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHcCCcEEEh
Confidence            47899999999999887 889999887665

>PTZ00035 Rad51 protein; Provisional

Probab=96.89  E-value=0.0061  Score=61.52  Aligned_cols=28  Identities=25%  Similarity=0.221  Sum_probs=23.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |++...-+.|+||||||||+++..+|..
T Consensus       114 Gi~~G~iteI~G~~GsGKT~l~~~l~~~  141 (337)
T PTZ00035        114 GIETGSITELFGEFRTGKTQLCHTLCVT  141 (337)
T ss_pred             CCCCCeEEEEECCCCCchhHHHHHHHHH
Confidence            5666666899999999999999998854

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.88  E-value=0.0081  Score=67.20  Aligned_cols=97  Identities=16%  Similarity=0.342  Sum_probs=55.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CC----------cEEE---Eeccc---ccC--------hHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KF----------DIYD---LDLSA---VQS--------NSELRFLLLTMP  293 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~----------~~~~---l~~s~---~~~--------~~~l~~~~~~~~  293 (449)
                      .+.++|.||.+.|||++.+.++-..     |.          ++++   .+.++   +..        -..+..++....
T Consensus       327 ~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~  406 (782)
T PRK00409        327 KTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKAD  406 (782)
T ss_pred             ceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCC
Confidence            3568999999999999999887542     32          1111   11111   110        122334555567


Q ss_pred             CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC
Q 013128          294 SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK  358 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~  358 (449)
                      .+++++|||+..-..             ..........++..+-.      .+..+|+||++.+.
T Consensus       407 ~~sLvLlDE~~~GtD-------------p~eg~ala~aile~l~~------~~~~vIitTH~~el  452 (782)
T PRK00409        407 KNSLVLFDELGAGTD-------------PDEGAALAISILEYLRK------RGAKIIATTHYKEL  452 (782)
T ss_pred             cCcEEEecCCCCCCC-------------HHHHHHHHHHHHHHHHH------CCCEEEEECChHHH
Confidence            899999999975321             11122233345554422      23477888887543

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.87  E-value=0.00099  Score=59.83  Aligned_cols=29  Identities=28%  Similarity=0.655  Sum_probs=26.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.+.|++|+|||++++.+|+.++++++..
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~   31 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISA   31 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecH
Confidence            68999999999999999999999987764

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>TIGR00416 sms DNA repair protein RadA

Probab=96.86  E-value=0.0073  Score=63.41  Aligned_cols=68  Identities=22%  Similarity=0.228  Sum_probs=45.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC-----------------------hHHHHHHHHcC
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS-----------------------NSELRFLLLTM  292 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~-----------------------~~~l~~~~~~~  292 (449)
                      |++...-+||+|+||+|||+|+..+|..+   +.++++++..+-..                       -..+...+ ..
T Consensus        90 Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i-~~  168 (454)
T TIGR00416        90 GIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANI-EE  168 (454)
T ss_pred             CccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHH-Hh
Confidence            56666779999999999999999998766   34566665432110                       01111111 22


Q ss_pred             CCCceEEeeccchhh
Q 013128          293 PSRSMLVIEDIDCSV  307 (449)
Q Consensus       293 ~~~~Il~iDeiD~l~  307 (449)
                      .++.+++||.|..+.
T Consensus       169 ~~~~~vVIDSIq~l~  183 (454)
T TIGR00416       169 ENPQACVIDSIQTLY  183 (454)
T ss_pred             cCCcEEEEecchhhc
Confidence            468899999999874

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)).

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

Probab=96.86  E-value=0.0036  Score=56.66  Aligned_cols=26  Identities=27%  Similarity=0.511  Sum_probs=23.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +..+.|.||+|+|||+|++.|+..+.
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~~~   53 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRLYD   53 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            45689999999999999999999873

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.

>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=96.86  E-value=0.019  Score=57.18  Aligned_cols=29  Identities=38%  Similarity=0.399  Sum_probs=25.3

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      .+..+-|+|+=|+|||++++.+-+++...
T Consensus        19 ~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen   19 DPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            46779999999999999999999988544

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 [].

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.83  E-value=0.00084  Score=60.21  Aligned_cols=26  Identities=35%  Similarity=0.672  Sum_probs=21.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      |.|.|+||||||||+++++.. |++++
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            689999999999999999999 77765

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

Probab=96.83  E-value=0.0024  Score=54.74  Aligned_cols=64  Identities=27%  Similarity=0.325  Sum_probs=43.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC--------------------cEEEEecccccChHHHHHH--HHcCCCCceEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF--------------------DIYDLDLSAVQSNSELRFL--LLTMPSRSMLVI  300 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~--------------------~~~~l~~s~~~~~~~l~~~--~~~~~~~~Il~i  300 (449)
                      ..-++|+|+=|+|||++++++|..++.                    +++.+|+-.+.+..++..+  .......+|.+|
T Consensus        15 g~vi~L~GdLGaGKTtf~r~l~~~lg~~~~V~SPTF~l~~~Y~~~~~~l~H~DLYRl~~~~e~~~~g~~e~~~~~~i~~I   94 (123)
T PF02367_consen   15 GDVILLSGDLGAGKTTFVRGLARALGIDEEVTSPTFSLVNEYEGGNIPLYHFDLYRLEDPEELEDLGLEEYLFEDGICVI   94 (123)
T ss_dssp             -EEEEEEESTTSSHHHHHHHHHHHTT--S----TTTTSEEEEEETTEEEEEEE-TT-SSTHHHHHCTTTTCSSSSEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCCCcCCCCeEEEEEecCCCceEEEeeccccCCHHHHHHCCchhhhCCCCEEEE
Confidence            346999999999999999999999964                    3455666666655554432  233356888888


Q ss_pred             eccchh
Q 013128          301 EDIDCS  306 (449)
Q Consensus       301 DeiD~l  306 (449)
                      |=-+.+
T Consensus        95 EW~e~~  100 (123)
T PF02367_consen   95 EWPERL  100 (123)
T ss_dssp             ESGGGG
T ss_pred             ECcccc
Confidence            855544

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

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=96.83  E-value=0.0011  Score=61.70  Aligned_cols=35  Identities=37%  Similarity=0.574  Sum_probs=27.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      -++|+||+|||||.++-++|+.+|.+++.+|--..
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq~   37 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVISLDRIQC   37 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEEE-SGGG
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEEecceec
Confidence            47899999999999999999999999999885444

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.83  E-value=0.0011  Score=65.66  Aligned_cols=31  Identities=29%  Similarity=0.295  Sum_probs=26.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-CCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-KFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l  274 (449)
                      .-++|.|||||||||+++.++..+ +..+++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~~   34 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVNR   34 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEec
Confidence            458899999999999999999999 6655543

>PRK14526 adenylate kinase; Provisional

Probab=96.80  E-value=0.0012  Score=62.14  Aligned_cols=28  Identities=29%  Similarity=0.718  Sum_probs=25.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ++|.||||+|||++++.+|..++...+.
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999999876654

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=96.77  E-value=0.03  Score=55.33  Aligned_cols=28  Identities=25%  Similarity=0.356  Sum_probs=25.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      |-.+++.||+|||||++|..+|..++.+
T Consensus        92 p~iIlI~G~sgsGKStlA~~La~~l~~~  119 (301)
T PRK04220         92 PIIILIGGASGVGTSTIAFELASRLGIR  119 (301)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            4568999999999999999999999887

>PHA00350 putative assembly protein

Probab=96.77  E-value=0.0025  Score=65.23  Aligned_cols=121  Identities=12%  Similarity=0.101  Sum_probs=62.3

Q ss_pred             ceEEeCCCCCCHHHHHHH--HHHHc--CCcEEEEecccccCh--------------------------HHHHHHHHcCCC
Q 013128          245 GYLLYGPPGTGKSSLIAA--MANQL--KFDIYDLDLSAVQSN--------------------------SELRFLLLTMPS  294 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~a--iA~~l--~~~~~~l~~s~~~~~--------------------------~~l~~~~~~~~~  294 (449)
                      -+|++|.||+|||+.+-.  |-..+  |..++. ++..+.-+                          ..+...+.-.+.
T Consensus         3 I~l~tG~pGSGKT~~aV~~~i~palk~GR~V~T-NI~Gl~le~i~~~~~~~p~~~~li~i~~~~~~~~~~~~~~~~w~p~   81 (399)
T PHA00350          3 IYAIVGRPGSYKSYEAVVYHIIPALKDGRKVIT-NIPGLNLDVFEKVFGEFPSTARLIRIVDRNLEGFESMNRPFSWRPR   81 (399)
T ss_pred             eEEEecCCCCchhHHHHHHHHHHHHHCCCEEEE-CCCCCCHHHHHhhcccCcccceeEEeccccccchhhhccccccCCC
Confidence            368899999999998775  33333  665542 33322100                          001111111346


Q ss_pred             CceEEeeccchhhhcccccch-hhhh-ccchh---hHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          295 RSMLVIEDIDCSVKLQNRESS-EVQA-TNQEE---NKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       295 ~~Il~iDeiD~l~~~~~~~~~-~~~~-~~~~~---~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                      .++|||||+..+++.+..... +.-. .....   ....-..+++++..-   ...+.=||++|.++..||..++.  ++
T Consensus        82 gaLIViDEaq~~~p~r~~~~~~~~~~~p~~~~~~~~~~~p~~~i~~l~~H---RH~G~DIiliTQ~~~~Id~~iR~--lv  156 (399)
T PHA00350         82 GALYVIDEAQMIFPKRLGFKMANIFKRPFTDFEPHLPEGPENFLEAFMRH---RHYNWDIILLTPNIRKIHSDIRA--MI  156 (399)
T ss_pred             CCEEEEECchhhcCCCccccccccccccccccccccccCCHHHHHHHHHh---cccCceEEEEeCCHHHhhHHHHH--hh
Confidence            789999999999875422100 0000 00000   000011233333321   12345578888898899887765  66


Q ss_pred             ce
Q 013128          370 DM  371 (449)
Q Consensus       370 d~  371 (449)
                      ++
T Consensus       157 E~  158 (399)
T PHA00350        157 EM  158 (399)
T ss_pred             hh
Confidence            65

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.77  E-value=0.0016  Score=57.78  Aligned_cols=30  Identities=37%  Similarity=0.575  Sum_probs=25.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +++.|+||+|||++++.++..+   +...+.++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~   34 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLD   34 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            6899999999999999999998   66666654

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.76  E-value=0.012  Score=53.82  Aligned_cols=69  Identities=10%  Similarity=0.046  Sum_probs=41.2

Q ss_pred             eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc--CCCHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHh
Q 013128          371 MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV--NVTPAEVAGELMKSTNAEVSLNGLVKFLHAKMTQ  443 (449)
Q Consensus       371 ~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~--~~tpa~i~~~l~~~~~~~~al~~l~~~l~~~~~~  443 (449)
                      +.|.+-+|+.++.+.-+.    ..+.+..+.|..-+...  ++..++--.+.+-++|.+.|+..+...+......
T Consensus       116 v~IFi~pPs~eeL~~RL~----~Rgtds~e~I~~Rl~~a~~Ei~~~~~fdyvivNdd~e~a~~~l~~ii~aer~~  186 (191)
T COG0194         116 VSIFILPPSLEELERRLK----GRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSIILAERLR  186 (191)
T ss_pred             EEEEEcCCCHHHHHHHHH----ccCCCCHHHHHHHHHHHHHHHHHHHhCCEEEECccHHHHHHHHHHHHHHHHHH
Confidence            557888888877554443    33444555554444332  1222222233345889999999999988876443

>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=96.76  E-value=0.0063  Score=55.15  Aligned_cols=25  Identities=32%  Similarity=0.565  Sum_probs=22.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||.|+|||+|++.|+..+
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3458899999999999999999986

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

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.76  E-value=0.029  Score=65.51  Aligned_cols=127  Identities=17%  Similarity=0.226  Sum_probs=79.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHH----------------HHHHHcCCCCceEEeeccchhh
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSEL----------------RFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l----------------~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      -.+|+.||..+|||+++..+|.+.|-.++.++-..-.+-.+.                .-+.....+.--|++||+....
T Consensus       889 fP~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVLDELNLAp  968 (4600)
T COG5271         889 FPLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVLDELNLAP  968 (4600)
T ss_pred             CcEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhcCcEEEeeccccCc
Confidence            359999999999999999999999999999985544321111                1223334566789999997542


Q ss_pred             hcccccchhhhhccchhhHHHHHHHHHHhcCccc-------cCCCCeEEEEEcCCCC------CCCccccCCCccceEEE
Q 013128          308 KLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS-------CCGEGRIIVFTTNHKE------KLDPALLRPGRMDMHLH  374 (449)
Q Consensus       308 ~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~-------~~~~~~iiI~tTN~~~------~ld~aLlrpgR~d~~i~  374 (449)
                      .               ..-..++.||.---.+.-       .+..+..+++|-|.|.      .|..|++.  || ..++
T Consensus       969 T---------------DVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRN--RF-lE~h 1030 (4600)
T COG5271         969 T---------------DVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRN--RF-LEMH 1030 (4600)
T ss_pred             H---------------HHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHh--hh-Hhhh
Confidence            1               112234444421111110       0123345666777663      36788887  88 5677


Q ss_pred             eCCCCHHHHHHHHH
Q 013128          375 MSYCNTSVFKQLAF  388 (449)
Q Consensus       375 l~~p~~~~r~~l~~  388 (449)
                      |..-.+.+...|+.
T Consensus      1031 FddipedEle~ILh 1044 (4600)
T COG5271        1031 FDDIPEDELEEILH 1044 (4600)
T ss_pred             cccCcHHHHHHHHh
Confidence            76666666666654

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.76  E-value=0.0013  Score=60.54  Aligned_cols=30  Identities=33%  Similarity=0.547  Sum_probs=25.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ..+.|.||+|+||||+++.|+..++.+++.
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~~   32 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLLV   32 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEEE
Confidence            358899999999999999999998876544

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=96.74  E-value=0.0042  Score=65.66  Aligned_cols=119  Identities=20%  Similarity=0.313  Sum_probs=67.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc--ccc------ChHHHHHHHHc-----CCCCceEEeeccchhhhcccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS--AVQ------SNSELRFLLLT-----MPSRSMLVIEDIDCSVKLQNR  312 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s--~~~------~~~~l~~~~~~-----~~~~~Il~iDeiD~l~~~~~~  312 (449)
                      +||.|.||||||.+.+.+++-....++.-..+  .+.      ...--+..-.+     ...++|-+|||+|.+-. ++|
T Consensus       485 vLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASavGLTa~v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMnd-qDR  563 (854)
T KOG0477|consen  485 VLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAVGLTAYVRKDPVTREWTLEAGALVLADKGVCLIDEFDKMND-QDR  563 (854)
T ss_pred             EEEecCCCccHHHHHHHHHhcCcceeEeccCCccccceeEEEeeCCccceeeeccCeEEEccCceEEeehhhhhcc-ccc
Confidence            99999999999999999999988777754321  110      01001111111     14688999999999854 222


Q ss_pred             cchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC-------------CCCccccCCCccceEEEe
Q 013128          313 ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE-------------KLDPALLRPGRMDMHLHM  375 (449)
Q Consensus       313 ~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~-------------~ld~aLlrpgR~d~~i~l  375 (449)
                      ..-... ..++.....-.++...+.+       ...||+|+|...             .|-..+++  |||+..-+
T Consensus       564 tSIHEA-MEQQSISISKAGIVtsLqA-------rctvIAAanPigGRY~~s~tFaqNV~ltePIlS--RFDiLcVv  629 (854)
T KOG0477|consen  564 TSIHEA-MEQQSISISKAGIVTSLQA-------RCTVIAAANPIGGRYNPSLTFAQNVDLTEPILS--RFDILCVV  629 (854)
T ss_pred             chHHHH-HHhcchhhhhhhHHHHHHh-------hhhhheecCCCCCccCCccchhhccccccchhh--hcceeeee
Confidence            221110 0111112222335555432       236788888731             24445666  89986665

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.73  E-value=0.0064  Score=57.44  Aligned_cols=61  Identities=21%  Similarity=0.305  Sum_probs=38.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH-----cCCc---------EEEEecccc------cC-h-------HHHHHHHHcCCCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ-----LKFD---------IYDLDLSAV------QS-N-------SELRFLLLTMPSR  295 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~-----l~~~---------~~~l~~s~~------~~-~-------~~l~~~~~~~~~~  295 (449)
                      +-++|.||.|+|||++.+.+|..     .+..         ++.--...+      .. .       ..+..++....++
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~~~~~~ls~g~s~f~~e~~~l~~~l~~~~~~  110 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATER  110 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccCCchhhhccCcchHHHHHHHHHHHHHhCCCC
Confidence            46899999999999999999742     2221         111000111      10 0       2345566667899


Q ss_pred             ceEEeeccc
Q 013128          296 SMLVIEDID  304 (449)
Q Consensus       296 ~Il~iDeiD  304 (449)
                      ++++|||..
T Consensus       111 ~llllDEp~  119 (216)
T cd03284         111 SLVLLDEIG  119 (216)
T ss_pred             eEEEEecCC
Confidence            999999984

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 clam

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.73  E-value=0.005  Score=61.65  Aligned_cols=25  Identities=36%  Similarity=0.737  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.++++.||+|+|||+++++++.++
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~~  172 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINEM  172 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999999874

>PRK10867 signal recognition particle protein; Provisional

Probab=96.73  E-value=0.19  Score=52.45  Aligned_cols=65  Identities=14%  Similarity=0.252  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccccc
Q 013128          216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAVQ  280 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~~  280 (449)
                      .+++.+.+.+...+.....--......+.-+++.||+|+||||++..+|..+    |..+..+++....
T Consensus        73 ~~~~~v~~el~~~l~~~~~~~~~~~~~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R  141 (433)
T PRK10867         73 QVIKIVNDELVEILGGENSELNLAAKPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYR  141 (433)
T ss_pred             HHHHHHHHHHHHHhCCCcceeeecCCCCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccc
Confidence            3455566566665543211011122335678999999999999999888866    5667767665544

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.71  E-value=0.0051  Score=61.58  Aligned_cols=25  Identities=24%  Similarity=0.523  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.++|+.||+|+||||++++++.++
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i  168 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999986

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.71  E-value=0.0076  Score=60.28  Aligned_cols=27  Identities=26%  Similarity=0.238  Sum_probs=23.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      |++...-+.++||||+|||+++..+|.
T Consensus        92 Gi~~g~i~~i~G~~g~GKT~l~~~~~~  118 (316)
T TIGR02239        92 GIETGSITEIFGEFRTGKTQLCHTLAV  118 (316)
T ss_pred             CCCCCeEEEEECCCCCCcCHHHHHHHH
Confidence            556666689999999999999998886

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).

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.69  E-value=0.0079  Score=60.72  Aligned_cols=28  Identities=25%  Similarity=0.239  Sum_probs=23.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |++...-++++|+||+|||+++..+|-.
T Consensus       119 G~~~g~i~~i~G~~g~GKT~l~~~l~~~  146 (342)
T PLN03186        119 GIETGSITEIYGEFRTGKTQLCHTLCVT  146 (342)
T ss_pred             CCcCceEEEEECCCCCCccHHHHHHHHH
Confidence            4555666899999999999999988743

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.69  E-value=0.029  Score=57.93  Aligned_cols=36  Identities=22%  Similarity=0.386  Sum_probs=26.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSA  278 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~  278 (449)
                      +..++|.||+|+||||++..+|..+    |..+..+++..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            3458899999999999999999754    34454444433

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.67  E-value=0.0075  Score=54.16  Aligned_cols=64  Identities=25%  Similarity=0.429  Sum_probs=39.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCc---------------EEEEe---------ccccc-ChHHHHHHHHcCC--CCc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFD---------------IYDLD---------LSAVQ-SNSELRFLLLTMP--SRS  296 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~---------------~~~l~---------~s~~~-~~~~l~~~~~~~~--~~~  296 (449)
                      +..++.||.|+|||+++++++-.+...               +-..+         ++.-. .-..+...+....  .|.
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~lS~G~~~~~~la~~L~~~~~~~~~  101 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQLSGGEKELSALALILALASLKPRP  101 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcchhhhccCcccCCCcceeeEEEEehheeeccccHHHHHHHHHHHHhcCCCCCC
Confidence            478899999999999999986544211               11111         11110 1123344455444  899


Q ss_pred             eEEeeccchhh
Q 013128          297 MLVIEDIDCSV  307 (449)
Q Consensus       297 Il~iDeiD~l~  307 (449)
                      +++|||+..-.
T Consensus       102 llllDEp~~gl  112 (162)
T cd03227         102 LYILDEIDRGL  112 (162)
T ss_pred             EEEEeCCCCCC
Confidence            99999998654

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.67  E-value=0.0059  Score=56.83  Aligned_cols=37  Identities=32%  Similarity=0.353  Sum_probs=27.8

Q ss_pred             ChhHHhhh--cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          231 GKEYYTRI--GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       231 ~~~~~~~~--g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.+.-+++  |+|.+.-+|+.|+.|||||-|.+.+|-=+
T Consensus        14 ndelDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~   52 (235)
T COG2874          14 NDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGF   52 (235)
T ss_pred             cHHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHH
Confidence            34444555  46666668999999999999999888544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.67  E-value=0.0019  Score=62.72  Aligned_cols=39  Identities=18%  Similarity=0.118  Sum_probs=30.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      |++....+|++||||||||+++..+|...   +.++..++..
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            66667779999999999999999876643   5566655543

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.65  E-value=0.0016  Score=62.68  Aligned_cols=31  Identities=35%  Similarity=0.596  Sum_probs=26.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      ++|.|+||+|||++|++++..+   +.+++.++.
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~   35 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGT   35 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEcc
Confidence            6899999999999999999988   456666654

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.65  E-value=0.0021  Score=63.81  Aligned_cols=25  Identities=28%  Similarity=0.626  Sum_probs=23.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.++|+.||+|+|||++++++++++
T Consensus       132 ~~~ilI~G~tGSGKTTll~al~~~i  156 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLANALLAEI  156 (299)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999987

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.

>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=96.64  E-value=0.0076  Score=55.07  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=20.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +.-+.|.||.|+|||||.++++..
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~   44 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYA   44 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc
Confidence            445889999999999999999743

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.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.64  E-value=0.0021  Score=59.89  Aligned_cols=29  Identities=31%  Similarity=0.444  Sum_probs=25.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      +.-+++.|+||+|||++++.+|.+++...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            45689999999999999999999988754

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.63  E-value=0.0026  Score=60.93  Aligned_cols=39  Identities=28%  Similarity=0.187  Sum_probs=29.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      |++.+..+|++||||||||+++..++.+.   |...+.+...
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~e   58 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE   58 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEee
Confidence            67777889999999999999998766542   5566665543

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.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.63  E-value=0.0075  Score=66.71  Aligned_cols=70  Identities=17%  Similarity=0.214  Sum_probs=43.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH---cCCcEEEEeccccc---------------------ChHHHH---HHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ---LKFDIYDLDLSAVQ---------------------SNSELR---FLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~---l~~~~~~l~~s~~~---------------------~~~~l~---~~~~~  291 (449)
                      |++..+.++++||||||||+|+..++..   .+-.+..++...-.                     ......   ..+.+
T Consensus        56 Gip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~  135 (790)
T PRK09519         56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (790)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHHHHHHcCCChhHeEEecCCCHHHHHHHHHHHhh
Confidence            4666677999999999999999654433   24445554432210                     111111   11223


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+|+||-|..+..
T Consensus       136 ~~~~~LVVIDSI~aL~~  152 (790)
T PRK09519        136 SGALDIVVIDSVAALVP  152 (790)
T ss_pred             cCCCeEEEEcchhhhcc
Confidence            34688999999998874

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.62  E-value=0.0019  Score=61.12  Aligned_cols=37  Identities=24%  Similarity=0.345  Sum_probs=27.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~  275 (449)
                      |++.+..+|+.||||||||+++..++...    |..++.+.
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs   55 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVS   55 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEE
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEE
Confidence            67777789999999999999998766433    55655554

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 ....

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.61  E-value=0.0027  Score=61.64  Aligned_cols=40  Identities=23%  Similarity=0.290  Sum_probs=31.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      |.+..+.+|++|+||||||+++...+...   |.+++.+....
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence            56677889999999999999999888776   55566665443

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.60  E-value=0.01  Score=57.52  Aligned_cols=107  Identities=20%  Similarity=0.188  Sum_probs=58.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEecccccChHHHH-----------------------
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSAVQSNSELR-----------------------  286 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~~~~~~~l~-----------------------  286 (449)
                      |++.+.-+=|+||||||||.|+-.+|-..         +..++++|...-.....+.                       
T Consensus        34 Gi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~  113 (256)
T PF08423_consen   34 GIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVF  113 (256)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-S
T ss_pred             CCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecC
Confidence            34333335599999999999999887654         3347777755432211111                       


Q ss_pred             ------HHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          287 ------FLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       287 ------~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                            .++..      ..+-.+|+||-|-.++...-....     +.......+..+++.|-.+...  .++.||.|
T Consensus       114 ~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalfr~e~~~~~-----~~~~R~~~L~~~~~~L~~lA~~--~~iaVvvT  184 (256)
T PF08423_consen  114 DLEELLELLEQLPKLLSESKIKLIVIDSIAALFRSEFSGRG-----DLAERQRMLARLARILKRLARK--YNIAVVVT  184 (256)
T ss_dssp             SHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHHHHHSGSTT-----THHHHHHHHHHHHHHHHHHHHH--TT-EEEEE
T ss_pred             CHHHHHHHHHHHHhhccccceEEEEecchHHHHHHHHccch-----hhHHHHHHHHHHHHHHHHHHHh--CCceEEee
Confidence                  11111      135679999999998752111000     1122345566666666655443  33444443

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 ....

>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=96.60  E-value=0.0028  Score=61.87  Aligned_cols=61  Identities=16%  Similarity=0.281  Sum_probs=33.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc----------ChHHHHHHH----Hc-CCCCceEEeeccchh
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ----------SNSELRFLL----LT-MPSRSMLVIEDIDCS  306 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~----------~~~~l~~~~----~~-~~~~~Il~iDeiD~l  306 (449)
                      ++|+|.||+|||++|+.|+..+   +..+..++-..+.          .+...+..+    .+ .....|+++|+...+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYi   82 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYI   82 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchH
Confidence            7899999999999999999986   5666666533221          122222221    11 245689999988755

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.58  E-value=0.018  Score=63.98  Aligned_cols=32  Identities=25%  Similarity=0.369  Sum_probs=25.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---C--CcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---K--FDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~--~~~~~l~  275 (449)
                      +-++|.|+||||||++++++...+   +  ..++-+.
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~A  375 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAA  375 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEe
Confidence            468899999999999999997766   3  4455444

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.57  E-value=0.0029  Score=57.37  Aligned_cols=35  Identities=26%  Similarity=0.380  Sum_probs=27.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      +..+.|.|+||+|||+++++++..+   +.++..++..
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~D   41 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDGD   41 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcCc
Confidence            3468899999999999999999988   3445555543

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=96.57  E-value=0.012  Score=53.90  Aligned_cols=25  Identities=32%  Similarity=0.662  Sum_probs=22.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -.+.+.||.|+|||||.+.+|.-+.
T Consensus        29 e~~~i~G~NG~GKTtLLRilaGLl~   53 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAGLLR   53 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHcccC
Confidence            3488999999999999999999884

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.57  E-value=0.0023  Score=58.17  Aligned_cols=26  Identities=27%  Similarity=0.424  Sum_probs=23.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-++|.|+||+|||++++++++.+.
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            44688999999999999999999985

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.56  E-value=0.0096  Score=63.05  Aligned_cols=86  Identities=19%  Similarity=0.366  Sum_probs=53.7

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe-----
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQLK---FDIYDLD-----  275 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~-----  275 (449)
                      +.+++++.+.++..+.+...+.    .           +.| +|+.||+|+||||+..++.++++   .+++.+.     
T Consensus       218 ~~~l~~Lg~~~~~~~~l~~~~~----~-----------~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~  282 (486)
T TIGR02533       218 RLDLETLGMSPELLSRFERLIR----R-----------PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY  282 (486)
T ss_pred             CCCHHHcCCCHHHHHHHHHHHh----c-----------CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeee
Confidence            4578888888877666554332    1           345 78999999999999999988884   3344442     


Q ss_pred             -cccc-----cC--hHHHHHHHHc--CCCCceEEeeccch
Q 013128          276 -LSAV-----QS--NSELRFLLLT--MPSRSMLVIEDIDC  305 (449)
Q Consensus       276 -~s~~-----~~--~~~l~~~~~~--~~~~~Il~iDeiD~  305 (449)
                       ...+     ..  .......+..  ...|-||++.||-.
T Consensus       283 ~~~~~~q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEiRd  322 (486)
T TIGR02533       283 QIEGIGQIQVNPKIGLTFAAGLRAILRQDPDIIMVGEIRD  322 (486)
T ss_pred             ecCCCceEEEccccCccHHHHHHHHHhcCCCEEEEeCCCC
Confidence             1111     00  0111112211  25799999999864

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.

>PRK10646 ADP-binding protein; Provisional

Probab=96.56  E-value=0.019  Score=51.13  Aligned_cols=26  Identities=27%  Similarity=0.450  Sum_probs=23.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-++|.|+=|+|||++++++|+.++.
T Consensus        29 ~vi~L~GdLGaGKTtf~rgl~~~Lg~   54 (153)
T PRK10646         29 TVIYLYGDLGAGKTTFSRGFLQALGH   54 (153)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            35899999999999999999999974

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.56  E-value=0.0082  Score=54.00  Aligned_cols=25  Identities=32%  Similarity=0.541  Sum_probs=19.7

Q ss_pred             cceEEeCCCCCCHHH-HHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSS-LIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~-la~aiA~~l~  268 (449)
                      +.+++.||+|||||. ++..+...+.
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~   50 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALK   50 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhc
Confidence            579999999999999 5555555553

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=96.56  E-value=0.0023  Score=68.73  Aligned_cols=31  Identities=23%  Similarity=0.380  Sum_probs=29.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -++|.|+||+|||++.+.+|+.++++++++|
T Consensus         8 ~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D   38 (542)
T PRK14021          8 QAVIIGMMGAGKTRVGKEVAQMMRLPFADAD   38 (542)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3889999999999999999999999999987

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.55  E-value=0.0098  Score=62.04  Aligned_cols=51  Identities=22%  Similarity=0.363  Sum_probs=40.5

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      ..+|+.+.+.+...+.+...+.               .|.| +|+.||.|+|||++..++.++++.+
T Consensus       234 ~l~l~~Lg~~~~~~~~~~~~~~---------------~p~GliLvTGPTGSGKTTTLY~~L~~ln~~  285 (500)
T COG2804         234 ILDLEKLGMSPFQLARLLRLLN---------------RPQGLILVTGPTGSGKTTTLYAALSELNTP  285 (500)
T ss_pred             cCCHHHhCCCHHHHHHHHHHHh---------------CCCeEEEEeCCCCCCHHHHHHHHHHHhcCC
Confidence            4568999999988887766553               1456 6678999999999999999999643

>PLN02165 adenylate isopentenyltransferase

Probab=96.54  E-value=0.0023  Score=63.96  Aligned_cols=37  Identities=27%  Similarity=0.437  Sum_probs=30.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +..+.|.||+|+|||+|+..||..++..++..|--.+
T Consensus        43 g~iivIiGPTGSGKStLA~~LA~~l~~eIIsaDs~Qv   79 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVDLATRFPSEIINSDKMQV   79 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHcCCceecCChhee
Confidence            3458999999999999999999999988777654433

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.54  E-value=0.002  Score=56.81  Aligned_cols=167  Identities=17%  Similarity=0.250  Sum_probs=84.6

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhcc
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATN  321 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~  321 (449)
                      .+-.+++-|++|||||+++++++.+++.+|++-  .++....+....-...+      +.|=|.+               
T Consensus        11 ~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~dg--Dd~Hp~~NveKM~~Gip------LnD~DR~---------------   67 (191)
T KOG3354|consen   11 FKYVIVVMGVSGSGKSTIGKALSEELGLKFIDG--DDLHPPANVEKMTQGIP------LNDDDRW---------------   67 (191)
T ss_pred             CceeEEEEecCCCChhhHHHHHHHHhCCccccc--ccCCCHHHHHHHhcCCC------CCccccc---------------
Confidence            345688899999999999999999999988754  44544444333222211      1111211               


Q ss_pred             chhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC----CCCCcccc--CCCccc-eEEEeCCCCHHHHHHHHHHHhCcC
Q 013128          322 QEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK----EKLDPALL--RPGRMD-MHLHMSYCNTSVFKQLAFNYLGIS  394 (449)
Q Consensus       322 ~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~----~~ld~aLl--rpgR~d-~~i~l~~p~~~~r~~l~~~~l~~~  394 (449)
                       ......-..+...++      .++.+|++++.-.    +.|-.++-  +||.++ ..++|=+... .+..|+++.....
T Consensus        68 -pWL~~i~~~~~~~l~------~~q~vVlACSaLKk~YRdILr~sl~~gk~~~~~~~~l~fi~l~~-s~evi~~Rl~~R~  139 (191)
T KOG3354|consen   68 -PWLKKIAVELRKALA------SGQGVVLACSALKKKYRDILRHSLKDGKPGKCPESQLHFILLSA-SFEVILKRLKKRK  139 (191)
T ss_pred             -HHHHHHHHHHHHHhh------cCCeEEEEhHHHHHHHHHHHHhhcccCCccCCccceEEEeeeec-cHHHHHHHHhhcc
Confidence             111222222222222      1233444444221    22222332  344444 5555555554 6678888888888


Q ss_pred             CCCCHHHHHH-HHHccCCCH---HHHHHHHhcCCCHHHHHHHHHHHHHH
Q 013128          395 HHYLFEQIEE-LIKEVNVTP---AEVAGELMKSTNAEVSLNGLVKFLHA  439 (449)
Q Consensus       395 ~~~l~~~i~~-l~~~~~~tp---a~i~~~l~~~~~~~~al~~l~~~l~~  439 (449)
                      +|-...++-+ -++..+...   .+|..+=.++.++++.++.+.+-+..
T Consensus       140 gHFMp~~lleSQf~~LE~p~~~e~div~isv~~~~~e~iv~tI~k~~~~  188 (191)
T KOG3354|consen  140 GHFMPADLLESQFATLEAPDADEEDIVTISVKTYSVEEIVDTIVKMVAL  188 (191)
T ss_pred             cccCCHHHHHHHHHhccCCCCCccceEEEeeccCCHHHHHHHHHHHHHh
Confidence            8776544322 111111111   11211112335677777777776654

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.53  E-value=0.0058  Score=61.16  Aligned_cols=61  Identities=21%  Similarity=0.236  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHcCh-hHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          216 ELKREITEDLENFMNGK-EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~-~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      .+++.+.+.+...+... ..+. .....+.-++|.||+|+||||++..+|..+   +..+.-+++.
T Consensus        87 ~~~~~l~~~l~~~l~~~~~~~~-~~~~~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~D  151 (318)
T PRK10416         87 ELKELLKEELAEILEPVEKPLN-IEEKKPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGD  151 (318)
T ss_pred             HHHHHHHHHHHHHhCcCCcccc-ccCCCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            34555665665555421 1111 111234568899999999999999999988   4455555443

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.52  E-value=0.0057  Score=60.93  Aligned_cols=40  Identities=18%  Similarity=0.194  Sum_probs=30.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~  278 (449)
                      |++.+.-++++||||||||+++..+|...         +-.+++++...
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            56666678999999999999999998763         23667776544

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.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.52  E-value=0.003  Score=61.62  Aligned_cols=53  Identities=32%  Similarity=0.523  Sum_probs=39.1

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHcC----CcEEEE
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQLK----FDIYDL  274 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l~----~~~~~l  274 (449)
                      .+..+|+.|..++-+.+ +.+                  .++| ||+.||.|+|||+..+||-+++|    .+++.+
T Consensus       103 ~~i~~~e~LglP~i~~~-~~~------------------~~~GLILVTGpTGSGKSTTlAamId~iN~~~~~HIlTI  160 (353)
T COG2805         103 SKIPTLEELGLPPIVRE-LAE------------------SPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTI  160 (353)
T ss_pred             ccCCCHHHcCCCHHHHH-HHh------------------CCCceEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEe
Confidence            45568999888875554 221                  1567 67789999999999999999996    345544

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=96.52  E-value=0.0057  Score=63.38  Aligned_cols=138  Identities=19%  Similarity=0.278  Sum_probs=73.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc-cc-------cChHHHHHHHHc-----CCCCceEEeeccchhhhccc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS-AV-------QSNSELRFLLLT-----MPSRSMLVIEDIDCSVKLQN  311 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s-~~-------~~~~~l~~~~~~-----~~~~~Il~iDeiD~l~~~~~  311 (449)
                      ++||.|.|||.||.|.+-+-.-.-.-+|.-.-+ +.       .-++.-+....+     ....+|++|||+|.+-. .+
T Consensus       366 NVLLLGDPgtAKSQlLKFvEkvsPIaVYTSGKGSSAAGLTASV~RD~~tReFylEGGAMVLADgGVvCIDEFDKMre-~D  444 (729)
T KOG0481|consen  366 NVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVIRDPSTREFYLEGGAMVLADGGVVCIDEFDKMRE-DD  444 (729)
T ss_pred             eEEEecCCchhHHHHHHHHHhcCceEEEecCCCcccccceeeEEecCCcceEEEecceEEEecCCEEEeehhhccCc-hh
Confidence            499999999999999998877665555542211 11       001111111111     13678999999998743 01


Q ss_pred             ccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC-----------CCC--CccccCCCccceEEEeCCC
Q 013128          312 RESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK-----------EKL--DPALLRPGRMDMHLHMSYC  378 (449)
Q Consensus       312 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-----------~~l--d~aLlrpgR~d~~i~l~~p  378 (449)
                      |..-     ...-.+.++|---.   |+....+...-|+++.|.+           +.|  .|.++.  |||+.+-+..-
T Consensus       445 RVAI-----HEAMEQQTISIAKA---GITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILS--RFDmIFIVKD~  514 (729)
T KOG0481|consen  445 RVAI-----HEAMEQQTISIAKA---GITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILS--RFDMIFIVKDE  514 (729)
T ss_pred             hhHH-----HHHHHhhhHHHhhh---cceeeecchhhhhhhcCCccccccccCCcccccchhhhHhh--hccEEEEEecc
Confidence            1000     00011122221111   2222222333466777764           223  378888  99997777543


Q ss_pred             -CHHHHHHHHHHHhCc
Q 013128          379 -NTSVFKQLAFNYLGI  393 (449)
Q Consensus       379 -~~~~r~~l~~~~l~~  393 (449)
                       +++.=..|+++.+..
T Consensus       515 h~~~~D~~lAkHVI~v  530 (729)
T KOG0481|consen  515 HDEERDITLAKHVINV  530 (729)
T ss_pred             CcchhhhHHHHHhhhh
Confidence             444455666666654

>PRK14529 adenylate kinase; Provisional

Probab=96.51  E-value=0.002  Score=61.14  Aligned_cols=28  Identities=25%  Similarity=0.535  Sum_probs=25.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ++|.||||+||||+++.||..+++..+.
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~~is   30 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLAHIE   30 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCcc
Confidence            7899999999999999999999987653

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.51  E-value=0.1  Score=49.95  Aligned_cols=156  Identities=17%  Similarity=0.182  Sum_probs=89.5

Q ss_pred             Ccc-eEEeCCCCCCHHHHHHHHHHHcCCc---EEEEecccccC--------------------------hHHHHHHHHcC
Q 013128          243 KRG-YLLYGPPGTGKSSLIAAMANQLKFD---IYDLDLSAVQS--------------------------NSELRFLLLTM  292 (449)
Q Consensus       243 ~rg-~LL~GPpGtGKT~la~aiA~~l~~~---~~~l~~s~~~~--------------------------~~~l~~~~~~~  292 (449)
                      .+| +.+.|+-|||||.+++|+..-++-+   ++.++...+..                          ...|..++.+.
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g  129 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKG  129 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhC
Confidence            344 6688999999999999887777432   22333222211                          12334455556


Q ss_pred             CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCc--------ccc
Q 013128          293 PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDP--------ALL  364 (449)
Q Consensus       293 ~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~--------aLl  364 (449)
                      ..|.++++||.+.+..               ..-..+.-|.|.-++...  .-.+++|+=.    +|.+        .+-
T Consensus       130 ~r~v~l~vdEah~L~~---------------~~le~Lrll~nl~~~~~~--~l~ivL~Gqp----~L~~~lr~~~l~e~~  188 (269)
T COG3267         130 KRPVVLMVDEAHDLND---------------SALEALRLLTNLEEDSSK--LLSIVLIGQP----KLRPRLRLPVLRELE  188 (269)
T ss_pred             CCCeEEeehhHhhhCh---------------hHHHHHHHHHhhcccccC--ceeeeecCCc----ccchhhchHHHHhhh
Confidence            6789999999998753               011122223333322211  1223444421    1222        223


Q ss_pred             CCCccceEEEeCCCCHHHHHHHHHHHhCcC--CCCCH--HHHHHHHHccCCCHHHHHHHHh
Q 013128          365 RPGRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHYLF--EQIEELIKEVNVTPAEVAGELM  421 (449)
Q Consensus       365 rpgR~d~~i~l~~p~~~~r~~l~~~~l~~~--~~~l~--~~i~~l~~~~~~tpa~i~~~l~  421 (449)
                      .  |++..|++++.+.++-...++..|+..  +.+++  +.+..+-....-.|.-|.+.+.
T Consensus       189 ~--R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         189 Q--RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             h--eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            4  898889999999998888888888753  34443  2333333333447777766654

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=96.50  E-value=0.0027  Score=58.01  Aligned_cols=29  Identities=31%  Similarity=0.432  Sum_probs=25.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.|.|+||+|||++++.+++ +|+++++.|
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~i~~D   30 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPVIDAD   30 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCEEecC
Confidence            67999999999999999999 888877665

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>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=96.50  E-value=0.013  Score=54.84  Aligned_cols=24  Identities=42%  Similarity=0.533  Sum_probs=19.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+.+.||+|||||+||-+.|-++
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~   43 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALEL   43 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH
Confidence            468899999999999999999776

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PF00488 MutS_V: MutS domain V C-terminus

Probab=96.49  E-value=0.015  Score=55.57  Aligned_cols=97  Identities=20%  Similarity=0.352  Sum_probs=55.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-----CC----c-----E-----EEEecc-cccC--------hHHHHHHHHcCCCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-----KF----D-----I-----YDLDLS-AVQS--------NSELRFLLLTMPSR  295 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-----~~----~-----~-----~~l~~s-~~~~--------~~~l~~~~~~~~~~  295 (449)
                      +.++|.||..+|||++.+++|-..     |.    .     +     ..+... ++..        -.++..++....++
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~  123 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEK  123 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TT
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccc
Confidence            678999999999999999988655     31    1     1     111111 1111        14456777778899


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK  358 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~  358 (449)
                      ++++|||+-.-.             ...+.......++..+-..     .+..+|+||+..+-
T Consensus       124 sLvliDE~g~gT-------------~~~eg~ai~~aile~l~~~-----~~~~~i~~TH~~~l  168 (235)
T PF00488_consen  124 SLVLIDELGRGT-------------NPEEGIAIAIAILEYLLEK-----SGCFVIIATHFHEL  168 (235)
T ss_dssp             EEEEEESTTTTS-------------SHHHHHHHHHHHHHHHHHT-----TT-EEEEEES-GGG
T ss_pred             eeeecccccCCC-------------ChhHHHHHHHHHHHHHHHh-----ccccEEEEeccchh
Confidence            999999996521             1122233344455555321     13467888887653

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>TIGR00959 ffh signal recognition particle protein

Probab=96.48  E-value=0.31  Score=50.82  Aligned_cols=65  Identities=15%  Similarity=0.235  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccccc
Q 013128          216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAVQ  280 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~~  280 (449)
                      .+.+.+.+.+...+.....--......+..+++.||||+|||+++..+|..+    +..+..+++....
T Consensus        72 ~~~~~v~~eL~~~l~~~~~~~~~~~~~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R  140 (428)
T TIGR00959        72 QFIKIVHEELVAILGGENASLNLAKKPPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYR  140 (428)
T ss_pred             HHHHHHHHHHHHHhCCCCcccccCCCCCEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccc
Confidence            3455555555555543211011112235679999999999999999998875    4566666666543

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.48  E-value=0.0023  Score=58.25  Aligned_cols=25  Identities=28%  Similarity=0.425  Sum_probs=22.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -++|.||||+|||+++++|+..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4789999999999999999998864

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.48  E-value=0.0081  Score=58.80  Aligned_cols=62  Identities=23%  Similarity=0.244  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHcCh-hHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          217 LKREITEDLENFMNGK-EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       217 ~k~~i~~~l~~~~~~~-~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      ..+.+.+.+...+... ..+. .....++.++|.||||+|||+++..+|..+   +..+.-+++...
T Consensus        46 ~~~~~~e~l~~~~~~~~~~~~-~~~~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~  111 (272)
T TIGR00064        46 LKEILKEYLKEILKETDLELI-VEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTF  111 (272)
T ss_pred             HHHHHHHHHHHHHcccchhhc-ccCCCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCC
Confidence            4445555555554432 1111 112234668888999999999999999887   555655555443

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.

>PTZ00301 uridine kinase; Provisional

Probab=96.47  E-value=0.037  Score=52.02  Aligned_cols=90  Identities=12%  Similarity=0.006  Sum_probs=46.7

Q ss_pred             eEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHH-------HHH
Q 013128          347 RIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEV-------AGE  419 (449)
Q Consensus       347 ~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i-------~~~  419 (449)
                      .+||.--++. .-++.+..  .+|..|++..|....+.....+-....+.....-+..........-++.       +..
T Consensus       108 ~ViIvEGi~~-l~~~~l~~--l~D~~ifvd~~~d~~~~Rr~~Rd~~~rG~~~e~v~~~~~~~v~~~~~~~I~p~k~~ADi  184 (210)
T PTZ00301        108 SVLIVEGILL-FTNAELRN--EMDCLIFVDTPLDICLIRRAKRDMRERGRTFESVIEQYEATVRPMYYAYVEPSKVYADI  184 (210)
T ss_pred             cEEEEechhh-hCCHHHHH--hCCEEEEEeCChhHHHHHHHhhhHHhcCCCHHHHHHHHHHhhcccHHHHcCccccCCcE
Confidence            3555555554 12467766  8999999998877666655555544334443333333332211111111       112


Q ss_pred             Hhc-CCCHHHHHHHHHHHHHH
Q 013128          420 LMK-STNAEVSLNGLVKFLHA  439 (449)
Q Consensus       420 l~~-~~~~~~al~~l~~~l~~  439 (449)
                      ++. ..+.+.++..+...++.
T Consensus       185 Ii~~~~~~~~~~~~~~~~~~~  205 (210)
T PTZ00301        185 IVPSWKDNSVAVGVLRAKLNH  205 (210)
T ss_pred             EEcCCCcchHHHHHHHHHHHH
Confidence            222 23567777777666554

>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=96.45  E-value=0.0029  Score=58.85  Aligned_cols=39  Identities=23%  Similarity=0.347  Sum_probs=30.0

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEeccccc
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAVQ  280 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~~  280 (449)
                      .|.-+++.|+||+|||+++..+...+ +..++.++...+.
T Consensus        14 ~P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r   53 (199)
T PF06414_consen   14 KPTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFR   53 (199)
T ss_dssp             S-EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGG
T ss_pred             CCEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHH
Confidence            36779999999999999999999998 7777888776664

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.

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

Probab=96.45  E-value=0.0067  Score=66.89  Aligned_cols=29  Identities=24%  Similarity=0.312  Sum_probs=24.3

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++++.-+-+.|++|||||||++.+.+...
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly~  524 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLYK  524 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            33344499999999999999999999883

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.44  E-value=0.012  Score=62.32  Aligned_cols=64  Identities=25%  Similarity=0.329  Sum_probs=41.5

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEeccc--c--------------------cChHHHHHHHHcCCC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSA--V--------------------QSNSELRFLLLTMPS  294 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~--~--------------------~~~~~l~~~~~~~~~  294 (449)
                      ++..+.|.||+|+|||+++..||..+     +..+..++...  .                    .+...+...+.....
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~  428 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRD  428 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhcc
Confidence            34568899999999999999999865     22343333221  1                    112345555555566


Q ss_pred             CceEEeeccch
Q 013128          295 RSMLVIEDIDC  305 (449)
Q Consensus       295 ~~Il~iDeiD~  305 (449)
                      ..+||||..-.
T Consensus       429 ~DLVLIDTaG~  439 (559)
T PRK12727        429 YKLVLIDTAGM  439 (559)
T ss_pred             CCEEEecCCCc
Confidence            77888888754

>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=96.43  E-value=0.014  Score=52.87  Aligned_cols=25  Identities=40%  Similarity=0.619  Sum_probs=22.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +..+.|.||.|+|||+|++.||..+
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999976

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.42  E-value=0.0024  Score=58.75  Aligned_cols=26  Identities=27%  Similarity=0.588  Sum_probs=23.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +..+++.||+|+|||+++++++..+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            45799999999999999999999874

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.

>PRK12338 hypothetical protein; Provisional

Probab=96.41  E-value=0.003  Score=62.88  Aligned_cols=29  Identities=24%  Similarity=0.343  Sum_probs=25.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      |.-+++.|+||||||++++++|..++...
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~   32 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKH   32 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeE
Confidence            45789999999999999999999998754

>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=96.40  E-value=0.0032  Score=56.23  Aligned_cols=37  Identities=30%  Similarity=0.438  Sum_probs=30.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      ..|.|.|.||+|||++|+++...|   +.+++.+|...+.
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR   42 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLR   42 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchh
Confidence            357899999999999999999988   6788888766554

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 ....

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=96.40  E-value=0.017  Score=54.62  Aligned_cols=63  Identities=19%  Similarity=0.311  Sum_probs=42.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CC---------cE-----EEEecc-cccC--------hHHHHHHHHcCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KF---------DI-----YDLDLS-AVQS--------NSELRFLLLTMPS  294 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~---------~~-----~~l~~s-~~~~--------~~~l~~~~~~~~~  294 (449)
                      ++.++|.||.|.|||++.+.++...     |.         ++     ..+... ++..        -.++..++.....
T Consensus        30 ~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  109 (218)
T cd03286          30 PRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATP  109 (218)
T ss_pred             CcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCcccccccCcchHHHHHHHHHHHHHhCCC
Confidence            4578999999999999999887653     21         11     111111 1111        1445567777889


Q ss_pred             CceEEeeccch
Q 013128          295 RSMLVIEDIDC  305 (449)
Q Consensus       295 ~~Il~iDeiD~  305 (449)
                      +++++|||+..
T Consensus       110 ~sLvLlDE~~~  120 (218)
T cd03286         110 DSLVILDELGR  120 (218)
T ss_pred             CeEEEEecccC
Confidence            99999999864

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

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=96.40  E-value=0.022  Score=50.15  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=19.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|+||+|||+|+.++++.
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999875

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>PRK04328 hypothetical protein; Provisional

Probab=96.40  E-value=0.0044  Score=59.86  Aligned_cols=38  Identities=32%  Similarity=0.261  Sum_probs=28.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH-c--CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ-L--KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~-l--~~~~~~l~~  276 (449)
                      |++.+..+|++||||||||+|+..++.+ +  |.+.+.++.
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~   59 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVAL   59 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEe
Confidence            5667778999999999999998876654 2  455555544

>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=96.38  E-value=0.0027  Score=57.56  Aligned_cols=22  Identities=36%  Similarity=0.860  Sum_probs=20.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++|.|+||+||||+++.+++++
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            7899999999999999999998

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.

>PRK10436 hypothetical protein; Provisional

Probab=96.36  E-value=0.016  Score=60.83  Aligned_cols=86  Identities=17%  Similarity=0.419  Sum_probs=53.8

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe-----
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQLK---FDIYDLD-----  275 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~-----  275 (449)
                      +.+++++.+.+...+.+.+.+.    .           +.| +|+.||+|+||||+..++.++++   .+++.+.     
T Consensus       194 ~~~L~~LG~~~~~~~~l~~~~~----~-----------~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE~  258 (462)
T PRK10436        194 ALDLETLGMTPAQLAQFRQALQ----Q-----------PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVEI  258 (462)
T ss_pred             CCCHHHcCcCHHHHHHHHHHHH----h-----------cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCccc
Confidence            3478899888877666654432    1           344 78899999999999999888874   3344432     


Q ss_pred             -cccc-----c--ChHHHHHHHHcC--CCCceEEeeccch
Q 013128          276 -LSAV-----Q--SNSELRFLLLTM--PSRSMLVIEDIDC  305 (449)
Q Consensus       276 -~s~~-----~--~~~~l~~~~~~~--~~~~Il~iDeiD~  305 (449)
                       +..+     .  ....+...+...  ..|-||++.||-.
T Consensus       259 ~l~gi~Q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEIRD  298 (462)
T PRK10436        259 PLAGINQTQIHPKAGLTFQRVLRALLRQDPDVIMVGEIRD  298 (462)
T ss_pred             cCCCcceEeeCCccCcCHHHHHHHHhcCCCCEEEECCCCC
Confidence             1111     1  011222222222  4799999999863

>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=96.35  E-value=0.0032  Score=58.55  Aligned_cols=25  Identities=40%  Similarity=0.648  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |+-++|.||+|+||||++.-+|.++
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~   25 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARL   25 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHH
Confidence            4568999999999999999999888

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 ....

>COG3378 Phage associated DNA primase [General function prediction only]

Probab=96.35  E-value=0.013  Score=62.01  Aligned_cols=91  Identities=20%  Similarity=0.407  Sum_probs=55.3

Q ss_pred             cccccC-CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC-cEEEEecccccChHHH
Q 013128          208 FKTLAL-DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF-DIYDLDLSAVQSNSEL  285 (449)
Q Consensus       208 f~~l~g-~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~-~~~~l~~s~~~~~~~l  285 (449)
                      ++++.+ +.++..-+.+.+-.-+...       ..+...+.|+||-|+|||+++..|.+-+|. .+-.+..+.+.....-
T Consensus       201 L~~~~~~d~el~~ll~~i~g~~l~g~-------~~~~k~~~l~G~G~nGKstf~~li~~llG~~n~~s~~~~~~~~~~~~  273 (517)
T COG3378         201 LDRVAGGDPELRNLLQRIIGASLTGR-------VSEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAPLTDLEADDRH  273 (517)
T ss_pred             HHHhhcCCHHHHHHHHHHHhheecCc-------ccceeEEEEEcCCCCChHHHHHHHHHHhccchhccccHHHhhhhccC
Confidence            456655 5555444444433222221       335678999999999999999999999975 4444555544422222


Q ss_pred             HHHHHcCCCCceEEeeccch
Q 013128          286 RFLLLTMPSRSMLVIEDIDC  305 (449)
Q Consensus       286 ~~~~~~~~~~~Il~iDeiD~  305 (449)
                      +.-++..-...++..+|.+.
T Consensus       274 ~~~~A~Lvg~~~v~~~E~~k  293 (517)
T COG3378         274 PFGLAALVGKRLVTVSETEK  293 (517)
T ss_pred             cchHHHhhCceEEEecCccc
Confidence            23344445667777777665

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.34  E-value=0.017  Score=59.07  Aligned_cols=27  Identities=41%  Similarity=0.655  Sum_probs=24.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +..+.+.||.|||||++++++.+.+..
T Consensus        22 ~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   22 GLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             CcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            567899999999999999999999844

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.34  E-value=0.0051  Score=58.29  Aligned_cols=37  Identities=22%  Similarity=0.155  Sum_probs=27.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |++.+..++++||||||||+++..++.+.   +..++.++
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            56667779999999999999999877543   44444444

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.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=96.32  E-value=0.0094  Score=54.66  Aligned_cols=24  Identities=42%  Similarity=0.721  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-.+++||||+|||+++..+|..+
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~   56 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAAL   56 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHH
Confidence            348899999999999999998876

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=96.32  E-value=0.032  Score=53.32  Aligned_cols=21  Identities=48%  Similarity=0.593  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+|.||||+|||+|+..+|-.
T Consensus         4 ~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHHH
Confidence            479999999999999999865

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.32  E-value=0.0046  Score=62.87  Aligned_cols=24  Identities=38%  Similarity=0.614  Sum_probs=22.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.||+|+||||+++++++++
T Consensus       135 glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       135 GIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            458999999999999999999987

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.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=96.31  E-value=0.0035  Score=57.21  Aligned_cols=35  Identities=26%  Similarity=0.406  Sum_probs=27.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      .-+.|.||+|+|||+++++++..++..  .++...+.
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~~--~i~gd~~~   38 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSAK--FIDGDDLH   38 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCE--EECCcccC
Confidence            458899999999999999999999874  34444443

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

Probab=96.30  E-value=0.011  Score=60.15  Aligned_cols=104  Identities=24%  Similarity=0.295  Sum_probs=60.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC-------CcEEEEeccccc--------------------ChHHHHHHHHcCCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK-------FDIYDLDLSAVQ--------------------SNSELRFLLLTMPSR  295 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~-------~~~~~l~~s~~~--------------------~~~~l~~~~~~~~~~  295 (449)
                      ++-+.|.||.|+||||.++-+|..+.       .-++.+|.-.+.                    +..++...+......
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~~~  282 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDC  282 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhhcC
Confidence            56688999999999999888888774       334454433332                    234444555555566


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCcccc
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALL  364 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLl  364 (449)
                      -+|++|=+...                ......+.+|-.+++...+  -...+++.+|...+.+...+-
T Consensus       283 d~ILVDTaGrs----------------~~D~~~i~el~~~~~~~~~--i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         283 DVILVDTAGRS----------------QYDKEKIEELKELIDVSHS--IEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             CEEEEeCCCCC----------------ccCHHHHHHHHHHHhcccc--ceEEEEEecCcchHHHHHHHH
Confidence            77777766542                2223455666666665422  122344444444444544443

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.30  E-value=0.0038  Score=57.61  Aligned_cols=29  Identities=17%  Similarity=0.227  Sum_probs=23.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc-CCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL-KFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l-~~~~~~l  274 (449)
                      +.+.|+||||||++|+.++..+ +..++.+
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~~~~~~i~~   31 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILPNCCVIHQ   31 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeEEcc
Confidence            5688999999999999999998 4444433

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.30  E-value=0.0055  Score=58.47  Aligned_cols=38  Identities=16%  Similarity=0.217  Sum_probs=30.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~  276 (449)
                      |.+++.-++|.||||+|||+++..+|...    +.+++.+++
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~   50 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL   50 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC
Confidence            66666779999999999999998887665    677776653

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.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.29  E-value=0.0059  Score=57.09  Aligned_cols=36  Identities=17%  Similarity=0.191  Sum_probs=27.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC-CcEEEEeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK-FDIYDLDLSA  278 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~-~~~~~l~~s~  278 (449)
                      +.-+.|.||+|||||||+++|+..++ ..+..++...
T Consensus         6 ~~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~D~   42 (209)
T PRK05480          6 PIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQDS   42 (209)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeCCc
Confidence            34588999999999999999999983 3444454443

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.29  E-value=0.0072  Score=61.37  Aligned_cols=24  Identities=38%  Similarity=0.563  Sum_probs=22.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+++.|.||||||.|+-.+|.++
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            458899999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=96.28  E-value=0.0032  Score=56.68  Aligned_cols=26  Identities=35%  Similarity=0.507  Sum_probs=22.5

Q ss_pred             eCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          249 YGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       249 ~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .||||||||+++++++..++..+++-
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~   26 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDG   26 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeC
Confidence            49999999999999999998765544

>cd04177 RSR1 RSR1 subgroup

Probab=96.28  E-value=0.024  Score=50.60  Aligned_cols=23  Identities=26%  Similarity=0.508  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .++|.|+||+|||++++++++..
T Consensus         3 ki~liG~~~~GKTsli~~~~~~~   25 (168)
T cd04177           3 KIVVLGAGGVGKSALTVQFVQNV   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999998554

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>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=96.27  E-value=0.0054  Score=55.48  Aligned_cols=35  Identities=26%  Similarity=0.298  Sum_probs=28.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ  280 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~  280 (449)
                      +++.||||+|||++++.+|..+   +..+..+++....
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~~~   40 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYR   40 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCCCC
Confidence            6889999999999999999886   6677777766543

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.

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=96.27  E-value=0.0098  Score=61.89  Aligned_cols=33  Identities=36%  Similarity=0.435  Sum_probs=28.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc-EEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD-IYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~-~~~l~  275 (449)
                      |.-+++.|+||||||+++..+|..++.. ++..|
T Consensus       255 p~vil~~G~~G~GKSt~a~~LA~~lg~~~ii~tD  288 (475)
T PRK12337        255 PLHVLIGGVSGVGKSVLASALAYRLGITRIVSTD  288 (475)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCcEEeehh
Confidence            6779999999999999999999999985 33433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	449
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		2e-15
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-13
2ce7_A	476	Edta Treated Length = 476		5e-13
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		5e-13
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		5e-13
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-12
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-11
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		4e-11
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-10
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		5e-10
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		7e-09
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		8e-09
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		1e-08
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		2e-08
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		2e-08
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		3e-08
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		4e-08
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		4e-08
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		4e-08
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		5e-08
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		5e-08
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		5e-08
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		5e-08
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		2e-07
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		4e-05
3vfd_A	389	Human Spastin Aaa Domain Length = 389		4e-05
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		8e-04

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 60/179 (33%), Positives = 91/179 (50%), Gaps = 13/179 (7%)
Query: 203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAA 262
           K  + FK +A + E K E+ E + +F+   E Y  +G    +G LL GPPGTGK+ L  A
Sbjct: 5   KPNVRFKDMAGNEEAKEEVVE-IVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKA 63
Query: 263 MANQLKFDIYDLDLSAV------QSNSELRFLLLTMPSR--SMLVIEDIDCSVKLQNRES 314
           +A +     + +  S+          S +R L  T   +  S++ I++ID   K  +R +
Sbjct: 64  VAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGK--SRAA 121
Query: 315 SEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHL 373
             V + N E  + TL+ LL  +DG  S      I++  TN  E LDPAL+RPGR D  +
Sbjct: 122 GGVVSGNDEREQ-TLNQLLAEMDGFGSENAP-VIVLAATNRPEILDPALMRPGRFDRQV 178

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 73.6 bits (179), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 93/184 (50%), Gaps = 14/184 (7%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           +TF  +   +E  RE+ E +E  +   E + R+G    +G LLYGPPGTGK+ L  A+A 
Sbjct: 178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAA 237
Query: 266 QLKFDIYDLDLSAV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEV 317
            +  +      S +      +S   +R  F         ++ ++++D    +  R  SE 
Sbjct: 238 TIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDA---IGGRRFSEG 294
Query: 318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSY 377
            + ++E  + TL  LL  +DG +   G+ +II+  TN  + LDPALLRPGR+D  + +  
Sbjct: 295 TSADREIQR-TLMELLTQMDG-FDNLGQTKIIM-ATNRPDTLDPALLRPGRLDRKVEIPL 351
Query: 378 CNTS 381
            N +
Sbjct: 352 PNEA 355

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 83/173 (47%), Gaps = 15/173 (8%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           +TFK +    E   E+ E +E F+     + RIG    +G LL GPPGTGK+ L  A+A 
Sbjct: 13  VTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAG 71
Query: 266 QLKFDIYDL------DLSAVQSNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNRESSEV 317
           +     + +      +L      + +R L     + +  ++ I++ID       R     
Sbjct: 72  EANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAV----GRHRGAG 127
Query: 318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
                +E + TL+ LL  +DG  S   EG I++  TN  + LDPALLRPGR D
Sbjct: 128 LGGGHDEREQTLNQLLVEMDGFDSK--EGIIVMAATNRPDILDPALLRPGRFD 178

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 85/183 (46%), Gaps = 14/183 (7%)
Query: 218 KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS 277
           K+EI E +E  +   + Y +IG    RG LLYGPPGTGK+ L+ A+AN  K     ++ S
Sbjct: 181 KQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGS 240
Query: 278 AV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL 329
                   +    +R  F L    + S++ I+++D        +  + Q  +  E +  L
Sbjct: 241 EFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIAT----KRFDAQTGSDREVQRIL 296
Query: 330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFN 389
             LL  +DG          ++  TN  + LDPALLRPGR+D  +          ++L F 
Sbjct: 297 IELLTQMDGFDQSTNVK--VIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFG 354
Query: 390 YLG 392
            + 
Sbjct: 355 TIA 357

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 15/188 (7%)
Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TF  +A   E K E+ E +E ++     + ++G    +G L+ GPPGTGK+ L  A+A +
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68
Query: 267 LKF--------DIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            K         D  ++ +    S     F      +  ++ I++ID       R+     
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAV----GRQRGAGL 124
Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYC 378
               +E + TL+ +L  +DG      EG I++  TN  + LDPALLRPGR D  + +   
Sbjct: 125 GGGHDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLP 182
Query: 379 NTSVFKQL 386
           +    +Q+
Sbjct: 183 DVRGREQI 190

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 82/173 (47%), Gaps = 15/173 (8%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           +TFK +    E   E+ E +E F+     + RIG    +G LL GPPGTG + L  A+A 
Sbjct: 13  VTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGATLLARAVAG 71
Query: 266 QLKFDIYDL------DLSAVQSNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNRESSEV 317
           +     + +      +L      + +R L     + +  ++ I++ID       R     
Sbjct: 72  EANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAV----GRHRGAG 127
Query: 318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
                +E + TL+ LL  +DG  S   EG I++  TN  + LDPALLRPGR D
Sbjct: 128 LGGGHDEREQTLNQLLVEMDGFDSK--EGIIVMAATNRPDILDPALLRPGRFD 178

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 93/176 (52%), Gaps = 14/176 (7%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           ++FK +A   E K E+ E   +++   E + ++G    +G LL GPPG GK+ L  A+A 
Sbjct: 3   VSFKDVAGMHEAKLEVRE-FVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT 61
Query: 266 QLKFDIYDL------DLSAVQSNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNRESSEV 317
           + +     +      ++      + +R L     +R+  ++ I++ID   K   R ++  
Sbjct: 62  EAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGK--KRSTTMS 119
Query: 318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHL 373
             +N EE + TL+ LL  +DG+ +   +  I++ +TN  + LD AL+RPGR+D H+
Sbjct: 120 GFSNTEEEQ-TLNQLLVEMDGMGTT--DHVIVLASTNRADILDGALMRPGRLDRHV 172

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/164 (32%), Positives = 81/164 (49%), Gaps = 22/164 (13%)
Query: 219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ-----LKFDIYD 273
           +EI E +E  +   E +  +G A  +G +LYGPPGTGK+ L  A+A+      ++    +
Sbjct: 158 KEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAE 217
Query: 274 LDLSAVQSNSELRFLLLTMP---SRSMLVIEDID----CSVKLQNRESSEVQATNQEENK 326
           L    +   S +   L  M    + S++ +++ID      V+      SEVQ T  E   
Sbjct: 218 LVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLE--- 274
Query: 327 VTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
                LLN +DG  +   +   I+  TN  + LDPALLRPGR+D
Sbjct: 275 -----LLNQLDGFETS--KNIKIIMATNRLDILDPALLRPGRID 311

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/190 (31%), Positives = 99/190 (52%), Gaps = 19/190 (10%)
Query: 212 ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ----- 266
            L+S+++ EI E +E  +   E Y  +G    +G +LYG PGTGK+ L  A+ANQ     
Sbjct: 186 GLESQIQ-EIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATF 244
Query: 267 LKFDIYDLDLSAVQSNSELR---FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQE 323
           L+    +L    +     L    F +    + S++ I++ID ++  +  +S+   +  + 
Sbjct: 245 LRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEID-AIGTKRYDSN---SGGER 300
Query: 324 ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVF 383
           E + T+  LLN +DG +   G+ ++I   TN  E LDPAL+RPGR+D  +     + S  
Sbjct: 301 EIQRTMLELLNQLDG-FDDRGDVKVI-MATNKIETLDPALIRPGRIDRKILFENPDLSTK 358
Query: 384 KQLAFNYLGI 393
           K++    LGI
Sbjct: 359 KKI----LGI 364

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 62.4 bits (150), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 83/160 (51%), Gaps = 14/160 (8%)
Query: 219 REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ-----LKFDIYD 273
           +EI E +E  +   E + ++G    +G LLYGPPGTGK+ L  A+A +     ++    +
Sbjct: 27  QEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSE 86
Query: 274 LDLSAVQSNSELR---FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLS 330
           L    +   + L    F L    + S++ I++ID    +  + +  +   ++E  + TL 
Sbjct: 87  LVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDA---IAAKRTDALTGGDREVQR-TLM 142
Query: 331 GLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
            LL  +DG +   G+ +II   TN  + LDPA+LRPGR D
Sbjct: 143 QLLAEMDG-FDARGDVKII-GATNRPDILDPAILRPGRFD 180

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 58.5 bits (140), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 228 FMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--------DIYDLDLSAV 279
           F+     +  +G    +G LL GPPG GK+ L  A+A + +         D  ++ +   
Sbjct: 49  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 108
Query: 280 QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL 339
            +     F      +  ++ I++ID    +  +  S V   N E  + TL+ LL  +DG 
Sbjct: 109 AARVRDLFETAKRHAPCIVFIDEIDA---VGRKRGSGVGGGNDEREQ-TLNQLLVEMDGF 164
Query: 340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQL 386
                   +++  TN  + LDPALLRPGR D  + +   +    +Q+
Sbjct: 165 EKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI 209

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 58.2 bits (139), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 228 FMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--------DIYDLDLSAV 279
           F+     +  +G    +G LL GPPG GK+ L  A+A + +         D  ++ +   
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 117
Query: 280 QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL 339
            +     F      +  ++ I++ID    +  +  S V   N E  + TL+ LL  +DG 
Sbjct: 118 AARVRDLFETAKRHAPCIVFIDEIDA---VGRKRGSGVGGGNDEREQ-TLNQLLVEMDGF 173
Query: 340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQL 386
                   +++  TN  + LDPALLRPGR D  + +   +    +Q+
Sbjct: 174 EKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI 218

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 228 FMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--------DIYDLDLSAV 279
           F+     +  +G    +G LL GPPG GK+ L  A+A + +         D  ++ +   
Sbjct: 34  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 93
Query: 280 QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL 339
            +     F      +  ++ I++ID    +  +  S V   N E  + TL+ LL  +DG 
Sbjct: 94  AARVRDLFETAKRHAPCIVFIDEIDA---VGRKRGSGVGGGNDEREQ-TLNQLLVEMDGF 149
Query: 340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQL 386
                   +++  TN  + LDPALLRPGR D  + +   +    +Q+
Sbjct: 150 EKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI 194

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 228 FMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--------DIYDLDLSAV 279
           F+     +  +G    +G LL GPPG GK+ L  A+A + +         D  ++ +   
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 117
Query: 280 QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL 339
            +     F      +  ++ I++ID    +  +  S V   N E  + TL+ LL  +DG 
Sbjct: 118 AARVRDLFETAKRHAPCIVFIDEIDA---VGRKRGSGVGGGNDEREQ-TLNQLLVEMDGF 173
Query: 340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQL 386
                   +++  TN  + LDPALLRPGR D  + +   +    +Q+
Sbjct: 174 EKDTAI--VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQI 218

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/184 (26%), Positives = 83/184 (45%), Gaps = 27/184 (14%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           +T+  +    +++ E+T  +   +   + +  +G     G LL GPPG GK+ L  A+AN
Sbjct: 7   VTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVAN 66
Query: 266 QLKFDIYD------LDLSAVQSNSELRFLLLTMPSRSMLVI--EDID--CSVKLQNRESS 315
           +   +         L++   +S   +R +     + +  VI  +++D  C  +      +
Sbjct: 67  ESGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGA 126
Query: 316 EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF---TTNHKEKLDPALLRPGRMDMH 372
            V+  NQ         LL  +DGL     E R  VF    TN  + +DPA+LRPGR+D  
Sbjct: 127 SVRVVNQ---------LLTEMDGL-----EARQQVFIMAATNRPDIIDPAILRPGRLDKT 172
Query: 373 LHMS 376
           L + 
Sbjct: 173 LFVG 176

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/179 (22%), Positives = 86/179 (48%), Gaps = 14/179 (7%)
Query: 206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN 265
           +T++ +    ++KRE+ E ++  +   + + + G    +G L YGPPG GK+ L  A+AN
Sbjct: 12  VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN 71
Query: 266 QLKFDIYDLDLSAV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEV 317
           + + +   +    +      +S + +R  F      +  +L  +++D   K +     + 
Sbjct: 72  ECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDG 131
Query: 318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMS 376
                      ++ +L  +DG+ +   +   I+  TN  + +DPA+LRPGR+D  +++ 
Sbjct: 132 GGAADR----VINQILTEMDGMST--KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIP 184

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 83/173 (47%), Gaps = 19/173 (10%)
Query: 212 ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ----- 266
            LD +++ E+ E +   M   + +  +G    +G L+YGPPGTGK+ L  A A Q     
Sbjct: 185 GLDKQIE-ELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATF 243
Query: 267 LKFDIYDLDLSAVQSNSEL---RFLLLTMPSRSMLVIEDIDC-SVKLQNRESSEVQATNQ 322
           LK     L    +   ++L    F L    + +++ I+++D    K  + E S       
Sbjct: 244 LKLAAPQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKS-----GD 298
Query: 323 EENKVTLSGLLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLH 374
            E + T+  LLN +DG  S   + R+ V   TN  + LDPALLR GR+D  + 
Sbjct: 299 REVQRTMLELLNQLDGFSS---DDRVKVLAATNRVDVLDPALLRSGRLDRKIE 348

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 19/171 (11%)
Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL 276
           +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     F I   ++
Sbjct: 215 QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI 274
Query: 277 S---AVQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG 331
               A +S S LR  F      + +++ I+++D     + +   EV+       +  +S 
Sbjct: 275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE-------RRIVSQ 327
Query: 332 LLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTS 381
           LL  +DGL        +IV   TN    +DPAL R GR D  + +   + +
Sbjct: 328 LLTLMDGLKQ---RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDAT 375

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/154 (29%), Positives = 73/154 (47%), Gaps = 18/154 (11%)
Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ-----LKFDIYDLDLSAVQSNSELRF 287
           E +  +G    +G LLYGPPGTGK+    A+AN+     ++    +L    V   + +  
Sbjct: 233 ERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVR 292
Query: 288 LLLTMPSRS----MLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC 343
            L  M +R+    ++  ++ID     +  +     A    E + T+  L+  +DG     
Sbjct: 293 ELFEM-ARTKKACIIFFDEIDAVGGARFDDG----AGGDNEVQRTMLELITQLDGFDP-- 345
Query: 344 GEGRI-IVFTTNHKEKLDPALLRPGRMDMHLHMS 376
             G I ++F TN    LDPALLRPGR+D  +  S
Sbjct: 346 -RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFS 378

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 49/208 (23%), Positives = 91/208 (43%), Gaps = 23/208 (11%)
Query: 240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN--------SELRFLLLT 291
           R   +G LL+GPPGTGK+ +   +A+Q     + +  S++ S             F +  
Sbjct: 114 RGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVAR 173
Query: 292 MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF 351
               +++ I++ID    L  R   E      E ++   +  L  +DG  +   +  ++V 
Sbjct: 174 CQQPAVIFIDEIDS--LLSQRGDGE-----HESSRRIKTEFLVQLDGATTSSEDRILVVG 226
Query: 352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEVN 410
            TN  +++D A  R  R+   L++     S  KQ+  N +      L  E+IE+++++ +
Sbjct: 227 ATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSD 284
Query: 411 VTPAEVAGELMKSTNAEVSLNGLVKFLH 438
                 +G  M     E SL G ++ L 
Sbjct: 285 A----FSGADMTQLCREASL-GPIRSLQ 307

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/142 (31%), Positives = 73/142 (51%), Gaps = 18/142 (12%)
Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSL---IAAMANQLKFDIYDLDLSA--VQSNSELRF 287
           E +T + RA  RG LL+GPPG GK+ L   +AA +N   F+I    L++  V    +L  
Sbjct: 139 ELFTGL-RAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVR 197
Query: 288 LLLTMPSR---SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG 344
            L  +      S++ I+ +D S+  + RE       +    ++    L+ F DG+ S  G
Sbjct: 198 ALFAVARELQPSIIFIDQVD-SLLCERREGE-----HDASRRLKTEFLIEF-DGVQS-AG 249
Query: 345 EGRIIVF-TTNHKEKLDPALLR 365
           + R++V   TN  ++LD A+LR
Sbjct: 250 DDRVLVMGATNRPQELDEAVLR 271

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 60/129 (46%), Gaps = 16/129 (12%)
Query: 245 GYLLYGPPGTGKSSL---IAAMANQLKFDIYDLDLSA--VQSNSELRFLLLTMPSR---S 296
           G LLYGPPGTGKS L   +A  AN   F +   DL +  +  + +L   L  M      S
Sbjct: 62  GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPS 121
Query: 297 MLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK 356
           ++ I+++D     +    SE     + E  V ++G+ N          +G +++  TN  
Sbjct: 122 IIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGVGN--------DSQGVLVLGATNIP 173
Query: 357 EKLDPALLR 365
            +LD A+ R
Sbjct: 174 WQLDSAIRR 182

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	449
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-20
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-15
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	5e-17
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	9e-15
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	1e-14
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	5e-14
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-13
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	6e-13
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	7e-13
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	7e-13
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	8e-13
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	1e-12
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	1e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-09
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	3e-12
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	3e-12
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	1e-10
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	2e-08
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	3e-08
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	5e-08
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	3e-07
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	9e-07
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	2e-06
2fna_A	357	Conserved hypothetical protein; structural genomic	4e-05
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	4e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	5e-05
2qgz_A	308	Helicase loader, putative primosome component; str	6e-05
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	6e-05
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	1e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	1e-04
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	2e-04
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	2e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	3e-04
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	3e-04

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score = 82.2 bits (203), Expect = 5e-17
 Identities = 49/167 (29%), Positives = 77/167 (46%), Gaps = 20/167 (11%)

Query: 213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIY 272
              +L  +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+     +
Sbjct: 209 CRKQL-AQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFF 267

Query: 273 DLDLSAV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEE 324
            ++   +      +S S LR  F      + +++ I+++D       RE        + E
Sbjct: 268 LINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIA--PKREK----THGEVE 321

Query: 325 NKVTLSGLLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMD 370
            ++ +S LL  +DGL        +IV   TN    +DPAL R GR D
Sbjct: 322 RRI-VSQLLTLMDGL---KQRAHVIVMAATNRPNSIDPALRRFGRFD 364

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 73.7 bits (181), Expect = 9e-15
 Identities = 33/167 (19%), Positives = 58/167 (34%), Gaps = 32/167 (19%)

Query: 232 KEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSEL------ 285
           K +             ++G  G GKS     +  ++   I  + +SA     EL      
Sbjct: 25  KNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKM--GINPIMMSA----GELESGNAG 78

Query: 286 --------RFLLLTMPSR----SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLL 333
                   R+       R      L I D+D +   +   +++    NQ  N  TL  + 
Sbjct: 79  EPAKLIRQRYREAAEIIRKGNMCCLFINDLD-AGAGRMGGTTQYTVNNQMVNA-TLMNIA 136

Query: 334 NF-----IDGLWSCCGEGRI-IVFTTNHKEKLDPALLRPGRMDMHLH 374
           +      + G+++     R+ I+ T N    L   L+R GRM+    
Sbjct: 137 DNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW 183

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 73.1 bits (180), Expect = 1e-14
 Identities = 51/167 (30%), Positives = 82/167 (49%), Gaps = 17/167 (10%)

Query: 213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIY 272
           L+ +  +EI E +E  +   E + ++G    +G LLYGPPGTGK+ L  A+A +      
Sbjct: 22  LEKQ-MQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFI 80

Query: 273 DLDLSA-VQ-----SNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEE 324
            +  S  V+       S ++  F L    + S++ I++ID ++    R  +        E
Sbjct: 81  RVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEID-AIA-AKRTDALTGGDR--E 136

Query: 325 NKVTLSGLLNFIDGLWSCCGEGRIIVF-TTNHKEKLDPALLRPGRMD 370
            + TL  LL  +DG  +    G + +   TN  + LDPA+LRPGR D
Sbjct: 137 VQRTLMQLLAEMDGFDA---RGDVKIIGATNRPDILDPAILRPGRFD 180

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score = 71.1 bits (175), Expect = 5e-14
 Identities = 50/190 (26%), Positives = 89/190 (46%), Gaps = 42/190 (22%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           +FK +A   E K E+ E   +++   E + ++G    +G LL GPPG GK+ L  A+A +
Sbjct: 4   SFKDVAGMHEAKLEVRE-FVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE 62

Query: 267 LK---FDIYDLDLSAVQSNSELRFLLLTM-----PSR-------------SMLVIEDIDC 305
            +     +         + +E     + +      +R              ++ I++ID 
Sbjct: 63  AQVPFLAM---------AGAE----FVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDA 109

Query: 306 SVKLQNRESSEVQATNQE-ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALL 364
             K   R ++    +N E E   TL+ LL  +DG+ +   +  I++ +TN  + LD AL+
Sbjct: 110 VGK--KRSTTMSGFSNTEEEQ--TLNQLLVEMDGMGT--TDHVIVLASTNRADILDGALM 163

Query: 365 RPGRMDMHLH 374
           RPGR+D H+ 
Sbjct: 164 RPGRLDRHVF 173

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score = 70.4 bits (173), Expect = 1e-13
 Identities = 43/185 (23%), Positives = 78/185 (42%), Gaps = 50/185 (27%)

Query: 216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           ++KRE+ E ++  +   + + + G    +G L YGPPG GK+ L  A+AN+         
Sbjct: 22  DVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--------- 72

Query: 276 LSAVQSNSELRFL------LLTM--------------------PSRSMLVIEDIDCSVKL 309
                   +  F+      LLTM                    P   +L  +++D   K 
Sbjct: 73  -------CQANFISIKGPELLTMWFGESEANVREIFDKARQAAP--CVLFFDELDSIAK- 122

Query: 310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM 369
             R  +        +  +  + +L  +DG+ +   +   I+  TN  + +DPA+LRPGR+
Sbjct: 123 -ARGGNIGDGGGAADRVI--NQILTEMDGMST--KKNVFIIGATNRPDIIDPAILRPGRL 177

Query: 370 DMHLH 374
           D  ++
Sbjct: 178 DQLIY 182

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score = 67.3 bits (165), Expect = 6e-13
 Identities = 53/174 (30%), Positives = 82/174 (47%), Gaps = 19/174 (10%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TFK +A   E K E+ E +E F+     +  +G    +G LL GPPG GK+ L  A+A +
Sbjct: 14  TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 72

Query: 267 LK---FDIYDLDLSAVQ-----SNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNRESSE 316
            +         D   V+       + +R L  T    +  ++ I++ID +V    R+   
Sbjct: 73  ARVPFITASGSDF--VEMFVGVGAARVRDLFETAKRHAPCIVFIDEID-AV---GRKRGS 126

Query: 317 VQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
                 +E + TL+ LL  +DG         +++  TN  + LDPALLRPGR D
Sbjct: 127 GVGGGNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFD 178

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 67.8 bits (166), Expect = 7e-13
 Identities = 53/178 (29%), Positives = 83/178 (46%), Gaps = 19/178 (10%)

Query: 203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAA 262
              +TFK +A   E K E+ E +E F+     +  +G    +G LL GPPG GK+ L  A
Sbjct: 34  APKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARA 92

Query: 263 MANQLK---FDIYDLDLSAVQ-----SNSELRFLLLTMPSRS--MLVIEDIDCSVKLQNR 312
           +A + +         D   V+       + +R L  T    +  ++ I++ID +V    R
Sbjct: 93  VAGEARVPFITASGSDF--VEMFVGVGAARVRDLFETAKRHAPCIVFIDEID-AV---GR 146

Query: 313 ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
           +         +E + TL+ LL  +DG         +++  TN  + LDPALLRPGR D
Sbjct: 147 KRGSGVGGGNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFD 202

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 67.3 bits (165), Expect = 7e-13
 Identities = 56/178 (31%), Positives = 87/178 (48%), Gaps = 19/178 (10%)

Query: 203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAA 262
           +   TF  +A   E K E+ E +E ++     + ++G    +G L+ GPPGTGK+ L  A
Sbjct: 6   QIKTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKA 64

Query: 263 MANQLK---FDIYDLDLSAVQ-----SNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNR 312
           +A + K   F I   D   V+       S +R  F      +  ++ I++ID +V    R
Sbjct: 65  IAGEAKVPFFTISGSDF--VEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID-AV---GR 118

Query: 313 ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
           +         +E + TL+ +L  +DG      EG I++  TN  + LDPALLRPGR D
Sbjct: 119 QRGAGLGGGHDEREQTLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFD 174

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score = 68.3 bits (167), Expect = 8e-13
 Identities = 57/246 (23%), Positives = 113/246 (45%), Gaps = 23/246 (9%)

Query: 173 EKAKAIKEESKVVKLHTVMHMRWDANNIVLKHP-MTFKTLALDSELKREITEDLENFMNG 231
           E A  + E  K ++   +  +    N I+   P + ++ +A     K  I E +   M  
Sbjct: 50  EPAHPVDERLKNLEPKMIELI---MNEIMDHGPPVNWEDIAGVEFAKATIKEIVVWPMLR 106

Query: 232 KEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS----NSE--L 285
            + +T +    K G LL+GPPGTGK+ +   +A+Q     + +  S++ S      E  +
Sbjct: 107 PDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMV 165

Query: 286 R--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC 343
           R  F +      +++ I++ID S+ L  R   E +++ + + +      L  +DG  +  
Sbjct: 166 RALFAVARCQQPAVIFIDEID-SL-LSQRGDGEHESSRRIKTE-----FLVQLDGATTSS 218

Query: 344 GEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-I 402
            +  ++V  TN  +++D A  R  R+   L++     S  KQ+  N +      L E+ I
Sbjct: 219 EDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEI 276

Query: 403 EELIKE 408
           E+++++
Sbjct: 277 EQIVQQ 282

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 67.2 bits (165), Expect = 1e-12
 Identities = 47/190 (24%), Positives = 73/190 (38%), Gaps = 63/190 (33%)

Query: 216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           +++ E+T  +   +   + +  +G     G LL GPPG GK+ L  A+AN+         
Sbjct: 17  DIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANE--------- 67

Query: 276 LSAVQSNSELRFL------LLTM--------------------PSRSMLVIEDIDCSVKL 309
                  S L F+      LL M                    P   ++  +++D     
Sbjct: 68  -------SGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAP--CVIFFDEVDALCPR 118

Query: 310 QNRESSEVQA--TNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF---TTNHKEKLDPALL 364
           ++   +       NQ         LL  +DGL     E R  VF    TN  + +DPA+L
Sbjct: 119 RSDRETGASVRVVNQ---------LLTEMDGL-----EARQQVFIMAATNRPDIIDPAIL 164

Query: 365 RPGRMDMHLH 374
           RPGR+D  L 
Sbjct: 165 RPGRLDKTLF 174

>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* Length = 268

 Score = 66.9 bits (164), Expect = 1e-12
 Identities = 58/185 (31%), Positives = 85/185 (45%), Gaps = 39/185 (21%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
            FK +A + E K E+ E ++ F+   E Y  +G    +G LL GPPGTGK+ L  A+A +
Sbjct: 9   RFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE 67

Query: 267 LK---FDIYDLDLSAVQSNSELRFLLLTM-----PSR-------------SMLVIEDIDC 305
                F +           S      + M      SR             S++ I++ID 
Sbjct: 68  AHVPFFSM---------GGSS----FIEMFVGLGASRVRDLFETAKKQAPSIIFIDEID- 113

Query: 306 SVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLR 365
           ++    R +  V + N E  + TL+ LL  +DG  S      I++  TN  E LDPAL+R
Sbjct: 114 AIGKS-RAAGGVVSGNDEREQ-TLNQLLAEMDGFGS-ENAPVIVLAATNRPEILDPALMR 170

Query: 366 PGRMD 370
           PGR D
Sbjct: 171 PGRFD 175

>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 = 68.3 bits (166), Expect = 2e-12
 Identities = 58/379 (15%), Positives = 117/379 (30%), Gaps = 100/379 (26%)

Query: 92  SEKEKTFEIALDRNEETFDVFKDVTLKWKLVYT-QVPSSMEYRN----PNLGDYNASLRS 146
            E +  ++  L   E+ F    +   K        + S  E  +     +         +
Sbjct: 12  GEHQYQYKDILSVFEDAF--VDNFDCKDVQDMPKSILSKEEIDHIIMSKD---------A 60

Query: 147 EVRHYEL--SFHKKHKDVVLNLYLPHVLEK-----AKAIKEESKVVKLHTVMHMR----- 194
                 L  +   K +++V   ++  VL          IK E +   + T M++      
Sbjct: 61  VSGTLRLFWTLLSKQEEMV-QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 195 WDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGT 254
           ++ N +  K+ ++        +   ++ + L      K              L+ G  G+
Sbjct: 120 YNDNQVFAKYNVSRL------QPYLKLRQALLELRPAK------------NVLIDGVLGS 161

Query: 255 GKSSLIAAMANQLK------FDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVK 308
           GK+ +   +    K      F I+ L+L    S   +  +L  +  +       ID +  
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ-------IDPNWT 214

Query: 309 LQNRESSEVQATNQEENKVTLSGLLNF---------IDGLWS----------CCGEGRII 349
               + S          +  L  LL           +  + +          C    +I+
Sbjct: 215 -SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC----KIL 269

Query: 350 VFTTNHK---EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELI 406
           + TT  K   + L  A      +D H  M+     V   L   YL           ++L 
Sbjct: 270 L-TTRFKQVTDFLSAATTTHISLD-HHSMTLTPDEVKSLLL-KYLDCR-------PQDLP 319

Query: 407 KEV-NVTPAEVA--GELMK 422
           +EV    P  ++   E ++
Sbjct: 320 REVLTTNPRRLSIIAESIR 338

>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 = 57.6 bits (138), Expect = 6e-09
 Identities = 44/323 (13%), Positives = 97/323 (30%), Gaps = 79/323 (24%)

Query: 5   KTVLSTAASLSASAMLIR--------SVANDFLPAEIYDYLDSKIHLVSQYFSSQLTIVV 56
           KT +       +  +  +        ++ N   P  + + L   ++ +   ++S+     
Sbjct: 163 KTWV-ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR----- 216

Query: 57  EEFQGFSINQVFEAANYYLGNKATTTSAQRFRVGKSEKEKTFEIAL---D--RNEETFDV 111
                 +I     +    L         +R       K K +E  L      +N + ++ 
Sbjct: 217 -SDHSSNIKLRIHSIQAEL---------RRLL-----KSKPYENCLLVLLNVQNAKAWNA 261

Query: 112 FKDVTLKWKLVYTQVPSSMEYRNPNLGDY-NASLRSEVR--HYELSFHKKHKDVVLNLYL 168
           F +++ K  L+ T        R   + D+ +A+  + +   H+ ++      D V +L L
Sbjct: 262 F-NLSCK-ILLTT--------RFKQVTDFLSAATTTHISLDHHSMTLTP---DEVKSLLL 308

Query: 169 PHVLEKAKAIKEE---------SKVVKLHTVMHMRWD----ANNIVLKHPMTFKTLALDS 215
            ++  + + +  E         S + +        WD     N   L   +      L+ 
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

Query: 216 ELKREITEDLENFMNGKEYYTRI-----GRAWKRGYLLYGPPGT-----GKSSLIAAMAN 265
              R++ + L  F         I        W    ++            K SL+     
Sbjct: 369 AEYRKMFDRLSVFPPS----AHIPTILLSLIW--FDVIKSDVMVVVNKLHKYSLVEKQPK 422

Query: 266 QLKFDIYDLDLSAVQSNSELRFL 288
           +    I  + L           L
Sbjct: 423 ESTISIPSIYLELKVKLENEYAL 445

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 66.2 bits (162), Expect = 3e-12
 Identities = 50/186 (26%), Positives = 83/186 (44%), Gaps = 20/186 (10%)

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS----NSE---- 284
           E +T +    K G LL+GPPG GK+ L  A+A +      ++  +++ S    + E    
Sbjct: 45  ELFTGLRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVR 103

Query: 285 LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG 344
             F +      S++ I+++D S+ L  R SSE +A+ + + +      L   DGL     
Sbjct: 104 ALFAVARHMQPSIIFIDEVD-SL-LSERSSSEHEASRRLKTE-----FLVEFDGLPGNPD 156

Query: 345 EGRIIVF-TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQI 402
             RI+V   TN  ++LD A LR  R    +++S  +    + L    L      L  E +
Sbjct: 157 GDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEAL 214

Query: 403 EELIKE 408
             L K 
Sbjct: 215 RRLAKI 220

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 66.8 bits (163), Expect = 3e-12
 Identities = 44/185 (23%), Positives = 83/185 (44%), Gaps = 19/185 (10%)

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS----NSE---- 284
           E +T +    + G LL+GPPG GK+ L  A+A +     +++  +++ S      E    
Sbjct: 139 ELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVR 197

Query: 285 LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG 344
             F +      S++ I+ +D S+ L  R   E  A+ + + +      L   DG+ S   
Sbjct: 198 ALFAVARELQPSIIFIDQVD-SL-LCERREGEHDASRRLKTE-----FLIEFDGVQSAGD 250

Query: 345 EGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE-QIE 403
           +  +++  TN  ++LD A+LR  R    +++S  N      L  N L      L + ++ 
Sbjct: 251 DRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELA 308

Query: 404 ELIKE 408
           +L + 
Sbjct: 309 QLARM 313

>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* Length = 272

 Score = 60.9 bits (148), Expect = 1e-10
 Identities = 33/169 (19%), Positives = 60/169 (35%), Gaps = 22/169 (13%)

Query: 215 SELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL 274
            +    + +D E  +   +   R         LL GPP +GK++L A +A +  F    +
Sbjct: 39  GDPVTRVLDDGELLVQQTKNSDRTPL---VSVLLEGPPHSGKTALAAKIAEESNFPFIKI 95

Query: 275 ----DLSAVQSNSELR-----FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEEN 325
                +      ++ +     F        S +V++DI+       R    V    +  N
Sbjct: 96  CSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIE-------RLLDYVPIGPRFSN 148

Query: 326 KVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLH 374
            V L  LL  +       G   +I+ TT+ K+ L   +         +H
Sbjct: 149 LV-LQALLVLLKKAPP-QGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH 194

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score = 55.7 bits (134), Expect = 2e-08
 Identities = 23/110 (20%), Positives = 43/110 (39%), Gaps = 10/110 (9%)

Query: 173 EKAKAIKEESKVVKLHTVMHMRWDANNIVLKH-PMTFKTLALDSELKREITEDLENF--- 228
               +   E      H      W      +K+ P   + +  +     ++   L N+   
Sbjct: 7   HHHHSSGLEVLFQGPHMASDKLW-----TVKYAPTNLQQVCGNKGSVMKLKNWLANWENS 61

Query: 229 -MNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS 277
             N  ++  + G    R  +LYGPPG GK++    +A +L +DI + + S
Sbjct: 62  KKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNAS 111

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score = 54.3 bits (131), Expect = 3e-08
 Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 21/147 (14%)

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS----NSE--LR 286
             +    +    G LLYGPPGTGKS L  A+A +     + +  S + S     SE  ++
Sbjct: 42  HLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVK 100

Query: 287 --FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG 344
             F +      S++ I+ +D ++    R   E +A+ + + +     LL  ++G+     
Sbjct: 101 QLFAMARENKPSIIFIDQVD-AL-TGTRGEGESEASRRIKTE-----LLVQMNGV--GND 151

Query: 345 EGRIIVF-TTNHKEKLDPALLRPGRMD 370
              ++V   TN   +LD A+ R  R +
Sbjct: 152 SQGVLVLGATNIPWQLDSAIRR--RFE 176

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 53.5 bits (129), Expect = 5e-08
 Identities = 42/148 (28%), Positives = 67/148 (45%), Gaps = 22/148 (14%)

Query: 233 EYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLDLSA---VQSNSEL 285
             +T     W+ G LL+GPPGTGKS L  A+A +      F I   DL +    +S   +
Sbjct: 36  HLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLV 94

Query: 286 R--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC 343
           +  F L      S++ I++ID S+   +R  +E +A  + + +      L  + G+    
Sbjct: 95  KNLFQLARENKPSIIFIDEID-SL-CGSRSENESEAARRIKTE-----FLVQMQGVGV-- 145

Query: 344 GEGRIIVF-TTNHKEKLDPALLRPGRMD 370
               I+V   TN    LD A+ R  R +
Sbjct: 146 DNDGILVLGATNIPWVLDSAIRR--RFE 171

>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* Length = 355

 Score = 51.4 bits (123), Expect = 3e-07
 Identities = 39/162 (24%), Positives = 71/162 (43%), Gaps = 21/162 (12%)

Query: 218 KREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS 277
           K  + E +   +     +    +    G LLYGPPGTGKS L  A+A +     + +  S
Sbjct: 60  KEALKEAVILPVKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSS 118

Query: 278 AVQS----NSE--LR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL 329
            + S     SE  ++  F +      S++ I+ +D ++    R   E +A+ + + +   
Sbjct: 119 DLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVD-AL-TGTRGEGESEASRRIKTE--- 173

Query: 330 SGLLNFIDGLWSCCGEGRIIVFT-TNHKEKLDPALLRPGRMD 370
             LL  ++G+        ++V   TN   +LD A+ R  R +
Sbjct: 174 --LLVQMNGV--GNDSQGVLVLGATNIPWQLDSAIRR--RFE 209

>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 Length = 444

 Score = 50.0 bits (119), Expect = 9e-07
 Identities = 56/291 (19%), Positives = 110/291 (37%), Gaps = 28/291 (9%)

Query: 91  KSEKEKTFEIALDRNEETFDVFKDVTLKWKLVYTQVPSSMEYRNPNLGDYNASLRSEVRH 150
           + +K   +E AL   +     F    +K+     Q   + +       +Y    R+E   
Sbjct: 20  QEDKAGNYEEALQLYQHAVQYFLH-VVKY---EAQGDKAKQSIRAKCTEYLD--RAEKLK 73

Query: 151 YELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMRWDANNIVLKH--PMTF 208
             L   +K     +       +++     +            ++      ++     + +
Sbjct: 74  EYLKKKEKKPQKPVKEEQSGPVDEKGNDSDGEAESDDPEKKKLQNQLQGAIVIERPNVKW 133

Query: 209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK 268
             +A     K  + E +   +     +T     W+ G LL+GPPGTGKS L  A+A +  
Sbjct: 134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEAN 192

Query: 269 ----FDIYDLDLSA---VQSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQA 319
               F I   DL +    +S   ++  F L      S++ I++ID S+   +R  +E +A
Sbjct: 193 NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEID-SL-CGSRSENESEA 250

Query: 320 TNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
             + + +      L  + G+     +G +++  TN    LD A+ R  R +
Sbjct: 251 ARRIKTE-----FLVQMQGV-GVDNDGILVLGATNIPWVLDSAIRR--RFE 293

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A Length = 377

 Score = 48.5 bits (115), Expect = 2e-06
 Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIED 302
           KR +L  GP  +GK++L AA+            L+       L F L     + ++V ED
Sbjct: 169 KRYWLFKGPIDSGKTTLAAALLELCGGKA----LNVNLPLDRLNFELGVAIDQFLVVFED 224

Query: 303 IDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE 345
           +  +        S     N       L  L +++DG      E
Sbjct: 225 VKGTGGESRDLPSGQGINN-------LDNLRDYLDGSVKVNLE 260

>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 Length = 357

 Score = 44.7 bits (105), Expect = 4e-05
 Identities = 20/134 (14%), Positives = 46/134 (34%), Gaps = 5/134 (3%)

Query: 223 EDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK-----FDIYDLDLS 277
           ++ ++F + ++   ++        L+ G   TGKSS+I    N+L       D+   +  
Sbjct: 10  DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 69

Query: 278 AVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID 337
              S  +    L    ++ +  +  +  ++K                N+       N ++
Sbjct: 70  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 129

Query: 338 GLWSCCGEGRIIVF 351
                  +  IIV 
Sbjct: 130 SFEQASKDNVIIVL 143

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 21/107 (19%), Positives = 46/107 (42%), Gaps = 15/107 (14%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           +   + L+ + + +     E F+   E   +      +G  L+G  G GK+ L+AA+AN+
Sbjct: 23  SLSDVDLNDDGRIKAIRFAERFVAEYEPGKK-----MKGLYLHGSFGVGKTYLLAAIANE 77

Query: 267 LK--------FDIYDL--DLSAVQSNSELRFLLLTMPSRSMLVIEDI 303
           L           + +L  +L     +  +   L  +    +L+++D+
Sbjct: 78  LAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDL 124

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Length = 226

 Score = 43.4 bits (103), Expect = 5e-05
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 247 LLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           L  GPPGTGK++   A+A  L  + +  +
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRDN 70

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 43.7 bits (103), Expect = 6e-05
 Identities = 22/108 (20%), Positives = 46/108 (42%), Gaps = 17/108 (15%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
               + +++  + E    +       ++  +   A ++G  LYG  G GKS L+AAMA++
Sbjct: 122 HLSDIDVNNASRMEAFSAI------LDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE 175

Query: 267 LK---------FDIYDL--DLSAVQSNSELRFLLLTMPSRSMLVIEDI 303
           L                  D+    SN  ++  +  + +  +L+++DI
Sbjct: 176 LSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDI 223

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 44.1 bits (105), Expect = 6e-05
 Identities = 27/91 (29%), Positives = 39/91 (42%), Gaps = 23/91 (25%)

Query: 174 KAKAIKEESKVVKLHTVMHMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKE 233
           +A+ + E  KV                      TFK +A   E K E+ E +E F+    
Sbjct: 18  RARVLTEAPKV----------------------TFKDVAGAEEAKEELKEIVE-FLKNPS 54

Query: 234 YYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
            +  +G    +G LL GPPG GK+ L  A+A
Sbjct: 55  RFHEMGARIPKGVLLVGPPGVGKTHLARAVA 85

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 328 TLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
           TL+ LL  +DG         +++  TN  + LDPALLRPGR D
Sbjct: 153 TLNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFD 193

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 247 LLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           L  GPPGTGK++   A+A  L  + +  +
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRDN 70

>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* Length = 476

 Score = 42.9 bits (102), Expect = 2e-04
 Identities = 23/43 (53%), Positives = 28/43 (65%), Gaps = 2/43 (4%)

Query: 328 TLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMD 370
           TL+ LL  +DG  S   EG I++  TN  + LDPALLRPGR D
Sbjct: 138 TLNQLLVEMDGFDS--KEGIIVMAATNRPDILDPALLRPGRFD 178

>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* Length = 476

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
           TFK +    E   E+ E +E F+     + RIG    +G LL GPPGTGK+ L  A+A
Sbjct: 14  TFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVA 70

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Length = 327

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 247 LLYGPPGTGKSSLIAAMANQLKFDIYD 273
           L  GPPG GK++   A+A +L  + + 
Sbjct: 50  LFAGPPGVGKTTAALALARELFGENWR 76

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 18/89 (20%), Positives = 32/89 (35%), Gaps = 11/89 (12%)

Query: 226 ENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------FDIYDL-- 274
              +  + +         +G    G PG GK+ L  A    +          FD  DL  
Sbjct: 21  RALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIF 80

Query: 275 DLSAVQSNSELRFLLLTMPSRSMLVIEDI 303
            L  +    +    L T+ +  +LV++D+
Sbjct: 81  RLKHLMDEGKDTKFLKTVLNSPVLVLDDL 109

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	449
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.98
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.96
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.96
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.95
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.95
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.95
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.95
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.95
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.94
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.94
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.93
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.93
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.92
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.92
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.92
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.92
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.91
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.91
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.83
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.79
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.79
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.77
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.76
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.75
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.74
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.73
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.71
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.71
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.7
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.7
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.69
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.68
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.67
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.66
3pvs_A	447	Replication-associated recombination protein A; ma	99.65
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.64
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.64
3bos_A	242	Putative DNA replication factor; P-loop containing	99.63
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.63
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.63
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.63
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.63
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.62
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.62
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.61
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.6
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.59
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.59
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.58
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.57
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.57
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.56
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.56
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.56
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.55
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.55
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.54
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.54
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.54
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.51
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.5
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.48
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.46
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.43
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.41
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.39
3co5_A	143	Putative two-component system transcriptional RES	99.37
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.35
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.32
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.31
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.29
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.28
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.26
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.14
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.04
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	98.99
2qgz_A	308	Helicase loader, putative primosome component; str	98.98
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.97
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.96
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.92
2fna_A	357	Conserved hypothetical protein; structural genomic	98.87
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.83
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.82
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.78
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.74
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.73
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.72
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.71
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.68
3f8t_A	506	Predicted ATPase involved in replication control,	98.45
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.35
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.3
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.05
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.02
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.01
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.82
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.78
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.71
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.68
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.63
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.6
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.6
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.6
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.58
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.58
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.57
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.57
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.56
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.55
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.51
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.5
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.5
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.48
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.48
1via_A	175	Shikimate kinase; structural genomics, transferase	97.46
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.46
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.45
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.45
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.43
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.43
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.42
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.42
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.37
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.36
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.36
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.34
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.34
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.31
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.31
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.31
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.3
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.27
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.27
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.26
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.25
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.25
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.24
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.24
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.23
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.22
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	97.22
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.22
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.22
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.21
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.2
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.2
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.2
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.18
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.17
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.16
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.15
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.14
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.13
3io5_A	333	Recombination and repair protein; storage dimer, i	97.1
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.1
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.08
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.04
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.04
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.04
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.03
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.02
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.02
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.02
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.01
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.95
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.92
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.9
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.88
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.88
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.86
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.86
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.86
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.85
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.85
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.82
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.82
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.81
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.8
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.79
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.77
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	96.75
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.75
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.74
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.74
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.64
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.63
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.63
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	96.61
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.6
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.58
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.58
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.57
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.56
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.55
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.53
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.53
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.52
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	96.46
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.46
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.45
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.44
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.44
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.44
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.43
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.41
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.4
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.39
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.39
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	96.38
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.36
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	96.33
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.32
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	96.31
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.29
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.26
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.26
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.24
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.24
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.22
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.21
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.2
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.2
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.18
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.18
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.18
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.17
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.16
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.15
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.14
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	96.11
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.1
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.08
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.03
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	96.03
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.02
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	95.98
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.98
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.98
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.97
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.96
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.95
2og2_A	359	Putative signal recognition particle receptor; nuc	95.95
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.93
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	95.89
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.88
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.86
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.86
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	95.84
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	95.84
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.84
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.82
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	95.82
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.82
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	95.8
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	95.8
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.79
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.79
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	95.77
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	95.75
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.75
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	95.75
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	95.74
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.73
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.73
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.7
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.7
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	95.69
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.69
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	95.69
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.68
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.68
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.66
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	95.65
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.64
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	95.63
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.62
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.57
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.55
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.54
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	95.5
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.49
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.47
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.47
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.42
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.42
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.39
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	95.39
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	95.39
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	95.38
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	95.31
3ice_A	422	Transcription termination factor RHO; transcriptio	95.31
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.3
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	95.3
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.29
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	95.29
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.27
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.26
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.24
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	95.21
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.18
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	95.13
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.12
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	95.12
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	95.09
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.07
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	95.07
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.07
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	95.07
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	95.07
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	95.06
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.05
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	95.02
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.02
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.02
2ged_A	193	SR-beta, signal recognition particle receptor beta	95.01
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	95.0
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.0
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.99
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	94.98
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.98
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.93
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.88
2xxa_A	433	Signal recognition particle protein; protein trans	94.87
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.87
3kw6_A	78	26S protease regulatory subunit 8; structural geno	94.86
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.83
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	94.82
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.74
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.73
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	94.71
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	94.71
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.71
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.7
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	94.67
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.64
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.63
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.62
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	94.62
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	94.61
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	94.61
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	94.6
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.59
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.59
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.58
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.57
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.54
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	94.54
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.54
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.54
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	94.53
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	94.52
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.51
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	94.49
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.49
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.43
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.41
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.4
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.4
3llu_A	196	RAS-related GTP-binding protein C; structural geno	94.38
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.36
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	94.35
2fh5_B	214	SR-beta, signal recognition particle receptor beta	94.35
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.33
1nrj_B	218	SR-beta, signal recognition particle receptor beta	94.32
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	94.31
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	94.3
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.27
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.26
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	94.24
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.23
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	94.23
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	94.22
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.21
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.18
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	94.17
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.15
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.15
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.13
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.11
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	94.07
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	94.05
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.04
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	94.02
1g6h_A	257	High-affinity branched-chain amino acid transport	94.02
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.01
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.98
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.98
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.97
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.96
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.93
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.93
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.91
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.9
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.9
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.89
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.85
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.85
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.82
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.82
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.81
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.79
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.79
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.77
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.77
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.75
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.74
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.74
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.69
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.67
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.65
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.65
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.64
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.64
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.63
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.62
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.6
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.58
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	93.54
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.53
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.51
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.48
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.44
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.42
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	93.4
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.35
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.32
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	93.32
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	93.32
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.31
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	93.31
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.31
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.3
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.3
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	93.3
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.29
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.28
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.27
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	93.27
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.23
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	93.2
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.17
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.16
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.16
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.14
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	93.14
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.12
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.11
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	93.09
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.03
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	93.02
2krk_A	86	26S protease regulatory subunit 8; structural geno	93.02
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.01
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	92.99
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.99
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	92.97
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	92.93
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.92
2hf9_A	226	Probable hydrogenase nickel incorporation protein	92.89
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.88
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	92.87
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.86
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	92.85
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.85
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.84
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	92.84
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.77
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.75
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.74
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.64
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	92.63
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	92.61
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.58
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	92.51
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	92.5
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.43
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	92.42
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	92.38
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	92.38
1qhl_A	227	Protein (cell division protein MUKB); SMC, chromos	92.37
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	92.37
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	92.35
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.3
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	92.29
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.29
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	92.27
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	92.26
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.23
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	92.05
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	92.03

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=4.5e-40  Score=332.84  Aligned_cols=214  Identities=24%  Similarity=0.325  Sum_probs=182.5

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+..+|++++|.+++|++|.+.+..++.+|+.|++.|+++++|+|||||||||||++|+|+|++++.+++.++++++.+
T Consensus       141 ~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~s  220 (405)
T 4b4t_J          141 KVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQ  220 (405)
T ss_dssp             CSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGSC
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhhc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999988853


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            +..++.+|..+  .+||||||||||++++.+......    .......++++||+.|||+.+  ..+++||+||
T Consensus       221 k~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~----~~~~~~~~l~~lL~~lDg~~~--~~~V~vIaAT  294 (405)
T 4b4t_J          221 KYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGG----GDSEVQRTMLELLNQLDGFET--SKNIKIIMAT  294 (405)
T ss_dssp             SSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSG----GGGHHHHHHHHHHHHHHTTTC--CCCEEEEEEE
T ss_pred             cccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCC----CcHHHHHHHHHHHHhhhccCC--CCCeEEEecc
Confidence                  45677776655  589999999999998755433221    234556789999999999976  4679999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |+|+.|||||+||||||++|++|.|+.++|++||+.++......-.-+++.+++.. ++|+|||..++.
T Consensus       295 Nrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~  363 (405)
T 4b4t_J          295 NRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCT  363 (405)
T ss_dssp             SCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             CChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999765433222456666654 699999988774

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.2e-39  Score=330.52  Aligned_cols=215  Identities=25%  Similarity=0.298  Sum_probs=181.6

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      ...+..+|++|+|.+++|++|.+.+..++.+++.|.+.|+++++|||||||||||||++|+|+|++++.+++.++++++.
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~  253 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELI  253 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGC
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhh
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999998875


Q ss_pred             C------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 S------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      +      +..++.+|..+  .+||||||||||+++..+......    .......++++||+.|||..+  .++++||+|
T Consensus       254 sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~----~~~~~~~~l~~LL~~lDg~~~--~~~ViVIaA  327 (437)
T 4b4t_I          254 QKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSG----GEREIQRTMLELLNQLDGFDD--RGDVKVIMA  327 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCS----SCCHHHHHHHHHHHHHHHCCC--SSSEEEEEE
T ss_pred             hccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCC----ccHHHHHHHHHHHHHhhCcCC--CCCEEEEEe
Confidence            3      34566666554  589999999999998755433221    234556789999999999865  467999999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      ||+++.|||||+||||||++|+||+|+.++|++||+.++......-.-+++.+++.. ++|+|||..++.
T Consensus       328 TNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  397 (437)
T 4b4t_I          328 TNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCT  397 (437)
T ss_dssp             ESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             CCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999999764332222456666554 699999988774

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=4.5e-39  Score=330.11  Aligned_cols=214  Identities=25%  Similarity=0.307  Sum_probs=181.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+..+|++|+|.+++|+.|.+.+..++.+++.|.+.|+++++|+|||||||||||++|+|+|++++.+++.++++++.+
T Consensus       174 ~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~s  253 (437)
T 4b4t_L          174 EQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVD  253 (437)
T ss_dssp             ESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCC
T ss_pred             cCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhcc
Confidence            35668999999999999999999999999999999999999999999999999999999999999999999999988853


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...++.+|..+  .+||||||||||+++..+...+..    .......++++||+.|||+.+  .++++||+||
T Consensus       254 k~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~----~~~~~~~~l~~lL~~lDg~~~--~~~vivI~AT  327 (437)
T 4b4t_L          254 KYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTS----ADREIQRTLMELLTQMDGFDN--LGQTKIIMAT  327 (437)
T ss_dssp             SSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCS----STTHHHHHHHHHHHHHHSSSC--TTSSEEEEEE
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCC----cchHHHHHHHHHHHHhhcccC--CCCeEEEEec
Confidence                  34456665544  589999999999998755333221    234456789999999999876  3679999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |+|+.|||||+||||||.+|+||+|+.++|++||+.++......-.-++..+++.+ ++|+|||..++.
T Consensus       328 Nrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~  396 (437)
T 4b4t_L          328 NRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCAT  396 (437)
T ss_dssp             SSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHH
T ss_pred             CCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999998754332222456666654 699999988774

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.1e-39  Score=332.34  Aligned_cols=234  Identities=21%  Similarity=0.254  Sum_probs=188.8

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      ...++.+|++|+|.+++|++|.+.+..|+.+++.|++.|+++++|||||||||||||++|+|+|++++.+++.++++++.
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~  252 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLV  252 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGC
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999998885


Q ss_pred             C------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 S------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      +      ...++.+|..+  ..||||||||||+++..+......    .......+++.||+.|||+.+  .++++||+|
T Consensus       253 ~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~----~~~~~~~~~~~lL~~ldg~~~--~~~ViVIaa  326 (434)
T 4b4t_M          253 QMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKS----GDREVQRTMLELLNQLDGFSS--DDRVKVLAA  326 (434)
T ss_dssp             SSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGG----TTHHHHHHHHHHHHHHTTSCS--SCSSEEEEE
T ss_pred             hcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCC----CchHHHHHHHHHHHHhhccCC--CCCEEEEEe
Confidence            3      35566666544  489999999999998754332211    224456789999999999976  467999999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhc-------CC
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMK-------ST  424 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~-------~~  424 (449)
                      ||+|+.|||||+||||||++|++|+|+.++|++||+.++......-.-+++.+++.. ++|+|||..++..       ..
T Consensus       327 TNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~eA~~~a~r~~  406 (434)
T 4b4t_M          327 TNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTVEAGMIALRNG  406 (434)
T ss_dssp             CSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcC
Confidence            999999999999999999999999999999999999998754322112345555554 6999999887742       12


Q ss_pred             CHHHHHHHHHHHHHHH
Q 013128          425 NAEVSLNGLVKFLHAK  440 (449)
Q Consensus       425 ~~~~al~~l~~~l~~~  440 (449)
                      ......+.+.+++++.
T Consensus       407 ~~~i~~~Df~~Al~~v  422 (434)
T 4b4t_M          407 QSSVKHEDFVEGISEV  422 (434)
T ss_dssp             CSSBCHHHHHHHHHSC
T ss_pred             CCCcCHHHHHHHHHHH
Confidence            2223345566665543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-38  Score=324.49  Aligned_cols=214  Identities=23%  Similarity=0.260  Sum_probs=180.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+..+|++|+|.+++|++|.+.+..++.+++.|.++|+++++|+|||||||||||++|+|+|++++.+++.++++.+.+
T Consensus       202 e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L~s  281 (467)
T 4b4t_H          202 EKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQ  281 (467)
T ss_dssp             SSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCC
T ss_pred             CCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHhhc
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999988854


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            +..++.+|..+  .+||||||||||.++..+......    .......+++.||+.|||...  .++++||+||
T Consensus       282 k~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~----~~~~~~~~l~~lL~~lDg~~~--~~~ViVIaAT  355 (467)
T 4b4t_H          282 KYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAG----GDNEVQRTMLELITQLDGFDP--RGNIKVMFAT  355 (467)
T ss_dssp             CSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCG----GGGHHHHHHHHHHHHHHSSCC--TTTEEEEEEC
T ss_pred             ccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCC----ccHHHHHHHHHHHHHhhccCC--CCcEEEEeCC
Confidence                  35566666654  589999999999998755433221    234556789999999999866  4679999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |+|+.|||||+||||||++|+||.|+.++|++||+.++......-.-+++.+++.. ++|+|||..++.
T Consensus       356 Nrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  424 (467)
T 4b4t_H          356 NRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCT  424 (467)
T ss_dssp             SCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             CCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999864332222345555543 699999988774

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.4e-38  Score=324.24  Aligned_cols=214  Identities=26%  Similarity=0.341  Sum_probs=180.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+..+|++++|.+++|+.|.+.+..++.+++.|.++|+++++|+|||||||||||++|+|+|++++.+++.++++++.+
T Consensus       165 ~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~  244 (428)
T 4b4t_K          165 EKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVH  244 (428)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCC
T ss_pred             CCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhc
Confidence            45567999999999999999999999999999999999999999999999999999999999999999999999988753


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...++.+|..+  ..||||||||+|+++..+......    .......++++||+.|||+.+.  .+++||+||
T Consensus       245 ~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~----~~~~~~r~l~~lL~~ldg~~~~--~~v~vI~aT  318 (428)
T 4b4t_K          245 KYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG----SDREVQRILIELLTQMDGFDQS--TNVKVIMAT  318 (428)
T ss_dssp             SSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSC----CCCHHHHHHHHHHHHHHHSCSS--CSEEEEEEE
T ss_pred             cccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCC----CChHHHHHHHHHHHHhhCCCCC--CCEEEEEec
Confidence                  35567776654  589999999999998755332211    2345578899999999999774  679999999


Q ss_pred             CCCCCCCccccCCCccceEEEeC-CCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMS-YCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~-~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |+++.|||||+||||||++|+|| +|+.++|+.|++.++......-.-+++.++... ++|+|||..++.
T Consensus       319 N~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          319 NRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             SCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            99999999999999999999997 899999999999998754322222355666554 699999988874

>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=100.00  E-value=3.3e-34  Score=313.02  Aligned_cols=213  Identities=21%  Similarity=0.327  Sum_probs=159.5

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc---
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV---  279 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~---  279 (449)
                      .+..+|++++|.+++|+.+.+.+..++.+++.|.+.|..+++|+|||||||||||++|+|+|++++.+++.++.+++   
T Consensus       471 ~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~s~  550 (806)
T 3cf2_A          471 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM  550 (806)
T ss_dssp             CCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHHTT
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhhcc
Confidence            35578999999999999999999999999999999999999999999999999999999999999999999998776   


Q ss_pred             ---cChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          280 ---QSNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       280 ---~~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                         .++..++.+|..+  ..||||||||||++++.++....+    ......+++++||+.|||+.+  ..+++||+|||
T Consensus       551 ~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~----~~~~~~rv~~~lL~~mdg~~~--~~~V~vi~aTN  624 (806)
T 3cf2_A          551 WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD----GGGAADRVINQILTEMDGMST--KKNVFIIGATN  624 (806)
T ss_dssp             TCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC------------------CHHHHHHHHHHHSSCS--SSSEEEECC-C
T ss_pred             ccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCC----CchHHHHHHHHHHHHHhCCCC--CCCEEEEEeCC
Confidence               3467788888765  579999999999998755432211    124456789999999999976  46799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      +|+.||||++||||||++|++|+|+.++|++||+.++......-.-+++.+++.. ++|+|||..++-
T Consensus       625 ~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~  692 (806)
T 3cf2_A          625 RPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  692 (806)
T ss_dssp             CSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHH
T ss_pred             CchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999765433334566666654 599999988873

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.98  E-value=2.3e-32  Score=298.42  Aligned_cols=209  Identities=23%  Similarity=0.290  Sum_probs=178.5

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      +..+|++|+|.+++|++|.+.+..++.+++.|..+|..+++|+|||||||||||+||+++|++++.+++.++++++.+  
T Consensus       199 ~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk~  278 (806)
T 3cf2_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (806)
T ss_dssp             SSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSSC
T ss_pred             CCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhccc
Confidence            346899999999999999999999999999999999999999999999999999999999999999999999887643  


Q ss_pred             ----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          282 ----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       282 ----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                          +..++.+|..+  .+||||||||||.+++.++...       ......++++||..|||+.+.  .+++||+|||+
T Consensus       279 ~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~-------~~~~~riv~~LL~~mdg~~~~--~~V~VIaaTN~  349 (806)
T 3cf2_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH-------GEVERRIVSQLLTLMDGLKQR--AHVIVMAATNR  349 (806)
T ss_dssp             TTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCC-------CTTHHHHHHHHHTHHHHCCGG--GCEEEEEECSS
T ss_pred             chHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCC-------ChHHHHHHHHHHHHHhccccc--CCEEEEEecCC
Confidence                45677777765  4799999999999987543321       234567899999999999764  56999999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      ++.|||||+|||||+.+|+++.|+.++|++|++.++.........++..++.. .+++++|+..++-
T Consensus       350 ~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~  416 (806)
T 3cf2_A          350 PNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (806)
T ss_dssp             TTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             hhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999876533333345666655 4699999987763

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=99.96  E-value=1.1e-28  Score=243.08  Aligned_cols=214  Identities=21%  Similarity=0.312  Sum_probs=172.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc-
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-  280 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~-  280 (449)
                      ..++.+|++++|.+++|+.+.+.+..++.+++.|...|..+++++|||||||||||++|+++|++++.+++.++++.+. 
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~   87 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLT   87 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHh
Confidence            3466789999999999999999999999999999999999999999999999999999999999999999999987652 


Q ss_pred             -----ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          281 -----SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       281 -----~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                           ....++.+|...  ..|+||||||||.+...+......    ........++.||..||++..  ..+++||+||
T Consensus        88 ~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~----~~~~~~~~~~~lL~~l~~~~~--~~~v~vi~at  161 (301)
T 3cf0_A           88 MWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD----GGGAADRVINQILTEMDGMST--KKNVFIIGAT  161 (301)
T ss_dssp             HHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCC----SSCSCCHHHHHHHHHHHSSCT--TSSEEEEEEE
T ss_pred             hhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCC----cchHHHHHHHHHHHHhhcccC--CCCEEEEEec
Confidence                 234455555554  468999999999987643321110    112334677889999998754  4579999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      |+++.||++++|||||+..++++.|+.++|.+|++.++..........++.+... .+++++||..++-
T Consensus       162 n~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~  230 (301)
T 3cf0_A          162 NRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  230 (301)
T ss_dssp             SCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHH
T ss_pred             CCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999976532211223334433 4699999987763

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.96  E-value=1.2e-28  Score=239.64  Aligned_cols=209  Identities=20%  Similarity=0.299  Sum_probs=162.8

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      +..+|++++|.+++|+.+.+.+..++.+++.++.++...++|++|+||||||||+|++++|++++..++.++...+.+  
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~~~   84 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMY   84 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCSST
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHhhh
Confidence            457899999999999999999999999999999999999999999999999999999999999999999999877643  


Q ss_pred             ----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          282 ----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       282 ----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                          ...+..+|...  ..|+|+++||+|.+...+....       .......++.++..|||...  ...++++++||+
T Consensus        85 ~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~-------~~~~~~~~~~~l~~Lsgg~~--~~~~i~ia~tn~  155 (274)
T 2x8a_A           85 VGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRE-------TGASVRVVNQLLTEMDGLEA--RQQVFIMAATNR  155 (274)
T ss_dssp             THHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC----------------CTTHHHHHHHHHHTCCS--TTCEEEEEEESC
T ss_pred             hhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCc-------chHHHHHHHHHHHhhhcccc--cCCEEEEeecCC
Confidence                23455666653  5799999999999865322110       11234567889999998754  356788999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC-CCCC--HHHHHHHHHc---cCCCHHHHHHHHh
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS-HHYL--FEQIEELIKE---VNVTPAEVAGELM  421 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~-~~~l--~~~i~~l~~~---~~~tpa~i~~~l~  421 (449)
                      |+.||+|++||||||.+|++++|+.++|++|++.++... ..++  .-+++.+...   .++|+|||..++-
T Consensus       156 p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~  227 (274)
T 2x8a_A          156 PDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR  227 (274)
T ss_dssp             GGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHH
T ss_pred             hhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHH
Confidence            999999999999999999999999999999999998642 1122  2234555553   3899999987763

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.95  E-value=6.2e-27  Score=232.80  Aligned_cols=207  Identities=21%  Similarity=0.270  Sum_probs=170.9

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEecccccC
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAVQS  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~~~  281 (449)
                      .++.+|++|+|.+++|+.+.+.+..++.+++.|.. +..+++|+|||||||||||++|+++|+++ +.+++.++++.+..
T Consensus         6 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~   84 (322)
T 1xwi_A            6 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS   84 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHh
Confidence            45678999999999999999999999999998874 35567899999999999999999999999 89999999887642


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...++.+|...  .+|+||||||||.+.+.+...       ........+++||..+|++... ..+++||+||
T Consensus        85 ~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~-------~~~~~~~~~~~ll~~ld~~~~~-~~~v~vI~at  156 (322)
T 1xwi_A           85 KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSEN-------ESEAARRIKTEFLVQMQGVGVD-NDGILVLGAT  156 (322)
T ss_dssp             SSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSC-------CTTHHHHHHHHHHHHHHCSSSC-CTTEEEEEEE
T ss_pred             hhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccc-------cchHHHHHHHHHHHHHhccccc-CCCEEEEEec
Confidence                  34555555443  579999999999997643322       1233456788999999997542 4679999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHcc-CCCHHHHHHHH
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      |+++.+|++++|  ||+..++++.|+.++|..|++.++......+ ...++.+.+.. +++++||..++
T Consensus       157 n~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          157 NIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             SCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999  9999999999999999999999998765554 45667777664 69999998776

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.95  E-value=2.7e-27  Score=230.25  Aligned_cols=216  Identities=24%  Similarity=0.275  Sum_probs=173.3

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...++.+|++++|.+++++.+.+.+..++..++.|...|...++++||+||||||||++|+++|++++.+++.++++.+
T Consensus         8 ~~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~   87 (285)
T 3h4m_A            8 VDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSEL   87 (285)
T ss_dssp             EESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGG
T ss_pred             ccCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHH
Confidence            33456778999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             cCh------HHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 QSN------SELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~~~------~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      ...      ..+..++..  ...|+||||||+|.+...+.....    .........+..+++.+++...  ...++||+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~----~~~~~~~~~l~~ll~~~~~~~~--~~~~~vI~  161 (285)
T 3h4m_A           88 VKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALT----GGDREVQRTLMQLLAEMDGFDA--RGDVKIIG  161 (285)
T ss_dssp             CCCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCC----GGGGHHHHHHHHHHHHHHTTCS--SSSEEEEE
T ss_pred             HHhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccC----CccHHHHHHHHHHHHHhhCCCC--CCCEEEEE
Confidence            431      233334433  347899999999999763322111    1123456678889999987754  35789999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |||.++.+|++++|||||+..++++.|+.+++.+|++.++..........+..+.... ++++++|..++.
T Consensus       162 ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~  232 (285)
T 3h4m_A          162 ATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICT  232 (285)
T ss_dssp             ECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             eCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999998765433333345555443 589999987664

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=99.95  E-value=4.6e-27  Score=225.33  Aligned_cols=211  Identities=25%  Similarity=0.350  Sum_probs=154.0

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC---
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS---  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~---  281 (449)
                      +.+|++++|.+++|+.+.+.+. ++..++.|...|...++++|||||||||||++|+++|++++.+++.++++.+..   
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~   80 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIG   80 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHH-HHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSST
T ss_pred             CCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhcc
Confidence            4689999999999999988765 577888899999999999999999999999999999999999999999987643   


Q ss_pred             ---hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          282 ---NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       282 ---~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                         ...+..++...  ..|+||+|||+|.+...+.......   ........+..|++.+++...  ...+++|+|||.+
T Consensus        81 ~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~---~~~~~~~~l~~ll~~~~~~~~--~~~~~vi~~tn~~  155 (262)
T 2qz4_A           81 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGF---SNTEEEQTLNQLLVEMDGMGT--TDHVIVLASTNRA  155 (262)
T ss_dssp             THHHHHHHHHHHHHHHTCSEEEEEECC----------------------CHHHHHHHHHHHTCCT--TCCEEEEEEESCG
T ss_pred             ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCc---cchhHHHHHHHHHHHhhCcCC--CCCEEEEecCCCh
Confidence               23344444443  3689999999999875332211100   123345678889999998644  4578999999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHH--HHHHHc-cCCCHHHHHHHHh
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQI--EELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i--~~l~~~-~~~tpa~i~~~l~  421 (449)
                      +.+|++++|||||+..++++.|+.++|.+|++.++..........+  ..+... .++++++|...+-
T Consensus       156 ~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          156 DILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             GGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             hhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999876555444332  445544 3699999977764

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=99.95  E-value=7.3e-27  Score=242.80  Aligned_cols=212  Identities=27%  Similarity=0.366  Sum_probs=167.0

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      ....+|++++|.++.|+++.+.+. ++..+..|.++|...++|+||+||||||||++++++|++++.+++.++++++.. 
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~-~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~   88 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVEL   88 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHH-HHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTC
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHH-HhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHH
Confidence            345689999999999999988765 577888999999999999999999999999999999999999999999887643 


Q ss_pred             -----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           ...++.+|..+  ..|+||||||||.+...+.....    ........+++.||..||++..  ..+++||+|||
T Consensus        89 ~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~----g~~~~~~~~l~~LL~~ld~~~~--~~~viVIaaTn  162 (476)
T 2ce7_A           89 FVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLG----GGHDEREQTLNQLLVEMDGFDS--KEGIIVMAATN  162 (476)
T ss_dssp             CTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC-------------CHHHHHHHHHHHHHHHSCG--GGTEEEEEEES
T ss_pred             HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccC----cCcHHHHHHHHHHHHHHhccCC--CCCEEEEEecC
Confidence                 23455555554  47999999999999753321110    1223456788999999998754  35799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      +++.|||+++|||||+..|.++.|+.++|++|++.++......-...+..+... .+++++||..++-
T Consensus       163 ~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~  230 (476)
T 2ce7_A          163 RPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVN  230 (476)
T ss_dssp             CGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             ChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHH
Confidence            999999999999999999999999999999999999875432211124444444 3689999977664

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=99.95  E-value=7.8e-27  Score=231.94  Aligned_cols=210  Identities=20%  Similarity=0.247  Sum_probs=170.1

Q ss_pred             ccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          201 VLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       201 ~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      ...++.+|++++|.+++|+.+.+.+..++..++.+.. +..+++++|||||||||||++|+++|++++.+++.++++.+.
T Consensus        10 ~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~   88 (322)
T 3eie_A           10 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV   88 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHH
T ss_pred             ecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHh
Confidence            3567789999999999999999999999999988877 445578999999999999999999999999999999987763


Q ss_pred             C------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 S------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      +      ...++.+|...  .+|+||||||||.+...+...       .........+.|+..+|++... ...++||+|
T Consensus        89 ~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~-------~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~a  160 (322)
T 3eie_A           89 SKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEG-------ESEASRRIKTELLVQMNGVGND-SQGVLVLGA  160 (322)
T ss_dssp             TTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC-------------CCTHHHHHHHHHHHGGGGTS-CCCEEEEEE
T ss_pred             hcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCC-------cchHHHHHHHHHHHHhcccccc-CCceEEEEe
Confidence            2      23344444433  578999999999997633221       1233456788999999988543 467899999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      ||+++.||++++|  ||+..++++.|+.++|.+|++.++......+ ...++.+.... +++++||..++-
T Consensus       161 tn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          161 TNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             ESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             cCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999  9999999999999999999999998766554 44667777665 599999987763

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.94  E-value=4.2e-26  Score=218.97  Aligned_cols=213  Identities=25%  Similarity=0.352  Sum_probs=162.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++.+|++++|.+++|+.+.+.+. ++..++.|+..|...++|+||+||||||||++++++|++++.+++.++++.+..
T Consensus         5 ~~~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~~   83 (257)
T 1lv7_A            5 DQIKTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVE   83 (257)
T ss_dssp             CSSCCCGGGSCSCHHHHHHTHHHHH-HHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTT
T ss_pred             cCCCCCHHHhcCcHHHHHHHHHHHH-HHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHHH
Confidence            4567899999999999999988664 577788888899989999999999999999999999999999999999887642


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...+..++...  ..|+|++|||+|.+...+.....    .........++.+|..+|+...  ...++||+||
T Consensus        84 ~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~----~~~~~~~~~~~~ll~~l~~~~~--~~~~~vI~~t  157 (257)
T 1lv7_A           84 MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLG----GGHDEREQTLNQMLVEMDGFEG--NEGIIVIAAT  157 (257)
T ss_dssp             SCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSC----CTTCHHHHHHHHHHHHHHTCCS--SSCEEEEEEE
T ss_pred             HhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcC----CCchHHHHHHHHHHHHhhCccc--CCCEEEEEee
Confidence                  34455555543  46899999999998753221110    0122344678899999998754  4568999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      |+++.+|++++|||||+..++++.|+.++|++|++.++......-...+..+... .+++++|+...+.
T Consensus       158 n~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~  226 (257)
T 1lv7_A          158 NRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (257)
T ss_dssp             SCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999875322111123333443 3589999987764

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=99.94  E-value=2.8e-26  Score=231.04  Aligned_cols=209  Identities=21%  Similarity=0.252  Sum_probs=166.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc-
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ-  280 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~-  280 (449)
                      ..++.+|++|+|.+++|+.+.+.+..++..++.|.. +..+++|+|||||||||||++|+++|++++.+++.++++.+. 
T Consensus        44 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~~  122 (355)
T 2qp9_X           44 EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS  122 (355)
T ss_dssp             ---CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHHS
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHhh
Confidence            445778999999999999999999999999998887 556678999999999999999999999999999999987653 


Q ss_pred             -----ChHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          281 -----SNSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       281 -----~~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                           ....++.+|...  ..|+||||||||.+...+...       .........+.||..||++... ...++||+||
T Consensus       123 ~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~-------~~~~~~~~~~~ll~~l~~~~~~-~~~v~vI~at  194 (355)
T 2qp9_X          123 KWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEG-------ESEASRRIKTELLVQMNGVGND-SQGVLVLGAT  194 (355)
T ss_dssp             CC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC-------------CTHHHHHHHHHHHHHHHCC----CCEEEEEEE
T ss_pred             hhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCC-------cchHHHHHHHHHHHHhhccccc-CCCeEEEeec
Confidence                 234455555443  479999999999987633221       1234456788899999987542 3568999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |.++.||++++|  ||+..++++.|+.++|..|++.++......+ ...++.++... +++++||..++-
T Consensus       195 n~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          195 NIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             SCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999  9999999999999999999999998765544 44667776655 599999987763

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=99.93  E-value=1.1e-25  Score=235.31  Aligned_cols=209  Identities=23%  Similarity=0.292  Sum_probs=172.3

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      .+.+|++++|.+..++.+.+.+..++..++.|..+|.+.++++|||||||||||++|+++|++++.+++.++|+.+.+  
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSC
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhh
Confidence            467899999999999999999999999999999999999999999999999999999999999999999999887643  


Q ss_pred             ----hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          282 ----NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       282 ----~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                          ...++.+|..+  ..|+||||||||.+.+.+....       ......+++.||..||+...  ...++||+|||+
T Consensus       279 ~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~-------~~~~~~~~~~LL~~ld~~~~--~~~v~vIaaTn~  349 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH-------GEVERRIVSQLLTLMDGLKQ--RAHVIVMAATNR  349 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCC-------CHHHHHHHHHHHHHHHHSCT--TSCEEEEEEESC
T ss_pred             cchhHHHHHHHHHHHHhcCCcEEEecchhhhcccccccc-------chHHHHHHHHHHHHhhcccc--CCceEEEEecCC
Confidence                23445555544  4689999999999986432211       23345678889999998754  457899999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      ++.||++++++|||+..++++.|+.++|.++++.++..........+..+... .+++++++..++-
T Consensus       350 ~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~  416 (489)
T 3hu3_A          350 PNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (489)
T ss_dssp             GGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             ccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHH
Confidence            99999999999999999999999999999999999875433333334555554 4699999977653

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=99.93  E-value=2.1e-25  Score=231.10  Aligned_cols=209  Identities=21%  Similarity=0.260  Sum_probs=166.8

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEeccccc
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAVQ  280 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~~  280 (449)
                      ..++.+|++|+|.+++|+.+.+.+..++..++.|.. +..+++|+|||||||||||++|+++|+++ +.+++.++++.+.
T Consensus       127 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l~  205 (444)
T 2zan_A          127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLV  205 (444)
T ss_dssp             CCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC---
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHHH
Confidence            456789999999999999999999999998888764 34556899999999999999999999999 8999999988764


Q ss_pred             C------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          281 S------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       281 ~------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      +      ...++.+|..  ...|+||||||||.+.+.+...       ........++.||..||++... ..+++||+|
T Consensus       206 ~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~-------~~~~~~~~~~~lL~~l~~~~~~-~~~v~vI~a  277 (444)
T 2zan_A          206 SKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSEN-------ESEAARRIKTEFLVQMQGVGVD-NDGILVLGA  277 (444)
T ss_dssp             ------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCC-------CCGGGHHHHHHHHTTTTCSSCC-CSSCEEEEE
T ss_pred             hhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCc-------cccHHHHHHHHHHHHHhCcccC-CCCEEEEec
Confidence            2      2334444443  3579999999999987643222       1233456788999999997542 467899999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      ||.++.||++++|  ||+..++++.|+.++|..|++.++......+ ...++.++... +++++||..++-
T Consensus       278 tn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          278 TNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             ESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999  9999999999999999999999998765444 34566666654 699999987763

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.93  E-value=7.1e-25  Score=229.11  Aligned_cols=211  Identities=26%  Similarity=0.342  Sum_probs=165.5

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC--
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS--  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~--  281 (449)
                      ++.+|++++|.++.|+.+.+.+. ++..+..|..+|...++|+||+||||||||+|++++|++++.+++.++++++..  
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~-~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHH-HHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHH-HhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            56789999999999999988664 567788899999999999999999999999999999999999999999887743  


Q ss_pred             ----hHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          282 ----NSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       282 ----~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                          ...++.+|....  .|+|+||||||.+...+.....    ........+++.||..|||...  ...++++++||+
T Consensus       105 ~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~----~~~~e~~~~l~~LL~~Ldg~~~--~~~viviAatn~  178 (499)
T 2dhr_A          105 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVG----GGNDEREQTLNQLLVEMDGFEK--DTAIVVMAATNR  178 (499)
T ss_dssp             TTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTT----TSSHHHHHHHHHHHHHGGGCCS--SCCCEEEECCSC
T ss_pred             hhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcC----CCcHHHHHHHHHHHHHhccccc--CccEEEEEecCC
Confidence                234566676654  5899999999998653321100    0123445788999999998754  356899999999


Q ss_pred             CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          356 KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       356 ~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      |+.||++++|||||+.+|+++.|+.++|++|++.++......-...+..+... .+++++|+.+++-
T Consensus       179 p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~  245 (499)
T 2dhr_A          179 PDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  245 (499)
T ss_dssp             GGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHH
T ss_pred             hhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999988764321111123334443 3588888877654

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=99.92  E-value=1.1e-26  Score=224.13  Aligned_cols=214  Identities=29%  Similarity=0.371  Sum_probs=157.7

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      .++.+|++++|.++.++.+.+.+. ++..++.|...|...++|+|||||||||||++|+++|++++.+++.++++.+.. 
T Consensus         5 ~~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~   83 (268)
T 2r62_A            5 KPNVRFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEM   83 (268)
T ss_dssp             CCCCCSTTSSSCTTTHHHHHHHHH-HHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTTS
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHH-HHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHHh
Confidence            456789999999999999988665 578889999999999999999999999999999999999999999998876532 


Q ss_pred             -----hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           ...++.++..  ...|+||||||+|.+...+...+...   ........++.|++.+++.... ...++||+|||
T Consensus        84 ~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~---~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~ttn  159 (268)
T 2r62_A           84 FVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVS---GNDEREQTLNQLLAEMDGFGSE-NAPVIVLAATN  159 (268)
T ss_dssp             CSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC-------------CCCSCSSTTTTTTTTTCSSCS-CSCCEEEECBS
T ss_pred             hcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCC---CchhHHHHHHHHHHHhhCcccC-CCCEEEEEecC
Confidence                 1112222222  24689999999999875332111100   1122234567788888876442 34589999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      .++.+|++++|+|||+..++++.|+.++|.++++.++......-...++.+... .+++++||...+-
T Consensus       160 ~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~  227 (268)
T 2r62_A          160 RPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIIN  227 (268)
T ss_dssp             CCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHH
T ss_pred             CchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999865322111112333333 3588888877654

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.92  E-value=1.5e-24  Score=221.04  Aligned_cols=212  Identities=21%  Similarity=0.269  Sum_probs=164.9

Q ss_pred             cccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          200 IVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       200 ~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +...+|.+|++++|.+.+++.+.+.+..+...++.|...+. .++++|||||||||||++|+++|++++.+++.++++.+
T Consensus       106 ~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l  184 (389)
T 3vfd_A          106 VDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRA-PARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL  184 (389)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGC-CCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC
T ss_pred             hccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCC-CCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHh
Confidence            33678899999999999999999999999998888887774 46899999999999999999999999999999999887


Q ss_pred             cC------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          280 QS------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       280 ~~------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      ..      ...+..++..  ...++||||||||.++..+...       ........+..|+..+++........++||+
T Consensus       185 ~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~-------~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~  257 (389)
T 3vfd_A          185 TSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREG-------EHDASRRLKTEFLIEFDGVQSAGDDRVLVMG  257 (389)
T ss_dssp             -------CHHHHHHHHHHHHHSSSEEEEEETGGGGC---------------CTHHHHHHHHHHHHHHHC-----CEEEEE
T ss_pred             hccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCc-------cchHHHHHHHHHHHHhhcccccCCCCEEEEE
Confidence            43      2334444433  3478999999999997633211       1233456778899999987665556789999


Q ss_pred             EcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHcc-CCCHHHHHHHHh
Q 013128          352 TTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       352 tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |||.++.||++++|  ||+..++++.|+.+++..+++.++...+..+. +.+..+.... +++++++..++-
T Consensus       258 atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          258 ATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             EESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999999999  99999999999999999999999987666554 4455555543 588888866653

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=99.92  E-value=3.2e-24  Score=205.43  Aligned_cols=213  Identities=26%  Similarity=0.336  Sum_probs=160.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++.+|++++|.++.+.++.+... .+..+..+..++...++|++|+||||||||+|++++|+.++..++.++...+..
T Consensus         9 ~~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~~~   87 (254)
T 1ixz_A            9 EAPKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVE   87 (254)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHH
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHHHH
Confidence            3456799999999999999887655 456778889999999999999999999999999999999999999998765421


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...+..++...  ..|++++|||||.+...+.....    .........++.+++.++|...  ...++++++|
T Consensus        88 ~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~----~~~~~~~~~~~~ll~~l~g~~~--~~~~i~~a~t  161 (254)
T 1ixz_A           88 MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVG----GGNDEREQTLNQLLVEMDGFEK--DTAIVVMAAT  161 (254)
T ss_dssp             SCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-------------CHHHHHHHHHHHHHHHTCCT--TCCEEEEEEE
T ss_pred             HHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCcccc----ccchHHHHHHHHHHHHHhCCCC--CCCEEEEEcc
Confidence                  23455566654  36899999999998653321100    0123345678889999998644  3457888999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |+|+.||++++|||||+.+++++.|+.++|.+|++.++......-...+..+.... +++++|+...+.
T Consensus       162 ~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          162 NRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             SCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999887543221111244444443 588899977764

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=99.92  E-value=3.1e-24  Score=216.32  Aligned_cols=210  Identities=22%  Similarity=0.318  Sum_probs=165.6

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++.+|++++|.+++++.+.+.+..++..++.|...+ ..++++||+||||||||++|+++|++++.+++.++++.+..
T Consensus        77 ~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~  155 (357)
T 3d8b_A           77 HGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTS  155 (357)
T ss_dssp             CSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCC
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhc
Confidence            34678999999999999999999999998888887765 45789999999999999999999999999999999988743


Q ss_pred             h------HHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 N------SELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ~------~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                      .      ..++.++..  ..+++||||||||.+...+...       ........++.||..+++.....+..++||+||
T Consensus       156 ~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~-------~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~at  228 (357)
T 3d8b_A          156 KWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDG-------EHESSRRIKTEFLVQLDGATTSSEDRILVVGAT  228 (357)
T ss_dssp             SSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC-------------CHHHHHHHHHHHHHHC----CCCCEEEEEEE
T ss_pred             cccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCC-------cchHHHHHHHHHHHHHhcccccCCCCEEEEEec
Confidence            2      233444433  3578999999999997533211       123445678889999998765545678999999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC-HHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL-FEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      |.++.+|+++++  ||+..++++.|+.+++..++..++......+ .+.++.+.... +++++++..++-
T Consensus       229 n~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          229 NRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             SCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999  9999999999999999999999987655555 34566666654 589999977654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.91  E-value=1e-23  Score=206.27  Aligned_cols=210  Identities=21%  Similarity=0.266  Sum_probs=161.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++.+|++++|.+++++.+.+.+..+..+++.|..++ .+++++||+||||||||++|+++|++++.+++.++++.+..
T Consensus        14 ~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~   92 (297)
T 3b9p_A           14 GGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTS   92 (297)
T ss_dssp             CSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSS
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhh
Confidence            45678999999999999999999999888888887766 34689999999999999999999999999999999987643


Q ss_pred             ------hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc-CCCCeEEEEE
Q 013128          282 ------NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC-CGEGRIIVFT  352 (449)
Q Consensus       282 ------~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-~~~~~iiI~t  352 (449)
                            ...++.++..  ..+|+||||||+|.+...+....       ........+.||..+|+.... .+..++||+|
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~-------~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~  165 (297)
T 3b9p_A           93 KYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSE-------HEASRRLKTEFLVEFDGLPGNPDGDRIVVLAA  165 (297)
T ss_dssp             SSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC------------CCSHHHHHHHHHHHHHCC------CEEEEEE
T ss_pred             cccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCc-------chHHHHHHHHHHHHHhcccccCCCCcEEEEee
Confidence                  1223333332  35789999999999976332211       122345667889999876542 2356899999


Q ss_pred             cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHc-cCCCHHHHHHHHh
Q 013128          353 TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       353 TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      ||.++.+|+++++  ||+..++++.|+.+++..+++.++......+. +.++.+... .+++++++..++-
T Consensus       166 tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          166 TNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             ESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             cCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999  99999999999999999999999876555443 345555544 3688888866553

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.91  E-value=3.9e-24  Score=209.80  Aligned_cols=164  Identities=15%  Similarity=0.120  Sum_probs=114.9

Q ss_pred             hhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------hHHHHHHHHc------CCCCceEEeeccc
Q 013128          237 RIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------NSELRFLLLT------MPSRSMLVIEDID  304 (449)
Q Consensus       237 ~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------~~~l~~~~~~------~~~~~Il~iDeiD  304 (449)
                      ..+..+++|+|||||||||||++|+++|++++.+++.++++++.+      ...++..|..      ...|+||+|||||
T Consensus        30 ~~~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD  109 (293)
T 3t15_A           30 LPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLD  109 (293)
T ss_dssp             CTTCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC
T ss_pred             cCCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechh
Confidence            346677899999999999999999999999999999999887743      2334445543      3479999999999


Q ss_pred             hhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc---------cCCCCeEEEEEcCCCCCCCccccCCCccceEEEe
Q 013128          305 CSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS---------CCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHM  375 (449)
Q Consensus       305 ~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~---------~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l  375 (449)
                      .+.+..+....     .......+.+.|++.||+...         .....++||+|||+++.||++|+|||||+.+|++
T Consensus       110 ~~~~~~~~~~~-----~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~~  184 (293)
T 3t15_A          110 AGAGRMGGTTQ-----YTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWA  184 (293)
T ss_dssp             -------------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEEC
T ss_pred             hhcCCCCCCcc-----ccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEeC
Confidence            98762221111     112344567889999885431         1235689999999999999999999999999985


Q ss_pred             CCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc
Q 013128          376 SYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE  408 (449)
Q Consensus       376 ~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~  408 (449)
                        |+.++|.+|++.++...+.. .+.+..+...
T Consensus       185 --P~~~~r~~Il~~~~~~~~~~-~~~l~~~~~~  214 (293)
T 3t15_A          185 --PTREDRIGVCTGIFRTDNVP-AEDVVKIVDN  214 (293)
T ss_dssp             --CCHHHHHHHHHHHHGGGCCC-HHHHHHHHHH
T ss_pred             --cCHHHHHHHHHHhccCCCCC-HHHHHHHhCC
Confidence              59999999999988754322 3444444443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.91  E-value=3.8e-23  Score=200.91  Aligned_cols=213  Identities=26%  Similarity=0.333  Sum_probs=159.6

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..++.+|++++|.++.++++.+... .+..+..+..++...++|++|+||||||||+|++++|+.++..++.+++..+..
T Consensus        33 ~~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~  111 (278)
T 1iy2_A           33 EAPKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVE  111 (278)
T ss_dssp             CCCCCCGGGSSSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHH
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHH
Confidence            3467899999999999999887655 456677888999999999999999999999999999999999999998765421


Q ss_pred             ------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          282 ------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       282 ------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                            ...+..++...  ..|+++++||+|.+...+.....    .........+..+++.++|...  ...++++++|
T Consensus       112 ~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~----~~~~~~~~~~~~ll~~lsgg~~--~~~~i~~a~t  185 (278)
T 1iy2_A          112 MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVG----GGNDEREQTLNQLLVEMDGFEK--DTAIVVMAAT  185 (278)
T ss_dssp             STTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC------------CHHHHHHHHHHHHHHTTCCT--TCCEEEEEEE
T ss_pred             HHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccC----CcchHHHHHHHHHHHHHhCCCC--CCCEEEEEec
Confidence                  23344555553  46899999999988653221100    0122345677889999998643  3457888999


Q ss_pred             CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHHh
Q 013128          354 NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELM  421 (449)
Q Consensus       354 N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l~  421 (449)
                      |+|+.||++++|||||+.+|+++.|+.++|.+|++.++......-...+..+... .+++++||...+.
T Consensus       186 ~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~  254 (278)
T 1iy2_A          186 NRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  254 (278)
T ss_dssp             SCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999998764321111123444444 3588888876664

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.83  E-value=3.1e-19  Score=177.61  Aligned_cols=196  Identities=15%  Similarity=0.170  Sum_probs=147.8

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      ..|..    ..+|.+|++++|.+..++.+...+.......        ....++||+||||||||++|+++|+.++.+++
T Consensus        17 ~~~~~----~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~--------~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~   84 (338)
T 3pfi_A           17 ETYET----SLRPSNFDGYIGQESIKKNLNVFIAAAKKRN--------ECLDHILFSGPAGLGKTTLANIISYEMSANIK   84 (338)
T ss_dssp             ----------CCCCSGGGCCSCHHHHHHHHHHHHHHHHTT--------SCCCCEEEECSTTSSHHHHHHHHHHHTTCCEE
T ss_pred             hhhhh----ccCCCCHHHhCChHHHHHHHHHHHHHHHhcC--------CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeE
Confidence            35654    6788899999999999999988887654321        23568999999999999999999999999999


Q ss_pred             EEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc-----------
Q 013128          273 DLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS-----------  341 (449)
Q Consensus       273 ~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~-----------  341 (449)
                      .+++..+.....+...+.....+++|||||||.+..                  .....|+..++....           
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~------------------~~~~~Ll~~l~~~~~~~~~~~~~~~~  146 (338)
T 3pfi_A           85 TTAAPMIEKSGDLAAILTNLSEGDILFIDEIHRLSP------------------AIEEVLYPAMEDYRLDIIIGSGPAAQ  146 (338)
T ss_dssp             EEEGGGCCSHHHHHHHHHTCCTTCEEEEETGGGCCH------------------HHHHHHHHHHHTSCC---------CC
T ss_pred             EecchhccchhHHHHHHHhccCCCEEEEechhhcCH------------------HHHHHHHHHHHhccchhhcccCcccc
Confidence            999998888888888888888999999999998742                  234456666654210           


Q ss_pred             ---cCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHHH
Q 013128          342 ---CCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEVA  417 (449)
Q Consensus       342 ---~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i~  417 (449)
                         .....+++|++||....++++|++  ||+..++++.|+.+++..++..++...+..+.++ ++.++....-++.++.
T Consensus       147 ~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~  224 (338)
T 3pfi_A          147 TIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIAL  224 (338)
T ss_dssp             CCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHH
T ss_pred             ceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHH
Confidence               001137899999999999999999  9999999999999999999999887655444433 3444443344555554


Q ss_pred             HHH
Q 013128          418 GEL  420 (449)
Q Consensus       418 ~~l  420 (449)
                      +.+
T Consensus       225 ~~l  227 (338)
T 3pfi_A          225 RLL  227 (338)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=99.79  E-value=3e-18  Score=169.05  Aligned_cols=191  Identities=18%  Similarity=0.201  Sum_probs=146.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ..+|.+|++++|.+..++.+...+.......        ..+.++||+||||||||++|+++++.++.+++.++++.+..
T Consensus         5 ~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~--------~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~   76 (324)
T 1hqc_A            5 ALRPKTLDEYIGQERLKQKLRVYLEAAKARK--------EPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEK   76 (324)
T ss_dssp             CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHC--------SCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCS
T ss_pred             ccCcccHHHhhCHHHHHHHHHHHHHHHHccC--------CCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCC
Confidence            4578899999999999998888776543211        12478999999999999999999999999999999998888


Q ss_pred             hHHHHHHHHc-CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc--------------cCCCC
Q 013128          282 NSELRFLLLT-MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS--------------CCGEG  346 (449)
Q Consensus       282 ~~~l~~~~~~-~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~--------------~~~~~  346 (449)
                      ...+...+.. ...+++|||||||.+..                  .....|+..++....              .....
T Consensus        77 ~~~l~~~l~~~~~~~~~l~lDEi~~l~~------------------~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~  138 (324)
T 1hqc_A           77 PGDLAAILANSLEEGDILFIDEIHRLSR------------------QAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPR  138 (324)
T ss_dssp             HHHHHHHHTTTCCTTCEEEETTTTSCCH------------------HHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCC
T ss_pred             hHHHHHHHHHhccCCCEEEEECCccccc------------------chHHHHHHHHHhhhhHHhccccccccccccCCCC
Confidence            7788877777 67899999999998742                  122345555543210              00124


Q ss_pred             eEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH-HHHHHHHccCCCHHHHHHHH
Q 013128          347 RIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE-QIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       347 ~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~-~i~~l~~~~~~tpa~i~~~l  420 (449)
                      +++|++||.+..++++|.+  ||+..+.++.|+.+++..++..++...+..+.+ .++.++....-.|.++.+.+
T Consensus       139 ~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l  211 (324)
T 1hqc_A          139 FTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLF  211 (324)
T ss_dssp             CEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHH
T ss_pred             EEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            7899999999999999998  998899999999999999999988765555544 34555554455666665554

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=99.79  E-value=3.3e-20  Score=192.82  Aligned_cols=169  Identities=14%  Similarity=0.063  Sum_probs=117.7

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC--CcEEEEecccccC
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK--FDIYDLDLSAVQS  281 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~--~~~~~l~~s~~~~  281 (449)
                      +...|++++|.++.++.+...+..+.        .|..+++++|||||||||||++|+++|++++  .+++.++++.+.+
T Consensus        32 ~~~~~~~iiG~~~~~~~l~~~~~~~~--------~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~~  103 (456)
T 2c9o_A           32 AKQAASGLVGQENAREACGVIVELIK--------SKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYS  103 (456)
T ss_dssp             BCSEETTEESCHHHHHHHHHHHHHHH--------TTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGCC
T ss_pred             hhhchhhccCHHHHHHHHHHHHHHHH--------hCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHHH
Confidence            34568999999999998887665433        2455678999999999999999999999999  9999999888753


Q ss_pred             h-----HHHHHHHHcC-----CCCceEEeeccchhhhcccccchhhhh------------ccchhhHHHHHHHHHHhcCc
Q 013128          282 N-----SELRFLLLTM-----PSRSMLVIEDIDCSVKLQNRESSEVQA------------TNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       282 ~-----~~l~~~~~~~-----~~~~Il~iDeiD~l~~~~~~~~~~~~~------------~~~~~~~~~ls~LL~~ldg~  339 (449)
                      .     ..+...|..+     ..|+||||||||.++..+.........            .+........+.++..++..
T Consensus       104 ~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~  183 (456)
T 2c9o_A          104 TEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKE  183 (456)
T ss_dssp             SSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHT
T ss_pred             HhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhc
Confidence            1     3366777665     479999999999998754332110000            00011112334466666522


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccce--EEEeCCCCH
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDM--HLHMSYCNT  380 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~--~i~l~~p~~  380 (449)
                      ....++.++|++|||+++.+|+++.||||||.  .+.+|.|+.
T Consensus       184 ~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~  226 (456)
T 2c9o_A          184 RVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKG  226 (456)
T ss_dssp             TCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCS
T ss_pred             cCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCch
Confidence            22224445666899999999999999999998  566677743

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.77  E-value=1.9e-18  Score=169.48  Aligned_cols=177  Identities=15%  Similarity=0.213  Sum_probs=132.4

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCC---cceEEeCCCCCCHHHHHHHHHHHcC-------CcEEEEecccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWK---RGYLLYGPPGTGKSSLIAAMANQLK-------FDIYDLDLSAV  279 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~---rg~LL~GPpGtGKT~la~aiA~~l~-------~~~~~l~~s~~  279 (449)
                      +++|.+++|+.|.+.+..+.. +..+.+.|...+   .++||+||||||||++|+++|+.++       .+++.++++.+
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~-~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l  110 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLV-ERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDL  110 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHH-HHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGT
T ss_pred             HccChHHHHHHHHHHHHHHHh-HHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHh
Confidence            689999999999988876553 555666665443   3599999999999999999999983       38999998877


Q ss_pred             cC------hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          280 QS------NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       280 ~~------~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                      ..      ...+...+... .++||||||+|.+...+..         .......++.|++.++..    ...+++|+||
T Consensus       111 ~~~~~g~~~~~~~~~~~~~-~~~vl~iDEid~l~~~~~~---------~~~~~~~~~~Ll~~l~~~----~~~~~~i~~~  176 (309)
T 3syl_A          111 VGQYIGHTAPKTKEVLKRA-MGGVLFIDEAYYLYRPDNE---------RDYGQEAIEILLQVMENN----RDDLVVILAG  176 (309)
T ss_dssp             CCSSTTCHHHHHHHHHHHH-TTSEEEEETGGGSCCCC------------CCTHHHHHHHHHHHHHC----TTTCEEEEEE
T ss_pred             hhhcccccHHHHHHHHHhc-CCCEEEEEChhhhccCCCc---------ccccHHHHHHHHHHHhcC----CCCEEEEEeC
Confidence            43      23344444443 5789999999998742211         112345677788888753    3467888888


Q ss_pred             CCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHH
Q 013128          354 NHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIE  403 (449)
Q Consensus       354 N~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~  403 (449)
                      |..+     .++|+|++  ||+.+++|+.|+.+++..|++.++...+..+.++..
T Consensus       177 ~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~  229 (309)
T 3syl_A          177 YADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAE  229 (309)
T ss_dssp             CHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHH
T ss_pred             ChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            8653     35799999  999999999999999999999999866555544443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=99.76  E-value=2.3e-17  Score=161.31  Aligned_cols=174  Identities=15%  Similarity=0.233  Sum_probs=124.2

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhh-cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRI-GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------  281 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~-g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------  281 (449)
                      +.++|.++.++.+...+............. +...+.++||+||||||||++|+++|+.++.+++.++++.+..      
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~   94 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGG
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCc
Confidence            358999999999988887654332211111 1123578999999999999999999999999999999987643      


Q ss_pred             --hHHHHHHHHcC-------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc------CCCC
Q 013128          282 --NSELRFLLLTM-------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC------CGEG  346 (449)
Q Consensus       282 --~~~l~~~~~~~-------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~------~~~~  346 (449)
                        ...+..++...       ..++||||||+|.+........      .........+.|+..+++....      ....
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~------~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  168 (310)
T 1ofh_A           95 EVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSG------ADVSREGVQRDLLPLVEGSTVSTKHGMVKTDH  168 (310)
T ss_dssp             STTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCS------SHHHHHHHHHHHHHHHHCCEEEETTEEEECTT
T ss_pred             cHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccc------cchhHHHHHHHHHHHhcCCeEecccccccCCc
Confidence              23355555443       2479999999999865322111      1112233467788888864210      1235


Q ss_pred             eEEEEE----cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHH
Q 013128          347 RIIVFT----TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNY  390 (449)
Q Consensus       347 ~iiI~t----TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~  390 (449)
                      +++|++    ++.+..++++|++  ||+..++|+.|+.+++..+++..
T Consensus       169 ~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~  214 (310)
T 1ofh_A          169 ILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEP  214 (310)
T ss_dssp             CEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             EEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhh
Confidence            778887    5677889999998  99999999999999999999853

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=99.75  E-value=9.1e-18  Score=166.05  Aligned_cols=159  Identities=16%  Similarity=0.151  Sum_probs=121.1

Q ss_pred             cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          192 HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       192 ~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      ...|..    ..+|.+|++++|.++.++.+.+.+.    .       | ..+..+|++||||||||++++++|++++.++
T Consensus        13 ~~~~~~----k~rP~~~~~ivg~~~~~~~l~~~l~----~-------~-~~~~~~L~~G~~G~GKT~la~~la~~l~~~~   76 (324)
T 3u61_B           13 EHILEQ----KYRPSTIDECILPAFDKETFKSITS----K-------G-KIPHIILHSPSPGTGKTTVAKALCHDVNADM   76 (324)
T ss_dssp             CSSHHH----HSCCCSTTTSCCCHHHHHHHHHHHH----T-------T-CCCSEEEECSSTTSSHHHHHHHHHHHTTEEE
T ss_pred             cchHHH----hhCCCCHHHHhCcHHHHHHHHHHHH----c-------C-CCCeEEEeeCcCCCCHHHHHHHHHHHhCCCE
Confidence            346765    7889999999999999888776664    1       1 2246789999999999999999999999999


Q ss_pred             EEEecccccChHHHHHH----HHcCC---CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC
Q 013128          272 YDLDLSAVQSNSELRFL----LLTMP---SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG  344 (449)
Q Consensus       272 ~~l~~s~~~~~~~l~~~----~~~~~---~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  344 (449)
                      +.++++... ...++..    ....+   .+.||+|||+|.+.+                 ......|+..++..    .
T Consensus        77 ~~i~~~~~~-~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~-----------------~~~~~~L~~~le~~----~  134 (324)
T 3u61_B           77 MFVNGSDCK-IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL-----------------AESQRHLRSFMEAY----S  134 (324)
T ss_dssp             EEEETTTCC-HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG-----------------HHHHHHHHHHHHHH----G
T ss_pred             EEEcccccC-HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc-----------------HHHHHHHHHHHHhC----C
Confidence            999987754 3333332    22222   688999999998851                 11234566666643    2


Q ss_pred             CCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          345 EGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       345 ~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      ..+.+|+|||.+..++++|.+  |+. .++|+.|+.+++..++..++
T Consensus       135 ~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~~  178 (324)
T 3u61_B          135 SNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQMI  178 (324)
T ss_dssp             GGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHHH
Confidence            346888999999999999999  885 69999999999887776654

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=99.74  E-value=5.9e-19  Score=181.14  Aligned_cols=163  Identities=13%  Similarity=0.159  Sum_probs=71.3

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcC-CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGR-AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------  281 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~-~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------  281 (449)
                      +.++|.++.|+.+...+..+.++...+...+. .+++++||+||||||||++|+++|+.++.+++.++++.+..      
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~   94 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeec
Confidence            36899999999998888776655544444333 35689999999999999999999999999999999876532      


Q ss_pred             --hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE-cCCCCC
Q 013128          282 --NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT-TNHKEK  358 (449)
Q Consensus       282 --~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t-TN~~~~  358 (449)
                        ...++.++...  ..++.+||+|.+....          .......+++.||+.|||+.+.  .. + +++ ||+++.
T Consensus        95 d~e~~lr~lf~~a--~~~~~~De~d~~~~~~----------~~~~e~rvl~~LL~~~dg~~~~--~~-v-~a~~TN~~~~  158 (444)
T 1g41_A           95 EVDSIIRDLTDSA--MKLVRQQEIAKNRARA----------EDVAEERILDALLPPAKNQWGE--VE-N-HDSHSSTRQA  158 (444)
T ss_dssp             CTHHHHHHHHHHH--HHHHHHHHHHSCC----------------------------------------------------
T ss_pred             cHHHHHHHHHHHH--Hhcchhhhhhhhhccc----------hhhHHHHHHHHHHHHhhccccc--cc-c-ccccccCHHH
Confidence              23444554433  2234578887654211          1233467899999999998663  22 3 444 999999


Q ss_pred             CCccccCCCccceEEEeCCCCHH-HHHHHH
Q 013128          359 LDPALLRPGRMDMHLHMSYCNTS-VFKQLA  387 (449)
Q Consensus       359 ld~aLlrpgR~d~~i~l~~p~~~-~r~~l~  387 (449)
                      ||+||+||||||.+|+++.|+.. .+.+++
T Consensus       159 ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          159 FRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             ------------------------------
T ss_pred             HHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            99999999999999999999987 455554

>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=99.73  E-value=5e-17  Score=149.85  Aligned_cols=177  Identities=15%  Similarity=0.188  Sum_probs=125.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEec
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDL  276 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~  276 (449)
                      ...|.+|++++|.++.++.+.+.+..    .         ...++||+||||||||++++++++.+     ...++.+++
T Consensus        10 ~~~p~~~~~~~g~~~~~~~l~~~l~~----~---------~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~   76 (226)
T 2chg_A           10 KYRPRTLDEVVGQDEVIQRLKGYVER----K---------NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNA   76 (226)
T ss_dssp             HTSCSSGGGCCSCHHHHHHHHHHHHT----T---------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEET
T ss_pred             hcCCCCHHHHcCcHHHHHHHHHHHhC----C---------CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEecc
Confidence            67889999999999888877766532    1         12459999999999999999999986     456888888


Q ss_pred             ccccChHHHHHHH---Hc-----CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeE
Q 013128          277 SAVQSNSELRFLL---LT-----MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI  348 (449)
Q Consensus       277 s~~~~~~~l~~~~---~~-----~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  348 (449)
                      +.......+...+   ..     ...+.||+|||+|.+..                  .....|+..++..    .....
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~------------------~~~~~l~~~l~~~----~~~~~  134 (226)
T 2chg_A           77 SDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA------------------DAQAALRRTMEMY----SKSCR  134 (226)
T ss_dssp             TCTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH------------------HHHHHHHHHHHHT----TTTEE
T ss_pred             ccccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH------------------HHHHHHHHHHHhc----CCCCe
Confidence            7765544443322   22     24689999999998743                  1234455555542    34578


Q ss_pred             EEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH-HHHHHHHccCCCHHHH
Q 013128          349 IVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE-QIEELIKEVNVTPAEV  416 (449)
Q Consensus       349 iI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~-~i~~l~~~~~~tpa~i  416 (449)
                      +|+|||.++.+++++.+  |+. .++++.++.++...++..++...+..+.+ .++.+.+...-.+..+
T Consensus       135 ~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~r~l  200 (226)
T 2chg_A          135 FILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKA  200 (226)
T ss_dssp             EEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHH
T ss_pred             EEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHH
Confidence            88999999999999999  887 89999999999999999877544333332 3333333333344433

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.71  E-value=1.9e-16  Score=152.77  Aligned_cols=167  Identities=18%  Similarity=0.199  Sum_probs=113.4

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-------
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-------  281 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-------  281 (449)
                      +.+++.....+.++.....+..   .....+...++++||+||||||||++|+++|+.++.+++.+++.+...       
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~---~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~~~  109 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQ---QTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAK  109 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHH---HHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHH---HHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchHHH
Confidence            4566766666666654222211   122223455789999999999999999999999999999998765321       


Q ss_pred             hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCC
Q 013128          282 NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL  359 (449)
Q Consensus       282 ~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l  359 (449)
                      ...+...+..  ...++||+|||||.+++.+...        .......+..|+..+++... .+..++||+|||.++.+
T Consensus       110 ~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~--------~~~~~~~l~~L~~~~~~~~~-~~~~~~ii~ttn~~~~l  180 (272)
T 1d2n_A          110 CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG--------PRFSNLVLQALLVLLKKAPP-QGRKLLIIGTTSRKDVL  180 (272)
T ss_dssp             HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTT--------TBCCHHHHHHHHHHTTCCCS-TTCEEEEEEEESCHHHH
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCC--------hhHHHHHHHHHHHHhcCccC-CCCCEEEEEecCChhhc
Confidence            1234445544  3568999999999987532111        11234456667777776532 24567899999999988


Q ss_pred             Cc-cccCCCccceEEEeCCCCH-HHHHHHHHH
Q 013128          360 DP-ALLRPGRMDMHLHMSYCNT-SVFKQLAFN  389 (449)
Q Consensus       360 d~-aLlrpgR~d~~i~l~~p~~-~~r~~l~~~  389 (449)
                      ++ .+.+  ||+..|++|.++. ++...++..
T Consensus       181 ~~~~l~~--rf~~~i~~p~l~~r~~i~~i~~~  210 (272)
T 1d2n_A          181 QEMEMLN--AFSTTIHVPNIATGEQLLEALEL  210 (272)
T ss_dssp             HHTTCTT--TSSEEEECCCEEEHHHHHHHHHH
T ss_pred             chhhhhc--ccceEEcCCCccHHHHHHHHHHh
Confidence            88 5555  9999999988776 666666654

>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=99.71  E-value=4.3e-16  Score=145.19  Aligned_cols=182  Identities=18%  Similarity=0.268  Sum_probs=129.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ...|.+|++++|.+..++.+...+..           + ..++.++|+||||||||++++++++.++.            
T Consensus        16 ~~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~   83 (250)
T 1njg_A           16 KWRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   83 (250)
T ss_dssp             HTCCCSGGGCCSCHHHHHHHHHHHHH-----------T-CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCS
T ss_pred             ccCCccHHHHhCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCccc
Confidence            56788999999999988888776642           1 11357999999999999999999998843            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.........+..++....      .+.+|+|||+|.+..                  ..+..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~------------------~~~~~  145 (250)
T 1njg_A           84 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR------------------HSFNA  145 (250)
T ss_dssp             HHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCH------------------HHHHH
T ss_pred             HHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccH------------------HHHHH
Confidence                        345555443333344555655532      578999999998632                  23455


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHccC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEVN  410 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~  410 (449)
                      |+..++..    +..+.+|++||.++.+++++.+  |+ ..++++.++.++..+++..++...+..+. +.++.+.+...
T Consensus       146 l~~~l~~~----~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  218 (250)
T 1njg_A          146 LLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAE  218 (250)
T ss_dssp             HHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHT
T ss_pred             HHHHHhcC----CCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence            77777643    3567899999999999999988  75 68999999999999999988865444433 23444444444


Q ss_pred             CCHHHHHHHH
Q 013128          411 VTPAEVAGEL  420 (449)
Q Consensus       411 ~tpa~i~~~l  420 (449)
                      -.|.++...+
T Consensus       219 G~~~~~~~~~  228 (250)
T 1njg_A          219 GSLRDALSLT  228 (250)
T ss_dssp             TCHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            4555554443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.70  E-value=2e-16  Score=158.91  Aligned_cols=184  Identities=18%  Similarity=0.125  Sum_probs=123.9

Q ss_pred             CCCC-cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEeccccc
Q 013128          204 HPMT-FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLSAVQ  280 (449)
Q Consensus       204 ~p~~-f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s~~~  280 (449)
                      +|.. |++++|.+..++.+...+.....        |..+++++||+||||||||++|+++|+.++.  +++.+++..+.
T Consensus        38 ~p~~~~~~ivG~~~~~~~l~~l~~~~~~--------~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  109 (368)
T 3uk6_A           38 EPRQASQGMVGQLAARRAAGVVLEMIRE--------GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIF  109 (368)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHHHHT--------TCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGS
T ss_pred             CcCcchhhccChHHHHHHHHHHHHHHHc--------CCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhh
Confidence            4555 99999999998876554433322        3334579999999999999999999999975  67777654421


Q ss_pred             C-------------------------------------------------------hHHHHHHHHcC-----------CC
Q 013128          281 S-------------------------------------------------------NSELRFLLLTM-----------PS  294 (449)
Q Consensus       281 ~-------------------------------------------------------~~~l~~~~~~~-----------~~  294 (449)
                      .                                                       ...++..+...           ..
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~  189 (368)
T 3uk6_A          110 SLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEII  189 (368)
T ss_dssp             CSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---C
T ss_pred             hcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhcccccc
Confidence            1                                                       11222222111           12


Q ss_pred             CceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc-----------CCCCCCCccc
Q 013128          295 RSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT-----------NHKEKLDPAL  363 (449)
Q Consensus       295 ~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT-----------N~~~~ld~aL  363 (449)
                      |+||||||+|.+..                  ..++.|+..++..    ...+++++|.           |.+..++++|
T Consensus       190 ~~vl~IDEi~~l~~------------------~~~~~L~~~le~~----~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l  247 (368)
T 3uk6_A          190 PGVLFIDEVHMLDI------------------ESFSFLNRALESD----MAPVLIMATNRGITRIRGTSYQSPHGIPIDL  247 (368)
T ss_dssp             BCEEEEESGGGSBH------------------HHHHHHHHHTTCT----TCCEEEEEESCSEEECBTSSCEEETTCCHHH
T ss_pred             CceEEEhhccccCh------------------HHHHHHHHHhhCc----CCCeeeeecccceeeeeccCCCCcccCCHHH
Confidence            68999999998742                  2445677777643    2234444443           3578899999


Q ss_pred             cCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccC-CCHHHHHHHH
Q 013128          364 LRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVN-VTPAEVAGEL  420 (449)
Q Consensus       364 lrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~-~tpa~i~~~l  420 (449)
                      ++  ||.. ++|++|+.+++..+++..+...+..+.++ ++.++.... -++.++...|
T Consensus       248 ~s--R~~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll  303 (368)
T 3uk6_A          248 LD--RLLI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLI  303 (368)
T ss_dssp             HT--TEEE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             Hh--hccE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHH
Confidence            99  9976 89999999999999999887665555444 344444443 5666665544

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.70  E-value=1.8e-16  Score=167.07  Aligned_cols=177  Identities=18%  Similarity=0.281  Sum_probs=121.9

Q ss_pred             cccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcC-hhHHhhhcC---CCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          192 HMRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNG-KEYYTRIGR---AWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       192 ~~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~-~~~~~~~g~---~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...|..    ..+|.+|++++|.++.++.+.+.+..+... +..++..|.   +.++++||+||||||||++|+++|+++
T Consensus        26 ~~lW~e----kyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           26 DKLWTV----KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             CCCHHH----HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCccc----ccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            346865    789999999999999999999888765432 222333333   256799999999999999999999999


Q ss_pred             CCcEEEEecccccChHHHHHHHH-------------c-------CCCCceEEeeccchhhhcccccchhhhhccchhhHH
Q 013128          268 KFDIYDLDLSAVQSNSELRFLLL-------------T-------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKV  327 (449)
Q Consensus       268 ~~~~~~l~~s~~~~~~~l~~~~~-------------~-------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~  327 (449)
                      +.+++.++++.......+...+.             .       ...++||+|||+|.+....               ..
T Consensus       102 ~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~---------------~~  166 (516)
T 1sxj_A          102 GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD---------------RG  166 (516)
T ss_dssp             TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS---------------TT
T ss_pred             CCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhh---------------HH
Confidence            99999999988766443332221             1       2467899999999986410               11


Q ss_pred             HHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          328 TLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       328 ~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .+..|++.++..    +..+|+|+++.....++ .+.   |+...+.|+.|+.+++..++...+..++
T Consensus       167 ~l~~L~~~l~~~----~~~iIli~~~~~~~~l~-~l~---~r~~~i~f~~~~~~~~~~~L~~i~~~~~  226 (516)
T 1sxj_A          167 GVGQLAQFCRKT----STPLILICNERNLPKMR-PFD---RVCLDIQFRRPDANSIKSRLMTIAIREK  226 (516)
T ss_dssp             HHHHHHHHHHHC----SSCEEEEESCTTSSTTG-GGT---TTSEEEECCCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhc----CCCEEEEEcCCCCccch-hhH---hceEEEEeCCCCHHHHHHHHHHHHHHcC
Confidence            244566666531    12233333333333443 354   4456899999999999999988765443

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=99.69  E-value=9.1e-18  Score=169.08  Aligned_cols=176  Identities=18%  Similarity=0.208  Sum_probs=119.5

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhh-hcC-CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC------
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTR-IGR-AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS------  281 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~-~g~-~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~------  281 (449)
                      .++|.+..++.+...+............ .+. ..+.++||+||||||||++|+++|+.++.+++.++++.+..      
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~   95 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGE   95 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhcccccccc
Confidence            3689999999998888654432211000 111 24678999999999999999999999999999999987753      


Q ss_pred             --hHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc-----------
Q 013128          282 --NSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC-----------  342 (449)
Q Consensus       282 --~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-----------  342 (449)
                        ...+..++...      ..++||||||||.+...+......    .......+.+.||..|||....           
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~----~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~  171 (363)
T 3hws_A           96 DVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSIT----RDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQ  171 (363)
T ss_dssp             HHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC-------CHHHHHHHHHHHHHHHHCC--------------
T ss_pred             cHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccc----cccchHHHHHHHHHHhcCceeeccCccccccCC
Confidence              22344455443      357899999999987643222111    1122234788899999954210           


Q ss_pred             ------CCCCeEEEEEcCCC----------CC-----------------------------------CCccccCCCccce
Q 013128          343 ------CGEGRIIVFTTNHK----------EK-----------------------------------LDPALLRPGRMDM  371 (449)
Q Consensus       343 ------~~~~~iiI~tTN~~----------~~-----------------------------------ld~aLlrpgR~d~  371 (449)
                            ...++++|+|+|..          ..                                   +.|+|+.  ||+.
T Consensus       172 ~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~  249 (363)
T 3hws_A          172 QEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPV  249 (363)
T ss_dssp             --CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCE
T ss_pred             CceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCe
Confidence                  11334555555532          11                                   6788887  9999


Q ss_pred             EEEeCCCCHHHHHHHHHHHh
Q 013128          372 HLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       372 ~i~l~~p~~~~r~~l~~~~l  391 (449)
                      .+.+++|+.+.+..|+...+
T Consensus       250 ~~~~~pl~~~~~~~I~~~~~  269 (363)
T 3hws_A          250 VATLNELSEEALIQILKEPK  269 (363)
T ss_dssp             EEECCCCCHHHHHHHHHSST
T ss_pred             eeecCCCCHHHHHHHHHHHH
Confidence            99999999999999998633

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.68  E-value=4.9e-17  Score=146.40  Aligned_cols=154  Identities=18%  Similarity=0.209  Sum_probs=107.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ...|.+|++++|.++..+.+.+.+..             ..++++||+||||||||++++++++.+          +.++
T Consensus        15 ~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~   81 (195)
T 1jbk_A           15 RAEQGKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRV   81 (195)
T ss_dssp             HHHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEE
T ss_pred             HHhhccccccccchHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcE
Confidence            34577899999999888777665421             225789999999999999999999997          7888


Q ss_pred             EEEecccccCh--------HHHHHHHH---cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc
Q 013128          272 YDLDLSAVQSN--------SELRFLLL---TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW  340 (449)
Q Consensus       272 ~~l~~s~~~~~--------~~l~~~~~---~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  340 (449)
                      +.+++..+...        ..+..++.   ....++||+|||+|.+...+....       ...   ....|...++.  
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~-------~~~---~~~~l~~~~~~--  149 (195)
T 1jbk_A           82 LALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADG-------AMD---AGNMLKPALAR--  149 (195)
T ss_dssp             EEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT-------------CCC---CHHHHHHHHHT--
T ss_pred             EEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccc-------hHH---HHHHHHHhhcc--
Confidence            88887665311        12333332   456788999999999865321100       011   12223333322  


Q ss_pred             ccCCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHH
Q 013128          341 SCCGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLA  387 (449)
Q Consensus       341 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~  387 (449)
                          ..+.+|++||.++     .+++++.+  ||+ .++++.|+.+++.+++
T Consensus       150 ----~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 ----GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ----TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             ----CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence                3567888888776     78999999  998 6999999999988764

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=99.67  E-value=2.7e-16  Score=166.61  Aligned_cols=160  Identities=19%  Similarity=0.148  Sum_probs=113.9

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChH----
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNS----  283 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~----  283 (449)
                      .++++|.+++++.+.+.+........       ..+..+||+||||||||++++++|+.++.++..++++.+....    
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~~~~-------~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g  152 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKLTKS-------LKGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRG  152 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHHSSS-------CCSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC---------
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhccc-------CCCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhh
Confidence            45689999999988766543322221       1355799999999999999999999999999999987754322    


Q ss_pred             -----------HHHHHHHcCC-CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc---------
Q 013128          284 -----------ELRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC---------  342 (449)
Q Consensus       284 -----------~l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~---------  342 (449)
                                 .+...+.... ...||||||||.+.....              ....+.||..||.....         
T Consensus       153 ~~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~~~--------------~~~~~~LL~~ld~~~~~~~~~~~~~~  218 (543)
T 3m6a_A          153 HRRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSDFR--------------GDPSSAMLEVLDPEQNSSFSDHYIEE  218 (543)
T ss_dssp             -----------CHHHHHHTTCSSSEEEEEEESSSCC-----------------------CCGGGTCTTTTTBCCCSSSCC
T ss_pred             HHHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhhhc--------------cCHHHHHHHHHhhhhcceeecccCCe
Confidence                       1223444442 445999999999864211              11345578888753211         


Q ss_pred             --CCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          343 --CGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       343 --~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                        .-..++||+|||.++.++|+|++  ||+ .|+++.|+.+++..|++.++
T Consensus       219 ~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          219 TFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             CCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTH
T ss_pred             eecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHH
Confidence              01457999999999999999999  996 69999999999999999887

>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=99.66  E-value=3.2e-16  Score=153.57  Aligned_cols=164  Identities=14%  Similarity=0.194  Sum_probs=119.8

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----  267 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----  267 (449)
                      ..|..    ..+|.+|++++|.++.++.+.+.+.    .       +.  ..++|||||||||||++++++|+.+     
T Consensus         5 ~~~~~----k~~p~~~~~~~g~~~~~~~l~~~l~----~-------~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~   67 (319)
T 2chq_A            5 EIWVE----KYRPRTLDEVVGQDEVIQRLKGYVE----R-------KN--IPHLLFSGPPGTGKTATAIALARDLFGENW   67 (319)
T ss_dssp             -CTTT----TTSCSSGGGSCSCHHHHHHHHTTTT----T-------TC--CCCEEEESSSSSSHHHHHHHHHHHHHTTCH
T ss_pred             ccHHH----hcCCCCHHHHhCCHHHHHHHHHHHh----C-------CC--CCeEEEECcCCcCHHHHHHHHHHHhcCCcc
Confidence            35754    7889999999999988887765442    1       11  2349999999999999999999997     


Q ss_pred             CCcEEEEecccccChHHH---HHHHH-cC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          268 KFDIYDLDLSAVQSNSEL---RFLLL-TM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       268 ~~~~~~l~~s~~~~~~~l---~~~~~-~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                      +.+++.++++.......+   ...+. ..    ..+.||+|||+|.+..                  ...+.|+..++..
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~------------------~~~~~L~~~le~~  129 (319)
T 2chq_A           68 RDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA------------------DAQAALRRTMEMY  129 (319)
T ss_dssp             HHHCEEEETTSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH------------------HHHHTTGGGTSSS
T ss_pred             cCCeEEEeCccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH------------------HHHHHHHHHHHhc
Confidence            346788888765332222   22222 21    3578999999998742                  1234466666642


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                          +..+++|++||.+..+++++.+  |+. .+.++.|+.++...++..++...+..+
T Consensus       130 ----~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i  181 (319)
T 2chq_A          130 ----SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKI  181 (319)
T ss_dssp             ----SSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTTCCCB
T ss_pred             ----CCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHcCCCC
Confidence                3567889999999999999999  775 799999999999999998876554444

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.65  E-value=8.8e-16  Score=158.81  Aligned_cols=151  Identities=21%  Similarity=0.287  Sum_probs=111.1

Q ss_pred             cCCCCCcccccCCHHHH---HHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc
Q 013128          202 LKHPMTFKTLALDSELK---REITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k---~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~  278 (449)
                      ..+|.+|++++|.+.++   +.+...+..           |.  ..++|||||||||||++|+++|+.++.+++.+++..
T Consensus        19 r~rP~~l~~ivGq~~~~~~~~~L~~~i~~-----------~~--~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~~   85 (447)
T 3pvs_A           19 RMRPENLAQYIGQQHLLAAGKPLPRAIEA-----------GH--LHSMILWGPPGTGKTTLAEVIARYANADVERISAVT   85 (447)
T ss_dssp             HTCCCSTTTCCSCHHHHSTTSHHHHHHHH-----------TC--CCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETTT
T ss_pred             HhCCCCHHHhCCcHHHHhchHHHHHHHHc-----------CC--CcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEecc
Confidence            57899999999999887   455544431           11  258999999999999999999999999999998765


Q ss_pred             ccChHHHHHHHHc------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          279 VQSNSELRFLLLT------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       279 ~~~~~~l~~~~~~------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      .. ...++..+..      ...++||||||||.+..                  .....||..++.      ..+++|++
T Consensus        86 ~~-~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~------------------~~q~~LL~~le~------~~v~lI~a  140 (447)
T 3pvs_A           86 SG-VKEIREAIERARQNRNAGRRTILFVDEVHRFNK------------------SQQDAFLPHIED------GTITFIGA  140 (447)
T ss_dssp             CC-HHHHHHHHHHHHHHHHTTCCEEEEEETTTCC------------------------CCHHHHHT------TSCEEEEE
T ss_pred             CC-HHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCH------------------HHHHHHHHHHhc------CceEEEec
Confidence            43 2334333332      34789999999998843                  122347777764      23566655


Q ss_pred             c--CCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          353 T--NHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       353 T--N~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      |  |....++++|++  |+. .+.++.|+.++...++.+++..
T Consensus       141 tt~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~  180 (447)
T 3pvs_A          141 TTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMED  180 (447)
T ss_dssp             ESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHC
T ss_pred             CCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHH
Confidence            5  444689999999  885 6789999999999999998865

>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=99.64  E-value=1.6e-15  Score=149.15  Aligned_cols=164  Identities=14%  Similarity=0.200  Sum_probs=120.0

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      ..|..    ..+|.+|++++|.++.++.+...+..           |.  ..++||+||||||||++|+++|+.+.    
T Consensus        13 ~~~~~----k~~p~~~~~~~g~~~~~~~l~~~l~~-----------~~--~~~~ll~G~~G~GKT~la~~l~~~l~~~~~   75 (327)
T 1iqp_A           13 KPWVE----KYRPQRLDDIVGQEHIVKRLKHYVKT-----------GS--MPHLLFAGPPGVGKTTAALALARELFGENW   75 (327)
T ss_dssp             SCHHH----HTCCCSTTTCCSCHHHHHHHHHHHHH-----------TC--CCEEEEESCTTSSHHHHHHHHHHHHHGGGH
T ss_pred             Cchhh----ccCCCCHHHhhCCHHHHHHHHHHHHc-----------CC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcc
Confidence            46755    68999999999999998888766542           11  23599999999999999999999973    


Q ss_pred             -CcEEEEecccccChHH----HHHHHHcC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          269 -FDIYDLDLSAVQSNSE----LRFLLLTM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       269 -~~~~~l~~s~~~~~~~----l~~~~~~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                       ..++.+++++......    +.......    ..+.||+|||+|.+..                  ...+.|+..++..
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~------------------~~~~~L~~~le~~  137 (327)
T 1iqp_A           76 RHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ------------------DAQQALRRTMEMF  137 (327)
T ss_dssp             HHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH------------------HHHHHHHHHHHHT
T ss_pred             cCceEEeeccccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCH------------------HHHHHHHHHHHhc
Confidence             3477888765432222    22222222    3578999999998742                  1344566666642


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                          ...+.+|++||.++.+++++.+  |+. .+.++.++.++...++..++...+..+
T Consensus       138 ----~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~~~~~l~~~~~~~~~~~  189 (327)
T 1iqp_A          138 ----SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLEL  189 (327)
T ss_dssp             ----TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEE
T ss_pred             ----CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHHHHHHHHHHHHhcCCCC
Confidence                3457888899999999999988  775 799999999999999988876554433

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.64  E-value=1.9e-15  Score=149.86  Aligned_cols=155  Identities=15%  Similarity=0.160  Sum_probs=111.4

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNS  283 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~  283 (449)
                      .|..+++++|.++.++.+...+..               ++++||+||||||||++|+++|+.++.+++.++++......
T Consensus        22 ~~~~~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~   86 (331)
T 2r44_A           22 IDEVGKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPS   86 (331)
T ss_dssp             HHHHTTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHH
T ss_pred             HHHhccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChh
Confidence            344567899999988877665532               35899999999999999999999999999999875333222


Q ss_pred             HHHHH---------HHcCCC---CceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc-------cccCC
Q 013128          284 ELRFL---------LLTMPS---RSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL-------WSCCG  344 (449)
Q Consensus       284 ~l~~~---------~~~~~~---~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-------~~~~~  344 (449)
                      .+...         +.....   .+||+|||+|.+..                  .+.+.|+..|+..       ....+
T Consensus        87 ~l~g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~------------------~~~~~Ll~~l~~~~~~~~g~~~~~~  148 (331)
T 2r44_A           87 DLIGTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPA------------------KVQSALLECMQEKQVTIGDTTYPLD  148 (331)
T ss_dssp             HHHEEEEEETTTTEEEEEECTTCSSEEEEETGGGSCH------------------HHHHHHHHHHHHSEEEETTEEEECC
T ss_pred             hcCCceeecCCCCceEeccCcccccEEEEEccccCCH------------------HHHHHHHHHHhcCceeeCCEEEECC
Confidence            22100         000011   37999999998642                  2345566666521       11223


Q ss_pred             CCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          345 EGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       345 ~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      ..+++|+|+|..+     .++++|++  ||+.++++++|+.+++.++++..+..
T Consensus       149 ~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          149 NPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             SSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             CCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhcccc
Confidence            4567888888554     38999999  99999999999999999999998865

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.63  E-value=9.3e-16  Score=143.75  Aligned_cols=165  Identities=16%  Similarity=0.183  Sum_probs=107.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEeccc
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSA  278 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~  278 (449)
                      +.++.+|+++++.+ ..+.+++.+..+...+         .++++||+||||||||++++++|+++.   ..++.++++.
T Consensus        21 ~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~---------~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~   90 (242)
T 3bos_A           21 LPDDETFTSYYPAA-GNDELIGALKSAASGD---------GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGI   90 (242)
T ss_dssp             CCTTCSTTTSCC---CCHHHHHHHHHHHHTC---------SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGG
T ss_pred             CCCCCChhhccCCC-CCHHHHHHHHHHHhCC---------CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            44557999999832 1233444555544422         257899999999999999999999884   7888888877


Q ss_pred             ccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCe-EEEEEcCCCC
Q 013128          279 VQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGR-IIVFTTNHKE  357 (449)
Q Consensus       279 ~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~-iiI~tTN~~~  357 (449)
                      +...  +...+.....+.+|+|||+|.+...             .   .....|+..++.....  ... +|+.++..++
T Consensus        91 ~~~~--~~~~~~~~~~~~vliiDe~~~~~~~-------------~---~~~~~l~~~l~~~~~~--~~~~ii~~~~~~~~  150 (242)
T 3bos_A           91 HASI--STALLEGLEQFDLICIDDVDAVAGH-------------P---LWEEAIFDLYNRVAEQ--KRGSLIVSASASPM  150 (242)
T ss_dssp             GGGS--CGGGGTTGGGSSEEEEETGGGGTTC-------------H---HHHHHHHHHHHHHHHH--CSCEEEEEESSCTT
T ss_pred             HHHH--HHHHHHhccCCCEEEEeccccccCC-------------H---HHHHHHHHHHHHHHHc--CCCeEEEEcCCCHH
Confidence            6432  1122233456899999999987431             0   0122344444433221  223 4444444444


Q ss_pred             ---CCCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          358 ---KLDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       358 ---~ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                         .+++++.+  |+.  ..++++.|+.+++.+++..++...+..+
T Consensus       151 ~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~  194 (242)
T 3bos_A          151 EAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQL  194 (242)
T ss_dssp             TTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCC
T ss_pred             HHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCC
Confidence               45688888  775  8999999999999999998876444333

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.63  E-value=1.9e-15  Score=148.00  Aligned_cols=161  Identities=17%  Similarity=0.285  Sum_probs=116.1

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSEL  285 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l  285 (449)
                      +.++|.+..++.+...+......-.   . ...+...+||+||||||||++|+++|+.+   +.+++.++++.+......
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~---~-~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~   92 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV   92 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCS---C-TTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCC---C-CCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccH
Confidence            4578999999988888876542210   0 01122469999999999999999999998   566999999877554322


Q ss_pred             HHHH------------------HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC---
Q 013128          286 RFLL------------------LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG---  344 (449)
Q Consensus       286 ~~~~------------------~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~---  344 (449)
                      ..++                  ......+||+|||+|.+..                  ...+.|+..|+......+   
T Consensus        93 ~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~------------------~~~~~Ll~~le~~~~~~~~~~  154 (311)
T 4fcw_A           93 SRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAHP------------------DVFNILLQMLDDGRLTDSHGR  154 (311)
T ss_dssp             HHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSCH------------------HHHHHHHHHHHHSEEECTTSC
T ss_pred             HHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcCH------------------HHHHHHHHHHhcCEEEcCCCC
Confidence            2222                  1112458999999998742                  245667777764321111   


Q ss_pred             ----CCeEEEEEcCC--------------------------CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          345 ----EGRIIVFTTNH--------------------------KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       345 ----~~~iiI~tTN~--------------------------~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                          ..+++|+|||.                          ...++|+|+.  ||+..+.+++|+.+++..|+..++..
T Consensus       155 ~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~~  231 (311)
T 4fcw_A          155 TVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMSY  231 (311)
T ss_dssp             EEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTHH
T ss_pred             EEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence                35789999998                          4578899998  99999999999999999999988753

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.63  E-value=7.1e-15  Score=147.39  Aligned_cols=160  Identities=19%  Similarity=0.306  Sum_probs=118.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.++.++.+...+..           | ..+..+||+||||||||++++++|+.++.            
T Consensus         9 k~rp~~~~~~vg~~~~~~~L~~~l~~-----------~-~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~   76 (373)
T 1jr3_A            9 KWRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   76 (373)
T ss_dssp             HTCCCSTTTSCSCHHHHHHHHHHHHH-----------T-CCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSS
T ss_pred             hhCCCchhhccCcHHHHHHHHHHHHh-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCccc
Confidence            67899999999999998888776642           1 12457999999999999999999999854            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcC------CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTM------PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~------~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++...-.....++.++...      ..+.||+|||+|.+..                  ...+.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~------------------~~~~~  138 (373)
T 1jr3_A           77 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR------------------HSFNA  138 (373)
T ss_dssp             HHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCH------------------HHHHH
T ss_pred             HHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcH------------------HHHHH
Confidence                        34555544322223344444433      2468999999998732                  23456


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                      |+..++..    +..+++|++|+.+..+++++.+  |+ ..++++.|+.++...++..++...+..+
T Consensus       139 Ll~~le~~----~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~  198 (373)
T 1jr3_A          139 LLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAH  198 (373)
T ss_dssp             HHHHHHSC----CSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCB
T ss_pred             HHHHHhcC----CCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCC
Confidence            77777653    4568889999999999999998  76 6899999999999999998875443333

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.63  E-value=1.4e-15  Score=151.48  Aligned_cols=161  Identities=17%  Similarity=0.228  Sum_probs=117.1

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      ..|..    ..+|.+|++++|.+++++.+...+.    ..       .  ..++||+||||||||++++++|+.++    
T Consensus        25 ~~~~~----k~~p~~~~~i~g~~~~~~~l~~~l~----~~-------~--~~~~ll~G~~G~GKT~la~~la~~l~~~~~   87 (353)
T 1sxj_D           25 QPWVE----KYRPKNLDEVTAQDHAVTVLKKTLK----SA-------N--LPHMLFYGPPGTGKTSTILALTKELYGPDL   87 (353)
T ss_dssp             -CHHH----HTCCSSTTTCCSCCTTHHHHHHHTT----CT-------T--CCCEEEECSTTSSHHHHHHHHHHHHHHHHH
T ss_pred             ccHHH----hcCCCCHHHhhCCHHHHHHHHHHHh----cC-------C--CCEEEEECCCCCCHHHHHHHHHHHhCCCcc
Confidence            46765    6799999999999988877765542    11       1  23499999999999999999999964    


Q ss_pred             --CcEEEEecccccChHHHHH---HHHc---------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHH
Q 013128          269 --FDIYDLDLSAVQSNSELRF---LLLT---------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVT  328 (449)
Q Consensus       269 --~~~~~l~~s~~~~~~~l~~---~~~~---------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~  328 (449)
                        ..++.+++++......++.   .+..               ...+.||+|||+|.+..                  ..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~------------------~~  149 (353)
T 1sxj_D           88 MKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA------------------DA  149 (353)
T ss_dssp             HTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH------------------HH
T ss_pred             cccceEEEccccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCH------------------HH
Confidence              4688888877544332221   1111               23457999999998743                  12


Q ss_pred             HHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          329 LSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       329 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .+.|+..++..    .....+|++||+++.+++++.+  |+. .+.++.++.++...++...+...+
T Consensus       150 ~~~Ll~~le~~----~~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~~~  209 (353)
T 1sxj_D          150 QSALRRTMETY----SGVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALDASNAIDRLRFISEQEN  209 (353)
T ss_dssp             HHHHHHHHHHT----TTTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHhc----CCCceEEEEeCchhhCcchhhc--cCc-eEEeCCCCHHHHHHHHHHHHHHhC
Confidence            35566766643    2345677788999999999998  885 799999999999999988775443

>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=99.63  E-value=3.8e-15  Score=146.12  Aligned_cols=161  Identities=14%  Similarity=0.227  Sum_probs=118.5

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----  267 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----  267 (449)
                      ..|..    ...|.+|++++|.++.++.+.+.+..           +.  ...+||+||||||||++++++|+.+     
T Consensus         9 ~~~~~----~~~p~~~~~~~g~~~~~~~l~~~l~~-----------~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~   71 (323)
T 1sxj_B            9 LPWVE----KYRPQVLSDIVGNKETIDRLQQIAKD-----------GN--MPHMIISGMPGIGKTTSVHCLAHELLGRSY   71 (323)
T ss_dssp             CCHHH----HTCCSSGGGCCSCTHHHHHHHHHHHS-----------CC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGH
T ss_pred             CcHHH----hcCCCCHHHHHCCHHHHHHHHHHHHc-----------CC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcc
Confidence            35654    67899999999999988877766531           11  1239999999999999999999997     


Q ss_pred             CCcEEEEecccccChHHHHHHHHc---------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC
Q 013128          268 KFDIYDLDLSAVQSNSELRFLLLT---------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG  338 (449)
Q Consensus       268 ~~~~~~l~~s~~~~~~~l~~~~~~---------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  338 (449)
                      +.+++.+++++......++..+..         ...+.||+|||+|.+..                  ...+.|+..++.
T Consensus        72 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~------------------~~~~~L~~~le~  133 (323)
T 1sxj_B           72 ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA------------------GAQQALRRTMEL  133 (323)
T ss_dssp             HHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH------------------HHHHTTHHHHHH
T ss_pred             cCCEEEecCccccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH------------------HHHHHHHHHHhc
Confidence            456888887765444444433321         22478999999998743                  123345666653


Q ss_pred             ccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          339 LWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       339 ~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .    ....++|++||.++.+++++.+  |+. .++++.|+.++...++...+...+
T Consensus       134 ~----~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~  183 (323)
T 1sxj_B          134 Y----SNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLED  183 (323)
T ss_dssp             T----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHT
T ss_pred             c----CCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHHHHHHcC
Confidence            2    3457888899999999999998  764 799999999999999988765433

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=99.62  E-value=2.7e-15  Score=148.40  Aligned_cols=187  Identities=15%  Similarity=0.233  Sum_probs=118.2

Q ss_pred             cCCCCCccccc-CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          202 LKHPMTFKTLA-LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       202 ~~~p~~f~~l~-g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      +.+..+|++++ |.... . ....+......+.       ...++++||||||||||++++++++.+   +.+++.+++.
T Consensus         4 l~~~~~f~~fv~g~~~~-~-a~~~~~~~~~~~~-------~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~   74 (324)
T 1l8q_A            4 LNPKYTLENFIVGEGNR-L-AYEVVKEALENLG-------SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   74 (324)
T ss_dssp             CCTTCCSSSCCCCTTTH-H-HHHHHHHHHHTTT-------TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCCCCcccCCCCCcHH-H-HHHHHHHHHhCcC-------CCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHH
Confidence            44566899997 43322 2 2233444443321       124689999999999999999999999   8999999987


Q ss_pred             cccCh--H-----HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEE
Q 013128          278 AVQSN--S-----ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIV  350 (449)
Q Consensus       278 ~~~~~--~-----~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  350 (449)
                      .+...  .     ...........+.||+|||+|.+...+                .....++..++....  .+.++|+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~~~----------------~~~~~l~~~l~~~~~--~~~~iii  136 (324)
T 1l8q_A           75 DFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKE----------------RTQIEFFHIFNTLYL--LEKQIIL  136 (324)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTCH----------------HHHHHHHHHHHHHHH--TTCEEEE
T ss_pred             HHHHHHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccCCh----------------HHHHHHHHHHHHHHH--CCCeEEE
Confidence            65321  0     011112222358999999999975310                112234444433222  2345666


Q ss_pred             EEcCCCC---CCCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHH-HHHHHccCCCHHHHHHH
Q 013128          351 FTTNHKE---KLDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQI-EELIKEVNVTPAEVAGE  419 (449)
Q Consensus       351 ~tTN~~~---~ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i-~~l~~~~~~tpa~i~~~  419 (449)
                      ++++.+.   .++++|.+  ||.  ..+++++ +.+++..+++.++...+..+.++. +.++... -+..++...
T Consensus       137 ~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~  207 (324)
T 1l8q_A          137 ASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGK  207 (324)
T ss_dssp             EESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHH
T ss_pred             EecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHH
Confidence            6766665   68999998  886  7899999 999999999998875555554443 3334444 444444333

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.62  E-value=3.8e-15  Score=149.59  Aligned_cols=160  Identities=18%  Similarity=0.171  Sum_probs=115.1

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEecc
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLS  277 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s  277 (449)
                      .+++++|.++..+.+.+.+...+..         ..+++++|+||||||||++++++++.+         +..++.+++.
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~   87 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALRG---------EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNAR   87 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTSS---------CCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECC
Confidence            4588999999888887766544322         225789999999999999999999999         8888999987


Q ss_pred             cccCh----------------------HH-HHH---HHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          278 AVQSN----------------------SE-LRF---LLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       278 ~~~~~----------------------~~-l~~---~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                      ...+.                      .. +..   .+.....++||+|||+|.+....             .....+..
T Consensus        88 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~-------------~~~~~l~~  154 (387)
T 2v1u_A           88 HRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRP-------------GGQDLLYR  154 (387)
T ss_dssp             TSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHST-------------THHHHHHH
T ss_pred             cCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccC-------------CCChHHHh
Confidence            64321                      11 111   22223458899999999985310             02345556


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCC---CCCCccccCCCccce-EEEeCCCCHHHHHHHHHHHhC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMDM-HLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d~-~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      +++.++....  +..+++|++||.+   +.+++++.+  ||.. .++|++++.++...++...+.
T Consensus       155 l~~~~~~~~~--~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~  215 (387)
T 2v1u_A          155 ITRINQELGD--RVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAE  215 (387)
T ss_dssp             HHHGGGCC-------CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHH
T ss_pred             HhhchhhcCC--CceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHH
Confidence            6666554310  3467899999987   788999998  8875 899999999999999998875

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=99.61  E-value=4e-15  Score=150.39  Aligned_cols=174  Identities=17%  Similarity=0.224  Sum_probs=112.4

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHh-----------------hhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYT-----------------RIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~-----------------~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .++|.++.|+.+...+.........-.                 .-....+.++||+||||||||++|+++|+.++.+++
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~~  101 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIA  101 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            479999999999887754433221100                 011223568999999999999999999999999999


Q ss_pred             EEecccccC--------hHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC
Q 013128          273 DLDLSAVQS--------NSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG  338 (449)
Q Consensus       273 ~l~~s~~~~--------~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  338 (449)
                      .++++.+..        ...+..++....      .++||||||||.+...+......    .........+.|+..||+
T Consensus       102 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~----~~~~~~~~~~~Ll~~le~  177 (376)
T 1um8_A          102 ISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSIT----RDVSGEGVQQALLKIVEG  177 (376)
T ss_dssp             EEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC------------------CHHHHHHHHHHHHC
T ss_pred             EecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCcee----cccchHHHHHHHHHHhhc
Confidence            999887642        223444444332      67999999999987532111100    011122367788888886


Q ss_pred             ccc-----------------cCCCCeEEEEEcCCC-----------------------------------------CCCC
Q 013128          339 LWS-----------------CCGEGRIIVFTTNHK-----------------------------------------EKLD  360 (449)
Q Consensus       339 ~~~-----------------~~~~~~iiI~tTN~~-----------------------------------------~~ld  360 (449)
                      ..-                 -...++++|+|||..                                         ..+.
T Consensus       178 ~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  257 (376)
T 1um8_A          178 SLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLI  257 (376)
T ss_dssp             CEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCC
T ss_pred             cceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCC
Confidence            420                 001345777877720                                         1245


Q ss_pred             ccccCCCccceEEEeCCCCHHHHHHHHHH
Q 013128          361 PALLRPGRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       361 ~aLlrpgR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                      |+|+.  |++..+.|+.++.++...++..
T Consensus       258 p~l~~--R~~~~i~~~~l~~~~l~~i~~~  284 (376)
T 1um8_A          258 PELIG--RLPVLSTLDSISLEAMVDILQK  284 (376)
T ss_dssp             HHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             hHHhc--CCCceeeccCCCHHHHHHHHhh
Confidence            66766  8989999999999999988874

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.60  E-value=4.7e-14  Score=140.44  Aligned_cols=191  Identities=18%  Similarity=0.206  Sum_probs=131.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      ...|.+|+.++|.+.+++.+...+..-..       .| ..+..++|+||||||||+|++++|+.++.++...+......
T Consensus        18 ~lr~~~l~~~~g~~~~~~~l~~~i~~~~~-------~~-~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~   89 (334)
T 1in4_A           18 FLRPKSLDEFIGQENVKKKLSLALEAAKM-------RG-EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVK   89 (334)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHH-------HT-CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCS
T ss_pred             HcCCccHHHccCcHHHHHHHHHHHHHHHh-------cC-CCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcC
Confidence            56788999999998777766555433211       11 12367999999999999999999999999888777666655


Q ss_pred             hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc------cc--------CCCCe
Q 013128          282 NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW------SC--------CGEGR  347 (449)
Q Consensus       282 ~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~------~~--------~~~~~  347 (449)
                      ...+...+.....+.|++|||++.+...                  ....|+..++...      ..        .-..+
T Consensus        90 ~~~l~~~~~~~~~~~v~~iDE~~~l~~~------------------~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~  151 (334)
T 1in4_A           90 QGDMAAILTSLERGDVLFIDEIHRLNKA------------------VEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPF  151 (334)
T ss_dssp             HHHHHHHHHHCCTTCEEEEETGGGCCHH------------------HHHHHHHHHHTSCCCC---------------CCC
T ss_pred             HHHHHHHHHHccCCCEEEEcchhhcCHH------------------HHHHHHHHHHhcccceeeccCcccccccccCCCe
Confidence            6666666666667889999999987530                  1111233332110      00        01235


Q ss_pred             EEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCH-HHHHHHHHccCCCHHHHHHHH
Q 013128          348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLF-EQIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       348 iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~~tpa~i~~~l  420 (449)
                      .++.+|+++..|++++++  ||...+.+++++.+++.+++++.....+..+. +.+..++....=+|..+...|
T Consensus       152 ~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll  223 (334)
T 1in4_A          152 TLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  223 (334)
T ss_dssp             EEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            677899999999999999  99989999999999999999987654433343 334445555555565544433

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.59  E-value=1.3e-15  Score=136.77  Aligned_cols=147  Identities=19%  Similarity=0.218  Sum_probs=101.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ...|.+|++++|.++..+.+.+.+..             ..++++||+||||||||++++++|+.+          +.++
T Consensus        15 ~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~   81 (187)
T 2p65_A           15 LARAGKLDPVIGRDTEIRRAIQILSR-------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKL   81 (187)
T ss_dssp             HHHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEE
T ss_pred             HHhccccchhhcchHHHHHHHHHHhC-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeE
Confidence            34577899999999887777665421             225689999999999999999999998          7888


Q ss_pred             EEEecccccC--------hHHHHHH---HHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc
Q 013128          272 YDLDLSAVQS--------NSELRFL---LLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW  340 (449)
Q Consensus       272 ~~l~~s~~~~--------~~~l~~~---~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  340 (449)
                      +.+++..+..        ...+..+   +.....+.||+|||+|.+.+.+...         .........|+..++.  
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~---------~~~~~~~~~l~~~~~~--  150 (187)
T 2p65_A           82 VSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVA---------EGALDAGNILKPMLAR--  150 (187)
T ss_dssp             EEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSC---------TTSCCTHHHHHHHHHT--
T ss_pred             EEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhccccccc---------ccchHHHHHHHHHHhc--
Confidence            8888765421        1122222   3334568899999999986422100         0011223334444432  


Q ss_pred             ccCCCCeEEEEEcCCCC-----CCCccccCCCccceEEEeCCCC
Q 013128          341 SCCGEGRIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCN  379 (449)
Q Consensus       341 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~  379 (449)
                          ..+++|++||.++     .+|+++.+  ||+. ++++.|+
T Consensus       151 ----~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          151 ----GELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             ----TCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             ----CCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence                4567888888765     68999999  9985 9999885

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2.1e-14  Score=141.58  Aligned_cols=200  Identities=12%  Similarity=0.141  Sum_probs=131.3

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEeccccc
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDLSAVQ  280 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~s~~~  280 (449)
                      |.+.++..+.|...+...+...         .+.++|||||||||||++++++++++          ++.++.++|..+.
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~---------~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~   92 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSS---------QNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELA   92 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTT---------CCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC
T ss_pred             cCCHHHHHHHHHHHHHHHhcCC---------CCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccC
Confidence            4455566667776666666533         26789999999999999999999999          4567888887653


Q ss_pred             Ch----------------------HHHHHHHHcC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHH
Q 013128          281 SN----------------------SELRFLLLTM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN  334 (449)
Q Consensus       281 ~~----------------------~~l~~~~~~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~  334 (449)
                      +.                      ..+...|...    ..++||+|||+|.+..                 +..+-.|++
T Consensus        93 t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~-----------------q~~L~~l~~  155 (318)
T 3te6_A           93 GMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLS-----------------EKILQYFEK  155 (318)
T ss_dssp             --HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCC-----------------THHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhc-----------------chHHHHHHh
Confidence            32                      2345555543    4678999999999851                 123444554


Q ss_pred             HhcCccccCCCCeEEEEEcCCCCC----CCccccCCCccc-eEEEeCCCCHHHHHHHHHHHhCcCCCC------------
Q 013128          335 FIDGLWSCCGEGRIIVFTTNHKEK----LDPALLRPGRMD-MHLHMSYCNTSVFKQLAFNYLGISHHY------------  397 (449)
Q Consensus       335 ~ldg~~~~~~~~~iiI~tTN~~~~----ld~aLlrpgR~d-~~i~l~~p~~~~r~~l~~~~l~~~~~~------------  397 (449)
                      ...    .....++||+++|..+.    |++++.+  ||. ..|+|++++.++...|+++-+......            
T Consensus       156 ~~~----~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~  229 (318)
T 3te6_A          156 WIS----SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMT  229 (318)
T ss_dssp             HHH----CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEE
T ss_pred             ccc----ccCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHhhhcccccccccccccc
Confidence            332    12356889999999865    3555666  886 589999999999999999877542111            


Q ss_pred             ----CHH-HHHHHHH-----ccCCCHHHHHHHHhc-----CCCHHHHHHHHHHHHHHHHHh
Q 013128          398 ----LFE-QIEELIK-----EVNVTPAEVAGELMK-----STNAEVSLNGLVKFLHAKMTQ  443 (449)
Q Consensus       398 ----l~~-~i~~l~~-----~~~~tpa~i~~~l~~-----~~~~~~al~~l~~~l~~~~~~  443 (449)
                          +.+ .-+..-.     ...+++.-| +++.+     ++|...||+-+..+++....+
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~i~~~ai-~~~A~~vA~~~GD~R~Al~ilr~A~~~ae~e  289 (318)
T 3te6_A          230 IYNNIREGQNQKIPDNVIVINHKINNKIT-QLIAKNVANVSGSTEKAFKICEAAVEISKKD  289 (318)
T ss_dssp             ECCCC--------CTTEEEECEECCHHHH-HHHHHHHHHHHCSHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccCHHHH-HHHHHHHHhhCChHHHHHHHHHHHHHHHHHH
Confidence                000 0000000     012555444 44443     589999999999888876554

>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=99.58  E-value=1.5e-14  Score=145.54  Aligned_cols=151  Identities=17%  Similarity=0.257  Sum_probs=111.9

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----------CCcEEEEecc
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----------KFDIYDLDLS  277 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----------~~~~~~l~~s  277 (449)
                      ++++|.++..+.+.+.+..+....         .+++++|+||||||||++++++++++           +..++.+++.
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~---------~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~   90 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNE---------VKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCR   90 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTC---------CCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCC---------CCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECc
Confidence            789999999999998887766532         25689999999999999999999998           8999999876


Q ss_pred             ccc-Ch-----------------------HH-HHHHHHcCC-CCceEEeeccchhhhcccccchhhhhccchhhHHH-HH
Q 013128          278 AVQ-SN-----------------------SE-LRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVT-LS  330 (449)
Q Consensus       278 ~~~-~~-----------------------~~-l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~-ls  330 (449)
                      ... +.                       .. +..+..... .+.||+|||+|.+....              .... +.
T Consensus        91 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~--------------~~~~~l~  156 (384)
T 2qby_B           91 EVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRR--------------GGDIVLY  156 (384)
T ss_dssp             HHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHST--------------TSHHHHH
T ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCC--------------CCceeHH
Confidence            544 21                       11 112222112 23399999999985411              0112 33


Q ss_pred             HHHHHhcCccccCCCCeEEEEEcCCC---CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          331 GLLNFIDGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       331 ~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      .|+...        ..+.+|+|||.+   +.+++++.+  ||...++|++++.++..+++..++.
T Consensus       157 ~l~~~~--------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          157 QLLRSD--------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAE  211 (384)
T ss_dssp             HHHTSS--------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHH
T ss_pred             HHhcCC--------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHH
Confidence            344322        457889999987   788999988  8877999999999999999998874

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.57  E-value=2.1e-14  Score=143.34  Aligned_cols=186  Identities=14%  Similarity=0.170  Sum_probs=119.7

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-CC---
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-KF---  269 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-~~---  269 (449)
                      .|..    ..+|.+|++++|.++.++.+...+.   ..       |. .+. ++|+||||||||++++++|+++ +.   
T Consensus         3 ~w~~----kyrP~~~~~~vg~~~~~~~l~~~~~---~~-------~~-~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g   66 (354)
T 1sxj_E            3 LWVD----KYRPKSLNALSHNEELTNFLKSLSD---QP-------RD-LPH-LLLYGPNGTGKKTRCMALLESIFGPGVY   66 (354)
T ss_dssp             -CTT----TTCCCSGGGCCSCHHHHHHHHTTTT---CT-------TC-CCC-EEEECSTTSSHHHHHHTHHHHHSCTTCC
T ss_pred             cchh----ccCCCCHHHhcCCHHHHHHHHHHHh---hC-------CC-CCe-EEEECCCCCCHHHHHHHHHHHHcCCCCC
Confidence            4755    7899999999999887766654330   11       11 133 9999999999999999999964 21   


Q ss_pred             -------------------------cEEEEecccccChH--HHHHHHHc----------------CCCCceEEeeccchh
Q 013128          270 -------------------------DIYDLDLSAVQSNS--ELRFLLLT----------------MPSRSMLVIEDIDCS  306 (449)
Q Consensus       270 -------------------------~~~~l~~s~~~~~~--~l~~~~~~----------------~~~~~Il~iDeiD~l  306 (449)
                                               +++.++.+......  .++..+..                ..++.||+|||++.+
T Consensus        67 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L  146 (354)
T 1sxj_E           67 RLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSL  146 (354)
T ss_dssp             C------------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSS
T ss_pred             eEEecceeecccccccceeeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCcccc
Confidence                                     23344433322111  23332221                225679999999985


Q ss_pred             hhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHH
Q 013128          307 VKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQL  386 (449)
Q Consensus       307 ~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l  386 (449)
                      -.                  ...+.|+..++..    ..+..+|++||.++.+.+++.+  |+ ..+.|+.|+.++...+
T Consensus       147 ~~------------------~~~~~L~~~le~~----~~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~  201 (354)
T 1sxj_E          147 TK------------------DAQAALRRTMEKY----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTI  201 (354)
T ss_dssp             CH------------------HHHHHHHHHHHHS----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHH
T ss_pred             CH------------------HHHHHHHHHHHhh----cCCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHH
Confidence            21                  1234466666543    2457888999999999999998  87 7899999999999999


Q ss_pred             HHHHhCcCCCCCH--HHHHHHHHccCCCHHHHHHHH
Q 013128          387 AFNYLGISHHYLF--EQIEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       387 ~~~~l~~~~~~l~--~~i~~l~~~~~~tpa~i~~~l  420 (449)
                      +...+..++..+.  +.++.+++..+=++.++...|
T Consensus       202 l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          202 LSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             HHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            9988765443333  234444444444444444443

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=99.57  E-value=1.9e-14  Score=148.68  Aligned_cols=188  Identities=16%  Similarity=0.252  Sum_probs=116.2

Q ss_pred             cCCCCCccccc-CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEe
Q 013128          202 LKHPMTFKTLA-LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLD  275 (449)
Q Consensus       202 ~~~p~~f~~l~-g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~  275 (449)
                      +.+..+|++++ |.....  ....+..+...+      +.  .++++||||||||||+|++++|+++     +..++.++
T Consensus        98 l~~~~tfd~fv~g~~n~~--a~~~~~~~a~~~------~~--~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~  167 (440)
T 2z4s_A           98 LNPDYTFENFVVGPGNSF--AYHAALEVAKHP------GR--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT  167 (440)
T ss_dssp             CCTTCSGGGCCCCTTTHH--HHHHHHHHHHST------TS--SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEE
T ss_pred             CCCCCChhhcCCCCchHH--HHHHHHHHHhCC------CC--CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee
Confidence            44456899987 544332  233344444332      11  5689999999999999999999999     88899998


Q ss_pred             cccccCh-------HHHHHHHHcCC-CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCe
Q 013128          276 LSAVQSN-------SELRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGR  347 (449)
Q Consensus       276 ~s~~~~~-------~~l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  347 (449)
                      +..+...       .....+..... ++.||+|||+|.+.+..                .+...|+..++.+..  .+..
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~~----------------~~q~~l~~~l~~l~~--~~~~  229 (440)
T 2z4s_A          168 SEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKT----------------GVQTELFHTFNELHD--SGKQ  229 (440)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSCH----------------HHHHHHHHHHHHHHT--TTCE
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCCh----------------HHHHHHHHHHHHHHH--CCCe
Confidence            8765321       00111222234 78999999999885310                112234444443322  1234


Q ss_pred             EEEEEcCCCCC---CCccccCCCccc--eEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHHHHH
Q 013128          348 IIVFTTNHKEK---LDPALLRPGRMD--MHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEVAGE  419 (449)
Q Consensus       348 iiI~tTN~~~~---ld~aLlrpgR~d--~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i~~~  419 (449)
                      +||.|.+.+..   ++++|++  ||.  ..+.++.|+.+++..+++..+...+..+.++ ++.++....-++.++...
T Consensus       230 iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          230 IVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             EEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHHH
T ss_pred             EEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHH
Confidence            55545454544   8899999  886  7899999999999999998875433333322 333333334444444433

>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=99.56  E-value=5e-14  Score=141.12  Aligned_cols=159  Identities=19%  Similarity=0.229  Sum_probs=114.4

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc------CCcEEEEecccc
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL------KFDIYDLDLSAV  279 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l------~~~~~~l~~s~~  279 (449)
                      ..+++++|.++..+.+.+.+...+..         ..++.++|+||||||||++++++++.+      +..++.+++...
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~~~---------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~   87 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLYRE---------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQI   87 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGGGT---------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCC
Confidence            34588999998888887766443322         225689999999999999999999999      888999886543


Q ss_pred             cC----------------------hHH----HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHH
Q 013128          280 QS----------------------NSE----LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLL  333 (449)
Q Consensus       280 ~~----------------------~~~----l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL  333 (449)
                      .+                      ...    +...+.....+.||+|||+|.+....              ....+..|+
T Consensus        88 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~--------------~~~~l~~l~  153 (386)
T 2qby_A           88 DTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKY--------------NDDILYKLS  153 (386)
T ss_dssp             CSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSS--------------CSTHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccC--------------cCHHHHHHh
Confidence            21                      111    22233344458999999999986411              123466677


Q ss_pred             HHhcCccccCCCCeEEEEEcCCC---CCCCccccCCCccc-eEEEeCCCCHHHHHHHHHHHhC
Q 013128          334 NFIDGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMD-MHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       334 ~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d-~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      ..++..   .+..+.+|++||.+   +.+++++.+  |+. ..+++++++.++..+++...+.
T Consensus       154 ~~~~~~---~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~  211 (386)
T 2qby_A          154 RINSEV---NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQ  211 (386)
T ss_dssp             HHHHSC---CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHH
T ss_pred             hchhhc---CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHH
Confidence            777654   13467888899877   567888887  664 4899999999999999998764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.56  E-value=2.1e-14  Score=158.03  Aligned_cols=159  Identities=14%  Similarity=0.220  Sum_probs=114.4

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh---
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN---  282 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~---  282 (449)
                      +.++|.++.++.+.+.+........   . ...+..++||+||||||||++|+++|+.+   +.+++.++|+.+...   
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~---~-~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLK---D-PKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHST  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCS---C-TTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccC---C-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccccccc
Confidence            4688999998888887765442110   0 00111269999999999999999999998   688999999988642   


Q ss_pred             --HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc-------CCCCeEEEEEc
Q 013128          283 --SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC-------CGEGRIIVFTT  353 (449)
Q Consensus       283 --~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-------~~~~~iiI~tT  353 (449)
                        ..+...+. ...++||||||||.+..                  ..++.|++.||.-.-.       ....++||+||
T Consensus       567 ~~~~l~~~~~-~~~~~vl~lDEi~~~~~------------------~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~tt  627 (758)
T 3pxi_A          567 SGGQLTEKVR-RKPYSVVLLDAIEKAHP------------------DVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTS  627 (758)
T ss_dssp             C---CHHHHH-HCSSSEEEEECGGGSCH------------------HHHHHHHHHHHHSBCC-----CCBCTTCEEEEEE
T ss_pred             ccchhhHHHH-hCCCeEEEEeCccccCH------------------HHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeC
Confidence              22333332 24578999999998732                  3566788888742111       12356899999


Q ss_pred             CCCCC------------CCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          354 NHKEK------------LDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       354 N~~~~------------ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      |.+..            +.|+|+.  ||+..|.|++|+.+++..|+..++.
T Consensus       628 n~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~  676 (758)
T 3pxi_A          628 NVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSD  676 (758)
T ss_dssp             SSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHH
T ss_pred             CCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHH
Confidence            97654            7888888  9999999999999999999998875

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.56  E-value=4.3e-14  Score=147.15  Aligned_cols=148  Identities=18%  Similarity=0.181  Sum_probs=106.1

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ..+|.+|+.++|.++..+.+++.+..             ..+.++||+||||||||++|+++|+.+          +.++
T Consensus       173 ~~r~~~ld~iiGr~~~i~~l~~~l~r-------------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~  239 (468)
T 3pxg_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRV  239 (468)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCE
T ss_pred             HHhcCCCCCccCcHHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeE
Confidence            45778899999999998888776542             125689999999999999999999997          7889


Q ss_pred             EEEeccccc-C--hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC
Q 013128          272 YDLDLSAVQ-S--NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG  346 (449)
Q Consensus       272 ~~l~~s~~~-~--~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  346 (449)
                      +.++++.-. .  ...+..++..  ...++|||||     ..   .              ...+.|+..|+      .+.
T Consensus       240 ~~l~~~~~~~g~~e~~~~~~~~~~~~~~~~iLfiD-----~~---~--------------~a~~~L~~~L~------~g~  291 (468)
T 3pxg_A          240 MTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID-----AA---I--------------DASNILKPSLA------RGE  291 (468)
T ss_dssp             ECC----------CTTHHHHHHHHHTCCCCEEEEC-----C-------------------------CCCTT------SSS
T ss_pred             EEeeCCccccchHHHHHHHHHHHHHhcCCeEEEEe-----Cc---h--------------hHHHHHHHhhc------CCC
Confidence            988886211 1  1234444433  2468999999     10   0              01223444443      246


Q ss_pred             eEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          347 RIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       347 ~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +.+|++||..+     .+|++|.+  ||.. |.++.|+.+++..|++.++..
T Consensus       292 v~vI~at~~~e~~~~~~~~~al~~--Rf~~-i~v~~p~~e~~~~iL~~~~~~  340 (468)
T 3pxg_A          292 LQCIGATTLDEYRKYIEKDAALER--RFQP-IQVDQPSVDESIQILQGLRDR  340 (468)
T ss_dssp             CEEEEECCTTTTHHHHTTCSHHHH--SEEE-EECCCCCHHHHHHHHHHTTTT
T ss_pred             EEEEecCCHHHHHHHhhcCHHHHH--hCcc-ceeCCCCHHHHHHHHHHHHHH
Confidence            88999999987     69999999  9975 999999999999999988875

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.55  E-value=2e-14  Score=143.03  Aligned_cols=155  Identities=19%  Similarity=0.221  Sum_probs=101.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      ..+|.+|++++|.++.++.+...+   . .+         ...++||+||||||||++|+++|+.++.            
T Consensus        17 ~~~~~~f~~i~G~~~~~~~l~~~~---~-~~---------~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~   83 (350)
T 1g8p_A           17 TRPVFPFSAIVGQEDMKLALLLTA---V-DP---------GIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSP   83 (350)
T ss_dssp             -CCCCCGGGSCSCHHHHHHHHHHH---H-CG---------GGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCS
T ss_pred             CCCCCCchhccChHHHHHHHHHHh---h-CC---------CCceEEEECCCCccHHHHHHHHHHhCcccccccccccccc
Confidence            456788999999998776543221   1 11         1357999999999999999999999863            


Q ss_pred             ---------------------cEEEEecccccChHHH------HHHHHcC-----------CCCceEEeeccchhhhccc
Q 013128          270 ---------------------DIYDLDLSAVQSNSEL------RFLLLTM-----------PSRSMLVIEDIDCSVKLQN  311 (449)
Q Consensus       270 ---------------------~~~~l~~s~~~~~~~l------~~~~~~~-----------~~~~Il~iDeiD~l~~~~~  311 (449)
                                           +++.+..+.  +...+      ...+...           ..++||||||||.+..   
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~---  158 (350)
T 1g8p_A           84 NVEMIPDWATVLSTNVIRKPTPVVDLPLGV--SEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLED---  158 (350)
T ss_dssp             SGGGSCTTCCCSCCCEEEECCCEEEECTTC--CHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCH---
T ss_pred             ccccccchhhhhccccccCCCcccccCCCc--chhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCCH---
Confidence                                 122221111  11111      1111111           1378999999998743   


Q ss_pred             ccchhhhhccchhhHHHHHHHHHHhcCc---ccc------CCCCeEEEEEcCCCC-CCCccccCCCccceEEEeCCC-CH
Q 013128          312 RESSEVQATNQEENKVTLSGLLNFIDGL---WSC------CGEGRIIVFTTNHKE-KLDPALLRPGRMDMHLHMSYC-NT  380 (449)
Q Consensus       312 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~---~~~------~~~~~iiI~tTN~~~-~ld~aLlrpgR~d~~i~l~~p-~~  380 (449)
                                     .....|+..++.-   ...      .+..+++|+|||..+ .++++|++  ||+.++++++| +.
T Consensus       159 ---------------~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~  221 (350)
T 1g8p_A          159 ---------------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDV  221 (350)
T ss_dssp             ---------------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSH
T ss_pred             ---------------HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcH
Confidence                           2344566666531   111      112578889999755 89999999  99999999999 67


Q ss_pred             HHHHHHHHHHh
Q 013128          381 SVFKQLAFNYL  391 (449)
Q Consensus       381 ~~r~~l~~~~l  391 (449)
                      +.+..|+...+
T Consensus       222 ~~~~~il~~~~  232 (350)
T 1g8p_A          222 ETRVEVIRRRD  232 (350)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77778887643

>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=99.55  E-value=1.4e-13  Score=138.35  Aligned_cols=160  Identities=15%  Similarity=0.087  Sum_probs=116.6

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEecccccCh
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAVQSN  282 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~~~~  282 (449)
                      .+++++|.++..+.+.+.+........       +..+.++|+||||||||++++++++.+    +..++.+++....+.
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~-------~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~   87 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNF   87 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCC-------CCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCH
Confidence            348899999999999988877665421       112379999999999999999999999    678888987665432


Q ss_pred             HH--------------------------HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHh
Q 013128          283 SE--------------------------LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFI  336 (449)
Q Consensus       283 ~~--------------------------l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~l  336 (449)
                      ..                          +...+.....+.||+|||+|.+.                  ...+..|+..+
T Consensus        88 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~------------------~~~~~~L~~~~  149 (389)
T 1fnn_A           88 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLA------------------PDILSTFIRLG  149 (389)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSC------------------HHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccc------------------hHHHHHHHHHH
Confidence            11                          11222334568899999999872                  12455566766


Q ss_pred             cCccccCCCCeEEEEEcCCC---CCCCccccCCCccce-EEEeCCCCHHHHHHHHHHHhCc
Q 013128          337 DGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMDM-HLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       337 dg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d~-~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +.........+.+|++||.+   +.+++.+.+  |+.. .+++++++.++...++...+..
T Consensus       150 ~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~  208 (389)
T 1fnn_A          150 QEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  208 (389)
T ss_dssp             TCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             HhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHh
Confidence            54321101367888999988   778888888  8875 8999999999999999887653

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.54  E-value=6.2e-14  Score=156.21  Aligned_cols=159  Identities=18%  Similarity=0.197  Sum_probs=105.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ..+|.+|++++|.++..+.+.+.+..             ..++++||+||||||||++++++|+.+          +..+
T Consensus       163 ~~r~~~ld~viGr~~~i~~l~~~l~~-------------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~  229 (854)
T 1qvr_A          163 LAAEGKLDPVIGRDEEIRRVIQILLR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRI  229 (854)
T ss_dssp             HHHTTCSCCCCSCHHHHHHHHHHHHC-------------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEE
T ss_pred             HHhcCCCcccCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeE
Confidence            34577899999999888877765521             125689999999999999999999998          8899


Q ss_pred             EEEecccccCh--------HHHHHHHHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc
Q 013128          272 YDLDLSAVQSN--------SELRFLLLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW  340 (449)
Q Consensus       272 ~~l~~s~~~~~--------~~l~~~~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  340 (449)
                      +.++++.+...        ..+..++..   ...++||||||+|.+.+.....+          .....+.|...++.  
T Consensus       230 ~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g----------~~~~~~~L~~~l~~--  297 (854)
T 1qvr_A          230 VSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEG----------AVDAGNMLKPALAR--  297 (854)
T ss_dssp             EEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC-----------------------------HHHHHT--
T ss_pred             EEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccc----------hHHHHHHHHHHHhC--
Confidence            99998877421        234444443   24689999999999875322211          11122334444432  


Q ss_pred             ccCCCCeEEEEEcCCCC----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          341 SCCGEGRIIVFTTNHKE----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       341 ~~~~~~~iiI~tTN~~~----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                          .++.+|++||.++    .+|++|.+  ||+. |.++.|+.+++.++++.++.
T Consensus       298 ----~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~  346 (854)
T 1qvr_A          298 ----GELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKE  346 (854)
T ss_dssp             ----TCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHH
T ss_pred             ----CCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhh
Confidence                3567888888764    47999999  9986 99999999999999987664

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.54  E-value=4.3e-14  Score=135.66  Aligned_cols=156  Identities=15%  Similarity=0.090  Sum_probs=102.5

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEecccccCh
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQSN  282 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~~~  282 (449)
                      .+|++++|.....+.+.+.+......           +.++||+||||||||++|+++++.+.   .+++.++|+.+...
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~~-----------~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~   71 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAPL-----------DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN   71 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTTS-----------CSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHH
T ss_pred             cccccceeCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChh
Confidence            47999999999988888877665432           46899999999999999999999985   68999999887432


Q ss_pred             HHHHHHHH-----------------cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-c---
Q 013128          283 SELRFLLL-----------------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-S---  341 (449)
Q Consensus       283 ~~l~~~~~-----------------~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~---  341 (449)
                      .-...++.                 ....+++|||||||.+..                  .....|+..++... .   
T Consensus        72 ~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~------------------~~q~~Ll~~l~~~~~~~~g  133 (265)
T 2bjv_A           72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM------------------MVQEKLLRVIEYGELERVG  133 (265)
T ss_dssp             HHHHHHHCCC---------CCCCHHHHTTTSEEEEESGGGSCH------------------HHHHHHHHHHHHCEECCCC
T ss_pred             HHHHHhcCCcccccccccccccchhhhcCCcEEEEechHhcCH------------------HHHHHHHHHHHhCCeecCC
Confidence            11111111                 012468999999998743                  12344666665211 0   


Q ss_pred             ---cCCCCeEEEEEcCCC-------CCCCccccCCCccc-eEEEeCCCCH--HHHHHHHHHHhC
Q 013128          342 ---CCGEGRIIVFTTNHK-------EKLDPALLRPGRMD-MHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       342 ---~~~~~~iiI~tTN~~-------~~ld~aLlrpgR~d-~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                         .....+.+|+|||..       ..++++|..  ||. ..|.+|....  ++...++..++.
T Consensus       134 ~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l~  195 (265)
T 2bjv_A          134 GSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAFDVVQLPPLRERESDIMLMAEYFAI  195 (265)
T ss_dssp             C--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCSEEEECCCGGGCHHHHHHHHHHHHH
T ss_pred             CcccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcCcEEeCCChhhhhHHHHHHHHHHHH
Confidence               011346788899874       357888988  885 5778887765  667777776654

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.54  E-value=6.9e-14  Score=153.89  Aligned_cols=159  Identities=18%  Similarity=0.248  Sum_probs=114.8

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh------
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN------  282 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~------  282 (449)
                      +.++|.++.++.+...+.....+-.   .. ..+..++||+||||||||++|+++|+.++.+++.++++.+...      
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~---~~-~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~~~l  533 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLG---HE-HKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRL  533 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCS---CT-TSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSS
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccC---CC-CCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhHhhh
Confidence            3477888888877776654322100   00 0122369999999999999999999999999999999887431      


Q ss_pred             -------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc--C----
Q 013128          283 -------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC--C----  343 (449)
Q Consensus       283 -------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--~----  343 (449)
                                   ..+...+.. ..++||||||||.+.+                  .+++.|++.||.-.-.  .    
T Consensus       534 ~g~~~g~~g~~~~~~l~~~~~~-~~~~vl~lDEi~~~~~------------------~~~~~Ll~~le~~~~~~~~g~~~  594 (758)
T 1r6b_X          534 IGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAHP------------------DVFNILLQVMDNGTLTDNNGRKA  594 (758)
T ss_dssp             CCCCSCSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSCH------------------HHHHHHHHHHHHSEEEETTTEEE
T ss_pred             cCCCCCCcCccccchHHHHHHh-CCCcEEEEeCccccCH------------------HHHHHHHHHhcCcEEEcCCCCEE
Confidence                         122333333 4579999999998642                  3667788888732111  0    


Q ss_pred             -CCCeEEEEEcCCCC-------------------------CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          344 -GEGRIIVFTTNHKE-------------------------KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       344 -~~~~iiI~tTN~~~-------------------------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                       -.+++||+|||...                         .++|+|++  ||+..|.|++++.+++..|+..++.
T Consensus       595 ~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~  667 (758)
T 1r6b_X          595 DFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_dssp             ECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             ecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHH
Confidence             13578999999854                         57888988  9999999999999999999998875

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.51  E-value=1.7e-13  Score=136.52  Aligned_cols=161  Identities=20%  Similarity=0.322  Sum_probs=115.1

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      ..|..    ..+|.+|++++|.+++++.+...+.    .       |.  ..++||+||||||||++++++|+.+.    
T Consensus        13 ~~~~~----k~rp~~~~~~~g~~~~~~~L~~~i~----~-------g~--~~~~ll~Gp~G~GKTtla~~la~~l~~~~~   75 (340)
T 1sxj_C           13 LPWVE----KYRPETLDEVYGQNEVITTVRKFVD----E-------GK--LPHLLFYGPPGTGKTSTIVALAREIYGKNY   75 (340)
T ss_dssp             CCHHH----HTCCSSGGGCCSCHHHHHHHHHHHH----T-------TC--CCCEEEECSSSSSHHHHHHHHHHHHHTTSH
T ss_pred             CchHH----HhCCCcHHHhcCcHHHHHHHHHHHh----c-------CC--CceEEEECCCCCCHHHHHHHHHHHHcCCCc
Confidence            46755    6899999999999887776655543    1       11  12399999999999999999999973    


Q ss_pred             -CcEEEEecccccChHHHHHH---HHc-C----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          269 -FDIYDLDLSAVQSNSELRFL---LLT-M----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       269 -~~~~~l~~s~~~~~~~l~~~---~~~-~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                       ..+..++.++......++..   +.. .    ..+.|++|||+|.+..                  ...+.|+..++..
T Consensus        76 ~~~~~~~~~~~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~------------------~~~~~L~~~le~~  137 (340)
T 1sxj_C           76 SNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN------------------AAQNALRRVIERY  137 (340)
T ss_dssp             HHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH------------------HHHHHHHHHHHHT
T ss_pred             cceEEEEcCcccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCH------------------HHHHHHHHHHhcC
Confidence             34677777654433333322   221 1    2478999999998742                  1234566666643


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                          .....+|++||.+..+.+++.+  |+. .+.++.++.++....+...+..++
T Consensus       138 ----~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~~~~l~~~~~~~~  186 (340)
T 1sxj_C          138 ----TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAIERRIANVLVHEK  186 (340)
T ss_dssp             ----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             ----CCCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHHHHHHHHHHHHcC
Confidence                2456778889999999999999  875 689999999988888887774433

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.50  E-value=2.3e-13  Score=149.66  Aligned_cols=160  Identities=20%  Similarity=0.233  Sum_probs=112.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ...|..|++++|.++..+.+++.+..             ..+.++||+||||||||++|+++|+.+          +..+
T Consensus       179 ~~~~~~~d~~iGr~~~i~~l~~~l~~-------------~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~  245 (758)
T 1r6b_X          179 LARVGGIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTI  245 (758)
T ss_dssp             HHHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEE
T ss_pred             HHhcCCCCCccCCHHHHHHHHHHHhc-------------cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEE
Confidence            34677899999999888887765531             235789999999999999999999997          6778


Q ss_pred             EEEecccccC--------hHHHHHHHHcCC--CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccc
Q 013128          272 YDLDLSAVQS--------NSELRFLLLTMP--SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWS  341 (449)
Q Consensus       272 ~~l~~s~~~~--------~~~l~~~~~~~~--~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  341 (449)
                      +.++++.+..        ...+..++....  .++||||||+|.+.+.......         ...    ..+.+..+..
T Consensus       246 ~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~---------~~~----~~~~L~~~l~  312 (758)
T 1r6b_X          246 YSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG---------QVD----AANLIKPLLS  312 (758)
T ss_dssp             EECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSC---------HHH----HHHHHSSCSS
T ss_pred             EEEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcc---------hHH----HHHHHHHHHh
Confidence            8888766542        234555554443  5799999999998753221100         111    2222322222


Q ss_pred             cCCCCeEEEEEcCCC-----CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          342 CCGEGRIIVFTTNHK-----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~-----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                        ...+.+|++||.+     -.+|++|.+  ||+ .+.++.|+.+++.++++.+..
T Consensus       313 --~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~  363 (758)
T 1r6b_X          313 --SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_dssp             --SCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             --CCCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHH
Confidence              2457788888864     357899999  998 699999999999999987654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.48  E-value=2.8e-13  Score=149.02  Aligned_cols=148  Identities=18%  Similarity=0.185  Sum_probs=106.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcE
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDI  271 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~  271 (449)
                      ...|..|++++|.++.++.+.+.+..             ..+.++||+||||||||++|+++|+.+          +..+
T Consensus       173 ~~~~~~ld~iiG~~~~i~~l~~~l~~-------------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~  239 (758)
T 3pxi_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRV  239 (758)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCE
T ss_pred             HHhhCCCCCccCchHHHHHHHHHHhC-------------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeE
Confidence            45677899999999999888776532             225689999999999999999999997          7888


Q ss_pred             EEEecccc-c--ChHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC
Q 013128          272 YDLDLSAV-Q--SNSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG  346 (449)
Q Consensus       272 ~~l~~s~~-~--~~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  346 (449)
                      +.+++..- .  ....+..++..  ...++|||||     ..                 ....+.|+..++      ...
T Consensus       240 ~~~~~g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD-----~~-----------------~~~~~~L~~~l~------~~~  291 (758)
T 3pxi_A          240 MTLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID-----AA-----------------IDASNILKPSLA------RGE  291 (758)
T ss_dssp             ECC----------CTTHHHHHHHHHTCCCCEEEEC-----C-------------------------CCCTT------SSS
T ss_pred             EEecccccccchHHHHHHHHHHHHHhcCCEEEEEc-----Cc-----------------hhHHHHHHHHHh------cCC
Confidence            88887221 1  12234444443  2578999999     10                 001223444443      246


Q ss_pred             eEEEEEcCCCC-----CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          347 RIIVFTTNHKE-----KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       347 ~iiI~tTN~~~-----~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      +.+|+|||..+     .+|++|.|  ||. .|.++.|+.+++..|++.++..
T Consensus       292 v~~I~at~~~~~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~  340 (758)
T 3pxi_A          292 LQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDR  340 (758)
T ss_dssp             CEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTT
T ss_pred             EEEEeCCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHH
Confidence            88999999988     79999999  995 5999999999999999987765

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.46  E-value=9.8e-14  Score=121.28  Aligned_cols=132  Identities=12%  Similarity=0.077  Sum_probs=89.9

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELR  286 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~  286 (449)
                      +++|.....+.+.+.+.....           ....+||+||||||||++|+++++..   +.+++ ++|+.+.......
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~-----------~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~   69 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE-----------TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLN   69 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT-----------CCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHH
T ss_pred             CceeCCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhh
Confidence            467878888888877765533           24579999999999999999999987   67888 9999887654444


Q ss_pred             HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC-------CCC
Q 013128          287 FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK-------EKL  359 (449)
Q Consensus       287 ~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-------~~l  359 (449)
                      ..+... .+++|||||||.+..                  .....|+..|...    ...+.+|+|||.+       ..+
T Consensus        70 ~~~~~a-~~g~l~ldei~~l~~------------------~~q~~Ll~~l~~~----~~~~~~I~~t~~~~~~~~~~~~~  126 (145)
T 3n70_A           70 DFIALA-QGGTLVLSHPEHLTR------------------EQQYHLVQLQSQE----HRPFRLIGIGDTSLVELAASNHI  126 (145)
T ss_dssp             HHHHHH-TTSCEEEECGGGSCH------------------HHHHHHHHHHHSS----SCSSCEEEEESSCHHHHHHHSCC
T ss_pred             cHHHHc-CCcEEEEcChHHCCH------------------HHHHHHHHHHhhc----CCCEEEEEECCcCHHHHHHcCCC
Confidence            444433 568999999998743                  1234466666432    2345678888864       234


Q ss_pred             CccccCCCccc-eEEEeCCC
Q 013128          360 DPALLRPGRMD-MHLHMSYC  378 (449)
Q Consensus       360 d~aLlrpgR~d-~~i~l~~p  378 (449)
                      ++.|..  |+. ..|++|+.
T Consensus       127 ~~~L~~--rl~~~~i~lPpL  144 (145)
T 3n70_A          127 IAELYY--CFAMTQIACLPL  144 (145)
T ss_dssp             CHHHHH--HHHHHEEECCCC
T ss_pred             CHHHHH--HhcCCEEeCCCC
Confidence            555554  442 35777764

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.43  E-value=4.2e-12  Score=126.29  Aligned_cols=124  Identities=16%  Similarity=0.151  Sum_probs=95.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------------------------CcEEEEecc---cccChHHHHHHHHcC---
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------------------------FDIYDLDLS---AVQSNSELRFLLLTM---  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------------------------~~~~~l~~s---~~~~~~~l~~~~~~~---  292 (449)
                      +.+||||||||||||++|+++|+.+.                        .+++.++..   .-.....++.+....   
T Consensus        24 ~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~~i~~ir~l~~~~~~~  103 (334)
T 1a5t_A           24 HHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEH  103 (334)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTSC
T ss_pred             ceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCCCHHHHHHHHHHHhhc
Confidence            56799999999999999999999874                        356666653   222334455554443   


Q ss_pred             ---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          293 ---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       293 ---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                         ..+.|++|||+|.+..                  ...+.||..++..    +...++|++||.++.+.|++++  |+
T Consensus       104 ~~~~~~kvviIdead~l~~------------------~a~naLLk~lEep----~~~~~~Il~t~~~~~l~~ti~S--Rc  159 (334)
T 1a5t_A          104 ARLGGAKVVWVTDAALLTD------------------AAANALLKTLEEP----PAETWFFLATREPERLLATLRS--RC  159 (334)
T ss_dssp             CTTSSCEEEEESCGGGBCH------------------HHHHHHHHHHTSC----CTTEEEEEEESCGGGSCHHHHT--TS
T ss_pred             cccCCcEEEEECchhhcCH------------------HHHHHHHHHhcCC----CCCeEEEEEeCChHhCcHHHhh--cc
Confidence               2468999999998742                  2346688888753    4568888999999999999999  77


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHh
Q 013128          370 DMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       370 d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                       ..++|+.|+.++...++....
T Consensus       160 -~~~~~~~~~~~~~~~~L~~~~  180 (334)
T 1a5t_A          160 -RLHYLAPPPEQYAVTWLSREV  180 (334)
T ss_dssp             -EEEECCCCCHHHHHHHHHHHC
T ss_pred             -eeeeCCCCCHHHHHHHHHHhc
Confidence             469999999999998888775

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.41  E-value=1.2e-12  Score=128.64  Aligned_cols=153  Identities=15%  Similarity=0.128  Sum_probs=103.1

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHH
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSEL  285 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l  285 (449)
                      ++++|.....+.+.+.+.....           ...++||+||||||||++|+++++..   +.+++.++|+.+....-.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~-----------~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~   70 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAP-----------SDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLE   70 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCS-----------TTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhC-----------CCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHH
Confidence            3577888888888887765532           24689999999999999999999976   578999999887432111


Q ss_pred             HHHHHc-----------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc-c------
Q 013128          286 RFLLLT-----------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW-S------  341 (449)
Q Consensus       286 ~~~~~~-----------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~------  341 (449)
                      ..+|..                 ...+++|||||||.+..                  .....|+..++... .      
T Consensus        71 ~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~------------------~~q~~Ll~~l~~~~~~~~g~~~  132 (304)
T 1ojl_A           71 SELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP------------------LMQVRLLRAIQEREVQRVGSNQ  132 (304)
T ss_dssp             HHHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCH------------------HHHHHHHHHHHSSBCCBTTBCC
T ss_pred             HHhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCCH------------------HHHHHHHHHHhcCEeeecCCcc
Confidence            111111                 11357999999998843                  13345677766432 0      


Q ss_pred             cCCCCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCC--HHHHHHHHHHHhC
Q 013128          342 CCGEGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCN--TSVFKQLAFNYLG  392 (449)
Q Consensus       342 ~~~~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~--~~~r~~l~~~~l~  392 (449)
                      .....+.||+|||..       ..++++|..  || ...|++|++.  .++...|+..|+.
T Consensus       133 ~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~  191 (304)
T 1ojl_A          133 TISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLNVVAIEMPSLRQRREDIPLLADHFLR  191 (304)
T ss_dssp             CCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHSSEEEECCCSGGGGGGHHHHHHHHHH
T ss_pred             cccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcCeeEEeccCHHHhHhhHHHHHHHHHH
Confidence            011346788899875       246677777  77 4567888877  4667777777664

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.39  E-value=1.2e-12  Score=145.73  Aligned_cols=159  Identities=18%  Similarity=0.275  Sum_probs=114.0

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChH--
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNS--  283 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~--  283 (449)
                      +.++|.++.++.+...+........   . ...+..++||+||||||||++|+++|+.+   +.+++.++|+.+....  
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~---~-~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~  633 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV  633 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCS---C-SSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccC---C-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHH
Confidence            5678888888888777765432100   0 00112479999999999999999999999   7899999998775421  


Q ss_pred             -----------------HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccC---
Q 013128          284 -----------------ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCC---  343 (449)
Q Consensus       284 -----------------~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~---  343 (449)
                                       .+...+.. ...+||||||||.+..                  .+++.|+..||.-.-..   
T Consensus       634 s~l~g~~~~~~G~~~~g~l~~~~~~-~~~~vl~lDEi~~l~~------------------~~~~~Ll~~l~~~~~~~~~g  694 (854)
T 1qvr_A          634 SRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAHP------------------DVFNILLQILDDGRLTDSHG  694 (854)
T ss_dssp             GGC--------------CHHHHHHH-CSSEEEEESSGGGSCH------------------HHHHHHHHHHTTTEECCSSS
T ss_pred             HHHcCCCCCCcCccccchHHHHHHh-CCCeEEEEecccccCH------------------HHHHHHHHHhccCceECCCC
Confidence                             12222222 3468999999998632                  36677889888432110   


Q ss_pred             ----CCCeEEEEEcCC--------------------------CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          344 ----GEGRIIVFTTNH--------------------------KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       344 ----~~~~iiI~tTN~--------------------------~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                          -.+.+||+|||.                          ...+.|+|+.  |++..+.+++|+.++...|+..++.
T Consensus       695 ~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~  771 (854)
T 1qvr_A          695 RTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  771 (854)
T ss_dssp             CCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             CEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHH
Confidence                135789999997                          2346777877  9999999999999999999998875

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.37  E-value=2.5e-13  Score=118.43  Aligned_cols=132  Identities=11%  Similarity=0.019  Sum_probs=87.0

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLL  289 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~  289 (449)
                      +++|.....+.+.+.+..+...           ..++||+||||||||++|+++++..+ +++.++|+.+.... ....+
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~-----------~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~~-~~~~~   71 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKR-----------TSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLIDM-PMELL   71 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTC-----------SSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHHC-HHHHH
T ss_pred             CceeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChHh-hhhHH
Confidence            4678888888888888766432           35799999999999999999999988 99999988764321 23334


Q ss_pred             HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC-CCC----Ccccc
Q 013128          290 LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK-EKL----DPALL  364 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~l----d~aLl  364 (449)
                      .. ..+++|||||||.+..                  .....|+..++...   ...+.+|+|||.+ +.+    ++.|.
T Consensus        72 ~~-a~~~~l~lDei~~l~~------------------~~q~~Ll~~l~~~~---~~~~~iI~~tn~~~~~~~~~~~~~L~  129 (143)
T 3co5_A           72 QK-AEGGVLYVGDIAQYSR------------------NIQTGITFIIGKAE---RCRVRVIASCSYAAGSDGISCEEKLA  129 (143)
T ss_dssp             HH-TTTSEEEEEECTTCCH------------------HHHHHHHHHHHHHT---TTTCEEEEEEEECTTTC--CHHHHHH
T ss_pred             Hh-CCCCeEEEeChHHCCH------------------HHHHHHHHHHHhCC---CCCEEEEEecCCCHHHHHhCccHHHH
Confidence            33 3478999999998743                  12233555555321   2346677777754 332    23333


Q ss_pred             CCCcc-ceEEEeCCC
Q 013128          365 RPGRM-DMHLHMSYC  378 (449)
Q Consensus       365 rpgR~-d~~i~l~~p  378 (449)
                      .  |+ ...|++|+.
T Consensus       130 ~--rl~~~~i~lPpL  142 (143)
T 3co5_A          130 G--LFSESVVRIPPL  142 (143)
T ss_dssp             H--HSSSEEEEECCC
T ss_pred             H--HhcCcEEeCCCC
Confidence            3  43 346777764

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.35  E-value=4.1e-12  Score=132.75  Aligned_cols=146  Identities=18%  Similarity=0.135  Sum_probs=94.7

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEecccccChHHH--
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLSAVQSNSEL--  285 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s~~~~~~~l--  285 (449)
                      .++|.+++++.+...+.   .            +.++||+||||||||++|+++|+.++.  ++..+.+.- .+...+  
T Consensus        23 ~ivGq~~~i~~l~~al~---~------------~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~-~t~~dL~G   86 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAAL---S------------GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF-STPEEVFG   86 (500)
T ss_dssp             TCSSCHHHHHHHHHHHH---H------------TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTT-CCHHHHHC
T ss_pred             hhHHHHHHHHHHHHHHh---c------------CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhc-CCHHHhcC
Confidence            46788877776654432   1            358999999999999999999999953  444444432 111111  


Q ss_pred             ---------HHHHHcCC-----CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-------ccccCC
Q 013128          286 ---------RFLLLTMP-----SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-------LWSCCG  344 (449)
Q Consensus       286 ---------~~~~~~~~-----~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-------~~~~~~  344 (449)
                               ...+....     .++|||||||+.+.+                  .+.+.|+..|+.       .... -
T Consensus        87 ~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~~~------------------~~q~~LL~~lee~~v~i~G~~~~-~  147 (500)
T 3nbx_X           87 PLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAGP------------------AILNTLLTAINERQFRNGAHVEK-I  147 (500)
T ss_dssp             CBC----------CBCCTTSGGGCSEEEEESGGGCCH------------------HHHHHHHHHHHSSEEECSSSEEE-C
T ss_pred             cccHHHHhhchhHHhhhccCCCcceeeeHHhHhhhcH------------------HHHHHHHHHHHHHhccCCCCcCC-c
Confidence                     11122111     356899999986532                  355668887752       2111 1


Q ss_pred             CCeEEEEEcCCCCC---CCccccCCCccceEEEeCCCCH-HHHHHHHHHHhC
Q 013128          345 EGRIIVFTTNHKEK---LDPALLRPGRMDMHLHMSYCNT-SVFKQLAFNYLG  392 (449)
Q Consensus       345 ~~~iiI~tTN~~~~---ld~aLlrpgR~d~~i~l~~p~~-~~r~~l~~~~l~  392 (449)
                      ..+++|+|||....   ..+++++  ||..++++|+|+. +++..|+.....
T Consensus       148 ~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~~  197 (500)
T 3nbx_X          148 PMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQD  197 (500)
T ss_dssp             CCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCCC
T ss_pred             chhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhcccc
Confidence            23467888886422   4469999  9999999999997 778888887653

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.32  E-value=5.9e-12  Score=123.73  Aligned_cols=123  Identities=15%  Similarity=0.228  Sum_probs=94.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc------CCcEEEEeccc-ccChHHHHHHHHcC---C---CCceEEeeccchhhhc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL------KFDIYDLDLSA-VQSNSELRFLLLTM---P---SRSMLVIEDIDCSVKL  309 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l------~~~~~~l~~s~-~~~~~~l~~~~~~~---~---~~~Il~iDeiD~l~~~  309 (449)
                      ...||||||||||||++|+++|+.+      +.+++.++.++ -.....++.++...   +   ...|++|||+|.+.. 
T Consensus        18 ~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~-   96 (305)
T 2gno_A           18 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ-   96 (305)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH-
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCH-
Confidence            3589999999999999999999974      56888888764 23333444444332   2   357999999998842 


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHH
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~  389 (449)
                                       ...+.||..|+..    +...++|++||.++++.|++++  |   .++|+.|+.++..+.+..
T Consensus        97 -----------------~a~naLLk~LEep----~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~L~~  150 (305)
T 2gno_A           97 -----------------QAANAFLKALEEP----PEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDLVKE  150 (305)
T ss_dssp             -----------------HHHHHTHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHHHHH
T ss_pred             -----------------HHHHHHHHHHhCC----CCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHHHHH
Confidence                             2356688888753    4567888888999999999999  7   789999999998888887


Q ss_pred             HhC
Q 013128          390 YLG  392 (449)
Q Consensus       390 ~l~  392 (449)
                      .++
T Consensus       151 ~~~  153 (305)
T 2gno_A          151 KIG  153 (305)
T ss_dssp             HHT
T ss_pred             HhC
Confidence            764

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.31  E-value=3.3e-13  Score=144.35  Aligned_cols=127  Identities=18%  Similarity=0.248  Sum_probs=87.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe----cccccC---hHHHH-------HHHHcCCCCceEEeeccchhhhcc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD----LSAVQS---NSELR-------FLLLTMPSRSMLVIEDIDCSVKLQ  310 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~----~s~~~~---~~~l~-------~~~~~~~~~~Il~iDeiD~l~~~~  310 (449)
                      ++||+||||||||++|+++|+.++..++...    +..+..   .....       ..+. ...++|++|||||.+..  
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~-~A~~gil~IDEid~l~~--  405 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALV-LADGGIAVIDEIDKMRD--  405 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGGTSSCSEEECHHH-HHSSSEECCTTTTCCCS--
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeeccccccccccCCeeE-ecCCCcEEeehhhhCCH--
Confidence            7999999999999999999999987666432    122110   00000       0000 12468999999998742  


Q ss_pred             cccchhhhhccchhhHHHHHHHHHHhcCc---------cccCCCCeEEEEEcCCCC-------------CCCccccCCCc
Q 013128          311 NRESSEVQATNQEENKVTLSGLLNFIDGL---------WSCCGEGRIIVFTTNHKE-------------KLDPALLRPGR  368 (449)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~-------------~ld~aLlrpgR  368 (449)
                                      ...+.|+..|+.-         ....+..+.||+|||.+.             .|+++|++  |
T Consensus       406 ----------------~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~--R  467 (595)
T 3f9v_A          406 ----------------EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILS--R  467 (595)
T ss_dssp             ----------------HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGG--G
T ss_pred             ----------------hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHh--h
Confidence                            2345577777632         122234578999999986             89999999  9


Q ss_pred             cc-eEEEeCCCCHHHHHHHHHHHhCc
Q 013128          369 MD-MHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       369 ~d-~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      || ..+..++|+.+ ...|+++.+..
T Consensus       468 FDl~~~~~~~~~~e-~~~i~~~il~~  492 (595)
T 3f9v_A          468 FDLIFILKDQPGEQ-DRELANYILDV  492 (595)
T ss_dssp             CSCCEEECCTTHHH-HHHHHHHHHTT
T ss_pred             CeEEEEeCCCCCHH-HHHHHHHHHHH
Confidence            98 45666788888 88898888764

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.29  E-value=1.7e-11  Score=148.20  Aligned_cols=137  Identities=23%  Similarity=0.354  Sum_probs=96.7

Q ss_pred             CcceEEeCCCCCCHHHHH-HHHHHHcCCcEEEEecccccChHHHHHHHHcC-----------------CCCceEEeeccc
Q 013128          243 KRGYLLYGPPGTGKSSLI-AAMANQLKFDIYDLDLSAVQSNSELRFLLLTM-----------------PSRSMLVIEDID  304 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la-~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~-----------------~~~~Il~iDeiD  304 (449)
                      ++++||+||||||||++| +++++..++.++.++++...+...+...+...                 .+++||||||||
T Consensus      1267 ~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEin 1346 (2695)
T 4akg_A         1267 KRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEIN 1346 (2695)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccc
Confidence            479999999999999999 55555558889999999888776666555421                 235799999999


Q ss_pred             hhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC------CCeEEEEEcCCCC-----CCCccccCCCccceEE
Q 013128          305 CSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG------EGRIIVFTTNHKE-----KLDPALLRPGRMDMHL  373 (449)
Q Consensus       305 ~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~-----~ld~aLlrpgR~d~~i  373 (449)
                      ....  ++-+.       ......+.+++. ..|++....      ..+.+|+|||++.     .|+|+|+|  || ..+
T Consensus      1347 mp~~--d~yg~-------q~~lelLRq~le-~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi 1413 (2695)
T 4akg_A         1347 LPKL--DKYGS-------QNVVLFLRQLME-KQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR--HA-AIL 1413 (2695)
T ss_dssp             CSCC--CSSSC-------CHHHHHHHHHHH-TSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--TE-EEE
T ss_pred             cccc--cccCc-------hhHHHHHHHHHh-cCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--ee-eEE
Confidence            6432  11110       111223333332 224443211      2478999999995     79999999  99 679


Q ss_pred             EeCCCCHHHHHHHHHHHhC
Q 013128          374 HMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       374 ~l~~p~~~~r~~l~~~~l~  392 (449)
                      .++.|+.++++.|+..++.
T Consensus      1414 ~i~~P~~~~l~~I~~~il~ 1432 (2695)
T 4akg_A         1414 YLGYPSGKSLSQIYEIYYK 1432 (2695)
T ss_dssp             ECCCCTTTHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHH
Confidence            9999999999999988774

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=99.28  E-value=4.5e-12  Score=114.28  Aligned_cols=130  Identities=16%  Similarity=0.205  Sum_probs=82.2

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccc
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSA  278 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~  278 (449)
                      ..+.+|++++......+.+.+.+..+...-      ..+.+.+++|+||||||||+|++++|+.+    |..++.+++.+
T Consensus         4 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~------~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~   77 (180)
T 3ec2_A            4 YWNANLDTYHPKNVSQNRALLTIRVFVHNF------NPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKD   77 (180)
T ss_dssp             CTTCCSSSCCCCSHHHHHHHHHHHHHHHSC------CGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHH
T ss_pred             hhhCccccccCCCHHHHHHHHHHHHHHHhc------cccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            356799999886555666667776666532      22336789999999999999999999988    66666666554


Q ss_pred             ccChH-------HHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEE
Q 013128          279 VQSNS-------ELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVF  351 (449)
Q Consensus       279 ~~~~~-------~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  351 (449)
                      +...-       .....+....++.+|+|||++....             .......+..+++..   ..   .+..+|+
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~~~-------------~~~~~~~l~~ll~~~---~~---~~~~ii~  138 (180)
T 3ec2_A           78 LIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSERL-------------SDWQRELISYIITYR---YN---NLKSTII  138 (180)
T ss_dssp             HHHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSSCC-------------CHHHHHHHHHHHHHH---HH---TTCEEEE
T ss_pred             HHHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCCcC-------------CHHHHHHHHHHHHHH---HH---cCCCEEE
Confidence            42110       0002233334789999999985421             122223444444433   11   3457788


Q ss_pred             EcCCCC
Q 013128          352 TTNHKE  357 (449)
Q Consensus       352 tTN~~~  357 (449)
                      |||.+.
T Consensus       139 tsn~~~  144 (180)
T 3ec2_A          139 TTNYSL  144 (180)
T ss_dssp             ECCCCS
T ss_pred             EcCCCh
Confidence            888764

>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=99.26  E-value=6.4e-11  Score=119.99  Aligned_cols=164  Identities=10%  Similarity=0.103  Sum_probs=106.6

Q ss_pred             CcccccCCHHHHHHHHHHH-HHHHcChhHHhhhcCCCCcceEE--eCCCCCCHHHHHHHHHHHc---------CCcEEEE
Q 013128          207 TFKTLALDSELKREITEDL-ENFMNGKEYYTRIGRAWKRGYLL--YGPPGTGKSSLIAAMANQL---------KFDIYDL  274 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l-~~~~~~~~~~~~~g~~~~rg~LL--~GPpGtGKT~la~aiA~~l---------~~~~~~l  274 (449)
                      ..+.++|.++..+.+.+.+ ........       ..++.++|  +||||||||++++++++.+         +..++.+
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~-------~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~   92 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAG-------LSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYV   92 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSC-------BCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCC-------CCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEE
Confidence            3478899999888888877 65544300       11467999  9999999999999999987         4567778


Q ss_pred             ecccccCh----------------------HH----HHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHH
Q 013128          275 DLSAVQSN----------------------SE----LRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVT  328 (449)
Q Consensus       275 ~~s~~~~~----------------------~~----l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~  328 (449)
                      ++....+.                      ..    +...+.....+.||+|||+|.+...+.            .....
T Consensus        93 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~------------~~~~~  160 (412)
T 1w5s_A           93 NAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPR------------IAAED  160 (412)
T ss_dssp             EGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTT------------SCHHH
T ss_pred             ECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccC------------cchHH
Confidence            76432211                      11    112222234688999999998853100            01234


Q ss_pred             HHHHHHHhcCccccCC--CCeEEEEEcCCCC---CCC---ccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          329 LSGLLNFIDGLWSCCG--EGRIIVFTTNHKE---KLD---PALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       329 ls~LL~~ldg~~~~~~--~~~iiI~tTN~~~---~ld---~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      +..|+..++.... .+  ..+.+|+|||.++   .++   +.+.+  ++...++++.++.++..+++...+.
T Consensus       161 l~~l~~~~~~~~~-~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~  229 (412)
T 1w5s_A          161 LYTLLRVHEEIPS-RDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAE  229 (412)
T ss_dssp             HHHHHTHHHHSCC-TTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccc-CCCCceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHH
Confidence            4445555543210 02  4577888887664   344   56666  5555599999999999999987654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.14  E-value=4.8e-11  Score=109.36  Aligned_cols=97  Identities=20%  Similarity=0.273  Sum_probs=64.0

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC-CCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA-WKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~-~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      .+.+|+++++.+...+.+.+.+..++....      .. .+++++|+||||||||++++++++++   +..++.+++..+
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~   93 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEYE------PGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPEL   93 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHCC------SSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHH
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHhh------hccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHH
Confidence            456899998866555556666666654221      11 12789999999999999999999998   677877776543


Q ss_pred             cCh-------HHHHHHHHcCCCCceEEeeccchh
Q 013128          280 QSN-------SELRFLLLTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       280 ~~~-------~~l~~~~~~~~~~~Il~iDeiD~l  306 (449)
                      ...       ..+...+.....+.+|+|||++..
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~  127 (202)
T 2w58_A           94 FRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHHC---CCCHHHHHHHHHSSEEEEEEECCC
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            210       001112222234569999999765

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.04  E-value=5.1e-10  Score=102.78  Aligned_cols=114  Identities=20%  Similarity=0.205  Sum_probs=68.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      ++|.++++|||||||||||++|.++|+.+...++.+..+.  +.    ..+.......||+|||+|.-..          
T Consensus        54 ~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~--s~----f~l~~l~~~kIiiLDEad~~~~----------  117 (212)
T 1tue_A           54 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST--SH----FWLEPLTDTKVAMLDDATTTCW----------  117 (212)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS--SC----GGGGGGTTCSSEEEEEECHHHH----------
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc--ch----hhhcccCCCCEEEEECCCchhH----------
Confidence            3566778999999999999999999999976554332111  10    1122223456999999984311          


Q ss_pred             hccchhhHHHHHHHHHHhcCccc----cCC-----CCeEEEEEcCCC---CCCCccccCCCccceEEEeCCC
Q 013128          319 ATNQEENKVTLSGLLNFIDGLWS----CCG-----EGRIIVFTTNHK---EKLDPALLRPGRMDMHLHMSYC  378 (449)
Q Consensus       319 ~~~~~~~~~~ls~LL~~ldg~~~----~~~-----~~~iiI~tTN~~---~~ld~aLlrpgR~d~~i~l~~p  378 (449)
                             ...-..+-+.+||...    ...     ...-+|.|||..   +..-+.|.+  |+ ..+.++.|
T Consensus       118 -------~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~S--Ri-~~f~F~~~  179 (212)
T 1tue_A          118 -------TYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RI-TVFEFPNA  179 (212)
T ss_dssp             -------HHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SC-EEEECCSC
T ss_pred             -------HHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhh--hE-EEEEcCCC
Confidence                   1111235567777421    000     124678899974   222346666  77 46777644

>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=98.99  E-value=2.2e-10  Score=115.59  Aligned_cols=121  Identities=22%  Similarity=0.281  Sum_probs=86.8

Q ss_pred             hcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhh
Q 013128          238 IGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEV  317 (449)
Q Consensus       238 ~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~  317 (449)
                      .+++.+..++|+||||+||||+++++++.++..++.++...    ......+....+..++++||++.......+...  
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~~r~l~~--  237 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGESRDLPS--  237 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCC--
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHHHhhccc--
Confidence            36777889999999999999999999999987766543222    122333555567888999999987642111000  


Q ss_pred             hhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCC
Q 013128          318 QATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       318 ~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~  377 (449)
                           .......+.+.+.+||.       +.++++||+++.+ +++++|||++..+...+
T Consensus       238 -----~~~~~~~~~l~~~ldG~-------v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          238 -----GQGINNLDNLRDYLDGS-------VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             -----CSHHHHHHTTHHHHHCS-------SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             -----cCcchHHHHHHHHhcCC-------CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence                 00111456678888873       4568889999999 89999999999888766

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.98  E-value=3.5e-10  Score=111.21  Aligned_cols=97  Identities=23%  Similarity=0.375  Sum_probs=61.2

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----CcEEEEecccc
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLDLSAV  279 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----~~~~~l~~s~~  279 (449)
                      .+.+|+++.+....+..+.+.+..|+...      +.....+++||||||||||+|+.++|+++.    ..++.+.+..+
T Consensus       119 ~~~tfd~f~~~~~~~~~~~~~~~~~i~~~------~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l  192 (308)
T 2qgz_A          119 RHIHLSDIDVNNASRMEAFSAILDFVEQY------PSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSF  192 (308)
T ss_dssp             GSCCGGGSCCCSHHHHHHHHHHHHHHHHC------SCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHH
T ss_pred             HhCCHhhCcCCChHHHHHHHHHHHHHHhc------cccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHH
Confidence            35789999876544455555555555421      111257899999999999999999999765    77777765543


Q ss_pred             cC-------hHHHHHHHHcCCCCceEEeeccchh
Q 013128          280 QS-------NSELRFLLLTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       280 ~~-------~~~l~~~~~~~~~~~Il~iDeiD~l  306 (449)
                      ..       ...+...+.......+|+|||++..
T Consensus       193 ~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          193 AIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             HHHHHCCCC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            11       1111111111234679999999754

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.97  E-value=9.2e-10  Score=117.97  Aligned_cols=53  Identities=32%  Similarity=0.266  Sum_probs=43.2

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      ..+|.+|++++|.+.+++.+...+.               ....++|+||||||||+++++||+.+..
T Consensus        34 ~~rp~~l~~i~G~~~~l~~l~~~i~---------------~g~~vll~Gp~GtGKTtlar~ia~~l~~   86 (604)
T 3k1j_A           34 EVPEKLIDQVIGQEHAVEVIKTAAN---------------QKRHVLLIGEPGTGKSMLGQAMAELLPT   86 (604)
T ss_dssp             CCCSSHHHHCCSCHHHHHHHHHHHH---------------TTCCEEEECCTTSSHHHHHHHHHHTSCC
T ss_pred             cccccccceEECchhhHhhcccccc---------------CCCEEEEEeCCCCCHHHHHHHHhccCCc
Confidence            4578899999999888766654442               1358999999999999999999999853

>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=98.96  E-value=7e-10  Score=129.20  Aligned_cols=147  Identities=12%  Similarity=0.123  Sum_probs=91.8

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcC----------hhHHhh------hc------------CCCCcceEEeCCCCCCHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNG----------KEYYTR------IG------------RAWKRGYLLYGPPGTGKS  257 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~----------~~~~~~------~g------------~~~~rg~LL~GPpGtGKT  257 (449)
                      .+|+++.+..+.|+.+++.+..++.+          ++.++.      .|            .|..+.+|||||||||||
T Consensus      1017 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g~GKT 1096 (1706)
T 3cmw_A         1017 SSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKT 1096 (1706)
T ss_dssp             -------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHH
T ss_pred             ceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCCCChH
Confidence            67999999999999999999988844          445555      22            333444999999999999


Q ss_pred             HHHHHHHHHcC---CcEEEEeccc----------------cc------ChHHHHHHHH--cCCCCceEEeeccchhhhcc
Q 013128          258 SLIAAMANQLK---FDIYDLDLSA----------------VQ------SNSELRFLLL--TMPSRSMLVIEDIDCSVKLQ  310 (449)
Q Consensus       258 ~la~aiA~~l~---~~~~~l~~s~----------------~~------~~~~l~~~~~--~~~~~~Il~iDeiD~l~~~~  310 (449)
                      +||.++|.+..   -+...++...                +.      ++..++.++.  +...+++|++|++|++.+.+
T Consensus      1097 ~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~~~~ 1176 (1706)
T 3cmw_A         1097 TLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKA 1176 (1706)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHH
T ss_pred             HHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcCccc
Confidence            99999999873   3333333322                11      2334443333  34579999999999998753


Q ss_pred             cccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          311 NRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                      ..++. ....+.....+.++++|..||++...  .+++|| +||+.
T Consensus      1177 ~~~g~-~~~~~~~~~~r~~~q~l~~~~~~~~~--~~v~v~-~~n~~ 1218 (1706)
T 3cmw_A         1177 EIEGE-IGDSHMGLAARMMSQAMRKLAGNLKQ--SNTLLI-FINQI 1218 (1706)
T ss_dssp             HHHSC-TTCCCTTHHHHHHHHHHHHHHHHHHH--TTCEEE-EEECE
T ss_pred             ccccc-cccccccHHHHHHHHHHHHHHhhhcc--CCeEEE-Eeccc
Confidence            31111 10001234456799999999987653  345555 77764

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.92  E-value=1.8e-09  Score=94.75  Aligned_cols=58  Identities=17%  Similarity=0.201  Sum_probs=47.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhh
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      ...++|+||+|+|||+|++++++.+   |..++.++...+...       ....++.||+|||++.+.
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~-------~~~~~~~lLilDE~~~~~   96 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT-------DAAFEAEYLAVDQVEKLG   96 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC-------GGGGGCSEEEEESTTCCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH-------HHHhCCCEEEEeCccccC
Confidence            5679999999999999999999998   777888887776544       113468999999998753

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.87  E-value=3.4e-08  Score=97.35  Aligned_cols=174  Identities=17%  Similarity=0.113  Sum_probs=102.2

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc-----c
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV-----Q  280 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~-----~  280 (449)
                      ..-+.++|-++..+.+.+ +.    .            +.++|+||+|+|||+|++.+++.++..++.+++...     .
T Consensus        10 ~~~~~~~gR~~el~~L~~-l~----~------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (357)
T 2fna_A           10 DNRKDFFDREKEIEKLKG-LR----A------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI   72 (357)
T ss_dssp             CSGGGSCCCHHHHHHHHH-TC----S------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCC
T ss_pred             CCHHHhcChHHHHHHHHH-hc----C------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhccccCC
Confidence            345678888777666654 32    1            479999999999999999999999877777776542     0


Q ss_pred             Ch--------------------------------------------------HHHHHHHHcCC-CCceEEeeccchhhhc
Q 013128          281 SN--------------------------------------------------SELRFLLLTMP-SRSMLVIEDIDCSVKL  309 (449)
Q Consensus       281 ~~--------------------------------------------------~~l~~~~~~~~-~~~Il~iDeiD~l~~~  309 (449)
                      +.                                                  ..+...+.... .|.+|+|||++.+...
T Consensus        73 ~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~  152 (357)
T 2fna_A           73 SYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKL  152 (357)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGC
T ss_pred             CHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhcc
Confidence            10                                                  11222233322 3889999999987531


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC---------CCCccccCCCccceEEEeCCCCH
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE---------KLDPALLRPGRMDMHLHMSYCNT  380 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~---------~ld~aLlrpgR~d~~i~l~~p~~  380 (449)
                      ..           ......+..+.   +..     .++.+|+|+....         .....+  .||+...++++..+.
T Consensus       153 ~~-----------~~~~~~l~~~~---~~~-----~~~~~i~~g~~~~~l~~~l~~~~~~~~l--~~r~~~~i~l~~l~~  211 (357)
T 2fna_A          153 RG-----------VNLLPALAYAY---DNL-----KRIKFIMSGSEMGLLYDYLRVEDPESPL--FGRAFSTVELKPFSR  211 (357)
T ss_dssp             TT-----------CCCHHHHHHHH---HHC-----TTEEEEEEESSHHHHHHHTTTTCTTSTT--TTCCCEEEEECCCCH
T ss_pred             Cc-----------hhHHHHHHHHH---HcC-----CCeEEEEEcCchHHHHHHHhccCCCCcc--ccCccceeecCCCCH
Confidence            00           01111222222   211     2355666665432         111222  247667899999999


Q ss_pred             HHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHH
Q 013128          381 SVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       381 ~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~  418 (449)
                      ++..+++...++..+....+. ..+....+=.|.-+..
T Consensus       212 ~e~~~~l~~~~~~~~~~~~~~-~~i~~~t~G~P~~l~~  248 (357)
T 2fna_A          212 EEAIEFLRRGFQEADIDFKDY-EVVYEKIGGIPGWLTY  248 (357)
T ss_dssp             HHHHHHHHHHHHHHTCCCCCH-HHHHHHHCSCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCcH-HHHHHHhCCCHHHHHH
Confidence            999999987654211111111 4455555555654443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.83  E-value=2.4e-08  Score=121.87  Aligned_cols=135  Identities=18%  Similarity=0.332  Sum_probs=94.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEecccccChHHHHHHHHc------C------------CCCceEEeecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDLSAVQSNSELRFLLLT------M------------PSRSMLVIEDI  303 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~s~~~~~~~l~~~~~~------~------------~~~~Il~iDei  303 (449)
                      ++++||+||||||||++++.....+ +.+++.++++.-.+...+...+..      .            .+..|+||||+
T Consensus      1304 ~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDi 1383 (3245)
T 3vkg_A         1304 HRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEI 1383 (3245)
T ss_dssp             TCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEeccc
Confidence            4689999999999998886655544 778889999998887777666542      1            12469999999


Q ss_pred             chhhhcccccchhhhhccchhhHHHHHHHHHHhc--CccccCC------CCeEEEEEcCCC-----CCCCccccCCCccc
Q 013128          304 DCSVKLQNRESSEVQATNQEENKVTLSGLLNFID--GLWSCCG------EGRIIVFTTNHK-----EKLDPALLRPGRMD  370 (449)
Q Consensus       304 D~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld--g~~~~~~------~~~iiI~tTN~~-----~~ld~aLlrpgR~d  370 (449)
                      +....  +.          ...+..+.-|...+|  |.+....      ..+.+|+|+|++     ..|+++|+|  ||.
T Consensus      1384 Nmp~~--D~----------yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~F~ 1449 (3245)
T 3vkg_A         1384 NLPST--DK----------YGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--HAP 1449 (3245)
T ss_dssp             TCCCC--CT----------TSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--TCC
T ss_pred             CCCCc--cc----------cccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--hce
Confidence            86422  11          111223444445555  2222111      346789999988     358999999  995


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhC
Q 013128          371 MHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       371 ~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      + +.+++|+.++...|+..++.
T Consensus      1450 v-i~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1450 I-LLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             E-EECCCCCHHHHHHHHHHHHH
T ss_pred             E-EEeCCCCHHHHHHHHHHHHH
Confidence            5 99999999999999876653

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.82  E-value=7.4e-09  Score=95.25  Aligned_cols=120  Identities=14%  Similarity=0.164  Sum_probs=78.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc--------C-CcEEEEecccccC---------------------hHHHHHHHH-cC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL--------K-FDIYDLDLSAVQS---------------------NSELRFLLL-TM  292 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l--------~-~~~~~l~~s~~~~---------------------~~~l~~~~~-~~  292 (449)
                      -.+|++|+||||||++|.+++...        | .+++..++..+..                     ...+...+. ..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~   85 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKPE   85 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSGG
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhccc
Confidence            468999999999999998875443        3 6676665543321                     012222210 12


Q ss_pred             CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceE
Q 013128          293 PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMH  372 (449)
Q Consensus       293 ~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~  372 (449)
                      ..++||+|||++.+.+.+... .       +.     ..++..+..-   .....-||++|++++.|+.++..  |++.+
T Consensus        86 ~~~~vliIDEAq~l~~~~~~~-~-------e~-----~rll~~l~~~---r~~~~~iil~tq~~~~l~~~lr~--ri~~~  147 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSAG-S-------KI-----PENVQWLNTH---RHQGIDIFVLTQGPKLLDQNLRT--LVRKH  147 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCTT-C-------CC-----CHHHHGGGGT---TTTTCEEEEEESCGGGBCHHHHT--TEEEE
T ss_pred             cCceEEEEEChhhhccCcccc-c-------hh-----HHHHHHHHhc---CcCCeEEEEECCCHHHHhHHHHH--HhheE
Confidence            358999999999986532111 0       00     1255555432   23456788888889999999988  99999


Q ss_pred             EEeCCCCHH
Q 013128          373 LHMSYCNTS  381 (449)
Q Consensus       373 i~l~~p~~~  381 (449)
                      ++++.+...
T Consensus       148 ~~l~~~~~~  156 (199)
T 2r2a_A          148 YHIASNKMG  156 (199)
T ss_dssp             EEEEECSSC
T ss_pred             EEEcCcccC
Confidence            999876543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.78  E-value=9.3e-07  Score=86.79  Aligned_cols=180  Identities=18%  Similarity=0.131  Sum_probs=105.6

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc---
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ---  280 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~---  280 (449)
                      ++..-+.++|.++..+.+.+.+..               ++.++|+||+|+|||+|++.+++..+  .+.+++....   
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~---------------~~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~   69 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN---------------YPLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAER   69 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH---------------CSEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTT
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc---------------CCeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeecccccc
Confidence            344456789988888877765532               15799999999999999999999986  5556553321   


Q ss_pred             ---Ch---------------------------------------HHHHHHHHcC---CCCceEEeeccchhhhcccccch
Q 013128          281 ---SN---------------------------------------SELRFLLLTM---PSRSMLVIEDIDCSVKLQNRESS  315 (449)
Q Consensus       281 ---~~---------------------------------------~~l~~~~~~~---~~~~Il~iDeiD~l~~~~~~~~~  315 (449)
                         +.                                       ..+...+...   ..|.+|+|||++.+.....    
T Consensus        70 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~----  145 (350)
T 2qen_A           70 GHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGS----  145 (350)
T ss_dssp             TCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTT----
T ss_pred             cCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCc----
Confidence               10                                       1111111111   1389999999998753100    


Q ss_pred             hhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC---------CCCccccCCCccceEEEeCCCCHHHHHHH
Q 013128          316 EVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE---------KLDPALLRPGRMDMHLHMSYCNTSVFKQL  386 (449)
Q Consensus       316 ~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~---------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l  386 (449)
                             ......+..|-..++..     ..+.+|+|+....         .....+.  ||....+++++.+.++..++
T Consensus       146 -------~~~~~~~~~L~~~~~~~-----~~~~~il~g~~~~~l~~~l~~~~~~~~l~--~~~~~~i~l~pl~~~e~~~~  211 (350)
T 2qen_A          146 -------RGGKELLALFAYAYDSL-----PNLKIILTGSEVGLLHDFLKITDYESPLY--GRIAGEVLVKPFDKDTSVEF  211 (350)
T ss_dssp             -------TTTHHHHHHHHHHHHHC-----TTEEEEEEESSHHHHHHHHCTTCTTSTTT--TCCCEEEECCCCCHHHHHHH
T ss_pred             -------cchhhHHHHHHHHHHhc-----CCeEEEEECCcHHHHHHHHhhcCCCCccc--cCccceeeCCCCCHHHHHHH
Confidence                   00111222222333321     2455566654321         1122232  46667899999999999999


Q ss_pred             HHHHhCcCCCCC-HHHHHHHHHccCCCHHHHHH
Q 013128          387 AFNYLGISHHYL-FEQIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       387 ~~~~l~~~~~~l-~~~i~~l~~~~~~tpa~i~~  418 (449)
                      +...+...+... .+.+..+....+=.|.-+..
T Consensus       212 l~~~~~~~~~~~~~~~~~~i~~~tgG~P~~l~~  244 (350)
T 2qen_A          212 LKRGFREVNLDVPENEIEEAVELLDGIPGWLVV  244 (350)
T ss_dssp             HHHHHHTTTCCCCHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            988765433333 34555666666666655543

>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=98.74  E-value=4.4e-08  Score=93.73  Aligned_cols=119  Identities=17%  Similarity=0.251  Sum_probs=69.8

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhc
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQAT  320 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~  320 (449)
                      +++++++||||||||||+++.|+|+.+.. .-.++.+.   .   ...+.....+.|++.||....-.            
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~~~l-~G~vn~~~---~---~f~l~~~~~k~i~l~Ee~~~~~d------------  162 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHTVPF-YGCVNWTN---E---NFPFNDCVDKMVIWWEEGKMTAK------------  162 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSC-EEECCTTC---S---SCTTGGGSSCSEEEECSCCEETT------------
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhhhcc-cceeeccc---c---ccccccccccEEEEeccccchhH------------
Confidence            44678999999999999999999998755 22223221   1   11344445667777777765321            


Q ss_pred             cchhhHHHHHHHHHHhcCcccc----CC-----CCeEEEEEcCC-C----------CCCCccccCCCccceEEEeC----
Q 013128          321 NQEENKVTLSGLLNFIDGLWSC----CG-----EGRIIVFTTNH-K----------EKLDPALLRPGRMDMHLHMS----  376 (449)
Q Consensus       321 ~~~~~~~~ls~LL~~ldg~~~~----~~-----~~~iiI~tTN~-~----------~~ld~aLlrpgR~d~~i~l~----  376 (449)
                          ....   +-+.++|-.-.    ..     ....+|+|||. +          +...++|.+  |+ ..+.|+    
T Consensus       163 ----~~~~---lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~s--R~-~~f~F~~~~p  232 (267)
T 1u0j_A          163 ----VVES---AKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQD--RM-FKFELTRRLD  232 (267)
T ss_dssp             ----THHH---HHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHT--TE-EEEECCSCCC
T ss_pred             ----HHHH---HHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhh--hE-EEEECCCcCC
Confidence                0011   22233421110    00     23467788886 2          245578888  87 668887    


Q ss_pred             ----CCCHHHHHHHHH
Q 013128          377 ----YCNTSVFKQLAF  388 (449)
Q Consensus       377 ----~p~~~~r~~l~~  388 (449)
                          ..+.++-+..+.
T Consensus       233 ~~~~~lt~~~~~~f~~  248 (267)
T 1u0j_A          233 HDFGKVTKQEVKDFFR  248 (267)
T ss_dssp             TTSCCCCHHHHHHHHH
T ss_pred             cccCCCCHHHHHHHHH
Confidence                456666666555

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=98.73  E-value=4.3e-09  Score=103.20  Aligned_cols=113  Identities=16%  Similarity=0.198  Sum_probs=63.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc--EEEEecc----ccc-C-hHHH---HHHHHcCCCCceEEeeccchhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD--IYDLDLS----AVQ-S-NSEL---RFLLLTMPSRSMLVIEDIDCSV  307 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~--~~~l~~s----~~~-~-~~~l---~~~~~~~~~~~Il~iDeiD~l~  307 (449)
                      |.+.++.++|+||||||||+|+.++|...+..  ++.+...    ... + +..+   ...+.+.  + +||||+++.+.
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~--~-LLVIDsI~aL~  195 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQH--R-VIVIDSLKNVI  195 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHC--S-EEEEECCTTTC
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhC--C-EEEEecccccc
Confidence            44445668999999999999999999876544  4444111    111 1 1112   2223322  3 99999999985


Q ss_pred             hcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccc
Q 013128          308 KLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPAL  363 (449)
Q Consensus       308 ~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aL  363 (449)
                      ......+      ........+.+++..|+++...  .++.+|++|| +...|+++
T Consensus       196 ~~~~~~s------~~G~v~~~lrqlL~~L~~~~k~--~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          196 GAAGGNT------TSGGISRGAFDLLSDIGAMAAS--RGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             -----------------CCHHHHHHHHHHHHHHHH--HTCEEEEECC-CSSCSSSH
T ss_pred             ccccccc------ccchHHHHHHHHHHHHHHHHhh--CCCEEEEEeC-CcccchhH
Confidence            4221100      0011133455666666555332  3467788888 56666664

>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=98.72  E-value=8.4e-08  Score=116.44  Aligned_cols=133  Identities=15%  Similarity=0.186  Sum_probs=95.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCC-CCceEEeeccchhhhcccccchhhhhcc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATN  321 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~  321 (449)
                      ..|.+++||||||||++++++|+.+|.+++.++|+.-.+...+...|.... .++.+++|||+.+-..       .    
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~DE~nr~~~e-------v----  713 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEK-------V----  713 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEETTTSSCHH-------H----
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeehhhhhcChH-------H----
Confidence            468999999999999999999999999999999999888888887776654 4799999999986420       0    


Q ss_pred             chhhHHHHHHHHHHhc---------CccccCCCCeEEEEEcC----CCCCCCccccCCCccceEEEeCCCCHHHHHHHHH
Q 013128          322 QEENKVTLSGLLNFID---------GLWSCCGEGRIIVFTTN----HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       322 ~~~~~~~ls~LL~~ld---------g~~~~~~~~~iiI~tTN----~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~  388 (449)
                      -......+..+++.+.         |..-.......|++|.|    ....|+++|.+  || +.|.|.+|+.+...++..
T Consensus       714 Ls~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~~i~ei~l  790 (2695)
T 4akg_A          714 LSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SF-REFSMKSPQSGTIAEMIL  790 (2695)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TE-EEEECCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--he-EEEEeeCCCHHHHHHHHH
Confidence            0000111111222221         11111123456788888    34679999998  88 689999999988777754


Q ss_pred             H
Q 013128          389 N  389 (449)
Q Consensus       389 ~  389 (449)
                      .
T Consensus       791 ~  791 (2695)
T 4akg_A          791 Q  791 (2695)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=98.71  E-value=2.6e-07  Score=93.56  Aligned_cols=174  Identities=16%  Similarity=0.154  Sum_probs=107.5

Q ss_pred             cccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEecccccChHH
Q 013128          208 FKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQSNSE  284 (449)
Q Consensus       208 f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~~~~~  284 (449)
                      ++.++|.....+.+.+.+.....           ....+||+|++||||+++|+++.....   .+++.++|+.+..+.-
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~a~-----------~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~  204 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKISC-----------AECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIF  204 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHHTT-----------CCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHH
T ss_pred             chhhhhccHHhhHHHHHHHHhcC-----------CCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHH
Confidence            44567776666777776655322           135689999999999999999998874   6899999998754322


Q ss_pred             HHHHHHc-----------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-ccccCC--
Q 013128          285 LRFLLLT-----------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSCCG--  344 (449)
Q Consensus       285 l~~~~~~-----------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~~~--  344 (449)
                      -..+|..                 ....++||||||+.+..                  .....||..++. .....|  
T Consensus       205 ~~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~------------------~~q~~Ll~~l~~~~~~~~g~~  266 (387)
T 1ny5_A          205 EAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSL------------------EAQAKLLRVIESGKFYRLGGR  266 (387)
T ss_dssp             HHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCH------------------HHHHHHHHHHHHSEECCBTCC
T ss_pred             HHHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhCCH------------------HHHHHHHHHHhcCcEEeCCCC
Confidence            2223321                 12467999999998843                  233446666652 111111  


Q ss_pred             ----CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCCH--HHHHHHHHHHhCcC-------CCCCHHHHH
Q 013128          345 ----EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCNT--SVFKQLAFNYLGIS-------HHYLFEQIE  403 (449)
Q Consensus       345 ----~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~~--~~r~~l~~~~l~~~-------~~~l~~~i~  403 (449)
                          -.+-||+|||..       ..+.+.|.-  |+ ...|++|+...  ++...|+..|+...       ...+.++..
T Consensus       267 ~~~~~~~rii~at~~~l~~~~~~g~fr~dl~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~  344 (387)
T 1ny5_A          267 KEIEVNVRILAATNRNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQ  344 (387)
T ss_dssp             SBEECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHH
T ss_pred             ceeeccEEEEEeCCCCHHHHHHcCCccHHHHH--hhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHH
Confidence                235688888863       233444443  44 35688888754  77777887777431       112445555


Q ss_pred             HHHHccCCC
Q 013128          404 ELIKEVNVT  412 (449)
Q Consensus       404 ~l~~~~~~t  412 (449)
                      +.+....|.
T Consensus       345 ~~l~~~~wp  353 (387)
T 1ny5_A          345 ELLLSYPWY  353 (387)
T ss_dssp             HHHHHSCCT
T ss_pred             HHHHhCCCC
Confidence            555555553

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=98.68  E-value=4.8e-07  Score=90.98  Aligned_cols=152  Identities=15%  Similarity=0.184  Sum_probs=98.0

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCc--EEEEecccccChHHHHH
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD--IYDLDLSAVQSNSELRF  287 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~--~~~l~~s~~~~~~~l~~  287 (449)
                      .++|.......+.+.+......           ...+|++|++||||+.+++++....+..  ++.++|+.+..+.-...
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~~-----------~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~  198 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAKS-----------KAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESE  198 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHTS-----------CSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHH
T ss_pred             cccccchHHHHHHhhhhhhhcc-----------chhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHH
Confidence            4667666666666655443321           3469999999999999999999887543  99999998865433333


Q ss_pred             HHHc-----------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC-ccccCCC----
Q 013128          288 LLLT-----------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG-LWSCCGE----  345 (449)
Q Consensus       288 ~~~~-----------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~~~~~----  345 (449)
                      +|..                 ....+.||||||+.+..                  .....||..++. .....|+    
T Consensus       199 lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~------------------~~Q~~Ll~~l~~~~~~~~g~~~~~  260 (368)
T 3dzd_A          199 LFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQ------------------RVQAKLLRVLETGSFTRLGGNQKI  260 (368)
T ss_dssp             HHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGSCH------------------HHHHHHHHHHHHSEECCBTCCCBE
T ss_pred             hcCccccccCCcccccCChHhhcCCCeEEecChhhCCH------------------HHHHHHHHHHHhCCcccCCCCcce
Confidence            3321                 12457899999999843                  234456777652 1111111    


Q ss_pred             --CeEEEEEcCCC-------CCCCccccCCCccc-eEEEeCCCCH--HHHHHHHHHHhC
Q 013128          346 --GRIIVFTTNHK-------EKLDPALLRPGRMD-MHLHMSYCNT--SVFKQLAFNYLG  392 (449)
Q Consensus       346 --~~iiI~tTN~~-------~~ld~aLlrpgR~d-~~i~l~~p~~--~~r~~l~~~~l~  392 (449)
                        .+-+|+|||..       ..+.+.|..  |+. ..|++|+...  ++...|+..|+.
T Consensus       261 ~~~~rii~at~~~l~~~v~~g~fr~dL~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          261 EVDIRVISATNKNLEEEIKKGNFREDLYY--RLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             ECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             eeeeEEEEecCCCHHHHHHcCCccHHHHH--HhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence              34577777753       223334443  443 3688998877  778888887774

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=98.45  E-value=2.1e-07  Score=95.46  Aligned_cols=139  Identities=14%  Similarity=0.150  Sum_probs=83.0

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHH-HHHcCCcEEEEecccccChHHHHHH-
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAM-ANQLKFDIYDLDLSAVQSNSELRFL-  288 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~ai-A~~l~~~~~~l~~s~~~~~~~l~~~-  288 (449)
                      +.|.+++|+.+.-.+   ..+-..     ....-++||.|+||| ||++++++ ++.+....|.....  .+...+... 
T Consensus       215 I~G~e~vK~aLll~L---~GG~~k-----~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~--ss~~gLt~s~  283 (506)
T 3f8t_A          215 LPGAEEVGKMLALQL---FSCVGK-----NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRR--TELTDLTAVL  283 (506)
T ss_dssp             STTCHHHHHHHHHHH---TTCCSS-----GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGG--CCHHHHSEEE
T ss_pred             cCCCHHHHHHHHHHH---cCCccc-----cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCC--CCccCceEEE
Confidence            788888887775443   221100     011226999999999 99999999 77766555432211  111111000 


Q ss_pred             -----------HHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc-------CccccCCCCeEEE
Q 013128          289 -----------LLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID-------GLWSCCGEGRIIV  350 (449)
Q Consensus       289 -----------~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld-------g~~~~~~~~~iiI  350 (449)
                                 ........|++||||+.+..                  .+.+.|+..|+       |.  ..+....||
T Consensus       284 r~~tG~~~~~G~l~LAdgGvl~lDEIn~~~~------------------~~qsaLlEaMEe~~VtI~G~--~lparf~VI  343 (506)
T 3f8t_A          284 KEDRGWALRAGAAVLADGGILAVDHLEGAPE------------------PHRWALMEAMDKGTVTVDGI--ALNARCAVL  343 (506)
T ss_dssp             EESSSEEEEECHHHHTTTSEEEEECCTTCCH------------------HHHHHHHHHHHHSEEEETTE--EEECCCEEE
T ss_pred             EcCCCcccCCCeeEEcCCCeeehHhhhhCCH------------------HHHHHHHHHHhCCcEEECCE--EcCCCeEEE
Confidence                       00013468999999998742                  35566777765       22  223457899


Q ss_pred             EEcCCCC-----------CCCccccCCCccceEEE-eCCCCHHH
Q 013128          351 FTTNHKE-----------KLDPALLRPGRMDMHLH-MSYCNTSV  382 (449)
Q Consensus       351 ~tTN~~~-----------~ld~aLlrpgR~d~~i~-l~~p~~~~  382 (449)
                      +|+|..+           .|+++++.  |||..+. +++|+.+.
T Consensus       344 AA~NP~~~yd~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          344 AAINPGEQWPSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             EEECCCC--CCSCGGGGCCSCHHHHT--TCSEEEETTC------
T ss_pred             EEeCcccccCCCCCccccCCChHHhh--heeeEEEecCCCChhH
Confidence            9999875           78899999  9987554 56776543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.35  E-value=1.8e-06  Score=105.80  Aligned_cols=132  Identities=15%  Similarity=0.134  Sum_probs=94.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCC-CCceEEeeccchhhhcccccchhhhhccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMP-SRSMLVIEDIDCSVKLQNRESSEVQATNQ  322 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~  322 (449)
                      .|..+.||+|||||.+++.+|+.+|..++.++|+.-.+...+.++|.... .++..++|||+.+-.              
T Consensus       605 ~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~~--------------  670 (3245)
T 3vkg_A          605 MGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEE--------------  670 (3245)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSCH--------------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCCH--------------
Confidence            46689999999999999999999999999999999888877877776654 578899999998732              


Q ss_pred             hhhHHHHHHHHH----Hh---------c-CccccCCCCeEEEEEcCC----CCCCCccccCCCccceEEEeCCCCHHHHH
Q 013128          323 EENKVTLSGLLN----FI---------D-GLWSCCGEGRIIVFTTNH----KEKLDPALLRPGRMDMHLHMSYCNTSVFK  384 (449)
Q Consensus       323 ~~~~~~ls~LL~----~l---------d-g~~~~~~~~~iiI~tTN~----~~~ld~aLlrpgR~d~~i~l~~p~~~~r~  384 (449)
                      +.. ..+++.+.    .+         + |-.-......-|++|.|.    ...|+++|..  || +.|.|+.|+.+...
T Consensus       671 ~vL-Svv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~--lF-r~v~m~~Pd~~~i~  746 (3245)
T 3vkg_A          671 RIL-SAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKK--LF-RSMAMIKPDREMIA  746 (3245)
T ss_dssp             HHH-HHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHT--TE-EEEECCSCCHHHHH
T ss_pred             HHH-HHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHh--hc-EEEEEeCCCHHHHH
Confidence            111 11111111    11         1 211111234567888884    4689999999  88 66999999998887


Q ss_pred             HHHHHHhCc
Q 013128          385 QLAFNYLGI  393 (449)
Q Consensus       385 ~l~~~~l~~  393 (449)
                      ++.-.-.|.
T Consensus       747 ei~L~s~Gf  755 (3245)
T 3vkg_A          747 QVMLYSQGF  755 (3245)
T ss_dssp             HHHHHTTTC
T ss_pred             HHHHHHccc
Confidence            776544443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.30  E-value=5.9e-07  Score=106.05  Aligned_cols=112  Identities=13%  Similarity=0.133  Sum_probs=69.0

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc---------------------ChHHHHH---HHHcC
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ---------------------SNSELRF---LLLTM  292 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~---------------------~~~~l~~---~~~~~  292 (449)
                      ++.+++++||||||||||+||.++|.+.   |..+..++.....                     ....+..   .+.+.
T Consensus      1424 i~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr~ 1503 (2050)
T 3cmu_A         1424 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS 1503 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHhc
Confidence            7778899999999999999999998876   4556666554321                     1112222   23334


Q ss_pred             CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC
Q 013128          293 PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH  355 (449)
Q Consensus       293 ~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  355 (449)
                      .++++||||+++.+.+....++. ..........+.++++|..|++....  .+ ++|.+||.
T Consensus      1504 ~~~~lVVIDsi~al~p~~~~~g~-~~~~~~~~~~R~lsqlL~~L~~~~~~--~~-v~VI~tNq 1562 (2050)
T 3cmu_A         1504 GAVDVIVVDSVAALTPKAEIEGE-IGDSHMGLAARMMSQAMRKLAGNLKQ--SN-TLLIFINQ 1562 (2050)
T ss_dssp             TCCSEEEESCGGGCCCHHHHHSC-TTCCCTTHHHHHHHHHHHHHHHHHHT--TT-CEEEEEEC
T ss_pred             CCCCEEEEcChhHhccccccccc-ccccccchHHHHHHHHHHHHHHHHHh--CC-cEEEEEcc
Confidence            68999999999988763211110 00001111345678888888877653  33 44555554

>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=98.05  E-value=2e-05  Score=77.96  Aligned_cols=126  Identities=14%  Similarity=0.115  Sum_probs=81.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CC-c--EEEEecccccChHHHHHHHHc---CCCCceEEeeccch-hhhcccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KF-D--IYDLDLSAVQSNSELRFLLLT---MPSRSMLVIEDIDC-SVKLQNR  312 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~-~--~~~l~~s~~~~~~~l~~~~~~---~~~~~Il~iDeiD~-l~~~~~~  312 (449)
                      ...||||||+|+||++.++++++.+   +. +  ++.++  .-.+-.++......   ....-|++|||++. +..    
T Consensus        18 ~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~~----   91 (343)
T 1jr3_D           18 RAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSID--PNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNA----   91 (343)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECC--TTCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCCT----
T ss_pred             CcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEec--CCCCHHHHHHHhcCcCCccCCeEEEEECCCCCCCh----
Confidence            5689999999999999999999876   33 2  33333  21222233222221   24678999999987 521    


Q ss_pred             cchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC------CCCccccCCCccceEEEeCCCCHHHHHHH
Q 013128          313 ESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE------KLDPALLRPGRMDMHLHMSYCNTSVFKQL  386 (449)
Q Consensus       313 ~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l  386 (449)
                                    ...+.|+..++..    +...++|++++.++      .+-+++..  |. ..+.+..++.++....
T Consensus        92 --------------~~~~aLl~~le~p----~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~  150 (343)
T 1jr3_D           92 --------------AINEQLLTLTGLL----HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTCQTPEQAQLPRW  150 (343)
T ss_dssp             --------------THHHHHHHHHTTC----BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEECCCCTTHHHHH
T ss_pred             --------------HHHHHHHHHHhcC----CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHH
Confidence                          2345578888753    34456666555533      45567777  54 5688999998888888


Q ss_pred             HHHHhCcCC
Q 013128          387 AFNYLGISH  395 (449)
Q Consensus       387 ~~~~l~~~~  395 (449)
                      ++..+..++
T Consensus       151 l~~~~~~~g  159 (343)
T 1jr3_D          151 VAARAKQLN  159 (343)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHcC
Confidence            877765443

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.02  E-value=1.7e-05  Score=71.23  Aligned_cols=28  Identities=25%  Similarity=0.526  Sum_probs=23.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .+.|.||+|+|||||++.|++.++..+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i~~~   29 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGKRAI   29 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGGEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcCC
Confidence            3689999999999999999999865443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.01  E-value=8.9e-05  Score=78.55  Aligned_cols=162  Identities=21%  Similarity=0.233  Sum_probs=90.7

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHH-------cCCcEEEEecccc
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ-------LKFDIYDLDLSAV  279 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~-------l~~~~~~l~~s~~  279 (449)
                      ....++|.+...+.|.+.+..-           ....+-++|+||+|+|||+||..+++.       +...++.++++..
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~-----------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~  190 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKL-----------KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ  190 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTS-----------TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC
T ss_pred             CCCeecccHHHHHHHHHHHhcc-----------cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC
Confidence            3456889888888777655321           012456899999999999999998753       2223454444322


Q ss_pred             cCh-------------------------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHH
Q 013128          280 QSN-------------------------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVT  328 (449)
Q Consensus       280 ~~~-------------------------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~  328 (449)
                      ...                               ..+...+....++.+|||||++...                     
T Consensus       191 ~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~---------------------  249 (591)
T 1z6t_A          191 DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSW---------------------  249 (591)
T ss_dssp             CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHH---------------------
T ss_pred             chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHH---------------------
Confidence            100                               1122223333368999999997421                     


Q ss_pred             HHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEe-CCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHH
Q 013128          329 LSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHM-SYCNTSVFKQLAFNYLGISHHYLFEQIEELIK  407 (449)
Q Consensus       329 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l-~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~  407 (449)
                         .+..+       +.+..||+||........  .. |.. ..+.. ...+.++-.+++....+.......+...++++
T Consensus       250 ---~l~~l-------~~~~~ilvTsR~~~~~~~--~~-~~~-~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~  315 (591)
T 1z6t_A          250 ---VLKAF-------DSQCQILLTTRDKSVTDS--VM-GPK-YVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIK  315 (591)
T ss_dssp             ---HHHTT-------CSSCEEEEEESCGGGGTT--CC-SCE-EEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHH
T ss_pred             ---HHHHh-------cCCCeEEEECCCcHHHHh--cC-CCc-eEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence               12222       123466667765432111  11 222 22332 46888888999998886532223344555555


Q ss_pred             ccCCCHH
Q 013128          408 EVNVTPA  414 (449)
Q Consensus       408 ~~~~tpa  414 (449)
                      ..+--|.
T Consensus       316 ~~~G~PL  322 (591)
T 1z6t_A          316 ECKGSPL  322 (591)
T ss_dssp             HHTTCHH
T ss_pred             HhCCCcH
Confidence            5554453

>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=97.82  E-value=0.00017  Score=82.40  Aligned_cols=164  Identities=18%  Similarity=0.204  Sum_probs=96.2

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc-------CCcEEEEec
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL-------KFDIYDLDL  276 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l-------~~~~~~l~~  276 (449)
                      .|.....++|.++..++|.+.+...  .         ...+-+.|+|++|+|||+||+.+++..       ...++.+++
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~--~---------~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~  187 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKL--N---------GEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSI  187 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTT--T---------TSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEEC
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhc--c---------CCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEE
Confidence            3455567899998888887766321  0         113568899999999999999988762       223445555


Q ss_pred             ccccC---------------------------hHHHH----HHHHcCCCCceEEeeccchhhhcccccchhhhhccchhh
Q 013128          277 SAVQS---------------------------NSELR----FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEEN  325 (449)
Q Consensus       277 s~~~~---------------------------~~~l~----~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~  325 (449)
                      +....                           ...+.    ..+....++.+|||||++...                  
T Consensus       188 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~------------------  249 (1249)
T 3sfz_A          188 GKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW------------------  249 (1249)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH------------------
T ss_pred             CCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH------------------
Confidence            44211                           01111    111122348999999998531                  


Q ss_pred             HHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCC-CCHHHHHHHHHHHhCcCCCCCHHHHHH
Q 013128          326 KVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSY-CNTSVFKQLAFNYLGISHHYLFEQIEE  404 (449)
Q Consensus       326 ~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~-p~~~~r~~l~~~~l~~~~~~l~~~i~~  404 (449)
                            .+..+       +.+.-||.||..+.-... ..   .....+.++. ++.++-.+|+..+.......+.+...+
T Consensus       250 ------~~~~~-------~~~~~ilvTtR~~~~~~~-~~---~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~  312 (1249)
T 3sfz_A          250 ------VLKAF-------DNQCQILLTTRDKSVTDS-VM---GPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHS  312 (1249)
T ss_dssp             ------HHTTT-------CSSCEEEEEESSTTTTTT-CC---SCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHH
T ss_pred             ------HHHhh-------cCCCEEEEEcCCHHHHHh-hc---CCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHH
Confidence                  11111       123457777776543321 11   1234577775 888888999988876554444444555


Q ss_pred             HHHccCCCH
Q 013128          405 LIKEVNVTP  413 (449)
Q Consensus       405 l~~~~~~tp  413 (449)
                      +++..+--|
T Consensus       313 i~~~~~glP  321 (1249)
T 3sfz_A          313 IIKECKGSP  321 (1249)
T ss_dssp             HHHHTTTCH
T ss_pred             HHHHhCCCH
Confidence            555544334

>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=97.78  E-value=0.00013  Score=75.32  Aligned_cols=68  Identities=22%  Similarity=0.225  Sum_probs=40.3

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CC
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KF  269 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~  269 (449)
                      ..|..    ...|.+|++|  .+++++.+.. +..++...          ...++|.||||||||+++.+++..+   +.
T Consensus        12 ~~~~~----~~~p~~~~~L--n~~Q~~av~~-~~~~i~~~----------~~~~li~G~aGTGKT~ll~~~~~~l~~~~~   74 (459)
T 3upu_A           12 SGLVP----RGSHMTFDDL--TEGQKNAFNI-VMKAIKEK----------KHHVTINGPAGTGATTLTKFIIEALISTGE   74 (459)
T ss_dssp             -------------CCSSCC--CHHHHHHHHH-HHHHHHSS----------SCEEEEECCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCcc----ccCCCccccC--CHHHHHHHHH-HHHHHhcC----------CCEEEEEeCCCCCHHHHHHHHHHHHHhcCC
Confidence            45654    7888999886  4556555443 33344322          2379999999999999999999888   33


Q ss_pred             -cEEEEecc
Q 013128          270 -DIYDLDLS  277 (449)
Q Consensus       270 -~~~~l~~s  277 (449)
                       .++.+..+
T Consensus        75 ~~il~~a~T   83 (459)
T 3upu_A           75 TGIILAAPT   83 (459)
T ss_dssp             CCEEEEESS
T ss_pred             ceEEEecCc
Confidence             45555433

>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=97.71  E-value=0.00017  Score=65.88  Aligned_cols=40  Identities=23%  Similarity=0.172  Sum_probs=31.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~  278 (449)
                      |++.+.-++|+||||+|||+++..+|...+..++.++...
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            4555667999999999999999999985566777776543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.68  E-value=2.1e-05  Score=70.19  Aligned_cols=33  Identities=33%  Similarity=0.392  Sum_probs=29.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++.++|.||||||||++++.+|..+++++++.|
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d   37 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDSD   37 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            457999999999999999999999999988754

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.63  E-value=4.2e-05  Score=67.71  Aligned_cols=35  Identities=20%  Similarity=0.322  Sum_probs=30.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS  277 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s  277 (449)
                      +..++|.||||+||||+++++|..++.+++.++..
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~D   37 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVD   37 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCCeEEeccc
Confidence            35689999999999999999999999988877654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.60  E-value=3.2e-05  Score=70.24  Aligned_cols=33  Identities=36%  Similarity=0.458  Sum_probs=29.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ...++|.|||||||||+++++|..+++.+++.+
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            457999999999999999999999999887654

>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=97.60  E-value=0.00016  Score=72.04  Aligned_cols=70  Identities=14%  Similarity=0.126  Sum_probs=47.4

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hHHHH---HHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NSELR---FLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~~l~---~~~~~  291 (449)
                      |++...-++|+||||+|||+|+..+|..+   +..++.++......                     ..++.   ..+..
T Consensus        57 Gi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~  136 (356)
T 3hr8_A           57 GYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVR  136 (356)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhh
Confidence            45556679999999999999999999875   55666666543211                     11111   11223


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+++||.+..+.+
T Consensus       137 ~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             TSCCSEEEEECTTTCCC
T ss_pred             hcCCCeEEehHhhhhcC
Confidence            35688999999988764

>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=97.60  E-value=0.00012  Score=71.85  Aligned_cols=40  Identities=18%  Similarity=0.233  Sum_probs=31.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~  278 (449)
                      |++.+.-++|+||||+|||+++..+|...         +..++.++...
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            55666679999999999999999999875         45666666544

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.58  E-value=0.00038  Score=63.80  Aligned_cols=37  Identities=22%  Similarity=0.106  Sum_probs=27.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |++.+..++|+||||+|||+|++.+|..+   +..++.++
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            34445668999999999999999999765   34444443

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=97.58  E-value=6.1e-05  Score=66.01  Aligned_cols=32  Identities=28%  Similarity=0.319  Sum_probs=28.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      -++|.||||+||||+++.++..+++.+++.+.
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d~   34 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGSS   34 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCcc
Confidence            47899999999999999999999999887663

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.57  E-value=0.00023  Score=70.61  Aligned_cols=40  Identities=20%  Similarity=0.085  Sum_probs=31.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---------~~~~~~l~~s~  278 (449)
                      |++.+.-++|+||||+|||+++..+|...         +..++.++...
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            55666669999999999999999999873         45666666544

>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=97.57  E-value=0.0002  Score=66.39  Aligned_cols=40  Identities=20%  Similarity=0.181  Sum_probs=30.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH--c-------CCcEEEEeccc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ--L-------KFDIYDLDLSA  278 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~--l-------~~~~~~l~~s~  278 (449)
                      |++.+.-++|+||||+|||+|+..+|..  +       +...+.++...
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            4555667999999999999999999995  3       34566665543

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=97.56  E-value=3.6e-05  Score=68.96  Aligned_cols=33  Identities=27%  Similarity=0.406  Sum_probs=29.0

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .+.-++|.|+||+||||+++.++..+++.+++.
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~   36 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGLRLPLLSK   36 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcCCeEecH
Confidence            355689999999999999999999999887764

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.55  E-value=0.00017  Score=71.65  Aligned_cols=69  Identities=17%  Similarity=0.211  Sum_probs=46.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hHHHH---HHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NSELR---FLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~~l~---~~~~~  291 (449)
                      |++.++.++|+||||+|||+|+..+|..+   +..+..++......                     ..++.   ..+..
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~  136 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVR  136 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            45556679999999999999999998765   45666665433211                     11111   22333


Q ss_pred             CCCCceEEeeccchhh
Q 013128          292 MPSRSMLVIEDIDCSV  307 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~  307 (449)
                      ...+.+||||++..+.
T Consensus       137 ~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          137 SGALDIIVIDSVAALV  152 (349)
T ss_dssp             TTCCSEEEEECGGGCC
T ss_pred             cCCCCEEEEcChHhhc
Confidence            4568999999999886

>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=97.51  E-value=0.00023  Score=65.36  Aligned_cols=29  Identities=24%  Similarity=0.323  Sum_probs=24.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++...-+.|.||+|+|||+|++.++..+
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            45555669999999999999999999855

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.50  E-value=0.00018  Score=85.37  Aligned_cols=70  Identities=17%  Similarity=0.197  Sum_probs=53.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh------------------------HHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN------------------------SELRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~------------------------~~l~~~~~~  291 (449)
                      |++.++.+||+||||||||+|+.+++.+.   |.....+++......                        ..+...+.+
T Consensus      1077 gi~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~ 1156 (2050)
T 3cmu_A         1077 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1156 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHH
Confidence            57777889999999999999999998765   677777776654221                        123334555


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+|+||++..+.+
T Consensus      1157 ~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HTCCSEEEESCGGGCCC
T ss_pred             hCCCCEEEECCcccccc
Confidence            67899999999999854

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=97.50  E-value=0.00027  Score=70.27  Aligned_cols=29  Identities=24%  Similarity=0.323  Sum_probs=25.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++.+.-+.|+||||+|||+|+..+|...
T Consensus       127 gi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          127 GIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            55666679999999999999999999987

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.48  E-value=0.00014  Score=72.51  Aligned_cols=70  Identities=14%  Similarity=0.186  Sum_probs=48.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccccc---------------------ChHHHHHHH---Hc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQ---------------------SNSELRFLL---LT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~---------------------~~~~l~~~~---~~  291 (449)
                      |++.++.++|+||||+|||+||..+|..+   +..++.++.....                     +...+...+   ..
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~  138 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  138 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHh
Confidence            45566779999999999999999998775   5667777653221                     112222222   22


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+||||.+..+..
T Consensus       139 ~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          139 SGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             ccCCCEEEEcCHHHhcc
Confidence            35688999999998863

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=97.48  E-value=5.6e-05  Score=67.22  Aligned_cols=33  Identities=27%  Similarity=0.457  Sum_probs=29.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++.++|.||||+|||++++++|..+++.+++.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~d   43 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKYINVG   43 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEHH
Confidence            456999999999999999999999998887653

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.46  E-value=5.7e-05  Score=66.95  Aligned_cols=30  Identities=33%  Similarity=0.489  Sum_probs=27.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .++|.||||+||||+++++|..+++++++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~   35 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDS   35 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEcc
Confidence            589999999999999999999999887764

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.45  E-value=0.00043  Score=69.26  Aligned_cols=70  Identities=19%  Similarity=0.220  Sum_probs=47.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hHHHHHH---HHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NSELRFL---LLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~~l~~~---~~~  291 (449)
                      |++.++.++|+||||+|||+|+..+|..+   +..+..++...-..                     ...+...   +..
T Consensus        70 Gl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~  149 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  149 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHh
Confidence            45556679999999999999999988775   56666666543211                     1122222   223


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+||||.+..+..
T Consensus       150 ~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             TTCCSEEEEECTTTCCC
T ss_pred             cCCCCEEEEeChHHhcc
Confidence            35688999999998863

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=97.45  E-value=6.8e-05  Score=66.85  Aligned_cols=32  Identities=34%  Similarity=0.531  Sum_probs=28.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..|+|.|+||+|||++++.+|..+++++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            35899999999999999999999999987654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.43  E-value=7.5e-05  Score=65.75  Aligned_cols=31  Identities=42%  Similarity=0.735  Sum_probs=27.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..+.|.|||||||||+++.+|..++..+++.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id~   35 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDS   35 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEec
Confidence            4689999999999999999999999876653

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=97.43  E-value=7e-05  Score=67.15  Aligned_cols=33  Identities=30%  Similarity=0.514  Sum_probs=28.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH-cCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ-LKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~-l~~~~~~l~  275 (449)
                      +..++|.|+||||||++++.+|.. +|+++++++
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d   43 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEVG   43 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHH
Confidence            346999999999999999999999 788877654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.42  E-value=7.4e-05  Score=65.67  Aligned_cols=32  Identities=38%  Similarity=0.564  Sum_probs=29.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..++|.|+|||||||+++.+|..+++++++.+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~D   39 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTD   39 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            46899999999999999999999999988754

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.42  E-value=5e-05  Score=68.49  Aligned_cols=31  Identities=16%  Similarity=0.240  Sum_probs=23.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l  274 (449)
                      .-++++||||+|||+++..++..+   +..++.+
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~   37 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVF   37 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            457899999999999997676654   5554433

>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=97.37  E-value=0.0044  Score=65.11  Aligned_cols=160  Identities=13%  Similarity=0.085  Sum_probs=89.9

Q ss_pred             cCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHH----HcC--Cc-EEEEeccccc----
Q 013128          212 ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMAN----QLK--FD-IYDLDLSAVQ----  280 (449)
Q Consensus       212 ~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~----~l~--~~-~~~l~~s~~~----  280 (449)
                      +|.++.+++|.+.+..--          ....+.+.|+|++|+|||+||+.+++    ...  ++ .+.++.+...    
T Consensus       131 ~GR~~~~~~l~~~L~~~~----------~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~  200 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC----------DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST  200 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT----------TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHH
T ss_pred             CCchHHHHHHHHHHhccc----------CCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCH
Confidence            488888888888774311          11245688999999999999999997    232  22 2233433311    


Q ss_pred             --------------------------ChHHHHHHHH-c-CC-CCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          281 --------------------------SNSELRFLLL-T-MP-SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       281 --------------------------~~~~l~~~~~-~-~~-~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                                +...+...+. . .. ++.+|||||++....                    + .
T Consensus       201 ~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~--------------------~-~  259 (549)
T 2a5y_B          201 FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEET--------------------I-R  259 (549)
T ss_dssp             HHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHH--------------------H-H
T ss_pred             HHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchh--------------------h-c
Confidence                                      0011122221 1 13 389999999986321                    0 1


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC--CCCHHHHHHHHHcc
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH--HYLFEQIEELIKEV  409 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~--~~l~~~i~~l~~~~  409 (449)
                      +.. .        .+..||.||....-.   ..- +.....+.++..+.++-.+|+........  ..+.+...++++.-
T Consensus       260 ~~~-~--------~gs~ilvTTR~~~v~---~~~-~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c  326 (549)
T 2a5y_B          260 WAQ-E--------LRLRCLVTTRDVEIS---NAA-SQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELS  326 (549)
T ss_dssp             HHH-H--------TTCEEEEEESBGGGG---GGC-CSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHH
T ss_pred             ccc-c--------CCCEEEEEcCCHHHH---HHc-CCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHh
Confidence            111 1        223566777653221   110 11335689999999999999998854332  12223345555555


Q ss_pred             CCCHHH
Q 013128          410 NVTPAE  415 (449)
Q Consensus       410 ~~tpa~  415 (449)
                      +--|--
T Consensus       327 ~GlPLA  332 (549)
T 2a5y_B          327 SGNPAT  332 (549)
T ss_dssp             TTCHHH
T ss_pred             CCChHH
Confidence            555533

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.36  E-value=0.00026  Score=68.36  Aligned_cols=34  Identities=32%  Similarity=0.525  Sum_probs=28.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      +..++|.||||+||||+++.++..++...+.++.
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~   66 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   66 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            4568999999999999999999998545566654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.36  E-value=0.00011  Score=69.66  Aligned_cols=32  Identities=28%  Similarity=0.528  Sum_probs=29.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      -++|.||||||||++++++|..+++.++..|.
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~~~~i~~D~   34 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETGWPVVALDR   34 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCCEEECCS
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCCCeEEeccH
Confidence            47899999999999999999999999887764

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=97.34  E-value=9.7e-05  Score=64.93  Aligned_cols=32  Identities=22%  Similarity=0.447  Sum_probs=28.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..++|.|+||+|||++++.+|..+++++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~d   34 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEccc
Confidence            35899999999999999999999999877643

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=97.34  E-value=0.00012  Score=66.30  Aligned_cols=32  Identities=31%  Similarity=0.518  Sum_probs=28.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..|+|.||||+||||+++.++..+++.+++.+
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l~~~~i~~d   52 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKLGIPQISTG   52 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            45889999999999999999999999887663

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.31  E-value=0.00011  Score=64.14  Aligned_cols=29  Identities=24%  Similarity=0.405  Sum_probs=26.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      -++|.||||+||||+++.+ ..+|++++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEH
Confidence            5789999999999999999 9999987765

>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=97.31  E-value=0.0005  Score=72.90  Aligned_cols=51  Identities=25%  Similarity=0.268  Sum_probs=36.2

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      ....+++++.+...+    .            .+.+++.||||||||+++.+++..+   +..+..+..+
T Consensus       188 ~~L~~~Q~~Av~~~~----~------------~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT  241 (574)
T 3e1s_A          188 KGLSEEQASVLDQLA----G------------HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPT  241 (574)
T ss_dssp             TTCCHHHHHHHHHHT----T------------CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CCCCHHHHHHHHHHH----h------------CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCc
Confidence            345667776664432    1            3568999999999999999999866   5666655443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.31  E-value=0.00011  Score=65.55  Aligned_cols=32  Identities=19%  Similarity=0.348  Sum_probs=28.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.-|+|.|+|||||||+++.++..++..+++.
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   34 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYGYTHLSA   34 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            35689999999999999999999999877654

>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=97.30  E-value=0.00046  Score=65.99  Aligned_cols=29  Identities=31%  Similarity=0.286  Sum_probs=24.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++...-++|+||||+|||+|+..+|..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            44445669999999999999999999755

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.27  E-value=0.00016  Score=65.55  Aligned_cols=33  Identities=27%  Similarity=0.399  Sum_probs=28.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-++|.||||+||||+++.++..+++.+++.+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~d   50 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEGD   50 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeCC
Confidence            346999999999999999999999988776543

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.27  E-value=0.00013  Score=65.42  Aligned_cols=33  Identities=15%  Similarity=0.336  Sum_probs=29.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-++|.||||+||||+++.+|..++..+++.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~d   41 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG   41 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            356899999999999999999999998877654

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.26  E-value=0.00012  Score=67.50  Aligned_cols=31  Identities=19%  Similarity=0.416  Sum_probs=28.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.|+||+||||+++.+|..+++.+++.
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   36 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYGLAHLST   36 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCceEEeh
Confidence            4589999999999999999999999888765

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.25  E-value=0.00015  Score=63.47  Aligned_cols=31  Identities=29%  Similarity=0.449  Sum_probs=27.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .++|.|+||+||||+++.++..+++++++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   32 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDVD   32 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            3789999999999999999999999887654

>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=97.25  E-value=0.0005  Score=67.21  Aligned_cols=28  Identities=18%  Similarity=0.201  Sum_probs=24.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |++.+.-++|+||||+|||+++..+|..
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4555666999999999999999999976

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=97.24  E-value=0.00014  Score=64.81  Aligned_cols=33  Identities=18%  Similarity=0.340  Sum_probs=28.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-++|.|+|||||||+++.++..+++.+++.+
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   38 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAG   38 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEeeHH
Confidence            456899999999999999999999998777653

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.24  E-value=0.00012  Score=65.22  Aligned_cols=31  Identities=29%  Similarity=0.641  Sum_probs=27.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||||+++.+|..+++.+++.
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l~~~~i~~   35 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQELGFKKLST   35 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTCEEECH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEecH
Confidence            3588999999999999999999999876654

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=97.23  E-value=0.00013  Score=65.06  Aligned_cols=30  Identities=17%  Similarity=0.436  Sum_probs=26.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC-----CcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK-----FDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~-----~~~~~  273 (449)
                      .-++|.||||+||||+++.++..++     ++++.
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~   38 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVS   38 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEe
Confidence            4689999999999999999999997     66554

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.22  E-value=9.9e-05  Score=65.14  Aligned_cols=29  Identities=28%  Similarity=0.330  Sum_probs=24.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHH-HcCCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMAN-QLKFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~-~l~~~~~  272 (449)
                      .-++|.||||+||||+++.++. .+++.++
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~i   32 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEEe
Confidence            4689999999999999999999 4655444

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=97.22  E-value=0.0018  Score=72.56  Aligned_cols=55  Identities=18%  Similarity=0.240  Sum_probs=38.7

Q ss_pred             cCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc------CCcEEEEeccc
Q 013128          212 ALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL------KFDIYDLDLSA  278 (449)
Q Consensus       212 ~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l------~~~~~~l~~s~  278 (449)
                      +|.++..+.|.+.+...            ...+-+.|+||.|+|||+||+.+++..      ...++-++++.
T Consensus       131 VGRe~eLeeL~elL~~~------------d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~  191 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLEL------------RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN  191 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHC------------CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCC
T ss_pred             CCcHHHHHHHHHHHhcc------------CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCC
Confidence            78888888887766421            113578899999999999999998643      33455555443

>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=97.22  E-value=0.00017  Score=66.03  Aligned_cols=29  Identities=21%  Similarity=0.348  Sum_probs=26.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.+|..++..+++.
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            78999999999999999999999888766

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=97.22  E-value=0.00015  Score=64.84  Aligned_cols=36  Identities=31%  Similarity=0.331  Sum_probs=28.9

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      ..+..+.|.||||+||||+++.++..++...+.++.
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            334568999999999999999999987666655554

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.21  E-value=0.00015  Score=65.25  Aligned_cols=33  Identities=18%  Similarity=0.369  Sum_probs=28.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-|+|.||||+||||+++.+|..+++.+++.+
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   44 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLSTG   44 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            356899999999999999999999998776653

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=97.20  E-value=0.00019  Score=66.08  Aligned_cols=31  Identities=23%  Similarity=0.442  Sum_probs=27.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||||+++.+|..++..+++.
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            4589999999999999999999999877765

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.20  E-value=0.0004  Score=65.55  Aligned_cols=37  Identities=22%  Similarity=0.291  Sum_probs=30.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +..++|.||||+||||+++.++..++...+.++...+
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            4568999999999999999999999866666665544

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.20  E-value=0.00016  Score=67.01  Aligned_cols=32  Identities=16%  Similarity=0.401  Sum_probs=28.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.-++|.||||+||||+++.+|..++..+++.
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            35689999999999999999999999877765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.18  E-value=0.00019  Score=65.71  Aligned_cols=29  Identities=21%  Similarity=0.403  Sum_probs=26.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.+|..++..+++.
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKYEIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEeeH
Confidence            78999999999999999999999888766

>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=97.17  E-value=0.00086  Score=67.84  Aligned_cols=28  Identities=32%  Similarity=0.256  Sum_probs=23.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |++...-++|+||||+|||+|+..+|-.
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~~  201 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAVT  201 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHHH
Confidence            5566666999999999999999977644

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=97.16  E-value=0.00024  Score=62.63  Aligned_cols=31  Identities=35%  Similarity=0.530  Sum_probs=26.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||||+++.++..+|..+++.
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~   39 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDG   39 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEG
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEeC
Confidence            4588999999999999999999998766543

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.15  E-value=0.00023  Score=64.38  Aligned_cols=32  Identities=19%  Similarity=0.356  Sum_probs=28.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .-|+|.|||||||||+++.++..+++.+++.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            45889999999999999999999998777654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.14  E-value=0.00022  Score=63.20  Aligned_cols=29  Identities=21%  Similarity=0.271  Sum_probs=22.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .-++|.|+||+||||+++.++..++.+++
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            46889999999999999999999999877

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=97.13  E-value=0.00025  Score=66.00  Aligned_cols=31  Identities=26%  Similarity=0.408  Sum_probs=27.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..|+|.|+|||||||+++.+|..+++.++..
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   47 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   47 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            4589999999999999999999999887765

>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=97.10  E-value=0.0013  Score=64.28  Aligned_cols=69  Identities=17%  Similarity=0.085  Sum_probs=44.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEeccccc---------------------ChHHH-H---HH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAVQ---------------------SNSEL-R---FL  288 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~~---------------------~~~~l-~---~~  288 (449)
                      |++.. -++++||||+|||+|+..++..+     +..+..++...-.                     +..++ .   ..
T Consensus        25 Gl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~  103 (333)
T 3io5_A           25 GMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQ  103 (333)
T ss_dssp             CBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHH
T ss_pred             CCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHH
Confidence            45555 48899999999999987766554     4556666643221                     11122 1   11


Q ss_pred             H--HcCCCCceEEeeccchhhh
Q 013128          289 L--LTMPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       289 ~--~~~~~~~Il~iDeiD~l~~  308 (449)
                      +  .....+.+|+||-|..+.+
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCBC
T ss_pred             HHHhhccCceEEEEeccccccc
Confidence            2  2335789999999999864

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.10  E-value=0.00016  Score=66.68  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=27.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +..|+|.||||+||||+++.+|..++..++++
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   36 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLAHISA   36 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            45689999999999999999999999765543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.08  E-value=0.00037  Score=63.15  Aligned_cols=31  Identities=19%  Similarity=0.487  Sum_probs=26.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      +.-+.|.||+|+||||+++.++..+|..+++
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            4568899999999999999999999765543

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=97.04  E-value=0.0005  Score=60.97  Aligned_cols=34  Identities=29%  Similarity=0.379  Sum_probs=29.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +.-+.|.|++|+||||+++.++..+   |++++.++.
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~   41 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDG   41 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECC
Confidence            3458899999999999999999998   888887763

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.04  E-value=0.00038  Score=68.33  Aligned_cols=34  Identities=29%  Similarity=0.547  Sum_probs=30.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      +..++|.||+|||||+++..+|..++..++++|.
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds   38 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALPCELISVDS   38 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEEECT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCcEEeccc
Confidence            3578999999999999999999999998888864

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.04  E-value=0.00046  Score=61.50  Aligned_cols=30  Identities=17%  Similarity=0.208  Sum_probs=27.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +.|.|+||+||||+++.+++.+   |++++..+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            7899999999999999999998   89888775

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.03  E-value=0.00042  Score=64.16  Aligned_cols=30  Identities=20%  Similarity=0.513  Sum_probs=26.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      ++.++|.||||+||+|.|+.||..+++..+
T Consensus        29 ~kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           29 AKVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             CEEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            567889999999999999999999987654

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.02  E-value=0.00024  Score=70.48  Aligned_cols=51  Identities=20%  Similarity=0.369  Sum_probs=37.8

Q ss_pred             CHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          214 DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       214 ~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .+.+.+.+.+.+...+...+         ...++|.||||+|||++++++|+.++++++.
T Consensus         4 ~~~L~~~il~~l~~~i~~g~---------~~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A            4 THKLADDVLQLLDNRIEDNY---------RVCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             HHHHHHHHHHHHHHTTTTCS---------CEEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCC---------eeEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            35566667766665543221         2469999999999999999999999887743

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.02  E-value=0.00034  Score=65.68  Aligned_cols=33  Identities=18%  Similarity=0.387  Sum_probs=28.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.-++|.||||+||||+++.+++.++..+++.+
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~~   61 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTG   61 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEecH
Confidence            456899999999999999999999998877653

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=97.02  E-value=0.00028  Score=64.61  Aligned_cols=29  Identities=17%  Similarity=0.285  Sum_probs=26.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.+|..+++.++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            78999999999999999999999888765

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.01  E-value=0.0005  Score=80.64  Aligned_cols=70  Identities=16%  Similarity=0.208  Sum_probs=51.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hHHHHHH---HHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NSELRFL---LLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~~l~~~---~~~  291 (449)
                      |++.++.++|+||||||||+||.++|...   +..++.++......                     ...+..+   +.+
T Consensus        30 Gi~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~  109 (1706)
T 3cmw_A           30 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  109 (1706)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHh
Confidence            56777889999999999999999988763   67778877665322                     1222222   222


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+||||++..+..
T Consensus       110 ~~~~~LVVIDSLt~L~~  126 (1706)
T 3cmw_A          110 SGAVDVIVVDSVAALTP  126 (1706)
T ss_dssp             HTCCSEEEESCSTTCCC
T ss_pred             ccCCCEEEEcchhhhcc
Confidence            35789999999998865

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.95  E-value=0.00039  Score=64.28  Aligned_cols=29  Identities=21%  Similarity=0.473  Sum_probs=26.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.++..+++.++..
T Consensus         3 I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            78999999999999999999999876654

>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=96.92  E-value=0.00055  Score=62.84  Aligned_cols=28  Identities=29%  Similarity=0.564  Sum_probs=25.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ++|.||||+||+|.|+.||..+++..+.
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            6889999999999999999999887654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.90  E-value=0.00056  Score=61.49  Aligned_cols=29  Identities=28%  Similarity=0.691  Sum_probs=25.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      -+.|.|+||+||||+++.+|+.++..++.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            37899999999999999999999986653

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=96.88  E-value=0.00042  Score=62.72  Aligned_cols=30  Identities=30%  Similarity=0.333  Sum_probs=26.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -+.|.||+||||||+++.+|+ +|+.+++.+
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d   32 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDAD   32 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEcc
Confidence            478999999999999999999 898887765

>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=96.88  E-value=0.00063  Score=63.71  Aligned_cols=31  Identities=23%  Similarity=0.506  Sum_probs=26.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      +.-+.|.||||+||||+++.||..++...++
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~~   57 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHLS   57 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            4568999999999999999999999876543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.86  E-value=0.00053  Score=64.91  Aligned_cols=33  Identities=33%  Similarity=0.553  Sum_probs=29.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +..+.|.||+|+||||+++.+|..+++++++.+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~d   80 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLGYTFFDCD   80 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCcEEeCc
Confidence            356999999999999999999999999888754

>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=96.86  E-value=0.00066  Score=61.15  Aligned_cols=33  Identities=15%  Similarity=0.184  Sum_probs=28.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~~  276 (449)
                      .-|.|.||||+||||+++.++..+ +++++.++.
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~   38 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNF   38 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEES
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEec
Confidence            458899999999999999999999 588877653

>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=96.86  E-value=0.0028  Score=57.56  Aligned_cols=109  Identities=11%  Similarity=0.152  Sum_probs=67.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc--cC-h---------------------------------HH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV--QS-N---------------------------------SE  284 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~--~~-~---------------------------------~~  284 (449)
                      ..+++|+++|.||||+|-++|-..   |..+..+..-.-  .. +                                 ..
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~  108 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAV  108 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHH
Confidence            358899999999999999999887   777777743221  00 0                                 01


Q ss_pred             HHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCcc
Q 013128          285 LRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPA  362 (449)
Q Consensus       285 l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~a  362 (449)
                      +.......  ....+|+|||+-......               -.....++..+..    .++..-||+|+|.+   +++
T Consensus       109 l~~a~~~l~~~~yDlvILDEi~~al~~g---------------~l~~~ev~~~l~~----Rp~~~~vIlTGr~a---p~~  166 (196)
T 1g5t_A          109 WQHGKRMLADPLLDMVVLDELTYMVAYD---------------YLPLEEVISALNA----RPGHQTVIITGRGC---HRD  166 (196)
T ss_dssp             HHHHHHHTTCTTCSEEEEETHHHHHHTT---------------SSCHHHHHHHHHT----SCTTCEEEEECSSC---CHH
T ss_pred             HHHHHHHHhcCCCCEEEEeCCCccccCC---------------CCCHHHHHHHHHh----CcCCCEEEEECCCC---cHH
Confidence            11222222  456899999997653210               1122346666653    24667889999885   566


Q ss_pred             ccCCCccceEEEeC
Q 013128          363 LLRPGRMDMHLHMS  376 (449)
Q Consensus       363 LlrpgR~d~~i~l~  376 (449)
                      |+.  .-|.+-+|.
T Consensus       167 l~e--~AD~VTem~  178 (196)
T 1g5t_A          167 ILD--LADTVSELR  178 (196)
T ss_dssp             HHH--HCSEEEECC
T ss_pred             HHH--hCcceeeec
Confidence            666  666666654

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.85  E-value=0.00068  Score=62.24  Aligned_cols=31  Identities=35%  Similarity=0.587  Sum_probs=27.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .-+.|.||+||||||+++.++..+++++++.
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d~   36 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDS   36 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            3588999999999999999999999877653

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.82  E-value=0.00042  Score=61.66  Aligned_cols=24  Identities=33%  Similarity=0.517  Sum_probs=22.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -|+|.||||+||||+++.++..++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999886

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.82  E-value=0.00099  Score=60.28  Aligned_cols=33  Identities=33%  Similarity=0.342  Sum_probs=26.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +.-+.|.||+|+||||+++++|..+   |...+.++
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            4568899999999999999999998   55434444

>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=96.81  E-value=0.00076  Score=63.94  Aligned_cols=33  Identities=30%  Similarity=0.392  Sum_probs=28.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH---cCCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ---LKFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~---l~~~~~~l~~  276 (449)
                      .-|+|.|+||+||||+++.++..   .|+.++.++.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~   40 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGS   40 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECc
Confidence            45889999999999999999998   6888775543

>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=96.80  E-value=0.00065  Score=61.33  Aligned_cols=31  Identities=26%  Similarity=0.295  Sum_probs=28.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .+.|.||+|+|||++++.+|..+++++++.+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg~~~~d~d   34 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALGVPYLSSG   34 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCceeccc
Confidence            5789999999999999999999999888764

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=96.79  E-value=0.00057  Score=61.96  Aligned_cols=30  Identities=27%  Similarity=0.362  Sum_probs=26.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .+.|.||+||||||+++.+|. +|+++++.+
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~d   33 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDAD   33 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccchH
Confidence            477999999999999999998 888887654

>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=96.77  E-value=0.00091  Score=62.59  Aligned_cols=32  Identities=34%  Similarity=0.390  Sum_probs=28.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +..+.|.||||+||||+++.+|..+++.+++.
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg~~~~d~   40 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALGARYLDT   40 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            34688999999999999999999999887654

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=96.75  E-value=0.0011  Score=61.60  Aligned_cols=33  Identities=18%  Similarity=0.192  Sum_probs=27.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      -.+++.|+||||||+++-++|..+   |+++..++.
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~   42 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVV   42 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEe
Confidence            358999999999999999999887   777665544

>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=96.75  E-value=0.0033  Score=58.32  Aligned_cols=62  Identities=15%  Similarity=0.215  Sum_probs=40.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc-------ccc-------------ChHHHHHHHHcC---CCCceE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS-------AVQ-------------SNSELRFLLLTM---PSRSML  298 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s-------~~~-------------~~~~l~~~~~~~---~~~~Il  298 (449)
                      -++++||||+|||+++..++..+   +..++.+...       .+.             ...++...+...   ..+.+|
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvV   93 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVI   93 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEE
Confidence            47788999999999998888777   5556655211       111             112343334332   347899


Q ss_pred             Eeeccchh
Q 013128          299 VIEDIDCS  306 (449)
Q Consensus       299 ~iDeiD~l  306 (449)
                      +|||+..+
T Consensus        94 iIDEaQ~l  101 (223)
T 2b8t_A           94 GIDEVQFF  101 (223)
T ss_dssp             EECSGGGS
T ss_pred             EEecCccC
Confidence            99999865

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.74  E-value=0.0011  Score=59.83  Aligned_cols=31  Identities=26%  Similarity=0.343  Sum_probs=26.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC--cEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF--DIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l  274 (449)
                      .-|+|.||||+||||+++.++..++.  +++..
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~   37 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKRDVYLT   37 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTSCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcCCEEEe
Confidence            45889999999999999999999876  35443

>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=96.74  E-value=0.00075  Score=61.22  Aligned_cols=31  Identities=26%  Similarity=0.354  Sum_probs=27.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -+.|.|++||||||+++.++..+|+++++.|
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D   44 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVD   44 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECc
Confidence            4779999999999999999999999888765

>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=96.64  E-value=0.0078  Score=56.09  Aligned_cols=32  Identities=22%  Similarity=0.187  Sum_probs=26.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .+++.||+|+|||.++.+++..++..++.+-.
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P  141 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  141 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeC
Confidence            48999999999999999999998766665543

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.63  E-value=0.0009  Score=60.13  Aligned_cols=31  Identities=29%  Similarity=0.388  Sum_probs=27.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..+.|.|++||||||+++.+|.. |+.+++.+
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            45889999999999999999998 88887665

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.63  E-value=0.0033  Score=67.47  Aligned_cols=60  Identities=28%  Similarity=0.434  Sum_probs=40.0

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      |..|-+-.+++++++.|...+.    .           +.-.|++||||||||+++..+...+   +..+..+..+..
T Consensus       182 ~~~~~~~~LN~~Q~~AV~~al~----~-----------~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN~  244 (646)
T 4b3f_X          182 PLTFFNTCLDTSQKEAVLFALS----Q-----------KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNI  244 (646)
T ss_dssp             CCCCSSTTCCHHHHHHHHHHHH----C-----------SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHH
T ss_pred             cccccCCCCCHHHHHHHHHHhc----C-----------CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCchH
Confidence            3344344568888888876552    1           1247899999999998877666555   566666655543

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=96.61  E-value=0.0079  Score=61.70  Aligned_cols=75  Identities=13%  Similarity=0.166  Sum_probs=56.4

Q ss_pred             CceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCC-------------CCCCCc
Q 013128          295 RSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNH-------------KEKLDP  361 (449)
Q Consensus       295 ~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~-------------~~~ld~  361 (449)
                      |.|++|||+|.+..                  ...+.|+..|+.-    ... ++|++||.             ++.|+|
T Consensus       296 ~~VliIDEa~~l~~------------------~a~~aLlk~lEe~----~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~  352 (456)
T 2c9o_A          296 PGVLFVDEVHMLDI------------------ECFTYLHRALESS----IAP-IVIFASNRGNCVIRGTEDITSPHGIPL  352 (456)
T ss_dssp             ECEEEEESGGGCBH------------------HHHHHHHHHTTST----TCC-EEEEEECCSEEECBTTSSCEEETTCCH
T ss_pred             ceEEEEechhhcCH------------------HHHHHHHHHhhcc----CCC-EEEEecCCccccccccccccccccCCh
Confidence            47999999998842                  3567788888753    233 45544432             778999


Q ss_pred             cccCCCccceEEEeCCCCHHHHHHHHHHHhCcCC
Q 013128          362 ALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISH  395 (449)
Q Consensus       362 aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~  395 (449)
                      .+++  ||.. +.+++++.++..++++..+..++
T Consensus       353 ~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~~~  383 (456)
T 2c9o_A          353 DLLD--RVMI-IRTMLYTPQEMKQIIKIRAQTEG  383 (456)
T ss_dssp             HHHT--TEEE-EECCCCCHHHHHHHHHHHHHHHT
T ss_pred             hHHh--hcce-eeCCCCCHHHHHHHHHHHHHHhC
Confidence            9999  9976 69999999999999987765433

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.60  E-value=0.0054  Score=62.96  Aligned_cols=37  Identities=14%  Similarity=0.229  Sum_probs=29.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~  275 (449)
                      |++.+.-++|.||||+|||+++..+|..+    |.++..++
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            56656669999999999999999988765    44666655

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.58  E-value=0.0013  Score=60.18  Aligned_cols=32  Identities=28%  Similarity=0.393  Sum_probs=28.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ..+.|.|++|||||++++.++..+|+++++.+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~d   35 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDTG   35 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecCC
Confidence            46889999999999999999999998887754

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.58  E-value=0.0013  Score=59.67  Aligned_cols=27  Identities=26%  Similarity=0.512  Sum_probs=24.2

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .++-++|.||||+||||+++.++..++
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            356789999999999999999999985

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.57  E-value=0.0005  Score=62.37  Aligned_cols=28  Identities=21%  Similarity=0.214  Sum_probs=24.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      +.-|.|.|+|||||||+++.++..++..
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~   37 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNN   37 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            3458899999999999999999988544

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.56  E-value=0.00099  Score=65.64  Aligned_cols=36  Identities=31%  Similarity=0.482  Sum_probs=31.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      .-++|.||+|||||+|+..||..++..+++.|--.+
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~qv   76 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKMQV   76 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSSTT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccccccc
Confidence            468899999999999999999999998888776544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.55  E-value=0.0014  Score=58.23  Aligned_cols=26  Identities=15%  Similarity=0.436  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++-+.|.||+|+|||||++.++..+.
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            35688999999999999999999874

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=96.53  E-value=0.021  Score=59.97  Aligned_cols=73  Identities=4%  Similarity=0.118  Sum_probs=48.5

Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC--CCCccccCCCccceEE
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE--KLDPALLRPGRMDMHL  373 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~--~ld~aLlrpgR~d~~i  373 (449)
                      .+|+|||+..+.....           ......+..+...  |    ..-++-+|++|.+|.  .|+..+..  -|...|
T Consensus       345 ivvVIDE~~~L~~~~~-----------~~~~~~L~~Iar~--G----Ra~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI  405 (574)
T 2iut_A          345 IVVVVDEFADMMMIVG-----------KKVEELIARIAQK--A----RAAGIHLILATQRPSVDVITGLIKA--NIPTRI  405 (574)
T ss_dssp             EEEEESCCTTHHHHTC-----------HHHHHHHHHHHHH--C----TTTTEEEEEEESCCCTTTSCHHHHH--TCCEEE
T ss_pred             EEEEEeCHHHHhhhhh-----------HHHHHHHHHHHHH--H----hhCCeEEEEEecCcccccccHHHHh--hhccEE
Confidence            5899999998864211           1111222223221  1    135688999999987  78877766  677888


Q ss_pred             EeCCCCHHHHHHHH
Q 013128          374 HMSYCNTSVFKQLA  387 (449)
Q Consensus       374 ~l~~p~~~~r~~l~  387 (449)
                      .+...+..+-+.++
T Consensus       406 ~lrv~s~~Dsr~IL  419 (574)
T 2iut_A          406 AFQVSSKIDSRTIL  419 (574)
T ss_dssp             EECCSCHHHHHHHH
T ss_pred             EEEcCCHHHHHHhc
Confidence            89988888877776

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.53  E-value=0.0019  Score=60.88  Aligned_cols=30  Identities=33%  Similarity=0.591  Sum_probs=26.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ..+.|.||+|+||||+++.+|..+|+.+++
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d   57 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLLD   57 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcCC
Confidence            458899999999999999999999987765

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=96.52  E-value=0.0013  Score=60.23  Aligned_cols=31  Identities=35%  Similarity=0.469  Sum_probs=27.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .-+.|.|++|+||||+++.++. +|+++++.|
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~D   35 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDAD   35 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEcc
Confidence            4588999999999999999998 888877654

>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=96.46  E-value=0.0018  Score=62.96  Aligned_cols=34  Identities=24%  Similarity=0.521  Sum_probs=29.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      +.-++|.||+|+|||+|+..+|..++..++..|.
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   43 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKILPVELISVDS   43 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEECCT
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhCCCcEEeccc
Confidence            4568899999999999999999999988777654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.46  E-value=0.0019  Score=59.67  Aligned_cols=38  Identities=26%  Similarity=0.184  Sum_probs=28.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |++.+.-++|+||||+|||+++..+|..+   +..++.++.
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~   59 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVAL   59 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEc
Confidence            45556679999999999999988887654   455555543

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.45  E-value=0.0017  Score=60.42  Aligned_cols=33  Identities=24%  Similarity=0.423  Sum_probs=28.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +..+.|.|++|+|||++++.+|..+|+++++.+
T Consensus        16 ~~~i~i~G~~gsGKst~~~~l~~~lg~~~~d~d   48 (236)
T 1q3t_A           16 TIQIAIDGPASSGKSTVAKIIAKDFGFTYLDTG   48 (236)
T ss_dssp             CCEEEEECSSCSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCceecCC
Confidence            345889999999999999999999998877643

>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=96.44  E-value=0.0011  Score=63.84  Aligned_cols=31  Identities=26%  Similarity=0.310  Sum_probs=25.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-CCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-KFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l  274 (449)
                      .-|+|.||||+||||+++.++..+ ++.+++.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i~~   34 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNINR   34 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEECH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEecc
Confidence            468999999999999999999974 6655543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.44  E-value=0.0028  Score=56.40  Aligned_cols=33  Identities=30%  Similarity=0.512  Sum_probs=26.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~  275 (449)
                      +.-++|.|+||+||||+++.+|..++   ..+..++
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~   48 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLD   48 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEee
Confidence            34588999999999999999999884   4454444

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.44  E-value=0.0019  Score=57.61  Aligned_cols=25  Identities=40%  Similarity=0.631  Sum_probs=22.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -+.|.||+|+||||+++.++..++.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~~g   28 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQLDN   28 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSS
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCC
Confidence            4789999999999999999987654

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=96.43  E-value=0.0014  Score=59.68  Aligned_cols=33  Identities=24%  Similarity=0.307  Sum_probs=27.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .++++|.||+|+|||+|+.+++...+ .++..|.
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdDs   66 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIADDR   66 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEESSE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEecch
Confidence            46899999999999999999999877 6665543

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=96.41  E-value=0.0012  Score=59.96  Aligned_cols=32  Identities=19%  Similarity=0.265  Sum_probs=26.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-CCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-KFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-~~~~~~l~  275 (449)
                      .-+.|.||||+||||+++.++..+ +..++..+
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~D   54 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVISQD   54 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEeCC
Confidence            347899999999999999999988 55555443

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=96.40  E-value=0.0018  Score=60.92  Aligned_cols=27  Identities=26%  Similarity=0.192  Sum_probs=24.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      .-|.|.||||+||||+++.++..++.+
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~   49 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQN   49 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            458899999999999999999999976

>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=96.39  E-value=0.00081  Score=61.03  Aligned_cols=26  Identities=23%  Similarity=0.180  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-|+|.|+||+||||+++.++..++
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34588999999999999999999874

>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=96.39  E-value=0.023  Score=58.08  Aligned_cols=91  Identities=13%  Similarity=0.214  Sum_probs=62.2

Q ss_pred             HcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc------CCCCeEEEEEc----CCCCCC
Q 013128          290 LTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC------CGEGRIIVFTT----NHKEKL  359 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~------~~~~~iiI~tT----N~~~~l  359 (449)
                      ..+...+|+++||||.+....+...      .+....-+...||..+||....      ..+++++|+|.    +.+..+
T Consensus       246 ~~ae~~~il~~DEidki~~~~~~~~------~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dl  319 (444)
T 1g41_A          246 DAVEQNGIVFIDEIDKICKKGEYSG------ADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDL  319 (444)
T ss_dssp             HHHHHHCEEEEETGGGGSCCSSCSS------SHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGS
T ss_pred             HHhccCCeeeHHHHHHHhhccCCCC------CCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhc
Confidence            3334677999999999975322111      1112233556799999985322      23567888887    234345


Q ss_pred             CccccCCCccceEEEeCCCCHHHHHHHHH
Q 013128          360 DPALLRPGRMDMHLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       360 d~aLlrpgR~d~~i~l~~p~~~~r~~l~~  388 (449)
                      -|.|+.  ||+.+|.++.++.+++..|+.
T Consensus       320 ipel~~--R~~i~i~l~~lt~~e~~~Il~  346 (444)
T 1g41_A          320 IPELQG--RLPIRVELTALSAADFERILT  346 (444)
T ss_dssp             CHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             chHHhc--ccceeeeCCCCCHHHHHHHHH
Confidence            578887  999999999999999999984

>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=96.38  E-value=0.013  Score=49.88  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+.-
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.36  E-value=0.0017  Score=58.42  Aligned_cols=25  Identities=24%  Similarity=0.355  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||+|+||||+++.++..+
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            4568899999999999999999987

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=96.33  E-value=0.002  Score=63.63  Aligned_cols=32  Identities=25%  Similarity=0.367  Sum_probs=28.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .-++|.||+|+|||+++..+|..++..++..|
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~D   39 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGD   39 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceeccc
Confidence            46889999999999999999999997766655

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.32  E-value=0.0066  Score=54.89  Aligned_cols=36  Identities=14%  Similarity=0.214  Sum_probs=28.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      .-+.|.||+|+||||+++.++..+   +.+++.++....
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d~~   61 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDDH   61 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccCcc
Confidence            458899999999999999999986   666666654433

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=96.31  E-value=0.0032  Score=58.20  Aligned_cols=38  Identities=26%  Similarity=0.206  Sum_probs=28.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH----cCCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ----LKFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~----l~~~~~~l~~  276 (449)
                      |++.+.-++++|+||+|||+++..+|..    .+..++.+++
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~   67 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTL   67 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecc
Confidence            4555667999999999999999887643    2566666553

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=96.29  E-value=0.0021  Score=58.64  Aligned_cols=27  Identities=26%  Similarity=0.346  Sum_probs=23.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||+|+||||+++.++..+..
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            455889999999999999999998854

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.26  E-value=0.0041  Score=56.57  Aligned_cols=26  Identities=38%  Similarity=0.599  Sum_probs=22.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||+|+|||||++.|+..+.
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34578999999999999999999885

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=96.26  E-value=0.036  Score=50.33  Aligned_cols=59  Identities=19%  Similarity=0.178  Sum_probs=34.6

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhc---CCCCcceEEeCCCCCCHHHH-HHHHHHHc
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIG---RAWKRGYLLYGPPGTGKSSL-IAAMANQL  267 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g---~~~~rg~LL~GPpGtGKT~l-a~aiA~~l  267 (449)
                      .+|+++...+.+.+.+.+.   -+..+..|+...   ....+.+++.+|+|+|||.. +-.+...+
T Consensus        14 ~~f~~l~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           14 YKFDDMELDENLLRGVFGY---GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             CCGGGGTCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CChhhcCCCHHHHHHHHHC---CCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            5699988887777666432   111222222211   11135799999999999987 34444443

>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=96.24  E-value=0.003  Score=57.53  Aligned_cols=33  Identities=33%  Similarity=0.453  Sum_probs=27.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC----CcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~----~~~~~l~  275 (449)
                      +.-++|.|+||+||||+++.++..++    .+++.++
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            45588999999999999999999875    4566665

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=96.24  E-value=0.0076  Score=51.73  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+.-
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58999999999999999998764

>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=96.22  E-value=0.0015  Score=66.46  Aligned_cols=32  Identities=22%  Similarity=0.251  Sum_probs=26.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.-++|.||||+||||+++.++..+++.+++.
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~~~~~i~~  289 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNR  289 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGGTCEECCG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCcEEEcc
Confidence            45588999999999999999999998765543

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=96.21  E-value=0.0085  Score=61.15  Aligned_cols=59  Identities=17%  Similarity=0.243  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHcChh-HHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          217 LKREITEDLENFMNGKE-YYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       217 ~k~~i~~~l~~~~~~~~-~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +.+.+.+.+...+.... .+. .....++.+++.||||+||||++..+|..+   |..+..+++
T Consensus        73 ~~~~~~~~l~~ll~~~~~~~~-~~~~~~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~  135 (432)
T 2v3c_C           73 IIKIVYEELVKLLGEEAKKLE-LNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAA  135 (432)
T ss_dssp             HHHHHHHHHHHHHCCSCCCCC-CCSSSCCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECC
T ss_pred             HHHHHHHHHHHHhCCCCcCcc-ccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec
Confidence            44555555655554321 010 011224568999999999999999999987   355555554

>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=96.20  E-value=0.011  Score=57.09  Aligned_cols=59  Identities=17%  Similarity=0.247  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhc-CCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEecc
Q 013128          216 ELKREITEDLENFMNGKEYYTRIG-RAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLS  277 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g-~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s  277 (449)
                      .+++.+.+.+...+.....   .. ...+..++|.||+|+||||++..+|..+    |..+..+++.
T Consensus        80 ~~~~~~~~~l~~~l~~~~~---~~~~~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D  143 (296)
T 2px0_A           80 NVVGKLQEILCDMLPSADK---WQEPIHSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTD  143 (296)
T ss_dssp             THHHHHHHHHHTTSCCGGG---SCCCCCSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECC
T ss_pred             HHHHHHHHHHHHHhCCccc---ccccCCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            4455555555555432221   11 1234568899999999999999999876    4466655543

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.20  E-value=0.021  Score=51.06  Aligned_cols=25  Identities=24%  Similarity=0.332  Sum_probs=18.6

Q ss_pred             CcceEEeCCCCCCHHHH-HHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSL-IAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~l-a~aiA~~l  267 (449)
                      .+.+++.+|+|+|||.. +..+...+
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l   63 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERL   63 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHH
Confidence            35799999999999986 44444543

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.18  E-value=0.035  Score=57.70  Aligned_cols=41  Identities=7%  Similarity=0.101  Sum_probs=32.3

Q ss_pred             CeEEEEEcCCCC--CCCccccCCCccceEEEeCCCCHHHHHHHHH
Q 013128          346 GRIIVFTTNHKE--KLDPALLRPGRMDMHLHMSYCNTSVFKQLAF  388 (449)
Q Consensus       346 ~~iiI~tTN~~~--~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~  388 (449)
                      ++-+|++|.++.  .++..+..  -+...|.|...+..+.+.++.
T Consensus       332 GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv~s~~dsr~ilg  374 (512)
T 2ius_A          332 GIHLVLATQRPSVDVITGLIKA--NIPTRIAFTVSSKIDSRTILD  374 (512)
T ss_dssp             TEEEEEEESCCCTTTSCHHHHH--HCCEEEEECCSSHHHHHHHHS
T ss_pred             CcEEEEEecCCccccccHHHHh--hcCCeEEEEcCCHHHHHHhcC
Confidence            577888999886  57777766  677888888888888887765

>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=96.18  E-value=0.0034  Score=56.61  Aligned_cols=27  Identities=33%  Similarity=0.563  Sum_probs=23.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      |.++|.||+|+|||||++.+.....-.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~   28 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDS   28 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCC
Confidence            568999999999999999999887533

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=96.18  E-value=0.0022  Score=61.60  Aligned_cols=31  Identities=35%  Similarity=0.335  Sum_probs=26.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .-|.|.|+|||||||+++.++ .+|+++++.+
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~D  106 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDSD  106 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEehh
Confidence            358899999999999999999 6888776653

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.17  E-value=0.0031  Score=56.70  Aligned_cols=25  Identities=32%  Similarity=0.666  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|+||||+++.++..+.
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4578999999999999999999864

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.16  E-value=0.0047  Score=59.95  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHcChhHHhhhc--CCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          215 SELKREITEDLENFMNGKEYYTRIG--RAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~~~~~~g--~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||.|+||||+++.||..+
T Consensus        70 ~~~~~~~~~~l~~~l~~~~~~~~l~~~~~~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           70 SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             HHHHHHHHHHHHHHHCC--CCCSCCCCSSSCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcccccccccccCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4566667777776665432001122  2334458899999999999999999987

>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=96.15  E-value=0.0028  Score=61.81  Aligned_cols=33  Identities=21%  Similarity=0.316  Sum_probs=28.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .-++|.||+|+|||+|+..+|..++..++..|.
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   36 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDS   36 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECCG
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecCc
Confidence            457899999999999999999999877766553

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.14  E-value=0.0064  Score=61.99  Aligned_cols=60  Identities=13%  Similarity=0.181  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHcChh-HHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          215 SELKREITEDLENFMNGKE-YYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~-~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +.+++.+.+.+...+.... .... ....++-+++.||+|+||||++..+|..+   +..+..++
T Consensus        69 ~~v~~~v~~eL~~~L~~~~~~~~~-~~~~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           69 EWFISIVYDELSKLFGGDKEPNVN-PTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCCCCS-CCSSSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHHhcCcccccccc-ccCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            4455666666666665321 1111 11234568899999999999999999887   55555544

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=96.11  E-value=0.003  Score=57.54  Aligned_cols=30  Identities=13%  Similarity=0.176  Sum_probs=27.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      ..|.|.||+|||||++++.+|..+|+++++
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg~~~~D   36 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYNIPLYS   36 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTCCEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhCcCEEC
Confidence            458899999999999999999999999986

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=96.10  E-value=0.073  Score=48.15  Aligned_cols=60  Identities=20%  Similarity=0.195  Sum_probs=34.7

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +..+|+++...+++.+.+.+.   -+..+..|+...++   ..+.+++.+|+|+|||..+...+-.
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~   74 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDC---GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ   74 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHT---TCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             cCCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHH
Confidence            445788888887777666441   11112222221111   1356999999999999866554433

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.03  E-value=0.0078  Score=61.47  Aligned_cols=62  Identities=18%  Similarity=0.292  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          215 SELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      +.+++.+.+.+...+..+...... ...+.-+++.||+|+||||++..+|..+   |..+..+++.
T Consensus        73 ~~v~~~l~~eL~~~L~~~~~~~~~-~~~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D  137 (443)
T 3dm5_A           73 EHIIKIVYEELTKFLGTEAKPIEI-KEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSD  137 (443)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCCCC-CSSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHHHhcCccccccc-CCCCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            455666777777666542111111 1135668999999999999999999887   5666655543

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=96.03  E-value=0.061  Score=45.71  Aligned_cols=22  Identities=18%  Similarity=0.321  Sum_probs=19.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +++.|++|+|||+|+.++.+.-
T Consensus         3 i~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7899999999999999998643

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=96.02  E-value=0.0094  Score=51.03  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+.-
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999998654

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=95.98  E-value=0.042  Score=48.21  Aligned_cols=24  Identities=21%  Similarity=0.382  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      --++|.|++|+|||+|++.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            358999999999999999988765

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.98  E-value=0.0036  Score=56.63  Aligned_cols=26  Identities=35%  Similarity=0.612  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++-+.|.||+|+|||||++.|+..+.
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            45689999999999999999999764

>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=95.98  E-value=0.018  Score=48.86  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++++..
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            48999999999999999998764

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.97  E-value=0.01  Score=53.68  Aligned_cols=32  Identities=19%  Similarity=0.303  Sum_probs=26.2

Q ss_pred             cceEEeCCCCCCHH-HHHHHHHHHc--CCcEEEEe
Q 013128          244 RGYLLYGPPGTGKS-SLIAAMANQL--KFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT-~la~aiA~~l--~~~~~~l~  275 (449)
                      .-+++|||.|+||| .|++++.++.  +..++.+.
T Consensus        21 ~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~k   55 (195)
T 1w4r_A           21 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   55 (195)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEc
Confidence            35889999999999 9999998876  56666664

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.96  E-value=0.0089  Score=58.15  Aligned_cols=59  Identities=14%  Similarity=0.083  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          217 LKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       217 ~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +++.+.+.+...+...... .+....+.-+++.||+|+||||++..+|..+   +..+..+++
T Consensus        79 ~~~~~~~~l~~~l~~~~~~-~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A           79 ALESLKEIILEILNFDTKL-NVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             HHHHHHHHHHHHTCSCCCC-CCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHhCCCCCC-cccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            5666666666666543200 1112334568899999999999999999887   445554443

>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=95.95  E-value=0.0049  Score=56.08  Aligned_cols=26  Identities=27%  Similarity=0.501  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++-+.|.||+|+|||+|+++|+....
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            45588999999999999999999875

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.95  E-value=0.0064  Score=60.48  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHcChhHHhhhc--CCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          215 SELKREITEDLENFMNGKEYYTRIG--RAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~~~~~~g--~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||.|+||||+++.||..+
T Consensus       127 ~~~~~~l~~~l~~~l~~~~~~~~l~l~~~~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          127 SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             HHHHHHHHHHHHHHHCCC---CSCCCCSSSSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcccCCCcceecCCCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            4556666666666665432111222  2334558899999999999999999987

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.93  E-value=0.017  Score=50.24  Aligned_cols=23  Identities=35%  Similarity=0.556  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..+++.|++|+|||+|+.++.+.
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            35899999999999999999875

>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=95.89  E-value=0.025  Score=48.13  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            458999999999999999998753

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.88  E-value=0.0057  Score=53.50  Aligned_cols=25  Identities=28%  Similarity=0.371  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||.|+|||||+++|+..+
T Consensus        33 Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           33 AIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhC
Confidence            3458899999999999999999988

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.86  E-value=0.0033  Score=56.99  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=22.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|+||||+++.++..++
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4578999999999999999999987

>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=95.86  E-value=0.0048  Score=59.97  Aligned_cols=33  Identities=33%  Similarity=0.441  Sum_probs=27.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      .++.+..+.|.||+|+|||||++.|+..+.-.+
T Consensus       122 ~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I  154 (305)
T 2v9p_A          122 GIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSV  154 (305)
T ss_dssp             TCTTCSEEEEECSSSSSHHHHHHHHHHHHTCEE
T ss_pred             EecCCCEEEEECCCCCcHHHHHHHHhhhcCceE
Confidence            455566799999999999999999999984333

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=95.84  E-value=0.23  Score=44.17  Aligned_cols=19  Identities=37%  Similarity=0.377  Sum_probs=15.6

Q ss_pred             CcceEEeCCCCCCHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIA  261 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~  261 (449)
                      .+.+++.+|+|+|||..+.
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHH
T ss_pred             CCCEEEECCCCCchHHHHH
Confidence            3679999999999996543

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=95.84  E-value=0.019  Score=50.11  Aligned_cols=23  Identities=26%  Similarity=0.453  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+++.|++|+|||+|+.++.+.-
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58999999999999999998754

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.84  E-value=0.0051  Score=56.57  Aligned_cols=25  Identities=32%  Similarity=0.638  Sum_probs=22.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||+|+|||||++.|+..+
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            4458899999999999999999987

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=95.82  E-value=0.018  Score=64.07  Aligned_cols=100  Identities=14%  Similarity=0.166  Sum_probs=55.4

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc-----CC----cEEE----------Eecccc-c--------ChHHHHHHHHcCC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL-----KF----DIYD----------LDLSAV-Q--------SNSELRFLLLTMP  293 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l-----~~----~~~~----------l~~s~~-~--------~~~~l~~~~~~~~  293 (449)
                      .+..++|.||.|+||||+.+.+|.-.     +.    .-..          +...+. .        ...++..++....
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~~i~~~aq~g~~vpa~~~~i~~~d~i~~~ig~~d~l~~~~stfs~em~~~~~il~~a~  751 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKAT  751 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHHHHHHHHHHTCCBSSSEEEEECCSEEEEEC----------CCHHHHHHHHHHHHHHCC
T ss_pred             CCeEEEEECCCCCchHHHHHHHHHHHHHhhcCccccchhhhhhHHHHHHHhCChHHHHHHhHHHhhHHHHHHHHHHHhcc
Confidence            34568999999999999999987432     21    1111          111110 0        0123334455578


Q ss_pred             CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCC
Q 013128          294 SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL  359 (449)
Q Consensus       294 ~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l  359 (449)
                      .|++|++||.-.-..             ..........++..+-.     ..+..+|++|.+.+..
T Consensus       752 ~p~LlLLDEP~~GlD-------------~~~~~~i~~~il~~L~~-----~~g~tvl~vTH~~el~  799 (918)
T 3thx_B          752 SQSLVILDELGRGTS-------------THDGIAIAYATLEYFIR-----DVKSLTLFVTHYPPVC  799 (918)
T ss_dssp             TTCEEEEESTTTTSC-------------HHHHHHHHHHHHHHHHH-----TTCCEEEEECSCGGGG
T ss_pred             CCCEEEEeCCCCCCC-------------HHHHHHHHHHHHHHHHH-----hcCCeEEEEeCcHHHH
Confidence            999999999865331             11122233355555421     1235778888876543

>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=95.82  E-value=0.029  Score=48.76  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++++.-
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhhCC
Confidence            459999999999999999998753

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.82  E-value=0.0053  Score=55.77  Aligned_cols=26  Identities=27%  Similarity=0.556  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||+|+|||||+++|+..+.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            34588999999999999999999885

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=95.80  E-value=0.015  Score=51.35  Aligned_cols=24  Identities=38%  Similarity=0.540  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+++.|++|+|||+|+.++.+.-
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            358999999999999999999754

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=95.80  E-value=0.012  Score=50.35  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=18.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~  265 (449)
                      -++|.|+||+|||+|++++.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            488999999999999999864

>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=95.79  E-value=0.007  Score=62.60  Aligned_cols=25  Identities=32%  Similarity=0.457  Sum_probs=22.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +..+.|.||+|+||||+++.||..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            3458899999999999999999987

>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=95.79  E-value=0.014  Score=49.90  Aligned_cols=23  Identities=30%  Similarity=0.429  Sum_probs=20.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999874

>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=95.77  E-value=0.025  Score=49.53  Aligned_cols=23  Identities=26%  Similarity=0.502  Sum_probs=20.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -.++|.|++|+|||+|+.++.+.
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45899999999999999999974

>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=95.75  E-value=0.025  Score=63.11  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=19.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      +.-++|.||.|+||||+++.+|.
T Consensus       662 g~i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45689999999999999999853

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=95.75  E-value=0.0047  Score=59.31  Aligned_cols=29  Identities=24%  Similarity=0.264  Sum_probs=24.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++.+.-++|.||||+|||+|+..+|..+
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44555669999999999999999999876

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=95.75  E-value=0.07  Score=51.75  Aligned_cols=58  Identities=16%  Similarity=0.117  Sum_probs=33.3

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC----CCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA----WKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~----~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+|+++...+.+.+.+.+.   -+..+..++...++    ..+.+++.+|+|+|||..+...+-.
T Consensus         6 ~~f~~~~l~~~~~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~   67 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNK---GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE   67 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CchhhcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHH
Confidence            4577777777666655431   11112222221111    1357999999999999886554443

>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=95.74  E-value=0.035  Score=49.30  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..++|.|++|+|||+|+.++.+.-
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            358999999999999999998653

>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=95.73  E-value=0.0049  Score=62.09  Aligned_cols=32  Identities=25%  Similarity=0.447  Sum_probs=27.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .-++|.||+|+|||+|+..+|..++..++..|
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~~~iis~D   34 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFNGEVINSD   34 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHTEEEEECC
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCCCeEeecC
Confidence            45789999999999999999999988776654

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=95.73  E-value=0.023  Score=50.00  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998764

>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=95.70  E-value=0.043  Score=47.30  Aligned_cols=24  Identities=33%  Similarity=0.433  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999999998653

>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=95.70  E-value=0.02  Score=49.48  Aligned_cols=24  Identities=29%  Similarity=0.541  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            459999999999999999998754

>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=95.69  E-value=0.023  Score=48.40  Aligned_cols=22  Identities=27%  Similarity=0.490  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+++.|++|+|||+|+.++.+.
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            5899999999999999999874

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=95.69  E-value=0.014  Score=51.60  Aligned_cols=24  Identities=25%  Similarity=0.455  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.|++|+|||+|+.++.+.-
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            358999999999999999998743

>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=95.69  E-value=0.021  Score=49.14  Aligned_cols=23  Identities=39%  Similarity=0.645  Sum_probs=20.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      --+++.|+||+|||+|+.++.+.
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            35899999999999999999754

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.68  E-value=0.013  Score=57.27  Aligned_cols=61  Identities=25%  Similarity=0.369  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHcChhHH---hhhc--CCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          217 LKREITEDLENFMNGKEYY---TRIG--RAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       217 ~k~~i~~~l~~~~~~~~~~---~~~g--~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      +++.+.+.+...+.....-   ..+.  ...+..+++.||+|+||||++..+|..+   +..+..+++.
T Consensus        74 ~~~~~~~~l~~~l~~~~~~~~~~~l~~~~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D  142 (320)
T 1zu4_A           74 IKDALVESLYQAYTDNDWTNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAAD  142 (320)
T ss_dssp             HHHHHHHHHHHHHHCSCC----CCCCCCTTSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHhCcccccccccCccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            5555666666665433200   1121  2334568899999999999999999887   5566665544

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.68  E-value=0.0056  Score=57.01  Aligned_cols=29  Identities=21%  Similarity=0.432  Sum_probs=25.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +-|.||||+||||+++.+|..+++..+..
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             eeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            56889999999999999999999887654

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=95.66  E-value=0.0082  Score=63.95  Aligned_cols=33  Identities=30%  Similarity=0.434  Sum_probs=29.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +.-|+|.|+||+||||++++++..+   |.+++.++
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            3458899999999999999999999   99999886

>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=95.65  E-value=0.033  Score=61.01  Aligned_cols=23  Identities=22%  Similarity=0.367  Sum_probs=19.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..+++.||+|+|||+++..++..
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            45999999999999987777554

>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=95.64  E-value=0.0068  Score=55.98  Aligned_cols=27  Identities=37%  Similarity=0.582  Sum_probs=23.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||+|+|||||+++|+..+..
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~p   42 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQPL   42 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSCT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCCC
Confidence            455889999999999999999998863

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=95.63  E-value=0.031  Score=49.13  Aligned_cols=24  Identities=33%  Similarity=0.534  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.|++|+|||+|+.++.+.-
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999999998753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.62  E-value=0.0076  Score=57.19  Aligned_cols=25  Identities=40%  Similarity=0.604  Sum_probs=22.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-++|.||+|+||||++++++..+
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHHhC
Confidence            3458899999999999999999986

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.57  E-value=0.011  Score=57.57  Aligned_cols=38  Identities=18%  Similarity=0.197  Sum_probs=29.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |.+++.-++|.|+||+|||+++..+|...   +.++..+++
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~sl  104 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  104 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEEC
Confidence            55556669999999999999999998765   345655543

>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=95.55  E-value=0.01  Score=63.49  Aligned_cols=33  Identities=30%  Similarity=0.369  Sum_probs=24.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~  276 (449)
                      ...++.||||||||+++..++..+    +..+..+..
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~  232 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAP  232 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEES
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeC
Confidence            357899999999999988887765    334544433

>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=95.54  E-value=0.019  Score=58.28  Aligned_cols=50  Identities=22%  Similarity=0.389  Sum_probs=34.4

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.+++++....+.+..+ +.+   +..+          ...++|.||+|+||||+++++++.+.
T Consensus       143 ~~~l~~Lg~~~~~~~~L-~~l---~~~~----------ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          143 RLDLHSLGMTAHNHDNF-RRL---IKRP----------HGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             CCCGGGSCCCHHHHHHH-HHH---HTSS----------SEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CCCHHHcCCCHHHHHHH-HHH---HHhc----------CCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            34677887766554433 222   2211          23478999999999999999999985

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=95.50  E-value=0.043  Score=50.40  Aligned_cols=54  Identities=13%  Similarity=0.084  Sum_probs=31.5

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHHH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~la  260 (449)
                      ...+|+++...+.+.+.+.+.   -+..+..++...+   ...+.+++.+|+|+|||...
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~   79 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGLQEA---QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF   79 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHHHHT---TCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             ccCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHH
Confidence            345688888777776665431   1111222222111   11467999999999999854

>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=95.49  E-value=0.0072  Score=56.11  Aligned_cols=30  Identities=27%  Similarity=0.503  Sum_probs=25.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC--CcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK--FDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~--~~~~~  273 (449)
                      .-+.|.||||+||||+++.+++.++  .+++.
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~   58 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIM   58 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhcCCCcee
Confidence            3478899999999999999999996  45543

>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=95.47  E-value=0.018  Score=56.43  Aligned_cols=52  Identities=19%  Similarity=0.255  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHcChh---HHh-hhcCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          216 ELKREITEDLENFMNGKE---YYT-RIGRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~---~~~-~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.+.+.+...+....   ... ....+.+.-+.|.||+|+||||+++.||..+
T Consensus        98 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C           98 IIEEAVKEAVSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             HHHHHHHHHHHHHSCCSSCCCHHHHHHSSCSSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCccccchhhhcccCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            344555555655554321   000 0122334568899999999999999999987

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.47  E-value=0.0055  Score=53.96  Aligned_cols=20  Identities=30%  Similarity=0.446  Sum_probs=17.5

Q ss_pred             CcceEEeCCCCCCHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAA  262 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~a  262 (449)
                      +.-+.|.||+|+|||||+++
T Consensus         9 gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHH
Confidence            44588999999999999994

>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=95.42  E-value=0.0091  Score=57.58  Aligned_cols=27  Identities=30%  Similarity=0.305  Sum_probs=23.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||+|+||||+++.|+..++.
T Consensus        31 ~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           31 PLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            345789999999999999999998863

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.42  E-value=0.0029  Score=57.29  Aligned_cols=25  Identities=20%  Similarity=0.393  Sum_probs=22.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -+.|.||+|+||||+++.++..++.
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            3678999999999999999999853

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.39  E-value=0.04  Score=48.81  Aligned_cols=24  Identities=25%  Similarity=0.549  Sum_probs=21.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-.+++.|++|+|||+|+.++.+.
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346999999999999999999875

>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=95.39  E-value=0.019  Score=50.76  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=21.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|++|+|||+|+.++.+.-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            48999999999999999999765

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=95.39  E-value=0.0086  Score=53.58  Aligned_cols=33  Identities=21%  Similarity=0.275  Sum_probs=28.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV  279 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~  279 (449)
                      +|++|++|+|||++|..+|.. +.+++++.....
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~~   34 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQI   34 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCCC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCCC
Confidence            689999999999999999988 888888876543

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=95.38  E-value=0.0075  Score=55.90  Aligned_cols=30  Identities=20%  Similarity=0.230  Sum_probs=27.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .-|.+.|++|||||++++.+|..+|+++++
T Consensus        15 ~iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           15 LIITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            457899999999999999999999999876

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=95.31  E-value=0.017  Score=49.54  Aligned_cols=22  Identities=32%  Similarity=0.554  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+++.|++|+|||+|+.++.+.
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            5899999999999999999863

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.31  E-value=0.024  Score=56.79  Aligned_cols=66  Identities=15%  Similarity=0.244  Sum_probs=42.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEecccc-------------------cCh---HH---------HH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAV-------------------QSN---SE---------LR  286 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~-------------------~~~---~~---------l~  286 (449)
                      +.-++|.||+|||||+|++.||+..     +..++.+-+.+-                   .+.   .+         ..
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~I~~lIGER~~Ev~~~~~~~~~~vV~atadep~~~r~~~a~~alt~A  253 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKA  253 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEEEEEEESSCHHHHHHHHTTCSSEEEEECTTSCHHHHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeEEEEEecCChHHHHHHHHHhCeEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            3459999999999999999999875     333433322210                   011   11         11


Q ss_pred             HHHHcCCCCceEEeeccchhhh
Q 013128          287 FLLLTMPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       287 ~~~~~~~~~~Il~iDeiD~l~~  308 (449)
                      .-|....+..+|++|++.+++.
T Consensus       254 Eyfrd~G~dVLil~DslTR~A~  275 (422)
T 3ice_A          254 KRLVEHKKDVIILLDSITRLAR  275 (422)
T ss_dssp             HHHHHTSCEEEEEEECHHHHHH
T ss_pred             HHHHhcCCCEEEEEeCchHHHH
Confidence            2344566789999999998764

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.30  E-value=0.0088  Score=53.91  Aligned_cols=23  Identities=43%  Similarity=0.774  Sum_probs=21.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+.|.||+|+||||+++.|+..+
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            47899999999999999999987

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=95.30  E-value=0.036  Score=48.70  Aligned_cols=23  Identities=26%  Similarity=0.455  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      --+++.|++|+|||+|+.++.+.
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            35899999999999999999986

>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=95.29  E-value=0.011  Score=59.13  Aligned_cols=28  Identities=36%  Similarity=0.501  Sum_probs=23.7

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ..+..++|.||+|+||||+++++++.+.
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            3345589999999999999999999873

>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=95.29  E-value=0.072  Score=46.86  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+.-
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999998643

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=95.27  E-value=0.045  Score=47.26  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999876

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=95.26  E-value=0.0093  Score=59.27  Aligned_cols=23  Identities=48%  Similarity=0.699  Sum_probs=21.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.||+|+||||+++++++.+
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhcc
Confidence            58899999999999999999987

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=95.24  E-value=0.028  Score=48.95  Aligned_cols=24  Identities=25%  Similarity=0.422  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.|++|+|||+|+.++.+..
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            358999999999999999999753

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=95.21  E-value=0.043  Score=60.21  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=21.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +..++|.||.|+||||+.+.+|..
T Consensus       607 g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          607 RRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHHH
Confidence            456899999999999999999875

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.18  E-value=0.021  Score=59.27  Aligned_cols=59  Identities=10%  Similarity=0.146  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhcC--CCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          216 ELKREITEDLENFMNGKEYYTRIGR--AWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g~--~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      .+.+.+.+.+...+.....  .+..  ..++.+++.|+||+||||++..+|..+   |..+..+++
T Consensus        74 ~~~~~v~~eL~~ll~~~~~--~~~~~~~~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W           74 MIQHAVFKELVKLVDPGVK--AWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             HHHHHHHHHHHHHHCCCCC--CCCCCSS--EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHHhccccc--hhccccCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            3555666666666653210  1111  224568899999999999999999877   566665554

>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=95.13  E-value=0.031  Score=49.70  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.|++|+|||+|+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            458999999999999999998653

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.12  E-value=0.012  Score=54.90  Aligned_cols=26  Identities=19%  Similarity=0.193  Sum_probs=23.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      -+-|.||.|+||||+++.++..+|..
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchh
Confidence            47789999999999999999988754

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=95.12  E-value=0.026  Score=48.80  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+++.|++|+|||+|+.++.+.
T Consensus         8 ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999999854

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=95.09  E-value=0.03  Score=49.99  Aligned_cols=24  Identities=25%  Similarity=0.310  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-++|.|++|+|||+|+.++.+.-
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            359999999999999999999754

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.07  E-value=0.026  Score=55.21  Aligned_cols=24  Identities=21%  Similarity=0.158  Sum_probs=21.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -+-|.||+||||||+++.|+..++
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            477899999999999999999875

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=95.07  E-value=0.041  Score=49.24  Aligned_cols=23  Identities=17%  Similarity=0.338  Sum_probs=20.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-++|.|++|+|||+|+..+.+.
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhhC
Confidence            35899999999999999999864

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=95.07  E-value=0.017  Score=63.45  Aligned_cols=24  Identities=42%  Similarity=0.631  Sum_probs=20.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.||||||||+++..++..+
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            357899999999999988887765

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=95.07  E-value=0.01  Score=52.76  Aligned_cols=29  Identities=31%  Similarity=0.470  Sum_probs=24.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .+|+||.||+|+|||+++.++... |..++
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r-G~~lv   44 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR-GHQLV   44 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCeEe
Confidence            579999999999999999999885 54444

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=95.07  E-value=0.063  Score=47.59  Aligned_cols=23  Identities=17%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      .--+++.|++|+|||+|+.++..
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34599999999999999999864

>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=95.06  E-value=0.051  Score=47.74  Aligned_cols=23  Identities=17%  Similarity=0.268  Sum_probs=20.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..++|.|++|+|||+|+.++.+.
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            35999999999999999999864

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.05  E-value=0.0066  Score=56.00  Aligned_cols=26  Identities=23%  Similarity=0.356  Sum_probs=15.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHH-HHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMA-NQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA-~~l~  268 (449)
                      +.-+.|.||+|+||||+++.++ ..+.
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~~   53 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQKN   53 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC----
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            3458899999999999999999 8763

>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=95.02  E-value=0.014  Score=61.10  Aligned_cols=33  Identities=15%  Similarity=0.238  Sum_probs=26.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      +.-|+|.|+||+|||++++.+|.++   +.+...++
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s   70 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFN   70 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEec
Confidence            3468999999999999999999998   44444443

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.02  E-value=0.0051  Score=59.34  Aligned_cols=37  Identities=14%  Similarity=0.231  Sum_probs=26.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEeccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLDLSAVQ  280 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~s~~~  280 (449)
                      .-+.|.||+|+||||+++.++..++   ..+..+++..+.
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~~   45 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   45 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchhh
Confidence            3478999999999999999999876   445666666665

>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=95.02  E-value=0.014  Score=51.88  Aligned_cols=25  Identities=24%  Similarity=0.267  Sum_probs=22.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..-+.|.||+|+|||++++.++..+
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            3568899999999999999999875

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=95.01  E-value=0.022  Score=50.22  Aligned_cols=25  Identities=24%  Similarity=0.561  Sum_probs=22.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...+++.|++|+|||+|+.++++.-
T Consensus        48 ~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           48 QPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4569999999999999999998754

>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=95.00  E-value=0.025  Score=50.13  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            359999999999999999998754

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=95.00  E-value=0.14  Score=44.78  Aligned_cols=23  Identities=30%  Similarity=0.518  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+++.|++|+|||+|+.++++.
T Consensus        17 ~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           17 VRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999999865

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=94.99  E-value=0.054  Score=48.76  Aligned_cols=22  Identities=23%  Similarity=0.496  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .++|.|++|+|||+|+.++.+.
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999864

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=94.98  E-value=0.079  Score=48.25  Aligned_cols=53  Identities=15%  Similarity=0.084  Sum_probs=29.3

Q ss_pred             CCCccc-ccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHHH
Q 013128          205 PMTFKT-LALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       205 p~~f~~-l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~la  260 (449)
                      ..+|++ +...+++.+.+.+.   -+..+..++...+   ..++.+++.+|+|+|||...
T Consensus        18 ~~~f~~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~   74 (228)
T 3iuy_A           18 TCRFKDAFQQYPDLLKSIIRV---GILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSY   74 (228)
T ss_dssp             CCSHHHHHTTCHHHHHHHHHH---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             hhhHhhhhccCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHH
Confidence            346777 45566655554331   1112222222111   12457999999999999754

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=94.98  E-value=0.3  Score=47.72  Aligned_cols=54  Identities=20%  Similarity=0.233  Sum_probs=31.5

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhh-----hcCCCCcceEEeCCCCCCHHHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTR-----IGRAWKRGYLLYGPPGTGKSSLIAA  262 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~-----~g~~~~rg~LL~GPpGtGKT~la~a  262 (449)
                      .+|+++...+.+.+.+.+.   -+..+..++.     +-...++.+++.+|+|+|||..+..
T Consensus         5 ~~f~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~   63 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYAM---KFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL   63 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHH
Confidence            4677777777766665431   1111111221     1111237899999999999986543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.93  E-value=0.02  Score=58.49  Aligned_cols=38  Identities=13%  Similarity=0.113  Sum_probs=29.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~  276 (449)
                      |.+++.-++|.|+||+|||+++..+|...    +.++..+++
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~sl  237 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSL  237 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            56656669999999999999999988764    456666654

>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=94.88  E-value=0.016  Score=56.22  Aligned_cols=25  Identities=32%  Similarity=0.452  Sum_probs=22.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||+|+||||+++.+|..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4458899999999999999999987

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.87  E-value=0.029  Score=57.17  Aligned_cols=62  Identities=15%  Similarity=0.202  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccc
Q 013128          217 LKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSA  278 (449)
Q Consensus       217 ~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~  278 (449)
                      +.+.+.+.+...+.....--......++.+++.|++|+||||++..+|..+    |..+.-+++..
T Consensus        74 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A           74 FVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             THHHHHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             HHHHHHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            445555555555543210000111235678899999999999999999776    66777666653

>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=94.87  E-value=0.026  Score=49.88  Aligned_cols=32  Identities=13%  Similarity=0.242  Sum_probs=25.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      ..+.+.|++|+|||+++..++..+   ++.+..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            457899999999999999999886   45555444

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=94.86  E-value=0.022  Score=43.37  Aligned_cols=66  Identities=11%  Similarity=-0.034  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhc-------CCCHHHHHHHHHHHHHHHH
Q 013128          376 SYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMK-------STNAEVSLNGLVKFLHAKM  441 (449)
Q Consensus       376 ~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~-------~~~~~~al~~l~~~l~~~~  441 (449)
                      |.|+.++|++||+.++......-.-++..+++.+ ++|+|||..++..       ........+.+.+++++..
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v~   74 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVM   74 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence            6899999999999999865432223466666654 5999999887742       2222334455555555443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.83  E-value=0.0089  Score=62.32  Aligned_cols=32  Identities=16%  Similarity=0.288  Sum_probs=26.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC--cEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF--DIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l  274 (449)
                      +.++++.||+|+||||+++++++.+..  .++.+
T Consensus       260 g~~i~I~GptGSGKTTlL~aL~~~i~~~~giiti  293 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSI  293 (511)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEE
Confidence            456999999999999999999999843  34444

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=94.82  E-value=0.35  Score=44.42  Aligned_cols=53  Identities=11%  Similarity=0.082  Sum_probs=30.3

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHHH
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~la  260 (449)
                      ..+|+++...+.+.+.+.+.   -+..+..++...+   ..++.+++.+|+|+|||...
T Consensus        28 ~~~f~~~~l~~~l~~~l~~~---g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~   83 (242)
T 3fe2_A           28 VLNFYEANFPANVMDVIARQ---NFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSY   83 (242)
T ss_dssp             CSSTTTTTCCHHHHHHHHTT---TCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHH
Confidence            35788887777666555431   1111211221110   11357999999999999864

>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=94.74  E-value=0.033  Score=49.63  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..++|.|++|+|||+|+.++.+.-
T Consensus        29 ~ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           29 YKIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            469999999999999999998643

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.73  E-value=0.092  Score=45.97  Aligned_cols=23  Identities=13%  Similarity=0.367  Sum_probs=20.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      ...+++.|++|+|||+|+.++.+
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            34699999999999999999985

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=94.71  E-value=0.046  Score=50.08  Aligned_cols=22  Identities=27%  Similarity=0.469  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|.+|+|||+|+..+...
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            3899999999999999998754

>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=94.71  E-value=0.1  Score=60.55  Aligned_cols=29  Identities=24%  Similarity=0.352  Sum_probs=24.3

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +++.-+.|.||+|+|||||+++|.+++..
T Consensus       442 ~~G~~vaivG~sGsGKSTll~ll~~~~~~  470 (1321)
T 4f4c_A          442 NAGQTVALVGSSGCGKSTIISLLLRYYDV  470 (1321)
T ss_dssp             CTTCEEEEEECSSSCHHHHHHHHTTSSCC
T ss_pred             cCCcEEEEEecCCCcHHHHHHHhcccccc
Confidence            33445889999999999999999998853

>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=94.71  E-value=0.017  Score=56.20  Aligned_cols=26  Identities=19%  Similarity=0.093  Sum_probs=22.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||+|+|||||++.|+..+.
T Consensus        90 g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           90 PFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCchHHHHHHHHHhhcc
Confidence            33477999999999999999999874

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.70  E-value=0.018  Score=53.45  Aligned_cols=25  Identities=20%  Similarity=0.347  Sum_probs=22.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.|++|+||||+++.++..++
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            4588999999999999999999994

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=94.67  E-value=0.026  Score=50.49  Aligned_cols=24  Identities=33%  Similarity=0.519  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-++|.|++|+|||+|+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            358999999999999999998743

>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=94.64  E-value=0.053  Score=55.04  Aligned_cols=59  Identities=17%  Similarity=0.134  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          216 ELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      .+++.+.+.+...+....  ..+....+..+++.||+|+||||++..+|..+   +..+..+++
T Consensus        73 ~~~~~v~~~L~~~~~~~~--~~i~l~~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~  134 (425)
T 2ffh_A           73 VILATVYEALKEALGGEA--RLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (425)
T ss_dssp             HHHHHHHHHHHHHTTSSC--CCCCCCSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             HHHHHHHHHHHHHhCCCc--ccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeec
Confidence            345555555655554321  12222234568888999999999999999987   455555554

>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=94.63  E-value=0.017  Score=50.89  Aligned_cols=25  Identities=28%  Similarity=0.204  Sum_probs=22.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -.+|+||.|+|||+++.||+-.++.
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHcC
Confidence            4679999999999999999998763

>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=94.62  E-value=0.027  Score=51.67  Aligned_cols=31  Identities=29%  Similarity=0.346  Sum_probs=25.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC---CcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK---FDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l  274 (449)
                      .-|.|.||+|+||||+++.++..++   ++++..
T Consensus         7 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~   40 (213)
T 4edh_A            7 LFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLT   40 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccc
Confidence            3477889999999999999999884   555544

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=94.62  E-value=0.022  Score=49.63  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=9.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..++|.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45899999999999999998754

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=94.61  E-value=0.41  Score=44.76  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=15.4

Q ss_pred             cceEEeCCCCCCHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIA  261 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~  261 (449)
                      +.+++.+|+|+|||..+.
T Consensus        92 ~~~lv~a~TGsGKT~~~~  109 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFL  109 (262)
T ss_dssp             CCCEECCCTTSCHHHHHH
T ss_pred             CcEEEEccCCCCchHHHH
Confidence            579999999999998643

>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=94.61  E-value=0.023  Score=49.65  Aligned_cols=24  Identities=33%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      --+++.|++|+|||+|+.++.+.-
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999999998654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=94.60  E-value=0.023  Score=62.51  Aligned_cols=35  Identities=37%  Similarity=0.408  Sum_probs=25.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEeccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSA  278 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~  278 (449)
                      ..+|+.||||||||+++..++..+    +..+..+..+.
T Consensus       376 ~~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~tn  414 (802)
T 2xzl_A          376 PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSN  414 (802)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcH
Confidence            357899999999999987776554    44555554443

>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=94.59  E-value=0.04  Score=53.20  Aligned_cols=61  Identities=18%  Similarity=0.238  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHcChhHHhh-hcCCC-CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          216 ELKREITEDLENFMNGKEYYTR-IGRAW-KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       216 ~~k~~i~~~l~~~~~~~~~~~~-~g~~~-~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      .+++.+.+.+...+....  .. +.... +.-+++.||+|+|||+++..+|..+   +..+..+++.-
T Consensus        71 ~~~~~~~~~l~~~~~~~~--~~~i~~~~~~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D~  136 (297)
T 1j8m_F           71 WFIKIVYDELSNLFGGDK--EPKVIPDKIPYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADV  136 (297)
T ss_dssp             HHHHHHHHHHHHHTTCSC--CCCCSCSSSSEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECCC
T ss_pred             HHHHHHHHHHHHHhcccc--ccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecCC
Confidence            345556666665554321  11 11111 4457888999999999999999887   56666666543

>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=94.59  E-value=0.019  Score=60.62  Aligned_cols=33  Identities=21%  Similarity=0.129  Sum_probs=28.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC----CcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~----~~~~~l~~  276 (449)
                      ..|+|.|+||+||||++++++..++    .+++.++.
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~  433 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLG  433 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECc
Confidence            3478999999999999999999986    77777773

>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=94.58  E-value=0.016  Score=56.10  Aligned_cols=36  Identities=14%  Similarity=0.080  Sum_probs=27.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC-----CcEEEEecccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK-----FDIYDLDLSAV  279 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~-----~~~~~l~~s~~  279 (449)
                      .-+-|.||+|+||||+++.|+..++     -.+..+++...
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~vi~~d~~  121 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEEEecCCc
Confidence            3477999999999999999999876     12444554443

>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=94.57  E-value=0.0085  Score=56.51  Aligned_cols=29  Identities=14%  Similarity=0.339  Sum_probs=24.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-CCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-KFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-~~~~~  272 (449)
                      .-|.|.|++|+||||+++.++..+ +..++
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~~~~~i   54 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCEDWEVV   54 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEEE
Confidence            347889999999999999999999 44433

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.54  E-value=0.018  Score=51.36  Aligned_cols=23  Identities=30%  Similarity=0.528  Sum_probs=20.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+.|.||+|+|||+|++.+++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58899999999999999999863

>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=94.54  E-value=0.025  Score=60.28  Aligned_cols=25  Identities=36%  Similarity=0.628  Sum_probs=21.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+-+++.||||||||+++..+...+
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            3568999999999999998887665

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.54  E-value=0.02  Score=48.58  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++++.-
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999998753

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.54  E-value=0.028  Score=55.39  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=29.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |..++.-++|.|+||+|||+++..+|..+   +.++..+++
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            44445569999999999999999998875   566655543

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=94.53  E-value=0.15  Score=55.08  Aligned_cols=18  Identities=22%  Similarity=0.392  Sum_probs=16.2

Q ss_pred             CcceEEeCCCCCCHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la  260 (449)
                      .+.+++.||+|+|||..+
T Consensus        39 ~~~~lv~apTGsGKT~~~   56 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIA   56 (720)
T ss_dssp             TCEEEEECCGGGCHHHHH
T ss_pred             CCcEEEEcCCccHHHHHH
Confidence            567999999999999887

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=94.52  E-value=0.014  Score=51.45  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+.-
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            59999999999999999998654

>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=94.51  E-value=0.015  Score=54.26  Aligned_cols=27  Identities=26%  Similarity=0.362  Sum_probs=23.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||+++|+..+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl~~p   57 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCLDKP   57 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            345889999999999999999998754

>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=94.49  E-value=0.036  Score=48.94  Aligned_cols=23  Identities=30%  Similarity=0.547  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHHcC
Confidence            35899999999999999999874

>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=94.49  E-value=0.038  Score=56.68  Aligned_cols=23  Identities=30%  Similarity=0.574  Sum_probs=20.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .++|+||||+|||+|+..++...
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhh
Confidence            48999999999999999988765

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.43  E-value=0.025  Score=52.50  Aligned_cols=23  Identities=22%  Similarity=0.325  Sum_probs=18.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -|.|.||+|+||||+++.+++.+
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47788999999999999999998

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=94.41  E-value=0.041  Score=57.18  Aligned_cols=26  Identities=12%  Similarity=0.038  Sum_probs=23.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      ..|.|.|++||||||+++++|..|+.
T Consensus       396 ~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          396 FSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEecccCCCCHHHHHHHHHHHHHH
Confidence            45889999999999999999999985

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=94.40  E-value=0.018  Score=51.22  Aligned_cols=23  Identities=30%  Similarity=0.528  Sum_probs=20.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+.|.||+|+|||||++.+++..
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            47899999999999999999865

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.40  E-value=0.015  Score=54.19  Aligned_cols=25  Identities=32%  Similarity=0.445  Sum_probs=22.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||.|+|||||+++|+..+
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4458899999999999999999987

>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=94.38  E-value=0.065  Score=47.56  Aligned_cols=24  Identities=29%  Similarity=0.400  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      --++|.|++|+|||+|++.+.+..
T Consensus        21 ~ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           21 PRILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHSCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhcC
Confidence            359999999999999999887754

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.36  E-value=0.018  Score=52.61  Aligned_cols=23  Identities=39%  Similarity=0.439  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+.|.||.|+|||||+++|+..
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            45889999999999999999986

>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=94.35  E-value=0.03  Score=50.43  Aligned_cols=24  Identities=29%  Similarity=0.499  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..++|.|++|+|||+|+.++.+..
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            358999999999999999998653

>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=94.35  E-value=0.04  Score=49.52  Aligned_cols=24  Identities=25%  Similarity=0.348  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998754

>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=94.33  E-value=0.022  Score=48.60  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+..
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcCC
Confidence            358999999999999999998753

>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=94.32  E-value=0.026  Score=50.98  Aligned_cols=25  Identities=24%  Similarity=0.561  Sum_probs=22.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...++|.|++|+|||+|+.++++..
T Consensus        12 ~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           12 QPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3469999999999999999999865

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=94.31  E-value=0.13  Score=57.93  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=19.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMA  264 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA  264 (449)
                      +..++|.||.|+||||+++.++
T Consensus       789 g~i~~ItGpNgsGKSTlLr~iG  810 (1022)
T 2o8b_B          789 AYCVLVTGPNMGGKSTLMRQAG  810 (1022)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHH
Confidence            3568999999999999999984

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=94.30  E-value=0.025  Score=51.86  Aligned_cols=31  Identities=29%  Similarity=0.353  Sum_probs=27.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .+-|.|..|||||++++.++. +|+++++.|.
T Consensus        11 ~iglTGgigsGKStv~~~l~~-~g~~vidaD~   41 (210)
T 4i1u_A           11 AIGLTGGIGSGKTTVADLFAA-RGASLVDTDL   41 (210)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcEEECcH
Confidence            477999999999999999998 9999998774

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.27  E-value=0.013  Score=54.06  Aligned_cols=27  Identities=22%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||+++|+..+..
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl~~p   56 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLLDAP   56 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            345889999999999999999988754

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.26  E-value=0.034  Score=56.89  Aligned_cols=38  Identities=18%  Similarity=0.197  Sum_probs=29.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |..++.-++|.|+||+|||+++..+|...   |.++..+++
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSl  233 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  233 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEEC
Confidence            55555569999999999999999988776   566666654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=94.24  E-value=0.029  Score=49.71  Aligned_cols=22  Identities=27%  Similarity=0.610  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+++.|++|+|||+|+.++.+.
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999753

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.23  E-value=0.018  Score=54.51  Aligned_cols=27  Identities=22%  Similarity=0.278  Sum_probs=23.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||+++|+..+..
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl~~p   58 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFLEKP   58 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            344789999999999999999998854

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=94.23  E-value=0.079  Score=57.81  Aligned_cols=25  Identities=28%  Similarity=0.321  Sum_probs=21.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +..++|.||.|+||||+.+.+|...
T Consensus       576 g~i~~I~GpNGsGKSTlLr~iagl~  600 (765)
T 1ewq_A          576 HELVLITGPNMAGKSTFLRQTALIA  600 (765)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHhhh
Confidence            4568899999999999999998753

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=94.22  E-value=0.26  Score=47.02  Aligned_cols=31  Identities=16%  Similarity=0.234  Sum_probs=23.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      +.+++.+|+|+|||..+...+-..+...+.+
T Consensus        32 ~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv   62 (337)
T 2z0m_A           32 KNVVVRAKTGSGKTAAYAIPILELGMKSLVV   62 (337)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHhhcCCEEEE
Confidence            5799999999999987766665555544443

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.21  E-value=0.022  Score=53.28  Aligned_cols=26  Identities=35%  Similarity=0.535  Sum_probs=23.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-+.|.||.|+|||||+++|+..+..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~p   50 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            56789999999999999999998743

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=94.18  E-value=0.017  Score=53.01  Aligned_cols=27  Identities=30%  Similarity=0.452  Sum_probs=23.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||+++|+..+..
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~Gl~~p   61 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTISTYLKP   61 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            345889999999999999999998743

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=94.17  E-value=0.023  Score=56.41  Aligned_cols=28  Identities=21%  Similarity=0.353  Sum_probs=24.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      ..-+.|.||+|+|||||++.|+..+...
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            3458999999999999999999998654

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=94.15  E-value=0.014  Score=60.19  Aligned_cols=26  Identities=19%  Similarity=0.337  Sum_probs=23.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-|+|.|.||+|||++++.+|..++
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34689999999999999999999875

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=94.15  E-value=0.019  Score=53.76  Aligned_cols=26  Identities=23%  Similarity=0.428  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   53 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERFYQ   53 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999999873

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=94.13  E-value=0.018  Score=53.41  Aligned_cols=26  Identities=27%  Similarity=0.471  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
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            34588999999999999999999874

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=94.11  E-value=0.026  Score=48.74  Aligned_cols=22  Identities=32%  Similarity=0.594  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+.|.|+||+|||+|++++++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999863

>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=94.07  E-value=0.028  Score=48.08  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            358999999999999999998653

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=94.05  E-value=0.035  Score=51.06  Aligned_cols=28  Identities=21%  Similarity=0.258  Sum_probs=24.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      .-+.|.||+|+||||+++.+++.++.+.
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l~~~~   33 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKLQPNC   33 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHCSSE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcccc
Confidence            4578899999999999999999998743

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=94.04  E-value=0.021  Score=54.16  Aligned_cols=27  Identities=26%  Similarity=0.511  Sum_probs=23.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||+++|+..+..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl~~p   76 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLLEDF   76 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcCCCC
Confidence            345889999999999999999998754

>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=94.02  E-value=0.029  Score=48.51  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            458999999999999999998754

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=94.02  E-value=0.019  Score=54.25  Aligned_cols=25  Identities=44%  Similarity=0.686  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||.|+|||||+++|+..+.
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~~   58 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFLK   58 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            4488999999999999999999874

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=94.01  E-value=0.096  Score=50.39  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=26.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +..+.+.||+|+||||++..+|..+   +..+..+++
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~  134 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            4457788999999999999999887   455655554

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.98  E-value=0.046  Score=49.44  Aligned_cols=26  Identities=23%  Similarity=0.371  Sum_probs=22.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ...+++.|++|+|||+|+..++..+.
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            35688999999999999999999864

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.98  E-value=0.022  Score=54.30  Aligned_cols=26  Identities=35%  Similarity=0.533  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||++.|+..+.
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>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=93.97  E-value=0.025  Score=53.71  Aligned_cols=25  Identities=36%  Similarity=0.529  Sum_probs=21.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||.|+|||||++.|+..+
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999963

>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=93.96  E-value=0.032  Score=57.81  Aligned_cols=38  Identities=16%  Similarity=-0.004  Sum_probs=29.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~  276 (449)
                      |.+.+.-++|.|+||+|||+++..+|..+    +.++..+++
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~  279 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML  279 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec
Confidence            45555569999999999999999998776    445666654

>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=93.93  E-value=0.026  Score=48.25  Aligned_cols=23  Identities=35%  Similarity=0.560  Sum_probs=20.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999864

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.93  E-value=0.024  Score=54.00  Aligned_cols=25  Identities=24%  Similarity=0.422  Sum_probs=21.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .+.|.||+|+|||||+++|++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~~   28 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQVS   28 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCC
Confidence            4789999999999999999998743

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.91  E-value=0.022  Score=53.91  Aligned_cols=26  Identities=23%  Similarity=0.325  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccCC
Confidence            44588999999999999999998763

>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=93.90  E-value=0.02  Score=53.70  Aligned_cols=26  Identities=23%  Similarity=0.258  Sum_probs=22.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||++.|+..+.
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   60 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFYI   60 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.90  E-value=0.024  Score=49.84  Aligned_cols=22  Identities=23%  Similarity=0.597  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|++|+|||+|++.+++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999999873

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.89  E-value=0.08  Score=52.23  Aligned_cols=24  Identities=42%  Similarity=0.620  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+.|.|+||+|||||+.+++..+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            347899999999999999999865

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.85  E-value=0.018  Score=57.18  Aligned_cols=26  Identities=27%  Similarity=0.585  Sum_probs=23.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +..++|.||+|+|||||+++|+..+.
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            45699999999999999999999885

>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=93.85  E-value=0.024  Score=53.26  Aligned_cols=24  Identities=38%  Similarity=0.490  Sum_probs=21.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +.-+.|.||.|+|||||+++|+..
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            345889999999999999999996

>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=93.82  E-value=0.025  Score=53.46  Aligned_cols=26  Identities=27%  Similarity=0.523  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>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=93.82  E-value=0.022  Score=54.46  Aligned_cols=25  Identities=32%  Similarity=0.434  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||.|+|||||+++|+..+.
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCCC
Confidence            3488999999999999999999874

>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=93.81  E-value=0.022  Score=53.21  Aligned_cols=26  Identities=27%  Similarity=0.447  Sum_probs=22.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-+.|.||.|+|||||++.|+..+..
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl~~p   58 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGLVRA   58 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            44889999999999999999998754

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=93.79  E-value=0.024  Score=56.28  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||+++||....
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl~~   55 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGFEQ   55 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCchHHHHHHHHhcCCC
Confidence            3478999999999999999999874

>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=93.79  E-value=0.048  Score=53.88  Aligned_cols=32  Identities=31%  Similarity=0.409  Sum_probs=25.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      .-+.|.|+||+||||++.+++..+   +..+..++
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            458899999999999999999886   55544443

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.77  E-value=0.029  Score=55.76  Aligned_cols=25  Identities=40%  Similarity=0.611  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||.++||....
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCchHHHHHHHHhcCCC
Confidence            3478999999999999999999874

>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=93.77  E-value=0.02  Score=53.88  Aligned_cols=27  Identities=41%  Similarity=0.471  Sum_probs=23.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+.|.||.|+|||||++.|+..+..
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~Gl~~p   52 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAGMTSG   52 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            345889999999999999999998754

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.75  E-value=0.029  Score=49.16  Aligned_cols=23  Identities=30%  Similarity=0.543  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+.|.|++|+|||+|+.++++.
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            35899999999999999999974

>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=93.74  E-value=0.035  Score=47.53  Aligned_cols=23  Identities=22%  Similarity=0.424  Sum_probs=20.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..+++.|++|+|||+|+.++.+.
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            45899999999999999999764

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.74  E-value=0.033  Score=47.66  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=18.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~  265 (449)
                      -+++.|+||+|||+|+.++++
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            378999999999999999964

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=93.69  E-value=0.03  Score=55.59  Aligned_cols=25  Identities=32%  Similarity=0.493  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||.++||....
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~~   54 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAGIYK   54 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEEcCCCchHHHHHHHHHCCCC
Confidence            4478999999999999999999874

>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=93.67  E-value=0.034  Score=47.88  Aligned_cols=23  Identities=43%  Similarity=0.566  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+|+||.|+|||+++.||+-.+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999998755

>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=93.65  E-value=0.031  Score=55.74  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||.++||....
T Consensus        38 e~~~llGpnGsGKSTLLr~iaGl~~   62 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTLRMIAGLEE   62 (372)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCC
Confidence            4478999999999999999999874

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.65  E-value=0.024  Score=54.23  Aligned_cols=25  Identities=28%  Similarity=0.581  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||.|+|||||++.|+..+.
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3488999999999999999999874

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.64  E-value=0.027  Score=53.42  Aligned_cols=26  Identities=31%  Similarity=0.525  Sum_probs=22.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~~   58 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLIE   58 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34588999999999999999998874

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=93.64  E-value=0.032  Score=55.86  Aligned_cols=25  Identities=32%  Similarity=0.501  Sum_probs=22.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||+++||....
T Consensus        30 e~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEEcCCCchHHHHHHHHHcCCC
Confidence            3478999999999999999999884

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.63  E-value=0.028  Score=55.73  Aligned_cols=25  Identities=28%  Similarity=0.511  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||+++||....
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            4478999999999999999999874

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.62  E-value=0.025  Score=53.36  Aligned_cols=26  Identities=23%  Similarity=0.335  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||++.|+..+.
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            34588999999999999999999874

>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=93.60  E-value=0.032  Score=48.11  Aligned_cols=22  Identities=27%  Similarity=0.469  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+++.|++|+|||+|+.++++.
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            5899999999999999999864

>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=93.58  E-value=0.034  Score=51.86  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-|.|.||+|+||||+++.++..+
T Consensus        28 ~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           28 KFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            457889999999999999999988

>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=93.54  E-value=0.029  Score=58.56  Aligned_cols=29  Identities=28%  Similarity=0.330  Sum_probs=24.7

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++....++|.||||+|||+|++.+|...
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45555669999999999999999999876

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=93.53  E-value=0.025  Score=55.51  Aligned_cols=63  Identities=13%  Similarity=0.228  Sum_probs=39.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC--cEEEEecc-cc-----------c--ChHHHHHHHH--cCCCCceEEeeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF--DIYDLDLS-AV-----------Q--SNSELRFLLL--TMPSRSMLVIEDID  304 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~--~~~~l~~s-~~-----------~--~~~~l~~~~~--~~~~~~Il~iDeiD  304 (449)
                      +..++|.||+|+|||||+++|+..+..  ..+.++-. .+           .  .....+..+.  -...|.+|++||.-
T Consensus       171 g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~~r~~la~aL~~~p~ilildE~~  250 (330)
T 2pt7_A          171 GKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELR  250 (330)
T ss_dssp             TCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEECCCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeeccccccchhEEEEEeCCChhHHHHHHHHhhhCCCEEEEcCCC
Confidence            357999999999999999999999843  23333311 10           0  1112222222  23578999999975


Q ss_pred             h
Q 013128          305 C  305 (449)
Q Consensus       305 ~  305 (449)
                      .
T Consensus       251 ~  251 (330)
T 2pt7_A          251 S  251 (330)
T ss_dssp             S
T ss_pred             h
Confidence            3

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.51  E-value=0.041  Score=47.52  Aligned_cols=24  Identities=21%  Similarity=0.333  Sum_probs=20.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..-+++.|++|+|||+|+.++.+.
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            346899999999999999999863

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.48  E-value=0.021  Score=59.98  Aligned_cols=25  Identities=36%  Similarity=0.482  Sum_probs=22.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ..+.|.||+|+||||++++||..++
T Consensus       370 ~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          370 FTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             EEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCChHHHHHHHHHHhhc
Confidence            4588999999999999999999985

>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=93.44  E-value=0.031  Score=55.76  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||.++||..+.
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCcHHHHHHHHHHcCCC
Confidence            4478999999999999999999874

>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=93.42  E-value=0.03  Score=53.19  Aligned_cols=26  Identities=31%  Similarity=0.524  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl~~   62 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGYLS   62 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>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=93.40  E-value=0.045  Score=63.48  Aligned_cols=27  Identities=30%  Similarity=0.461  Sum_probs=23.1

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++.-+-|.||+|+|||||++++.+.+.
T Consensus      1104 ~Ge~vaIVG~SGsGKSTL~~lL~rl~~ 1130 (1321)
T 4f4c_A         1104 PGQTLALVGPSGCGKSTVVALLERFYD 1130 (1321)
T ss_dssp             TTCEEEEECSTTSSTTSHHHHHTTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCcc
Confidence            344488999999999999999998873

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.35  E-value=0.023  Score=50.17  Aligned_cols=24  Identities=33%  Similarity=0.430  Sum_probs=21.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..-+++.|++|+|||+|+.++.+.
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           23 LPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            356999999999999999999864

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=93.32  E-value=0.1  Score=52.19  Aligned_cols=63  Identities=14%  Similarity=0.233  Sum_probs=41.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEecccc-------------------cCh------------HHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAV-------------------QSN------------SELRFLL  289 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~-------------------~~~------------~~l~~~~  289 (449)
                      .+|.||||||||+|+..||+..     +..++.+-+.+-                   .+.            -.+..-|
T Consensus       178 ~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~V~~lIGER~~EV~d~~~~~~G~VV~atadep~~~r~~~a~~altiAEyf  257 (427)
T 3l0o_A          178 GMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDERPEEVTDIRESTNAIVIAAPFDMPPDKQVKVAELTLEMAKRL  257 (427)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHHHHCTTSEEEEEECSCCHHHHSSSSSSCCSEEEECCTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEecCCCCChhHHHHHHHHHHhhcCCCeEEEEEEeccCcchHHHHHHHhCCeEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999864     334333322110                   011            1112335


Q ss_pred             HcCCCCceEEeeccchhhh
Q 013128          290 LTMPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       290 ~~~~~~~Il~iDeiD~l~~  308 (449)
                      ....+..+|++|++-+.+.
T Consensus       258 rd~G~dVLil~DslTR~A~  276 (427)
T 3l0o_A          258 VEFNYDVVILLDSLTRLAR  276 (427)
T ss_dssp             HHTTCEEEEEEECHHHHHH
T ss_pred             HHcCCCEEEecccchHHHH
Confidence            5566788999999988764

>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=93.32  E-value=0.045  Score=47.34  Aligned_cols=24  Identities=25%  Similarity=0.447  Sum_probs=21.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            358999999999999999998753

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=93.32  E-value=0.037  Score=48.48  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      --+++.|++|+|||+|+..+++.
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            35899999999999999999875

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.31  E-value=0.057  Score=53.32  Aligned_cols=29  Identities=28%  Similarity=0.457  Sum_probs=25.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .-+.|.||+|+|||+|++.|++....+..
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~~~~~~g  100 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNGASADII  100 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCEE
Confidence            34889999999999999999999976644

>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=93.31  E-value=0.045  Score=48.13  Aligned_cols=24  Identities=29%  Similarity=0.391  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..++|.|++|+|||+|+.++.+.-
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999999998754

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=93.31  E-value=0.027  Score=55.69  Aligned_cols=25  Identities=24%  Similarity=0.527  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||++.||....
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCccHHHHHHHHHcCCC
Confidence            4478999999999999999999874

>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=93.30  E-value=0.073  Score=49.53  Aligned_cols=33  Identities=21%  Similarity=0.449  Sum_probs=26.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc--CCcEEEEec
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL--KFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l--~~~~~~l~~  276 (449)
                      ..+++.|.+|+||||++..+|..+  +..+..+++
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd~   49 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNL   49 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEEC
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            347788999999999999999876  556555553

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.30  E-value=0.044  Score=50.67  Aligned_cols=26  Identities=23%  Similarity=0.179  Sum_probs=22.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-|.|.|++|+||||+++.+++.++.
T Consensus        22 ~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           22 MFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34778899999999999999998754

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=93.30  E-value=0.34  Score=47.67  Aligned_cols=22  Identities=23%  Similarity=0.462  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+.+.|++|+|||||+.++.+.
T Consensus        36 ~I~vvG~~~sGKSSLln~l~g~   57 (360)
T 3t34_A           36 AIAVVGGQSSGKSSVLESIVGK   57 (360)
T ss_dssp             EEEEECBTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            5889999999999999999983

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.29  E-value=0.02  Score=50.66  Aligned_cols=25  Identities=28%  Similarity=0.400  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ..+.|.||+|+|||||++.|+..+.
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3578999999999999999999984

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.28  E-value=0.048  Score=53.60  Aligned_cols=24  Identities=38%  Similarity=0.499  Sum_probs=21.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+.|.||||+|||||+++++..+
T Consensus        56 ~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           56 IRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhh
Confidence            347899999999999999999876

>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=93.27  E-value=0.046  Score=47.46  Aligned_cols=22  Identities=18%  Similarity=0.392  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+++.|++|+|||+|+.++.+.
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            5899999999999999999864

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=93.27  E-value=0.12  Score=49.18  Aligned_cols=23  Identities=30%  Similarity=0.541  Sum_probs=20.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+.|.|+||+|||+|+.++++.
T Consensus         4 ~kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            4 TEIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHCC
Confidence            35889999999999999999874

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.23  E-value=0.043  Score=47.39  Aligned_cols=23  Identities=39%  Similarity=0.592  Sum_probs=20.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      --+++.|++|+|||+|+.++.+.
T Consensus        10 ~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           10 FKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHCSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999998753

>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=93.20  E-value=0.034  Score=58.01  Aligned_cols=28  Identities=25%  Similarity=0.331  Sum_probs=22.4

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHH--HHHHc
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAA--MANQL  267 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~a--iA~~l  267 (449)
                      ++.+..++|.||+|+|||+|++.  ++...
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~   65 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGII   65 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            34456799999999999999999  45544

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=93.17  E-value=0.064  Score=54.28  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=20.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+.|.||+|+|||||+++|++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            47799999999999999999954

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.16  E-value=0.04  Score=50.50  Aligned_cols=24  Identities=21%  Similarity=0.369  Sum_probs=21.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-|.|.|++|+||||.++.++..+
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            347889999999999999999988

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=93.16  E-value=0.034  Score=48.45  Aligned_cols=22  Identities=41%  Similarity=0.678  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+.|.|+||+|||+|+.++++.
T Consensus         6 ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            6 KVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999975

>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=93.14  E-value=0.05  Score=47.96  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|++|+|||+|+..+.+.-
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCcHHHHHHHHHhCC
Confidence            48999999999999999998753

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=93.14  E-value=0.099  Score=49.15  Aligned_cols=22  Identities=41%  Similarity=0.664  Sum_probs=20.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+.|.|+||+|||||+.++.+.
T Consensus         3 kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            3 HALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5789999999999999999875

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.12  E-value=0.032  Score=52.89  Aligned_cols=25  Identities=32%  Similarity=0.692  Sum_probs=22.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||.|+|||||++.|+..+
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            3458899999999999999999876

>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=93.11  E-value=0.051  Score=47.09  Aligned_cols=24  Identities=17%  Similarity=0.271  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~~   32 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSNT   32 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            458999999999999999998643

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=93.09  E-value=0.072  Score=54.32  Aligned_cols=29  Identities=31%  Similarity=0.461  Sum_probs=24.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .-+.|.||+|||||+|++.||+....+..
T Consensus       158 q~~~IvG~sGsGKSTLl~~Iag~~~~~~G  186 (438)
T 2dpy_A          158 QRMGLFAGSGVGKSVLLGMMARYTRADVI  186 (438)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcccCCCeE
Confidence            34889999999999999999999976543

>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=93.03  E-value=0.039  Score=47.80  Aligned_cols=22  Identities=32%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+++.|++|+|||+|+..+++.
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            5899999999999999999875

>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=93.02  E-value=0.053  Score=47.76  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|++|+|||+|+..+.+..
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999998887753

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=93.02  E-value=0.05  Score=42.37  Aligned_cols=68  Identities=13%  Similarity=0.003  Sum_probs=43.9

Q ss_pred             EeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHhc-------CCCHHHHHHHHHHHHHHHH
Q 013128          374 HMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELMK-------STNAEVSLNGLVKFLHAKM  441 (449)
Q Consensus       374 ~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~~-------~~~~~~al~~l~~~l~~~~  441 (449)
                      +-++|+.++|++|++.++......-.-+++.+++.+ +||+|||.+++..       ........+.+.++++..+
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~~~~I~~~df~~Al~~v~   82 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVM   82 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            457899999999999999865332222345566554 7999999888743       1222334455555555443

>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=93.01  E-value=0.053  Score=48.19  Aligned_cols=24  Identities=29%  Similarity=0.511  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            458999999999999999998764

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=92.99  E-value=0.022  Score=51.43  Aligned_cols=22  Identities=27%  Similarity=0.419  Sum_probs=19.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      --++|.|++|+|||+|+.++++
T Consensus        12 ~ki~vvG~~~~GKSsli~~l~~   33 (218)
T 4djt_A           12 YKICLIGDGGVGKTTYINRVLD   33 (218)
T ss_dssp             EEEEEECCTTSSHHHHHCBCTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3589999999999999999884

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.99  E-value=0.045  Score=48.49  Aligned_cols=23  Identities=26%  Similarity=0.489  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+++.|++|+|||+|+.++++.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999999973

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=92.97  E-value=0.053  Score=47.79  Aligned_cols=23  Identities=30%  Similarity=0.658  Sum_probs=20.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+++.|++|+|||+|+.++.+.-
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999998643

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=92.93  E-value=0.1  Score=52.00  Aligned_cols=34  Identities=18%  Similarity=0.239  Sum_probs=27.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      ..++++.||+|+|||++++.++..+   +..++.+|.
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~   71 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDP   71 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeC
Confidence            4579999999999999999998765   556666664

>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=92.92  E-value=0.084  Score=47.97  Aligned_cols=30  Identities=27%  Similarity=0.520  Sum_probs=24.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc--CCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL--KFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l--~~~~~~l  274 (449)
                      =|.|.|+.|+||||.++.++..|  +.+++..
T Consensus         4 FI~~EG~dGsGKsTq~~~L~~~L~~~~~v~~~   35 (205)
T 4hlc_A            4 FITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   35 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHCCCCEEEe
Confidence            36788999999999999999998  4555543

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=92.89  E-value=0.086  Score=47.75  Aligned_cols=24  Identities=29%  Similarity=0.549  Sum_probs=21.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-++|.|++|+|||+|+..++..+
T Consensus        39 ~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           39 VAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            468888999999999999999886

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=92.88  E-value=0.027  Score=55.82  Aligned_cols=25  Identities=24%  Similarity=0.515  Sum_probs=22.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+.|.||+|||||||.+.||....
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl~~   56 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGLDV   56 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            4478999999999999999999873

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=92.87  E-value=0.057  Score=47.66  Aligned_cols=24  Identities=21%  Similarity=0.313  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.++|.|++|+|||+|+.++.+.-
T Consensus        24 ~ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           24 LKIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            359999999999999999998754

>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=92.86  E-value=0.032  Score=53.77  Aligned_cols=26  Identities=27%  Similarity=0.471  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||+++|+..+.
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~~   89 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGELE   89 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            34488999999999999999999873

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.85  E-value=0.056  Score=48.25  Aligned_cols=23  Identities=35%  Similarity=0.560  Sum_probs=20.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-+++.|++|+|||+|+.++.+.
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45899999999999999999864

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.85  E-value=0.05  Score=55.85  Aligned_cols=27  Identities=22%  Similarity=0.208  Sum_probs=23.4

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+.-+.|.||.|+|||||++.|++.+
T Consensus       136 ~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          136 FEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            334558999999999999999999987

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.84  E-value=0.043  Score=47.97  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+++.|++|+|||+|+.++++.
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            3789999999999999999864

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=92.84  E-value=0.061  Score=52.33  Aligned_cols=29  Identities=24%  Similarity=0.381  Sum_probs=24.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      .+|+||.|++|+|||+++.++... |..++
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~-g~~lv  172 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR-GHRLV  172 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc-CCcee
Confidence            578999999999999999999885 54444

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.77  E-value=0.025  Score=50.64  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=20.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..-+.|.|++|+|||||++++++..
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~~   50 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQK   50 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC-
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3448999999999999999987543

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.75  E-value=0.051  Score=47.17  Aligned_cols=23  Identities=30%  Similarity=0.374  Sum_probs=20.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-++|.|++|+|||+|+.++.+.
T Consensus         7 ~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            7 RKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            45899999999999999999854

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.74  E-value=0.12  Score=54.27  Aligned_cols=32  Identities=31%  Similarity=0.352  Sum_probs=26.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~  275 (449)
                      .-++|.|+||+||||+++.++..++   .+++.++
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld  407 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLD  407 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEEC
Confidence            4588999999999999999999874   4555555

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=92.64  E-value=0.049  Score=54.69  Aligned_cols=25  Identities=36%  Similarity=0.517  Sum_probs=22.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.-+.|.||+|||||||+++||..+
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            3458899999999999999999865

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=92.63  E-value=0.045  Score=47.84  Aligned_cols=25  Identities=16%  Similarity=0.353  Sum_probs=21.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...+++.|++|+|||+|+.++.+.-
T Consensus        18 ~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           18 ELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            3469999999999999999998643

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=92.61  E-value=0.045  Score=49.56  Aligned_cols=23  Identities=26%  Similarity=0.600  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCCHHHHHHH-HHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAA-MANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~a-iA~~l  267 (449)
                      -+++.|++|+|||+|+.. +.+..
T Consensus        17 ki~v~G~~~~GKSsli~~~~~~~~   40 (221)
T 3gj0_A           17 KLVLVGDGGTGKTTFVKRHLTGEF   40 (221)
T ss_dssp             EEEEEECTTSSHHHHHTTBHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcCCC
Confidence            489999999999999999 54443

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.58  E-value=0.049  Score=47.73  Aligned_cols=24  Identities=33%  Similarity=0.419  Sum_probs=21.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-+++.|++|+|||+|+.++.+.-
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCc
Confidence            459999999999999999998753

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=92.51  E-value=0.046  Score=51.68  Aligned_cols=24  Identities=25%  Similarity=0.481  Sum_probs=21.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ..+.|.|+||+|||||+.++.+..
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~~   27 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGLR   27 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998753

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=92.50  E-value=0.056  Score=49.84  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=21.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .-++|.|++|+|||+|+.++.+..
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHcCCC
Confidence            459999999999999999998754

>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=92.43  E-value=0.035  Score=53.88  Aligned_cols=27  Identities=26%  Similarity=0.418  Sum_probs=23.5

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .+.-+.|.||.|+|||||++.|+..+.
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcCCC
Confidence            345588999999999999999999874

>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=92.42  E-value=0.066  Score=53.24  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+-|.||.|+|||||+++|+..+.
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL~~   79 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLLER   79 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>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=92.38  E-value=0.076  Score=47.15  Aligned_cols=22  Identities=36%  Similarity=0.516  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|+||+|||+|+..+++.
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~~   29 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAGV   29 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999864

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=92.38  E-value=2.3  Score=42.62  Aligned_cols=51  Identities=12%  Similarity=0.147  Sum_probs=30.6

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSL  259 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~l  259 (449)
                      .+|+++...+.+.+.+.+.   -+..+.-++...+   ...+.+++.+|+|+|||..
T Consensus        56 ~~f~~~~l~~~l~~~l~~~---g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a  109 (434)
T 2db3_A           56 QHFTSADLRDIIIDNVNKS---GYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAA  109 (434)
T ss_dssp             CCGGGSCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CChhhcCCCHHHHHHHHHc---CCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHH
Confidence            4688888777766655331   1112222222211   1246799999999999984

>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12

Probab=92.37  E-value=0.022  Score=52.82  Aligned_cols=23  Identities=39%  Similarity=0.488  Sum_probs=20.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.|.||+|+|||+|+++|+..+.
T Consensus        30 ~~i~GpnGsGKSTll~~i~g~~~   52 (227)
T 1qhl_A           30 TTLSGGNGAGKSTTMAAFVTALI   52 (227)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcccc
Confidence            45789999999999999999884

>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=92.37  E-value=0.064  Score=53.20  Aligned_cols=25  Identities=36%  Similarity=0.494  Sum_probs=22.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ..+.|.||+|+|||||+++|+....
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            4588999999999999999998665

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=92.35  E-value=0.06  Score=48.46  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      --+++.|++|+|||+|+..+++.
T Consensus        29 ~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           29 CKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999975

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=92.30  E-value=0.051  Score=52.40  Aligned_cols=26  Identities=38%  Similarity=0.507  Sum_probs=22.4

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-+.|.||+|+|||||+++|+.....
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             CeEEEECCCCCcHHHHHHHhcccccc
Confidence            45789999999999999999987654

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.29  E-value=0.063  Score=54.48  Aligned_cols=22  Identities=36%  Similarity=0.526  Sum_probs=20.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +.|.||+|+|||||+++|++..
T Consensus        45 vaLvG~nGaGKSTLln~L~G~~   66 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNTK   66 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTSC
T ss_pred             EEEECCCCCCHHHHHHHHhCcc
Confidence            7799999999999999999863

>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=92.29  E-value=0.069  Score=49.14  Aligned_cols=28  Identities=29%  Similarity=0.389  Sum_probs=22.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      -+.|.||.|+||||+++.|+.. +..+..
T Consensus        22 ~i~i~G~~GsGKSTl~~~L~~~-~g~v~~   49 (230)
T 2vp4_A           22 TVLIEGNIGSGKTTYLNHFEKY-KNDICL   49 (230)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG-TTTEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhc-cCCeEE
Confidence            3778999999999999999987 444443

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.27  E-value=0.064  Score=46.54  Aligned_cols=23  Identities=22%  Similarity=0.440  Sum_probs=20.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      ...+++.|++|+|||+|+.++.+
T Consensus        18 ~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           18 ELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            45699999999999999998873

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=92.26  E-value=0.059  Score=52.36  Aligned_cols=30  Identities=30%  Similarity=0.328  Sum_probs=24.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .+|+||.||+|+|||++|.++.. -|..++.
T Consensus       147 g~gvli~G~sG~GKStlal~l~~-~G~~lv~  176 (312)
T 1knx_A          147 GVGVLLTGRSGIGKSECALDLIN-KNHLFVG  176 (312)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT-TTCEEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH-cCCEEEe
Confidence            57899999999999999988765 4555553

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=92.23  E-value=0.12  Score=46.58  Aligned_cols=29  Identities=28%  Similarity=0.275  Sum_probs=24.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l  274 (449)
                      |.|.|+.|+||||.++.+++.|   |.+++..
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~t   34 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILK   34 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            4678999999999999999998   5666554

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.05  E-value=0.071  Score=46.94  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=20.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+++.|++|+|||+|+.++.+..
T Consensus        20 ki~v~G~~~~GKssli~~l~~~~   42 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYANDA   42 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999999763

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=92.03  E-value=0.34  Score=49.88  Aligned_cols=61  Identities=20%  Similarity=0.220  Sum_probs=38.9

Q ss_pred             eEEeCCCCCCHHHH-HHHHHHHcCCcEEEE--eccccc-ChHHHHHHHHcC--CCCceEEeeccchh
Q 013128          246 YLLYGPPGTGKSSL-IAAMANQLKFDIYDL--DLSAVQ-SNSELRFLLLTM--PSRSMLVIEDIDCS  306 (449)
Q Consensus       246 ~LL~GPpGtGKT~l-a~aiA~~l~~~~~~l--~~s~~~-~~~~l~~~~~~~--~~~~Il~iDeiD~l  306 (449)
                      .+|.|++|||||+| +..|++..+.+++.+  -+.+-. .-.++...+...  -..+++|.--.|..
T Consensus       165 ~~Ifg~~g~GKT~Lal~~I~~~~~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p  231 (502)
T 2qe7_A          165 ELIIGDRQTGKTTIAIDTIINQKGQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEP  231 (502)
T ss_dssp             CEEEECSSSCHHHHHHHHHHGGGSCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSC
T ss_pred             EEEECCCCCCchHHHHHHHHHhhcCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCC
Confidence            99999999999999 679999998886533  222221 112233333332  35778777666543

---

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	449
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	9e-31
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	1e-30
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	3e-28
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-21
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	8e-16
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	3e-15
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	1e-11
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	3e-10
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	5e-08
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	1e-07
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	4e-07
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	5e-06
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	7e-06
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	0.001
d1tuea_	205	c.37.1.20 (A:) Replication protein E1 helicase dom	0.002
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	0.003
d1zp6a1	176	c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {	0.004

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

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]

 Score =  117 bits (294), Expect = 9e-31
 Identities = 45/220 (20%), Positives = 94/220 (42%), Gaps = 15/220 (6%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           T++ +    ++KRE+ E ++  +   + + + G    +G L YGPPG GK+ L  A+AN+
Sbjct: 5   TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 64

Query: 267 LKFDIYDLDLSAVQS--------NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            + +   +    + +        N    F      +  +L  +++D   K +     +  
Sbjct: 65  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD-- 122

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYC 378
                     ++ +L  +DG+ +   +   I+  TN  + +DPA+LRPGR+D  +++   
Sbjct: 123 --GGGAADRVINQILTEMDGMSTK--KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLP 178

Query: 379 NTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVA 417
           +      +    L  S       +E L K     + A++ 
Sbjct: 179 DEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLT 218

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score =  116 bits (292), Expect = 1e-30
 Identities = 55/220 (25%), Positives = 91/220 (41%), Gaps = 16/220 (7%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TFK +A   E K E+ E +E F+     +  +G    +G LL GPPG GK+ L  A+A +
Sbjct: 7   TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 65

Query: 267 LKFDIYDLDLSAV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            +        S           + +R  F      +  ++ I++ID    +  +  S V 
Sbjct: 66  ARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEID---AVGRKRGSGVG 122

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYC 378
             N E  +  L+ LL  +DG         +++  TN  + LDPALLRPGR D  + +   
Sbjct: 123 GGNDEREQT-LNQLLVEMDGFEK--DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAP 179

Query: 379 NTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVA 417
           +    +Q+   +           +  L K       A++ 
Sbjct: 180 DVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLE 219

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score =  110 bits (276), Expect = 3e-28
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 15/181 (8%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
           TF  +A   E K E+ E +E ++     + ++G    +G L+ GPPGTGK+ L  A+A +
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 267 LKFDIYDLDLSAV------QSNSELR--FLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ 318
            K   + +  S           S +R  F      +  ++ I++ID    +  +  + + 
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID---AVGRQRGAGLG 125

Query: 319 ATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYC 378
             + E  + TL+ +L  +DG      EG I++  TN  + LDPALLRPGR D  + +   
Sbjct: 126 GGHDEREQ-TLNQMLVEMDGFEG--NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLP 182

Query: 379 N 379
           +
Sbjct: 183 D 183

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

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]

 Score = 91.2 bits (225), Expect = 2e-21
 Identities = 44/197 (22%), Positives = 77/197 (39%), Gaps = 13/197 (6%)

Query: 207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ 266
            +  +    +   +I E +E  +     +  IG    RG LLYGPPGTGK+ +  A+AN+
Sbjct: 2   GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 61

Query: 267 LKFDIYDLDLSAV------QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQAT 320
                + ++   +      +S S LR         +  +I   +       RE      T
Sbjct: 62  TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK-----T 116

Query: 321 NQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT 380
           + E  +  +S LL  +D          I++  TN    +DPAL R GR D  + +   + 
Sbjct: 117 HGEVERRIVSQLLTLMD--GLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDA 174

Query: 381 SVFKQLAFNYLGISHHY 397
           +   ++   +       
Sbjct: 175 TGRLEILQIHTKNMKLA 191

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 76.3 bits (187), Expect = 8e-16
 Identities = 35/256 (13%), Positives = 71/256 (27%), Gaps = 43/256 (16%)

Query: 147 EVRHYELSFHKKHKDVVLNLYLPHVLEKAKAIKEESKVVKLHTVMHMR------WDANNI 200
           + +     +H+KH      ++      +    ++    V     +            N  
Sbjct: 43  KEQPSHYKYHEKH-YANAAIFADSK-NQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRF 100

Query: 201 ---VLKHPMTFKT-LALDSELKREITEDLENFMNGKEY-------YTRIGRAWKRGYLLY 249
              + +  + F +  + D E        L   +   +                KR +L  
Sbjct: 101 NDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFK 160

Query: 250 GPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKL 309
           GP  +GK++L AA+         +++L   + N EL         + ++V ED+  +   
Sbjct: 161 GPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELG----VAIDQFLVVFEDVKGTGGE 216

Query: 310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG----------RIIVFTTNHKEKL 359
                S             L  L +++DG      E              + T N     
Sbjct: 217 SRDLPSGQ-------GINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNE---Y 266

Query: 360 DPALLRPGRMDMHLHM 375
                   R    +  
Sbjct: 267 SVPKTLQARFVKQIDF 282

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score = 73.5 bits (179), Expect = 3e-15
 Identities = 34/240 (14%), Positives = 68/240 (28%), Gaps = 21/240 (8%)

Query: 214 DSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD 273
           D + +  + ++LE  + GK+            +LL G PG+GK+SL +A+  + + ++  
Sbjct: 8   DKQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIV 62

Query: 274 LDLS----------AVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQE 323
           +D             +    E   +    P  + +    I            E      +
Sbjct: 63  IDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTD 122

Query: 324 ENKVTLSGLLNF---IDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT 380
               T + L               +    + T    E +        R            
Sbjct: 123 VPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVK 182

Query: 381 SV---FKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLNGLVKFL 437
           ++    + L    L         +  +L   +          L K  N +VS   +   L
Sbjct: 183 NLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTL 242

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

 Score = 63.5 bits (154), Expect = 1e-11
 Identities = 23/176 (13%), Positives = 54/176 (30%), Gaps = 22/176 (12%)

Query: 216 ELKREITEDLENFMNGKE---YYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFD-- 270
           +  R    DL   + G           R      ++ G   +GK+ L+ A+   L     
Sbjct: 93  QGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDK 152

Query: 271 IYDLDLSAV------QSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEE 324
              +             N  +  +   M    ++VI+ +  +V      ++     ++  
Sbjct: 153 YATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLK-NVIGAAGGNTTSGGISR-- 209

Query: 325 NKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE---KLDPALLRPGRMDMHLHMSY 377
                  LL+ I  + +    G +++ + N      K+   +    R +    +  
Sbjct: 210 ---GAFDLLSDIGAMAAS--RGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVIS 260

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 58.0 bits (139), Expect = 3e-10
 Identities = 27/157 (17%), Positives = 49/157 (31%), Gaps = 3/157 (1%)

Query: 220 EITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAV 279
            +T  L++     +      R      LL GPP +GK++L A +A +  F    +     
Sbjct: 17  PVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK 76

Query: 280 QSN-SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG 338
               SE                  + C V        +        + + L  LL  +  
Sbjct: 77  MIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKK 136

Query: 339 LWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHM 375
                    +I+ TT+ K+ L    +        +H+
Sbjct: 137 APPQG-RKLLIIGTTSRKDVLQEMEML-NAFSTTIHV 171

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.7 bits (122), Expect = 5e-08
 Identities = 27/179 (15%), Positives = 54/179 (30%), Gaps = 4/179 (2%)

Query: 205 PMTFKTLALDSELKREITEDLENFMNGKEY----YTRIGRAWKRGYLLYGPPGTGKSSLI 260
           P   + +  +     ++   L N+ N K+       + G    R  +LYGPPG GK++  
Sbjct: 10  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 69

Query: 261 AAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQAT 320
             +A +L +DI + + S V+S + L   +        +V                 V   
Sbjct: 70  HLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIM 129

Query: 321 NQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCN 379
           ++ +               +       +I+              R             +
Sbjct: 130 DEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANS 188

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score = 50.3 bits (119), Expect = 1e-07
 Identities = 34/205 (16%), Positives = 64/205 (31%), Gaps = 16/205 (7%)

Query: 205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
           P T         LK+++   LE     KE             LL+GPPG GK++L   +A
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEAAKARKEP--------LEHLLLFGPPGLGKTTLAHVIA 56

Query: 265 NQLKFDIYDLD-LSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQE 323
           ++L  ++      +  +       L  ++    +L I++I    +    E     A    
Sbjct: 57  HELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSR--QAEEHLYPAMEDF 114

Query: 324 ENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLH-MSYCNTSV 382
              + +                   ++  T     +   LL    +  HL   +    + 
Sbjct: 115 VMDIVIGQGPAARTIRLELPRF--TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQ 172

Query: 383 FKQLAFNYLGISHHYLFEQIEELIK 407
                   LG+      E   E+ +
Sbjct: 173 GVMRDARLLGVRITE--EAALEIGR 195

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

 Score = 48.4 bits (114), Expect = 4e-07
 Identities = 34/210 (16%), Positives = 72/210 (34%), Gaps = 13/210 (6%)

Query: 205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
           P +         +K++++  LE      E             LL GPPG GK++L   +A
Sbjct: 5   PKSLDEFIGQENVKKKLSLALEAAKMRGEVL--------DHVLLAGPPGLGKTTLAHIIA 56

Query: 265 NQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEE 324
           ++L+ +I+      +    ++  +L ++    +L I++I    K       E+  +  E+
Sbjct: 57  SELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAV----EELLYSAIED 112

Query: 325 NKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFK 384
            ++ +               +   +V  T     L   L     + + L   Y    + +
Sbjct: 113 FQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDF-YTVKELKE 171

Query: 385 QLAFNYLGISHHYLFEQIEELIKEVNVTPA 414
            +      +         E + K    TP 
Sbjct: 172 IIKRAASLMDVEIEDAAAEMIAKRSRGTPR 201

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 45.5 bits (106), Expect = 5e-06
 Identities = 28/220 (12%), Positives = 72/220 (32%), Gaps = 12/220 (5%)

Query: 223 EDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN 282
           ++ ++F + ++   ++        L+ G   TGKSS+I    N+L      LDL   +  
Sbjct: 9   DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 68

Query: 283 SELRFLLL--------TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLN 334
           + + +               + +  +     +++      +E++     +++++ + LL 
Sbjct: 69  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 128

Query: 335 FID---GLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL 391
             +                        L PAL         +      + +     +  +
Sbjct: 129 SFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRV 188

Query: 392 GISHHYLFEQIEELIKEVNVTPAEVAGELMKSTNAEVSLN 431
                 LF +    + E+     E A E ++    E  ++
Sbjct: 189 EDPESPLFGRAFSTV-ELKPFSREEAIEFLRRGFQEADID 227

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 45.2 bits (106), Expect = 7e-06
 Identities = 38/242 (15%), Positives = 83/242 (34%), Gaps = 53/242 (21%)

Query: 215 SELK-REITEDLENFMNGKEY------------YTRIGRAW-------KRGYLLYGPPGT 254
           SE+  REI  +L+  + G+              + R+            +  L+ GP G 
Sbjct: 1   SEMTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGV 60

Query: 255 GKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMP---------------SRSMLV 299
           GK+ +   +A         ++ +       +   + ++                   ++ 
Sbjct: 61  GKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVF 120

Query: 300 IEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRI----IVF-TTN 354
           I++ID   K+  +      +      +     LL  ++G       G +    I+F  + 
Sbjct: 121 IDEID---KICKKGEY---SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASG 174

Query: 355 HKEKLDPALLRP---GRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNV 411
             +   P+ L P   GR+ + + ++  + + F++     L   H  L EQ + L+    V
Sbjct: 175 AFQVARPSDLIPELQGRLPIRVELTALSAADFER----ILTEPHASLTEQYKALMATEGV 230

Query: 412 TP 413
             
Sbjct: 231 NI 232

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.8 bits (86), Expect = 0.001
 Identities = 29/232 (12%), Positives = 70/232 (30%), Gaps = 25/232 (10%)

Query: 205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMA 264
           P +   L+ + EL   +    +          R         LLYGP GTGK +   A+ 
Sbjct: 7   PKSLNALSHNEELTNFLKSLSDQ--------PRDLPH----LLLYGPNGTGKKTRCMALL 54

Query: 265 NQLKFDIYDLDLSAVQ-----SNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQA 319
             +           V+     SN +L   +++ P    +   D+  + ++  +E  +  A
Sbjct: 55  ESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 114

Query: 320 TNQEENKVTLSGLLN-----FIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLH 374
             ++ +       L       I    +   +          ++      L      M   
Sbjct: 115 QMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPI 174

Query: 375 MSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGELMKSTN 425
           ++   +                 +   +  +  E + +   ++   + +++N
Sbjct: 175 IAPIKSQCLLIRCPAPSDSEISTILSDV--VTNERIQLETKDILKRIAQASN 224

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]} Length = 205

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 6/65 (9%)

Query: 239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSML 298
           G   K   +  GP  TGKS    +  + ++  +          NS   F L  +    + 
Sbjct: 49  GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISF------VNSTSHFWLEPLTDTKVA 102

Query: 299 VIEDI 303
           +++D 
Sbjct: 103 MLDDA 107

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 37.1 bits (84), Expect = 0.003
 Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 7/74 (9%)

Query: 197 ANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGK 256
            ++ V       K L    +  +++   L N++                  L G PGTGK
Sbjct: 4   VDDSVFSPSYVPKRLPHREQQLQQLDILLGNWLRNP-------GHHYPRATLLGRPGTGK 56

Query: 257 SSLIAAMANQLKFD 270
           +  +  +    K  
Sbjct: 57  TVTLRKLWELYKDK 70

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]} Length = 176

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

 Score = 36.1 bits (82), Expect = 0.004
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 247 LLYGPPGTGKSSLIAAMANQLKFDIYDLD 275
           LL G PG+GKS++  A+AN          
Sbjct: 8   LLSGHPGSGKSTIAEALANLPGVPKVHFH 36

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	449
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.88
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.88
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.87
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.84
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.84
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.81
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.76
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.76
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.75
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.73
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.7
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.69
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.62
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.49
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.49
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.48
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.48
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.45
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.44
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.43
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.42
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.4
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.38
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.32
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.17
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.99
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.99
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.9
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.33
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.26
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.21
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.15
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.03
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.03
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.97
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.93
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.91
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.91
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.9
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.8
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.76
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.73
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.72
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.65
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.59
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.57
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.55
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.55
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.5
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.5
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.47
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.46
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.45
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.44
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.44
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.43
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.41
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.41
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.39
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.38
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.38
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.37
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.36
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.32
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.31
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.29
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.25
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.21
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.17
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	97.16
d1okkd2	207	GTPase domain of the signal recognition particle r	97.09
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.08
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.06
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.06
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.03
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.98
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.96
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.95
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.94
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.88
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.85
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.83
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.78
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.75
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.74
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.63
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.63
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.61
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.6
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.59
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.59
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.54
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.53
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.52
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.5
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.46
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.36
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.35
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.26
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.25
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.17
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.13
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.11
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.07
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.05
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.05
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	96.04
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	96.03
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.98
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.94
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	95.93
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.79
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.78
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.78
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	95.72
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.66
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.6
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.59
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	95.57
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.53
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	95.51
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.5
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.5
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	95.45
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	95.44
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	95.41
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	95.39
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.38
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.36
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	95.29
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	95.26
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.25
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	95.23
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.23
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.22
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.22
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	95.2
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.16
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.16
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	95.09
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	95.08
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.07
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	95.07
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	95.02
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.98
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.97
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	94.94
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.93
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.87
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.85
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.81
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.81
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.79
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.78
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.69
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.59
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.57
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.56
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.52
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.51
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.46
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.4
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.37
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.37
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	94.33
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.29
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.27
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.2
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	94.1
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.05
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	94.05
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.04
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.97
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.95
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.9
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.88
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.87
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.84
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.81
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	93.79
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.76
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.74
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.73
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.72
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.68
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	93.65
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	93.54
d1g2912	240	Maltose transport protein MalK, N-terminal domain	93.5
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	93.48
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.47
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.47
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.35
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.34
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.34
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.22
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	93.12
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.11
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.05
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.98
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	92.85
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.76
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.73
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.67
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	92.64
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.54
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	92.42
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	92.37
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.34
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	92.26
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	92.21
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	92.2
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	92.04
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	91.9
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.89
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.82
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	91.78
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	91.5
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	91.36
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	91.1
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.71
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	90.58
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.45
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	90.21
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.21
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	90.21
d1xpua3	289	Transcription termination factor Rho, ATPase domai	90.17
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	90.15
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.14
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	90.13
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	89.96
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	89.02
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	88.87
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	88.44
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	88.07
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	87.93
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	87.91
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	87.36
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	87.34
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	87.15
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	86.02
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	85.45
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	85.04
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	84.9
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	84.77
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	84.63
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	84.51
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	84.32
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	83.19
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.08
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	82.97
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	82.5
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	82.19
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	81.87
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	81.77
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	81.77
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	81.37
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	81.22
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	80.47
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	80.42

>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=100.00  E-value=1.5e-36  Score=289.81  Aligned_cols=212  Identities=25%  Similarity=0.359  Sum_probs=171.7

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc--
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ--  280 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~--  280 (449)
                      ..+.||++++|.+++|++|.+.+ .++..++.|+++|..+++|+|||||||||||++|+++|++++.+++.++++++.  
T Consensus         6 ~~~~t~~Di~Gl~~~k~~l~e~v-~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~~~   84 (256)
T d1lv7a_           6 QIKTTFADVAGCDEAKEEVAELV-EYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM   84 (256)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHH-HHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTS
T ss_pred             CCCCCHHHHhchHHHHHHHHHHH-HHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhhhc
Confidence            34579999999999999998866 578889999999999999999999999999999999999999999999998874  


Q ss_pred             ----ChHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          281 ----SNSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       281 ----~~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                          ++..++.+|..  ..+||||+|||+|.++..++.....    .......+++.||+.||++.+  ..+++||+|||
T Consensus        85 ~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~----~~~~~~~~~~~ll~~~d~~~~--~~~v~vIatTn  158 (256)
T d1lv7a_          85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGG----GHDEREQTLNQMLVEMDGFEG--NEGIIVIAATN  158 (256)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCC----TTCHHHHHHHHHHHHHHTCCS--SSCEEEEEEES
T ss_pred             chhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCC----CcHHHHHHHHHHHHHhhCCCC--CCCEEEEEeCC
Confidence                34667777665  4689999999999998644322211    123445678999999999865  46799999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHHh
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGELM  421 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l~  421 (449)
                      +|+.|||+++||||||.+|++++|+.++|.+|++.++......-..++..+.+.. ++|++||...+.
T Consensus       159 ~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~  226 (256)
T d1lv7a_         159 RPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (256)
T ss_dssp             CTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999876444334456666654 599999977763

>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=100.00  E-value=1.4e-36  Score=288.83  Aligned_cols=211  Identities=26%  Similarity=0.336  Sum_probs=172.2

Q ss_pred             CCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-
Q 013128          203 KHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-  281 (449)
Q Consensus       203 ~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-  281 (449)
                      .++.+|++|+|.+++|+.|.+. ..++.+++.|.+.|..+++|+|||||||||||++|+++|++++.+++.++++.+.+ 
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~~-i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~   81 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKEI-VEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM   81 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHH-HHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCcHHHHccHHHHHHHHHHH-HHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhc
Confidence            3557999999999999998765 46788999999999999999999999999999999999999999999999988742 


Q ss_pred             -----hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcC
Q 013128          282 -----NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTN  354 (449)
Q Consensus       282 -----~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  354 (449)
                           ...++.+|..  ..+||||+|||||.++..++.....    .......+++.||+.||++..  ...++||+|||
T Consensus        82 ~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~----~~~~~~~~~~~ll~~~d~~~~--~~~vivi~tTn  155 (247)
T d1ixza_          82 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGG----GNDEREQTLNQLLVEMDGFEK--DTAIVVMAATN  155 (247)
T ss_dssp             CTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC-------------CHHHHHHHHHHHHHHHTCCT--TCCEEEEEEES
T ss_pred             cccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCC----CcHHHHHHHHHHHHHhhCCCC--CCCEEEEEeCC
Confidence                 3556777655  4589999999999998644322211    223456789999999999865  46789999999


Q ss_pred             CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHH
Q 013128          355 HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       355 ~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      +++.||++++|||||+.+|+++.|+.++|++|++.++.........++..+.+.. ++|++||..++
T Consensus       156 ~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv  222 (247)
T d1ixza_         156 RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  222 (247)
T ss_dssp             CGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHH
Confidence            9999999999999999999999999999999999999865443333456666654 69999997765

>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=100.00  E-value=6.6e-36  Score=286.22  Aligned_cols=206  Identities=23%  Similarity=0.300  Sum_probs=173.9

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC----
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS----  281 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~----  281 (449)
                      .+|++|+|.++.|++|.+.+..++.+++.|++.|+++++|+|||||||||||++++++|++++.+++.++++.+.+    
T Consensus         1 ~~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g   80 (258)
T d1e32a2           1 VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG   80 (258)
T ss_dssp             CCGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTT
T ss_pred             CChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhcccccc
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999887643    


Q ss_pred             --hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC
Q 013128          282 --NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE  357 (449)
Q Consensus       282 --~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  357 (449)
                        ...++.+|..  ..+||||+|||+|.++..++..       ..+....+++.+++.+++...  ..+++||+|||+++
T Consensus        81 ~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~-------~~~~~~~~~~~~~~~~~~~~~--~~~vlvi~tTn~~~  151 (258)
T d1e32a2          81 ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKT-------HGEVERRIVSQLLTLMDGLKQ--RAHVIVMAATNRPN  151 (258)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHC-------CCTTHHHHHHHHHHHHHTCCC--SSCEEEEEEESCGG
T ss_pred             cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCC-------CCchHHHHHHHhccccccccc--cCCccEEEeCCCcc
Confidence              3455555554  4689999999999998644322       223445678889999998755  46799999999999


Q ss_pred             CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc-CCCHHHHHHHH
Q 013128          358 KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV-NVTPAEVAGEL  420 (449)
Q Consensus       358 ~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~tpa~i~~~l  420 (449)
                      .+|||++||||||.+|++++|+.++|++|++.+++........++..+.+.+ ++|++||..++
T Consensus       152 ~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv  215 (258)
T d1e32a2         152 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALC  215 (258)
T ss_dssp             GSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHH
T ss_pred             ccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHH
Confidence            9999999999999999999999999999999999764332222456666654 69999998775

>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=100.00  E-value=2.8e-35  Score=282.87  Aligned_cols=210  Identities=21%  Similarity=0.324  Sum_probs=167.7

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC---
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS---  281 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~---  281 (449)
                      ..+|++++|.+++|++|.+.+..++.+++.|.+.|.++++|+|||||||||||++|+++|++++.+++.++++.+.+   
T Consensus         3 ~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~~~   82 (265)
T d1r7ra3           3 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWF   82 (265)
T ss_dssp             CCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTSCT
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999877632   


Q ss_pred             ---hHHHHHHHHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC
Q 013128          282 ---NSELRFLLLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK  356 (449)
Q Consensus       282 ---~~~l~~~~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  356 (449)
                         ...++.+|..  ...||||+|||+|.++..++.....    .......+++.|++.||++...  .+++||+|||++
T Consensus        83 ~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~----~~~~~~~~~~~ll~~l~~~~~~--~~v~vi~ttn~~  156 (265)
T d1r7ra3          83 GESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD----GGGAADRVINQILTEMDGMSTK--KNVFIIGATNRP  156 (265)
T ss_dssp             TTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCT----THHHHHHHHHHHHHTCC--------CCEEEECCBSC
T ss_pred             cchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCC----CcHHHHHHHHHHHHHhhCcCCC--CCEEEEEeCCCc
Confidence               3556666644  4689999999999998643322111    1234556889999999998663  568999999999


Q ss_pred             CCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHc-cCCCHHHHHHHH
Q 013128          357 EKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKE-VNVTPAEVAGEL  420 (449)
Q Consensus       357 ~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~tpa~i~~~l  420 (449)
                      +.|||+++|||||+.+|++++|+.++|+.||+.++......-..+++.+... .++|++||..++
T Consensus       157 ~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv  221 (265)
T d1r7ra3         157 DIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEIC  221 (265)
T ss_dssp             TTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHH
T ss_pred             hhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHH
Confidence            9999999999999999999999999999999999875321111123444444 359999997765

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.88  E-value=6.4e-23  Score=193.91  Aligned_cols=169  Identities=17%  Similarity=0.179  Sum_probs=122.3

Q ss_pred             ccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-------
Q 013128          209 KTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-------  281 (449)
Q Consensus       209 ~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-------  281 (449)
                      +.+++..+..+.+++.+..+.....   .....+++|+|||||||||||++|+++|++++.+++.+++++...       
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~---~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~   85 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTK---NSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAK   85 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHH---HCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHh---ccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccch
Confidence            3466666677788888877775332   222345689999999999999999999999999999999876421       


Q ss_pred             hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCC
Q 013128          282 NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL  359 (449)
Q Consensus       282 ~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l  359 (449)
                      ...++.+|..+  .+||||||||||.+.+.+...        ....+.+++.|+..+|+.... +..++||+|||+++.+
T Consensus        86 ~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~--------~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~tTn~~~~l  156 (246)
T d1d2na_          86 CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG--------PRFSNLVLQALLVLLKKAPPQ-GRKLLIIGTTSRKDVL  156 (246)
T ss_dssp             HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTT--------TBCCHHHHHHHHHHTTCCCST-TCEEEEEEEESCHHHH
T ss_pred             hhhhhhhhhhhhhcccceeehhhhhhHhhhcccc--------cchhHHHHHHHHHHhcCCCcc-ccceeeeeccCChhhc
Confidence            23455666544  578999999999987633221        123356788899999987553 4568899999999999


Q ss_pred             CccccCCCccceEEEeCCCC-HHHHHHHHHHH
Q 013128          360 DPALLRPGRMDMHLHMSYCN-TSVFKQLAFNY  390 (449)
Q Consensus       360 d~aLlrpgR~d~~i~l~~p~-~~~r~~l~~~~  390 (449)
                      |++.++ +||+.+|++|.+. .+++..++...
T Consensus       157 d~~~~~-~rF~~~i~~P~~~~r~~il~~l~~~  187 (246)
T d1d2na_         157 QEMEML-NAFSTTIHVPNIATGEQLLEALELL  187 (246)
T ss_dssp             HHTTCT-TTSSEEEECCCEEEHHHHHHHHHHH
T ss_pred             cchhhc-CccceEEecCCchhHHHHHHHHHhc
Confidence            876443 5999999997654 34444444443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.88  E-value=6.2e-22  Score=185.26  Aligned_cols=191  Identities=18%  Similarity=0.200  Sum_probs=147.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS  281 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~  281 (449)
                      +-+|.+|++++|.+++++.+...+.......        ....++|||||||||||++|+++|++++.+++.++.+....
T Consensus         2 ~~RP~~~~divGqe~~~~~l~~~i~~~~~~~--------~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~   73 (238)
T d1in4a2           2 FLRPKSLDEFIGQENVKKKLSLALEAAKMRG--------EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVK   73 (238)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHHHT--------CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCS
T ss_pred             CCCCCcHHHcCChHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCccccc
Confidence            3579999999999999999988887654321        22468999999999999999999999999999999988888


Q ss_pred             hHHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc--------------cccCCCCe
Q 013128          282 NSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL--------------WSCCGEGR  347 (449)
Q Consensus       282 ~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--------------~~~~~~~~  347 (449)
                      ...+...+......++++|||+|.+....                  ...++..++..              .......+
T Consensus        74 ~~~~~~~~~~~~~~~~~~ide~~~~~~~~------------------~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (238)
T d1in4a2          74 QGDMAAILTSLERGDVLFIDEIHRLNKAV------------------EELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPF  135 (238)
T ss_dssp             HHHHHHHHHHCCTTCEEEEETGGGCCHHH------------------HHHHHHHHHTSCCCC---------------CCC
T ss_pred             HHHHHHHHHhhccCCchHHHHHHHhhhHH------------------HhhcccceeeeeeeeeecCcccccccccCCCCe
Confidence            88888888888899999999999885311                  11122222110              00012457


Q ss_pred             EEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHH-HHHHHHccCCCHHHHHHHH
Q 013128          348 IIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQ-IEELIKEVNVTPAEVAGEL  420 (449)
Q Consensus       348 iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~tpa~i~~~l  420 (449)
                      ++|++||++..+++++++  ||...+.++.|+.+++..+++.+...+...+.++ +..+++...-+++.+...|
T Consensus       136 ~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~ai~~l  207 (238)
T d1in4a2         136 TLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  207 (238)
T ss_dssp             EEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             EEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHHHHHH
Confidence            899999999999999999  9999999999999999999999998887776655 5555555566666655444

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.87  E-value=3.3e-25  Score=215.83  Aligned_cols=154  Identities=14%  Similarity=0.121  Sum_probs=118.6

Q ss_pred             ChhHHhhhcCCCCcceEE-eCCCCCCHHHHHHHHHHHcC--CcEEEEecccccC------hHHHHHHHHcCCCCceEEee
Q 013128          231 GKEYYTRIGRAWKRGYLL-YGPPGTGKSSLIAAMANQLK--FDIYDLDLSAVQS------NSELRFLLLTMPSRSMLVIE  301 (449)
Q Consensus       231 ~~~~~~~~g~~~~rg~LL-~GPpGtGKT~la~aiA~~l~--~~~~~l~~s~~~~------~~~l~~~~~~~~~~~Il~iD  301 (449)
                      .+..++.+|...++|+|| |||||||||.+|+++|.+++  .+++.++.+++.+      +..++.+|..+.+|||||||
T Consensus       110 ~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~D  189 (321)
T d1w44a_         110 SPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVID  189 (321)
T ss_dssp             CCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEE
T ss_pred             chHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEee
Confidence            344556666666777655 89999999999999999986  6789999888753      57788899888889999999


Q ss_pred             ccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC---CCCCccccCCCccceEEEeCCC
Q 013128          302 DIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRMDMHLHMSYC  378 (449)
Q Consensus       302 eiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~d~~i~l~~p  378 (449)
                      |||.+.+.+.....      ......++++||..|||+.+.  .+++||+|||+.   +.||++++|||||++++++++|
T Consensus       190 Eid~~~~~r~~~~~------~~~~~r~v~~lL~e~dg~~~~--~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~p  261 (321)
T d1w44a_         190 SLKNVIGAAGGNTT------SGGISRGAFDLLSDIGAMAAS--RGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVIST  261 (321)
T ss_dssp             CCTTTC-----------------CCHHHHHHHHHHHHHHHH--HTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEEC
T ss_pred             hhhhhccccccCCC------CCcchhhhhhhhhhccccccC--CCeEEEEeCCCcccccchhhhhhccCcccceeecCCC
Confidence            99999875533221      223356999999999999764  569999999952   2355666899999999999999


Q ss_pred             CHHHHHHHHHHHhC
Q 013128          379 NTSVFKQLAFNYLG  392 (449)
Q Consensus       379 ~~~~r~~l~~~~l~  392 (449)
                      +.+.+.+|+..+..
T Consensus       262 d~~~r~~il~~~~~  275 (321)
T d1w44a_         262 DVDGEWQVLTRTGE  275 (321)
T ss_dssp             SSTTEEEEEEECBT
T ss_pred             ChHHHHHHHHHhcc
Confidence            99999998876654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=99.84  E-value=7.7e-20  Score=171.03  Aligned_cols=187  Identities=18%  Similarity=0.208  Sum_probs=136.2

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNS  283 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~  283 (449)
                      +|.+|++++|.+++++.+...+..+...        ...+.++|||||||||||++|+++|+++++++..++.+......
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~~--------~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~   75 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKAR--------KEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPG   75 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTTS--------SSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhc--------CCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccch
Confidence            7999999999999999998887654432        22357899999999999999999999999999999988887655


Q ss_pred             HHHHHHHcC-CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc--------------cccCCCCeE
Q 013128          284 ELRFLLLTM-PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL--------------WSCCGEGRI  348 (449)
Q Consensus       284 ~l~~~~~~~-~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--------------~~~~~~~~i  348 (449)
                      .....+... ...+|++|||+|.+...                  ....++..++..              .......++
T Consensus        76 ~~~~~~~~~~~~~~i~~iDe~~~~~~~------------------~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~  137 (239)
T d1ixsb2          76 DLAAILANSLEEGDILFIDEIHRLSRQ------------------AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFT  137 (239)
T ss_dssp             HHHHHHHTTCCTTCEEEEETGGGCCHH------------------HHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCE
T ss_pred             hhHHHHHhhccCCCeeeeecccccchh------------------HHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEE
Confidence            555444444 46789999999987431                  111123333210              001123467


Q ss_pred             EEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH-HHHHHHHccCCCHHHHHH
Q 013128          349 IVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE-QIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       349 iI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~-~i~~l~~~~~~tpa~i~~  418 (449)
                      +|++||++...+++.++  |+...+.+..|+.+++.+++...+..++....+ .++.++....-++.....
T Consensus       138 ~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~  206 (239)
T d1ixsb2         138 LIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKR  206 (239)
T ss_dssp             EEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHH
T ss_pred             EEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHH
Confidence            88899999888888888  778889999999999999999988877655543 444455554445544433

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.84  E-value=9.4e-21  Score=184.77  Aligned_cols=174  Identities=15%  Similarity=0.231  Sum_probs=126.5

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhh-cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccC-------
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRI-GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQS-------  281 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~-g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~-------  281 (449)
                      .++|+++.|+.+...+..++++....... +..+++|+||+||||||||+||+++|+.++.+++.++++.+..       
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~   94 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   94 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGS
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeee
Confidence            36899999999988876554433222111 1124689999999999999999999999999999999988742       


Q ss_pred             -hHHHHHHHHcCC-------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCC------CCe
Q 013128          282 -NSELRFLLLTMP-------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCG------EGR  347 (449)
Q Consensus       282 -~~~l~~~~~~~~-------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~  347 (449)
                       +..++.++..+.       +||||||||||.+.+.+.....      +-....+++.||..+||.....+      ..+
T Consensus        95 ~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~------~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~i  168 (309)
T d1ofha_          95 VDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGA------DVSREGVQRDLLPLVEGSTVSTKHGMVKTDHI  168 (309)
T ss_dssp             TTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSS------HHHHHHHHHHHHHHHHCCEEEETTEEEECTTC
T ss_pred             ccccccccchhhhcccccccCCceEEehhhhhhhhhccCccc------chhhhHHHHHhhHHhcCCEEecCCeEEEccce
Confidence             345666776664       3899999999999763322211      11223467889999998643322      234


Q ss_pred             EEEEE----cCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q 013128          348 IIVFT----TNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYL  391 (449)
Q Consensus       348 iiI~t----TN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l  391 (449)
                      ++|++    ++.++.++|++++  ||+..+.++.|+.+++++++..+.
T Consensus       169 lfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~~  214 (309)
T d1ofha_         169 LFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPH  214 (309)
T ss_dssp             EEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             eEEeccchhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHHH
Confidence            45555    4667777888875  999999999999999999987543

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.81  E-value=1.6e-19  Score=169.81  Aligned_cols=177  Identities=18%  Similarity=0.273  Sum_probs=125.0

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChh----HHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKE----YYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~----~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .|..    .++|.+|++++|.++.+++|.+.+..+.....    .+...+..+.+++|||||||||||++|+++|++++.
T Consensus         3 lW~e----ky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~   78 (253)
T d1sxja2           3 LWTV----KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY   78 (253)
T ss_dssp             CHHH----HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             cccc----CcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4754    78999999999999999999998877654321    223445666788999999999999999999999999


Q ss_pred             cEEEEecccccChHHHHHHHHc--------------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          270 DIYDLDLSAVQSNSELRFLLLT--------------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       270 ~~~~l~~s~~~~~~~l~~~~~~--------------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                      +++.++++...+...+......                    .....++++||+|.+...               ....+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~---------------~~~~~  143 (253)
T d1sxja2          79 DILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG---------------DRGGV  143 (253)
T ss_dssp             EEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTT---------------STTHH
T ss_pred             hhhccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccc---------------hhhhh
Confidence            9999999888766554432211                    124679999999987531               11223


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCC
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHY  397 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~  397 (449)
                      ..++......    ...++++++++....+++ +.   |+...|+|+.|+.++++.++++++..++..
T Consensus       144 ~~~~~~~~~~----~~~ii~i~~~~~~~~~~~-l~---~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~  203 (253)
T d1sxja2         144 GQLAQFCRKT----STPLILICNERNLPKMRP-FD---RVCLDIQFRRPDANSIKSRLMTIAIREKFK  203 (253)
T ss_dssp             HHHHHHHHHC----SSCEEEEESCTTSSTTGG-GT---TTSEEEECCCCCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHhhhhccc----cccccccccccccccccc-cc---ceeeeeeccccchhHHHHHHHHHHHHhCCC
Confidence            3344443321    223444444555555554 43   556889999999999999999887654433

>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=99.76  E-value=1.6e-18  Score=161.08  Aligned_cols=164  Identities=14%  Similarity=0.169  Sum_probs=123.3

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      .+|..    .+.|.+|++++|.+++++.+...+...             ...++|||||||||||++|+++|++++    
T Consensus        12 ~~w~~----ky~P~~~~diig~~~~~~~l~~~i~~~-------------~~~~lll~Gp~G~GKTtla~~iak~l~~~~~   74 (231)
T d1iqpa2          12 KPWVE----KYRPQRLDDIVGQEHIVKRLKHYVKTG-------------SMPHLLFAGPPGVGKTTAALALARELFGENW   74 (231)
T ss_dssp             SCHHH----HTCCCSTTTCCSCHHHHHHHHHHHHHT-------------CCCEEEEESCTTSSHHHHHHHHHHHHHGGGH
T ss_pred             chHHH----HhCCCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCcHHHHHHHHHHHHHhccc
Confidence            46855    789999999999999988887766421             124699999999999999999999874    


Q ss_pred             -CcEEEEecccccChHHHHHHHH----c----CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCc
Q 013128          269 -FDIYDLDLSAVQSNSELRFLLL----T----MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGL  339 (449)
Q Consensus       269 -~~~~~l~~s~~~~~~~l~~~~~----~----~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  339 (449)
                       .+++.+++++......++....    .    ...+.|+++||+|.+..                  .....|+..++..
T Consensus        75 ~~~~~e~n~s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~------------------~~~~~ll~~l~~~  136 (231)
T d1iqpa2          75 RHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ------------------DAQQALRRTMEMF  136 (231)
T ss_dssp             HHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH------------------HHHHHHHHHHHHT
T ss_pred             CCCeeEEecCcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcch------------------hHHHHHhhhcccC
Confidence             5788888876543222222111    1    23678999999998753                  1223466666542


Q ss_pred             cccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCC
Q 013128          340 WSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYL  398 (449)
Q Consensus       340 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l  398 (449)
                          ...+++|++||++..+++++.+  |+ ..+.++.|+.++...++++.+..++..+
T Consensus       137 ----~~~~~~i~~~n~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~~~~e~i~i  188 (231)
T d1iqpa2         137 ----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLEL  188 (231)
T ss_dssp             ----TTTEEEEEEESCGGGSCHHHHH--TE-EEEECCCCCHHHHHHHHHHHHHTTTCEE
T ss_pred             ----CcceEEEeccCChhhchHhHhC--cc-ccccccccchhhHHHHHHHHHHHhCCCC
Confidence                3457889999999999999998  88 5699999999999999998887665544

>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=99.76  E-value=2e-17  Score=154.86  Aligned_cols=186  Identities=17%  Similarity=0.241  Sum_probs=133.7

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC------------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF------------  269 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~------------  269 (449)
                      .++|.+|++++|.+++++.+...+..    .        ..+.++|||||||||||++|+++|++++.            
T Consensus         5 KyrP~~~~dlig~~~~~~~L~~~i~~----~--------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~   72 (239)
T d1njfa_           5 KWRPQTFADVVGQEHVLTALANGLSL----G--------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   72 (239)
T ss_dssp             HTCCSSGGGSCSCHHHHHHHHHHHHT----T--------CCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCS
T ss_pred             hhCCCCHHHccChHHHHHHHHHHHHc----C--------CCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccc
Confidence            57899999999999888877665531    1        12567999999999999999999999843            


Q ss_pred             ------------cEEEEecccccChHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          270 ------------DIYDLDLSAVQSNSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       270 ------------~~~~l~~s~~~~~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                                  +++.++.++......++.++....      ...|++|||+|.+..                  ...+.
T Consensus        73 ~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~------------------~~q~~  134 (239)
T d1njfa_          73 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSR------------------HSFNA  134 (239)
T ss_dssp             HHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCH------------------HHHHH
T ss_pred             hHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCH------------------HHHHH
Confidence                        467777666555566666666553      345999999999742                  23456


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNV  411 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~  411 (449)
                      |+..|+..    +...++|++||.++.+.+++.+  |+ ..+.++.|+.++.+..+.+....++..             +
T Consensus       135 Llk~lE~~----~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~-------------~  194 (239)
T d1njfa_         135 LLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIA-------------H  194 (239)
T ss_dssp             HHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCC-------------B
T ss_pred             HHHHHhcC----CCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhccC-------------C
Confidence            88888753    3567899999999999999999  77 579999999999888888776654433             3


Q ss_pred             CHHHHHHHHhc-CCCHHHHHHHHHHHH
Q 013128          412 TPAEVAGELMK-STNAEVSLNGLVKFL  437 (449)
Q Consensus       412 tpa~i~~~l~~-~~~~~~al~~l~~~l  437 (449)
                      ++..+..+.-. .+|+..|+..+....
T Consensus       195 ~~~~l~~i~~~s~Gd~R~ain~l~~~~  221 (239)
T d1njfa_         195 EPRALQLLARAAEGSLRDALSLTDQAI  221 (239)
T ss_dssp             CHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            33333222222 346666776655433

>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=99.75  E-value=6.4e-18  Score=156.39  Aligned_cols=192  Identities=13%  Similarity=0.204  Sum_probs=138.4

Q ss_pred             ccccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----
Q 013128          193 MRWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----  268 (449)
Q Consensus       193 ~~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----  268 (449)
                      -+|..    .++|.+|++++|.+++++.+...+.    ...         ..++|||||||||||++|+++|++++    
T Consensus         3 ~pw~e----KyrP~~~~d~ig~~~~~~~L~~~~~----~~~---------~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~   65 (224)
T d1sxjb2           3 LPWVE----KYRPQVLSDIVGNKETIDRLQQIAK----DGN---------MPHMIISGMPGIGKTTSVHCLAHELLGRSY   65 (224)
T ss_dssp             CCHHH----HTCCSSGGGCCSCTHHHHHHHHHHH----SCC---------CCCEEEECSTTSSHHHHHHHHHHHHHGGGH
T ss_pred             CchHh----HhCCCCHHHhcCCHHHHHHHHHHHH----cCC---------CCeEEEECCCCCCchhhHHHHHHHHhcccc
Confidence            36865    7899999999999988887776553    211         23699999999999999999999986    


Q ss_pred             -CcEEEEecccccChHHHHHHHH----cC-----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcC
Q 013128          269 -FDIYDLDLSAVQSNSELRFLLL----TM-----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDG  338 (449)
Q Consensus       269 -~~~~~l~~s~~~~~~~l~~~~~----~~-----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  338 (449)
                       .+++.++.++..+...+...+.    ..     ....|++|||+|.+..                  .....|+..++.
T Consensus        66 ~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~------------------~~~~~ll~~~e~  127 (224)
T d1sxjb2          66 ADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA------------------GAQQALRRTMEL  127 (224)
T ss_dssp             HHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH------------------HHHHTTHHHHHH
T ss_pred             ccccccccccccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccch------------------hHHHHHhhhccc
Confidence             4588888887766544432222    11     2456999999998854                  122335566654


Q ss_pred             ccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHH
Q 013128          339 LWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAG  418 (449)
Q Consensus       339 ~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~  418 (449)
                      .    ....+++++|+..+.+.++|++  |+ ..|+|+.|+.++...++...+..++             ..+++..+..
T Consensus       128 ~----~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i~~~e~-------------~~i~~~~l~~  187 (224)
T d1sxjb2         128 Y----SNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLED-------------VKYTNDGLEA  187 (224)
T ss_dssp             T----TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHT-------------CCBCHHHHHH
T ss_pred             c----ccceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHHHHhcc-------------cCCCHHHHHH
Confidence            2    3557888999999999999999  87 5699999999999999887775443             3345444433


Q ss_pred             HHhc-CCCHHHHHHHHHHHHHH
Q 013128          419 ELMK-STNAEVSLNGLVKFLHA  439 (449)
Q Consensus       419 ~l~~-~~~~~~al~~l~~~l~~  439 (449)
                      .... ++|+..|+..|+.++..
T Consensus       188 I~~~s~Gd~R~ai~~Lq~~~~~  209 (224)
T d1sxjb2         188 IIFTAEGDMRQAINNLQSTVAG  209 (224)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCcHHHHHHHHHHHHHc
Confidence            3322 46888888888766543

>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=99.73  E-value=2.1e-17  Score=152.84  Aligned_cols=165  Identities=21%  Similarity=0.276  Sum_probs=121.3

Q ss_pred             cccccccccCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC----
Q 013128          194 RWDANNIVLKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF----  269 (449)
Q Consensus       194 ~w~~~~~~~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~----  269 (449)
                      +|..    .++|.+|++++|.+++++.+...+.    ...         ..++|||||||||||++|+++|++++.    
T Consensus         3 pw~e----kyrP~~~~divg~~~~~~~L~~~i~----~~~---------~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~   65 (227)
T d1sxjc2           3 PWVE----KYRPETLDEVYGQNEVITTVRKFVD----EGK---------LPHLLFYGPPGTGKTSTIVALAREIYGKNYS   65 (227)
T ss_dssp             CHHH----HTCCSSGGGCCSCHHHHHHHHHHHH----TTC---------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHH
T ss_pred             chhh----hhCCCCHHHccCcHHHHHHHHHHHH----cCC---------CCeEEEECCCCCChhHHHHHHHHHhhcCCCc
Confidence            5755    7899999999999988888776653    211         235999999999999999999999853    


Q ss_pred             -cEEEEecccccChHHHH----HHHHcC----CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcc
Q 013128          270 -DIYDLDLSAVQSNSELR----FLLLTM----PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLW  340 (449)
Q Consensus       270 -~~~~l~~s~~~~~~~l~----~~~~~~----~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  340 (449)
                       .++..+.++........    ......    .+..|++|||+|.+..                  ...+.|+..|+.. 
T Consensus        66 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~------------------~~~~~Ll~~le~~-  126 (227)
T d1sxjc2          66 NMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN------------------AAQNALRRVIERY-  126 (227)
T ss_dssp             HHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH------------------HHHHHHHHHHHHT-
T ss_pred             ceeEEecccccCCeeeeecchhhccccccccCCCeEEEEEeccccchh------------------hHHHHHHHHhhhc-
Confidence             35666666654432222    111111    2346999999998743                  2345577777653 


Q ss_pred             ccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHH
Q 013128          341 SCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFE  400 (449)
Q Consensus       341 ~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~  400 (449)
                         ....+++++||.+..+++++++  |+ ..+.|+.|+.++...++.+.+..++..+.+
T Consensus       127 ---~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~  180 (227)
T d1sxjc2         127 ---TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLSP  180 (227)
T ss_dssp             ---TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCH
T ss_pred             ---ccceeeccccCcHHHhHHHHHH--HH-hhhccccccccccccccccccccccccCCH
Confidence               3467888999999999999998  76 568999999999999999888766555543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=2.9e-17  Score=153.89  Aligned_cols=186  Identities=15%  Similarity=0.167  Sum_probs=119.3

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---Cc--------
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---FD--------  270 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---~~--------  270 (449)
                      .++|.+|++++|.+++++.+...    +....        ...++|||||||||||++|+++|+++.   ..        
T Consensus         4 ky~P~~~~diig~~~~~~~L~~~----~~~~~--------~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~   71 (252)
T d1sxje2           4 KYRPKSLNALSHNEELTNFLKSL----SDQPR--------DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQ   71 (252)
T ss_dssp             TTCCCSGGGCCSCHHHHHHHHTT----TTCTT--------CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-------
T ss_pred             ccCCCCHHHccCcHHHHHHHHHH----HHcCC--------CCCeEEEECCCCCCHHHHHHHHHHhhcCcccccccccccc
Confidence            78999999999998877766543    32221        134699999999999999999999872   11        


Q ss_pred             ------------------EEEEecccccCh-----HHHHHHHHc-------------CCCCceEEeeccchhhhcccccc
Q 013128          271 ------------------IYDLDLSAVQSN-----SELRFLLLT-------------MPSRSMLVIEDIDCSVKLQNRES  314 (449)
Q Consensus       271 ------------------~~~l~~s~~~~~-----~~l~~~~~~-------------~~~~~Il~iDeiD~l~~~~~~~~  314 (449)
                                        .+.+........     .........             .....+++|||+|.+..      
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~------  145 (252)
T d1sxje2          72 FVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTK------  145 (252)
T ss_dssp             -----------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCH------
T ss_pred             ccccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEecccccccc------
Confidence                              111111111111     011111111             12345999999998743      


Q ss_pred             hhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC
Q 013128          315 SEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS  394 (449)
Q Consensus       315 ~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~  394 (449)
                                  .....|+..++..    ...+.+|++||+++.+++++++  |+ ..|+|+.|+.++.++++...+..+
T Consensus       146 ------------~~~~~l~~~~e~~----~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~e  206 (252)
T d1sxje2         146 ------------DAQAALRRTMEKY----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNE  206 (252)
T ss_dssp             ------------HHHHHHHHHHHHS----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             ------------ccchhhhcccccc----cccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHHHHc
Confidence                        1234456666532    3457789999999999999998  88 589999999999999998766543


Q ss_pred             CCCCHHHHHHHHHccCCCHHHHHHHHhc--CCCHHHHHHHHHHHH
Q 013128          395 HHYLFEQIEELIKEVNVTPAEVAGELMK--STNAEVSLNGLVKFL  437 (449)
Q Consensus       395 ~~~l~~~i~~l~~~~~~tpa~i~~~l~~--~~~~~~al~~l~~~l  437 (449)
                      +..             +.+.++.+.+.+  .+|...|+..|+.+.
T Consensus       207 ~~~-------------~~~~~~l~~i~~~s~Gd~R~ai~~Lq~~~  238 (252)
T d1sxje2         207 RIQ-------------LETKDILKRIAQASNGNLRVSLLMLESMA  238 (252)
T ss_dssp             TCE-------------ECCSHHHHHHHHHHTTCHHHHHHHHTHHH
T ss_pred             CCC-------------CCcHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            322             222333344433  467777877666444

>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=99.69  E-value=1.6e-16  Score=147.42  Aligned_cols=189  Identities=16%  Similarity=0.164  Sum_probs=128.4

Q ss_pred             cCCCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc------CCcEEEEe
Q 013128          202 LKHPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL------KFDIYDLD  275 (449)
Q Consensus       202 ~~~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l------~~~~~~l~  275 (449)
                      .++|.+|++++|.+++++.+...+    ....         ...+||+||||||||++++++|+++      +...+.++
T Consensus         5 ky~P~~~~diig~~~~~~~l~~~i----~~~~---------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~   71 (237)
T d1sxjd2           5 KYRPKNLDEVTAQDHAVTVLKKTL----KSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN   71 (237)
T ss_dssp             HTCCSSTTTCCSCCTTHHHHHHHT----TCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC
T ss_pred             hhCCCCHHHccCcHHHHHHHHHHH----HcCC---------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhee
Confidence            789999999999998887766543    3221         2459999999999999999999997      56777777


Q ss_pred             cccccChHHHH----HHH-------------H-cCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc
Q 013128          276 LSAVQSNSELR----FLL-------------L-TMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID  337 (449)
Q Consensus       276 ~s~~~~~~~l~----~~~-------------~-~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld  337 (449)
                      .+.........    ...             . ......||+|||+|.+..                  ...+.++..++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~------------------~~~~~l~~~~~  133 (237)
T d1sxjd2          72 ASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA------------------DAQSALRRTME  133 (237)
T ss_dssp             SSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH------------------HHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCH------------------HHHHHHhhccc
Confidence            76654432211    110             1 112345899999998753                  12223444443


Q ss_pred             CccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHH
Q 013128          338 GLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVA  417 (449)
Q Consensus       338 g~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~  417 (449)
                      ..    ....++|.+++....+.+++.+  |+ .++.|+.|+.++...+++..+..++..             +++..+.
T Consensus       134 ~~----~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~-------------i~~~~l~  193 (237)
T d1sxjd2         134 TY----SGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVK-------------CDDGVLE  193 (237)
T ss_dssp             HT----TTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCC-------------CCHHHHH
T ss_pred             cc----cccccccccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCc-------------CCHHHHH
Confidence            22    2456788899999999999998  87 679999999999999998877654433             3433332


Q ss_pred             HHHhc-CCCHHHHHHHHHHHHHHHH
Q 013128          418 GELMK-STNAEVSLNGLVKFLHAKM  441 (449)
Q Consensus       418 ~~l~~-~~~~~~al~~l~~~l~~~~  441 (449)
                      .+.-. .+|...|+..|..+.....
T Consensus       194 ~ia~~s~gd~R~ai~~L~~~~~~~~  218 (237)
T d1sxjd2         194 RILDISAGDLRRGITLLQSASKGAQ  218 (237)
T ss_dssp             HHHHHTSSCHHHHHHHHHHTHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHhch
Confidence            22222 3577788877766554433

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.62  E-value=4.9e-16  Score=153.76  Aligned_cols=150  Identities=19%  Similarity=0.162  Sum_probs=102.7

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcC
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTM  292 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~  292 (449)
                      +.++++..+.+.+..++        .|+|.++++|||||||||||++|+++|++++.+++.+++++..+.    ..+...
T Consensus       132 ~~~~~~~~i~~~l~~~~--------~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~----~~l~~~  199 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMV--------YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLN----FELGVA  199 (362)
T ss_dssp             TSTTHHHHHHHHHHHHH--------HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHH----HHHGGG
T ss_pred             cccchHHHHHHHHHHHH--------hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhH----HHHHhH
Confidence            34456666666665443        367888999999999999999999999999999999998876443    234455


Q ss_pred             CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC----------eEEEEEcCCCCCCCcc
Q 013128          293 PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG----------RIIVFTTNHKEKLDPA  362 (449)
Q Consensus       293 ~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~----------~iiI~tTN~~~~ld~a  362 (449)
                      ..+.+.++||+++...........       ..-..+..|.+.+||....+.+.          ..+|+|||+   ++.+
T Consensus       200 ~~~~~~l~d~~~~~~~~~~~~~~~-------~~~DeiD~l~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~---~~~~  269 (362)
T d1svma_         200 IDQFLVVFEDVKGTGGESRDLPSG-------QGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNE---YSVP  269 (362)
T ss_dssp             TTCSCEEETTCCCSTTTTTTCCCC-------SHHHHHHTTHHHHHCSSCEEECCSSSCCEEECCCCEEEEECS---CCCC
T ss_pred             HHHHHHHHHHHHHhhhhccCCCCe-------EEEehHhhcccccCCcchhhhhhhhhchhhhccCCceeeccc---cccc
Confidence            667778888888765422221110       01112344566667653221111          247889996   5677


Q ss_pred             ccCCCccceEEEeCCCCHHHHH
Q 013128          363 LLRPGRMDMHLHMSYCNTSVFK  384 (449)
Q Consensus       363 LlrpgR~d~~i~l~~p~~~~r~  384 (449)
                      ++|||||++.+.++.|....+.
T Consensus       270 ~~r~~Rf~~~i~~~~~~~~~~~  291 (362)
T d1svma_         270 KTLQARFVKQIDFRPKDYLKHC  291 (362)
T ss_dssp             HHHHTTEEEEEECCCCHHHHHH
T ss_pred             ccccccCceEEeecCCCcHHHH
Confidence            8899999999999998876654

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.49  E-value=1.1e-13  Score=134.50  Aligned_cols=158  Identities=18%  Similarity=0.235  Sum_probs=113.4

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh-------
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN-------  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~-------  282 (449)
                      .++|+++.++.|...+.....+-.   +.. .+...+||.||||||||.||+++|..++.+++.++++.+.+.       
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~---~~~-~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l~   98 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLG---HEH-KPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI   98 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCS---CTT-SCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSSC
T ss_pred             eecChHHHHHHHHHHHHHHHccCC---CCC-CCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhhc
Confidence            578999999999887764432110   001 122358999999999999999999999999999999987532       


Q ss_pred             ------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc-------C
Q 013128          283 ------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC-------C  343 (449)
Q Consensus       283 ------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-------~  343 (449)
                                  ..+... ......+|+++||||...+                  .+.+.||+.+|.-.-.       .
T Consensus        99 g~~~gy~g~~~~~~l~~~-~~~~~~~vvl~DeieKa~~------------------~V~~~lLqild~G~ltd~~Gr~vd  159 (315)
T d1r6bx3          99 GAPPGYVGFDQGGLLTDA-VIKHPHAVLLLDEIEKAHP------------------DVFNILLQVMDNGTLTDNNGRKAD  159 (315)
T ss_dssp             CCCSCSHHHHHTTHHHHH-HHHCSSEEEEEETGGGSCH------------------HHHHHHHHHHHHSEEEETTTEEEE
T ss_pred             ccCCCccccccCChhhHH-HHhCccchhhhcccccccc------------------hHhhhhHHhhccceecCCCCCccC
Confidence                        112222 2345678999999998743                  2566788877632111       1


Q ss_pred             CCCeEEEEEcCCCC-------------------------CCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          344 GEGRIIVFTTNHKE-------------------------KLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       344 ~~~~iiI~tTN~~~-------------------------~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      -...|+|+|||--.                         .+.|.|+.  |+|..+.+.+.+.++...|+..++.
T Consensus       160 f~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         160 FRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             CTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             ccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHH
Confidence            24568999999421                         25677777  9999999999999999999987764

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.49  E-value=1e-13  Score=127.14  Aligned_cols=172  Identities=15%  Similarity=0.220  Sum_probs=107.2

Q ss_pred             CCCCccccc-CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          204 HPMTFKTLA-LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       204 ~p~~f~~l~-g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      +..||++.+ |....  .....+..+...+.       ...+.++||||||||||+|++|+|+++   +..++.++...+
T Consensus         5 ~~~tFdnF~vg~~N~--~a~~~~~~~~~~~~-------~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~   75 (213)
T d1l8qa2           5 PKYTLENFIVGEGNR--LAYEVVKEALENLG-------SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF   75 (213)
T ss_dssp             TTCCSSSCCCCTTTH--HHHHHHHHHHHTTT-------TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CCCChhhccCCCcHH--HHHHHHHHHHhCcC-------CCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH
Confidence            456899965 54322  23333334443321       112459999999999999999999998   567777776655


Q ss_pred             cCh-------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEE
Q 013128          280 QSN-------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFT  352 (449)
Q Consensus       280 ~~~-------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  352 (449)
                      ...       ..............+|+|||||.+.+.             ...+..+-.++|.+   ..  .+..+||.+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~~-------------~~~~~~lf~lin~~---~~--~~~~iiits  137 (213)
T d1l8qa2          76 AQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGK-------------ERTQIEFFHIFNTL---YL--LEKQIILAS  137 (213)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTC-------------HHHHHHHHHHHHHH---HH--TTCEEEEEE
T ss_pred             HHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcCc-------------hHHHHHHHHHHHHH---hh--ccceEEEec
Confidence            321       112233334456789999999998641             22223333344433   22  244566666


Q ss_pred             cCCCCCC---CccccCCCcc--ceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHH
Q 013128          353 TNHKEKL---DPALLRPGRM--DMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEEL  405 (449)
Q Consensus       353 TN~~~~l---d~aLlrpgR~--d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l  405 (449)
                      ...|..+   .+.|.+  |+  ...+.++ |+.+.+.++++.+....+..+.+++...
T Consensus       138 ~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~y  192 (213)
T d1l8qa2         138 DRHPQKLDGVSDRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDY  192 (213)
T ss_dssp             SSCGGGCTTSCHHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             CCcchhccccchHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            6677554   467776  54  4677786 6778899999988876666665554443

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.48  E-value=1.5e-12  Score=122.90  Aligned_cols=197  Identities=19%  Similarity=0.206  Sum_probs=127.9

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      .++.++|.++..+++.+.|.             ...++++||.||||+|||++++.+|..+          +..++.+++
T Consensus        16 ~ld~~igRd~Ei~~l~~iL~-------------r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~   82 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVLC-------------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI   82 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHHT-------------SSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCC
T ss_pred             CCCcccChHHHHHHHHHHHh-------------cCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeee
Confidence            46788998887777766552             1225789999999999999999999875          578999998


Q ss_pred             ccccC--------hHHHHHHHHcC--CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCC
Q 013128          277 SAVQS--------NSELRFLLLTM--PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEG  346 (449)
Q Consensus       277 s~~~~--------~~~l~~~~~~~--~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  346 (449)
                      +.+..        +..+..++...  ..+.||||||++.+++.....+.          ...   +-+.|....+  .++
T Consensus        83 ~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~----------~~d---~a~~Lkp~L~--rg~  147 (268)
T d1r6bx2          83 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGG----------QVD---AANLIKPLLS--SGK  147 (268)
T ss_dssp             C---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSC----------HHH---HHHHHSSCSS--SCC
T ss_pred             chHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCc----------ccc---HHHHhhHHHh--CCC
Confidence            88753        23444555543  45789999999999864322211          112   3334433333  246


Q ss_pred             eEEEEEcCC-----CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHH-----
Q 013128          347 RIIVFTTNH-----KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEV-----  416 (449)
Q Consensus       347 ~iiI~tTN~-----~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i-----  416 (449)
                      +-+|++|..     ...-|+||.|  || ..|.+..|+.++-..|+..+....        + .-....+++.-+     
T Consensus       148 i~vIgatT~eey~~~~e~d~al~r--rF-~~I~V~Eps~e~t~~IL~~~~~~~--------e-~~h~v~~~~~al~~~v~  215 (268)
T d1r6bx2         148 IRVIGSTTYQEFSNIFEKDRALAR--RF-QKIDITEPSIEETVQIINGLKPKY--------E-AHHDVRYTAKAVRAAVE  215 (268)
T ss_dssp             CEEEEEECHHHHHCCCCCTTSSGG--GE-EEEECCCCCHHHHHHHHHHHHHHH--------H-HHHTCCCCHHHHHHHHH
T ss_pred             CeEEEeCCHHHHHHHHhhcHHHHh--hh-cccccCCCCHHHHHHHHHHhhHHH--------h-ccCCEEeChHHHHHHHH
Confidence            677776653     2355899999  99 569999999999998887644321        0 001122333222     


Q ss_pred             -HHHHhc-CCCHHHHHHHHHHHHHHHHHh
Q 013128          417 -AGELMK-STNAEVSLNGLVKFLHAKMTQ  443 (449)
Q Consensus       417 -~~~l~~-~~~~~~al~~l~~~l~~~~~~  443 (449)
                       +...+. ..-|+.|++-|.++....+..
T Consensus       216 ls~ryi~~~~~PdKAIdllDea~a~~~~~  244 (268)
T d1r6bx2         216 LAVKYINDRHLPDKAIDVIDEAGARARLM  244 (268)
T ss_dssp             HHHHHCTTSCTTHHHHHHHHHHHHHHHHS
T ss_pred             HHHhhccCCCCCcHHHHHHHHHHHHHHhh
Confidence             333333 347999999888887766654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.48  E-value=8.5e-13  Score=120.29  Aligned_cols=122  Identities=16%  Similarity=0.155  Sum_probs=92.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------------------------CcEEEEeccccc---ChHHHHHHHHcC---
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------------------------FDIYDLDLSAVQ---SNSELRFLLLTM---  292 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------------------------~~~~~l~~s~~~---~~~~l~~~~~~~---  292 (449)
                      +.++||+||||+|||++|+++|+.+.                        .+++.+....-.   ....++.+....   
T Consensus        24 ~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~~  103 (207)
T d1a5ta2          24 HHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEH  103 (207)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTSC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhhhhc
Confidence            56799999999999999999999872                        345555433221   234444444432   


Q ss_pred             ---CCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCcc
Q 013128          293 ---PSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRM  369 (449)
Q Consensus       293 ---~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~  369 (449)
                         .+..|++|||+|.+..                  ...+.||..|+..    +..+++|++||+++.|.|++++  |+
T Consensus       104 ~~~~~~kviIide~d~l~~------------------~a~n~Llk~lEep----~~~~~fIl~t~~~~~ll~tI~S--Rc  159 (207)
T d1a5ta2         104 ARLGGAKVVWVTDAALLTD------------------AAANALLKTLEEP----PAETWFFLATREPERLLATLRS--RC  159 (207)
T ss_dssp             CTTSSCEEEEESCGGGBCH------------------HHHHHHHHHHTSC----CTTEEEEEEESCGGGSCHHHHT--TS
T ss_pred             cccCccceEEechhhhhhh------------------hhhHHHHHHHHhh----cccceeeeeecChhhhhhhhcc--ee
Confidence               2456999999998853                  3457799999864    4668999999999999999998  87


Q ss_pred             ceEEEeCCCCHHHHHHHHHH
Q 013128          370 DMHLHMSYCNTSVFKQLAFN  389 (449)
Q Consensus       370 d~~i~l~~p~~~~r~~l~~~  389 (449)
                       ..+.|+.|+.++...+++.
T Consensus       160 -~~i~~~~~~~~~~~~~L~~  178 (207)
T d1a5ta2         160 -RLHYLAPPPEQYAVTWLSR  178 (207)
T ss_dssp             -EEEECCCCCHHHHHHHHHH
T ss_pred             -EEEecCCCCHHHHHHHHHH
Confidence             7899999999888777754

>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=99.45  E-value=1.5e-12  Score=121.64  Aligned_cols=160  Identities=16%  Similarity=0.079  Sum_probs=108.4

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC----CcEEEEecccccCh
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK----FDIYDLDLSAVQSN  282 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~----~~~~~l~~s~~~~~  282 (449)
                      ..+++++.++..+.|.+.|...+.++.       ..++++||+||||||||++++++|+.+.    ..++.+++......
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~~-------~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~   86 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNF   86 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCCC-------CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhh
Confidence            456789999999999999887776553       2367899999999999999999999983    55666665544221


Q ss_pred             --------------------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHh
Q 013128          283 --------------------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFI  336 (449)
Q Consensus       283 --------------------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~l  336 (449)
                                                ..+...+.......++++|++|.+...               ....+..++..+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~---------------~~~~~~~~~~~~  151 (276)
T d1fnna2          87 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPD---------------ILSTFIRLGQEA  151 (276)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHH---------------HHHHHHHHTTCH
T ss_pred             hhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhh---------------hhhhHHHHHhcc
Confidence                                      112222334456778889998876431               111112222222


Q ss_pred             cCccccCCCCeEEEEEcCCC---CCCCccccCCCcc-ceEEEeCCCCHHHHHHHHHHHhCc
Q 013128          337 DGLWSCCGEGRIIVFTTNHK---EKLDPALLRPGRM-DMHLHMSYCNTSVFKQLAFNYLGI  393 (449)
Q Consensus       337 dg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgR~-d~~i~l~~p~~~~r~~l~~~~l~~  393 (449)
                      .   ......+++|+++|..   +.+++++.+  |+ ...|+|+.++.++..++++..+..
T Consensus       152 ~---~~~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~  207 (276)
T d1fnna2         152 D---KLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  207 (276)
T ss_dssp             H---HHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             c---cccccceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHHH
Confidence            1   1223456778888874   578888876  54 356899999999999999887653

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.44  E-value=1.1e-12  Score=129.54  Aligned_cols=196  Identities=18%  Similarity=0.228  Sum_probs=122.9

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhH------------------HhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          210 TLALDSELKREITEDLENFMNGKEY------------------YTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~------------------~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      -++|+++.|+.+-..+....++...                  .... ..++.++||.||+|||||.||+++|..++.++
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~-~~p~~niLfiGPTGvGKTElAk~LA~~~~~~~   96 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEV-ELSKSNILLIGPTGSGKTLMAQTLAKHLDIPI   96 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHT-TCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccc-cCCCcceeeeCCCCccHHHHHHHHHhhcccce
Confidence            5799999999887776543332111                  0111 23467799999999999999999999999999


Q ss_pred             EEEecccccC--------hHHHHHHHHcCC------CCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc
Q 013128          272 YDLDLSAVQS--------NSELRFLLLTMP------SRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID  337 (449)
Q Consensus       272 ~~l~~s~~~~--------~~~l~~~~~~~~------~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld  337 (449)
                      +.++++.+..        .+.+..++....      +.+|+++||+|...+........    .......+.+.||+.+|
T Consensus        97 ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~----~d~a~~~V~~~lLqild  172 (364)
T d1um8a_          97 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSIT----RDVSGEGVQQALLKIVE  172 (364)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC------------------CHHHHHHHHHHHH
T ss_pred             eehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhcccccccccc----ccccchHHHHhhhhhhc
Confidence            9999998865        455666655543      57999999999976522211110    11233456788999998


Q ss_pred             Ccccc---------CCCCeEEEEEcCC-------------------------------------------------CCCC
Q 013128          338 GLWSC---------CGEGRIIVFTTNH-------------------------------------------------KEKL  359 (449)
Q Consensus       338 g~~~~---------~~~~~iiI~tTN~-------------------------------------------------~~~l  359 (449)
                      +....         ...+.++|.|+|-                                                 +..+
T Consensus       173 ~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f  252 (364)
T d1um8a_         173 GSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGL  252 (364)
T ss_dssp             CCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTC
T ss_pred             CceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhhhh
Confidence            53211         1123456666664                                                 0113


Q ss_pred             CccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCCCCHHHHHHHHHcc----CCCHHHH
Q 013128          360 DPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHHYLFEQIEELIKEV----NVTPAEV  416 (449)
Q Consensus       360 d~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~----~~tpa~i  416 (449)
                      -|.|+.  |++..+.|...+.++..+|+....    ..+..+...++...    .+|+.-+
T Consensus       253 ~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~~~----~~l~kq~~~~l~~~gi~L~~td~a~  307 (364)
T d1um8a_         253 IPELIG--RLPVLSTLDSISLEAMVDILQKPK----NALIKQYQQLFKMDEVDLIFEEEAI  307 (364)
T ss_dssp             CHHHHT--TCCEEEECCCCCHHHHHHHHHSST----TCHHHHHHHHHHTTTCEEEECHHHH
T ss_pred             HHHHHH--HhcchhhHhhhhHHHHHHHHHHHH----HHHHHHHHHHHHhCCcEEEECHHHH
Confidence            455555  999999999999999999986322    23445555555443    3566444

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.43  E-value=1.6e-13  Score=133.09  Aligned_cols=157  Identities=18%  Similarity=0.283  Sum_probs=114.0

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCc-ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh---
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKR-GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN---  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~r-g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~---  282 (449)
                      .++|+++.++.|...+......-.     ....|. .+||+||||||||.+|+++|..+   +.+++.++++++...   
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~-----~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~   98 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLK-----DPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV   98 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCS-----CSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGG
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCC-----CCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhh
Confidence            468999999999887765533110     011133 57888999999999999999998   788999999877542   


Q ss_pred             ----------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCcccc----
Q 013128          283 ----------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSC----  342 (449)
Q Consensus       283 ----------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----  342 (449)
                                      ..+...+.. ...||++|||||...+                  ..++.|+..+|.-...    
T Consensus        99 ~~L~g~~~gyvG~~~~~~l~~~~~~-~p~~Vvl~DEieK~~~------------------~v~~~ll~~l~~g~~~~~~g  159 (315)
T d1qvra3          99 SRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAHP------------------DVFNILLQILDDGRLTDSHG  159 (315)
T ss_dssp             GGC--------------CHHHHHHH-CSSEEEEESSGGGSCH------------------HHHHHHHHHHTTTEECCSSS
T ss_pred             hhhcCCCCCCcCcccCChHHHHHHh-CCCcEEEEehHhhcCH------------------HHHHHHHHHhccCceeCCCC
Confidence                            123333332 3479999999998743                  3556677877743211    


Q ss_pred             ---CCCCeEEEEEcCC--------------------------CCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          343 ---CGEGRIIVFTTNH--------------------------KEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       343 ---~~~~~iiI~tTN~--------------------------~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                         .-.+.++|+|||-                          .+.+.|.|+.  |||..+.|.+.+.++..+++...+.
T Consensus       160 r~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l~  236 (315)
T d1qvra3         160 RTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  236 (315)
T ss_dssp             CCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             cEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHHH
Confidence               1145789999994                          2457888988  9999999999999999999886654

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.42  E-value=2.2e-12  Score=121.17  Aligned_cols=169  Identities=10%  Similarity=0.014  Sum_probs=106.7

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC---------CcEEEEecc
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK---------FDIYDLDLS  277 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~---------~~~~~l~~s  277 (449)
                      ..+.+.+.++..++|.+.+..++....    ........++||||||||||++++++++++.         ..+..+++.
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~----~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~   89 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGA----GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAF   89 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSS----CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCC----CCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccc
Confidence            346788888888999888876664321    0011122478899999999999999999973         344455555


Q ss_pred             cccCh--------------------------HHHHHHHHcCCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHH
Q 013128          278 AVQSN--------------------------SELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSG  331 (449)
Q Consensus       278 ~~~~~--------------------------~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~  331 (449)
                      ...+.                          ..+.........+.++++|++|.+.......         ......+..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~---------~~~~~~l~~  160 (287)
T d1w5sa2          90 NAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIA---------AEDLYTLLR  160 (287)
T ss_dssp             GCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSC---------HHHHHHHHT
T ss_pred             cccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccc---------hhHHHHHHH
Confidence            44321                          1112222334567899999999986422211         112233444


Q ss_pred             HHHHhcCccccCCCCeEEEEEcCCCCC------CCccccCCCccceEEEeCCCCHHHHHHHHHHHhC
Q 013128          332 LLNFIDGLWSCCGEGRIIVFTTNHKEK------LDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLG  392 (449)
Q Consensus       332 LL~~ldg~~~~~~~~~iiI~tTN~~~~------ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~  392 (449)
                      +.+.+.....  .....+|+.+|.++.      .++++.+  |+..+++++.++.++..++++..+.
T Consensus       161 l~~~l~~~~~--~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~  223 (287)
T d1w5sa2         161 VHEEIPSRDG--VNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAE  223 (287)
T ss_dssp             HHHHSCCTTS--CCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             HHHhcchhhc--ccceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHH
Confidence            5555544333  234555665555432      3467777  8999999999999999999987654

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.40  E-value=6e-13  Score=132.23  Aligned_cols=199  Identities=19%  Similarity=0.201  Sum_probs=116.5

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      .+|.++|.++..+++++.|.             ...+.++||.||||+|||.+++.+|..+          +..++.+++
T Consensus        20 ~ld~~~gr~~ei~~~~~~L~-------------r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~   86 (387)
T d1qvra2          20 KLDPVIGRDEEIRRVIQILL-------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM   86 (387)
T ss_dssp             CSCCCCSCHHHHHHHHHHHH-------------CSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             CCCCCcCcHHHHHHHHHHHh-------------cCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            46778999888888877664             1225789999999999999999999876          567999999


Q ss_pred             ccccCh--------HHHHHHHHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          277 SAVQSN--------SELRFLLLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       277 s~~~~~--------~~l~~~~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      +.+...        ..+..++..   ...+.||||||++.+++.....+.          ...-+-|...|..     |+
T Consensus        87 ~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~----------~d~a~~Lkp~L~r-----g~  151 (387)
T d1qvra2          87 GSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA----------VDAGNMLKPALAR-----GE  151 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC-----------------------------HHHHHT-----TC
T ss_pred             hhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCc----------ccHHHHHHHHHhC-----CC
Confidence            888543        233344433   345789999999999864322111          0112224444432     33


Q ss_pred             CeEEEEEcC----CCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcC--CCCC--H-HHHHHHHHccCCCHHHH
Q 013128          346 GRIIVFTTN----HKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGIS--HHYL--F-EQIEELIKEVNVTPAEV  416 (449)
Q Consensus       346 ~~iiI~tTN----~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~--~~~l--~-~~i~~l~~~~~~tpa~i  416 (449)
                      =.+|.+||.    ..+. |+||.|  ||. .|.+..|+.++-..|++......  .|.+  . +.+...+        ++
T Consensus       152 ~~~I~~tT~~ey~~~e~-d~al~r--rF~-~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v--------~l  219 (387)
T d1qvra2         152 LRLIGATTLDEYREIEK-DPALER--RFQ-PVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAA--------TL  219 (387)
T ss_dssp             CCEEEEECHHHHHHHTT-CTTTCS--CCC-CEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHH--------HH
T ss_pred             cceeeecCHHHHHHhcc-cHHHHH--hcc-cccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHH--------Hh
Confidence            334444442    1344 899999  995 59999999999998888654431  2222  2 2222221        23


Q ss_pred             HHHHhc-CCCHHHHHHHHHHHHHHHHHhhh
Q 013128          417 AGELMK-STNAEVSLNGLVKFLHAKMTQQQ  445 (449)
Q Consensus       417 ~~~l~~-~~~~~~al~~l~~~l~~~~~~~~  445 (449)
                      +...+. ..-|+.|++-|.++....+....
T Consensus       220 s~ryi~~r~~PdKAidlld~a~a~~~i~~~  249 (387)
T d1qvra2         220 SHRYITERRLPDKAIDLIDEAAARLRMALE  249 (387)
T ss_dssp             HHHHCCSSCTHHHHHHHHHHHHHHHHHTTT
T ss_pred             cccccccccChhhHHHHHHHHHHHHHhhcc
Confidence            333343 35788888888888877766543

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.38  E-value=5.4e-13  Score=119.61  Aligned_cols=149  Identities=18%  Similarity=0.199  Sum_probs=99.2

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc----------CCcEEEEec
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL----------KFDIYDLDL  276 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l----------~~~~~~l~~  276 (449)
                      .+|.++|.++..+++.+.|.    +         ..+.+++|.||||+|||++++.+|..+          +..++.+|+
T Consensus        20 ~ld~~igRd~Ei~~l~~iL~----r---------~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~   86 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQVLQ----R---------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHT----S---------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CCCCCcCcHHHHHHHHHHHh----c---------cCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            46778888877777765442    2         225789999999999999999999866          578999998


Q ss_pred             ccccCh--------HHHHHHHHc---CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCC
Q 013128          277 SAVQSN--------SELRFLLLT---MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGE  345 (449)
Q Consensus       277 s~~~~~--------~~l~~~~~~---~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  345 (449)
                      +.+...        ..+..++..   ...+.||||||++.+.+.....+.          ...-+-|...|..      +
T Consensus        87 ~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~----------~d~~~~Lkp~L~r------g  150 (195)
T d1jbka_          87 GALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA----------MDAGNMLKPALAR------G  150 (195)
T ss_dssp             HHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------C----------CCCHHHHHHHHHT------T
T ss_pred             HHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCc----------ccHHHHHHHHHhC------C
Confidence            887432        334445544   344689999999999863322111          0011224444432      3


Q ss_pred             CeEEEEEcCCC-----CCCCccccCCCccceEEEeCCCCHHHHHHHH
Q 013128          346 GRIIVFTTNHK-----EKLDPALLRPGRMDMHLHMSYCNTSVFKQLA  387 (449)
Q Consensus       346 ~~iiI~tTN~~-----~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~  387 (449)
                      ++.+|++|...     -.-|+||.|  || ..|.+..|+.++-..|+
T Consensus       151 ~l~~IgatT~eey~~~~e~d~aL~r--rF-~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         151 ELHCVGATTLDEYRQYIEKDAALER--RF-QKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             SCCEEEEECHHHHHHHTTTCHHHHT--TE-EEEECCCCCHHHHHTTC
T ss_pred             CceEEecCCHHHHHHHHHcCHHHHh--cC-CEeecCCCCHHHHHHHh
Confidence            45566555432     244999999  99 56999999998866553

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.32  E-value=6.7e-12  Score=122.26  Aligned_cols=147  Identities=20%  Similarity=0.248  Sum_probs=95.7

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC----------------
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF----------------  269 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~----------------  269 (449)
                      ..|.+|+|.+.+|..+.-.+.   . .         ...++||+||||||||++|++++.-|..                
T Consensus         4 ~~f~~I~Gq~~~kral~laa~---~-~---------~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~   70 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAV---D-P---------GIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEM   70 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHH---C-G---------GGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGG
T ss_pred             CChhhccCcHHHHHHHHHHHh---c-c---------CCCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCcccc
Confidence            479999999999887653321   1 1         1247999999999999999999987721                


Q ss_pred             -----------------cEEEEecccccChHHH------HHHHHcC-----------CCCceEEeeccchhhhcccccch
Q 013128          270 -----------------DIYDLDLSAVQSNSEL------RFLLLTM-----------PSRSMLVIEDIDCSVKLQNRESS  315 (449)
Q Consensus       270 -----------------~~~~l~~s~~~~~~~l------~~~~~~~-----------~~~~Il~iDeiD~l~~~~~~~~~  315 (449)
                                       +++....+  .+...+      ...+..-           ....|++||||+.+-+       
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~~-------  141 (333)
T d1g8pa_          71 IPDWATVLSTNVIRKPTPVVDLPLG--VSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLED-------  141 (333)
T ss_dssp             SCTTCCCSCCCEEEECCCEEEECTT--CCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCH-------
T ss_pred             ccchhhccccCcccccCceeeccCC--CCcccccCcchhhhccccCcceeeccccccccccEeecccHHHHHH-------
Confidence                             11111110  011111      1111111           1357999999997642       


Q ss_pred             hhhhccchhhHHHHHHHHHHhcC---------ccccCCCCeEEEEEcCCC-CCCCccccCCCccceEEEeCCCC-HHHHH
Q 013128          316 EVQATNQEENKVTLSGLLNFIDG---------LWSCCGEGRIIVFTTNHK-EKLDPALLRPGRMDMHLHMSYCN-TSVFK  384 (449)
Q Consensus       316 ~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~-~~ld~aLlrpgR~d~~i~l~~p~-~~~r~  384 (449)
                                 .+++.|+..|+.         .....+...++|+|+|.. ..+.+++++  ||+.++.+++|. .+.+.
T Consensus       142 -----------~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~  208 (333)
T d1g8pa_         142 -----------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRV  208 (333)
T ss_dssp             -----------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHH
T ss_pred             -----------HHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHH
Confidence                       477889998862         222223446888888875 569999999  999999999884 34444


Q ss_pred             HHH
Q 013128          385 QLA  387 (449)
Q Consensus       385 ~l~  387 (449)
                      .+.
T Consensus       209 ~~~  211 (333)
T d1g8pa_         209 EVI  211 (333)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.17  E-value=6.5e-11  Score=106.83  Aligned_cols=113  Identities=14%  Similarity=0.215  Sum_probs=86.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC------CcEEEEeccccc-ChHHHHHHHHc---CC---CCceEEeeccchhhhc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK------FDIYDLDLSAVQ-SNSELRFLLLT---MP---SRSMLVIEDIDCSVKL  309 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~------~~~~~l~~s~~~-~~~~l~~~~~~---~~---~~~Il~iDeiD~l~~~  309 (449)
                      +..+|||||||||||++|..++++..      .+++.+....-. .-..++.+...   .+   +.-|++|||+|.+.. 
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~-   93 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ-   93 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH-
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccch-
Confidence            56899999999999999999999883      478888765322 33455544333   22   345999999999843 


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCH
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNT  380 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~  380 (449)
                                       ...+.||..|+..    +...++|++|++++.|.|++++  |+ .++.++.|..
T Consensus        94 -----------------~aqNaLLK~LEEP----p~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          94 -----------------QAANAFLKALEEP----PEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             -----------------HHHHHTHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             -----------------hhhhHHHHHHhCC----CCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence                             3556799999863    4668899999999999999999  87 6688887753

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.00  E-value=2e-09  Score=108.27  Aligned_cols=71  Identities=15%  Similarity=0.241  Sum_probs=53.5

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhh-hcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTR-IGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~-~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      -++|+++.|+.+--.+....++-..-.. ..--.|.++||.||||||||.||+++|..++.||+.++++.+.
T Consensus        15 yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fT   86 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFT   86 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC
T ss_pred             cccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceee
Confidence            3789999999887766654432110000 0112367999999999999999999999999999999999884

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.99  E-value=9.5e-09  Score=95.12  Aligned_cols=198  Identities=16%  Similarity=0.109  Sum_probs=118.2

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccCh---
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSN---  282 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~---  282 (449)
                      ..-++++|-++..+.+.+.                 .++.++|+||+|+|||+|++.+++.++..+..+++......   
T Consensus         9 ~~~~~f~GR~~el~~l~~~-----------------~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~~~   71 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL-----------------RAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI   71 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT-----------------CSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCC
T ss_pred             CChhhCCChHHHHHHHHhc-----------------cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccccc
Confidence            3568889998777666431                 25789999999999999999999999998888876544211   


Q ss_pred             --H---------------------------------------------------HHHHHHHcCCCCceEEeeccchhhhc
Q 013128          283 --S---------------------------------------------------ELRFLLLTMPSRSMLVIEDIDCSVKL  309 (449)
Q Consensus       283 --~---------------------------------------------------~l~~~~~~~~~~~Il~iDeiD~l~~~  309 (449)
                        .                                                   -+..+.....++.++++||++.+...
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~  151 (283)
T d2fnaa2          72 SYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKL  151 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGC
T ss_pred             cHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhccc
Confidence              0                                                   01111222356788999999987531


Q ss_pred             ccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCC-------CCCCccccCCCccceEEEeCCCCHHH
Q 013128          310 QNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHK-------EKLDPALLRPGRMDMHLHMSYCNTSV  382 (449)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-------~~ld~aLlrpgR~d~~i~l~~p~~~~  382 (449)
                      ..              ...+..+...++.     ...+..+++....       ...+..-.-.||....++++..+.++
T Consensus       152 ~~--------------~~~~~~l~~~~~~-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e  212 (283)
T d2fnaa2         152 RG--------------VNLLPALAYAYDN-----LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREE  212 (283)
T ss_dssp             TT--------------CCCHHHHHHHHHH-----CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHH
T ss_pred             ch--------------HHHHHHHHHHHHh-----hhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHH
Confidence            11              1112222222222     1223333333221       11111111124667889999999999


Q ss_pred             HHHHHHHHhCcCCCCCHHHHHHHHHccCCCHHHHHHHH---hcCCCHHHHHHHHHHHHHHH
Q 013128          383 FKQLAFNYLGISHHYLFEQIEELIKEVNVTPAEVAGEL---MKSTNAEVSLNGLVKFLHAK  440 (449)
Q Consensus       383 r~~l~~~~l~~~~~~l~~~i~~l~~~~~~tpa~i~~~l---~~~~~~~~al~~l~~~l~~~  440 (449)
                      ..+++.+.+...+.. .++++.+.+..+=.|.-++.+.   ....+.+.+++.+++.....
T Consensus       213 ~~~~l~~~~~~~~~~-~~~~~~i~~~~~G~P~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (283)
T d2fnaa2         213 AIEFLRRGFQEADID-FKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKL  272 (283)
T ss_dssp             HHHHHHHHHHHHTCC-CCCHHHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhhcCCC-HHHHHHHHHHhCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            999998876543222 2235566666666676665443   34567788888777655443

>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=98.99  E-value=5.4e-09  Score=97.16  Aligned_cols=172  Identities=17%  Similarity=0.183  Sum_probs=103.9

Q ss_pred             ccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHHHHH
Q 013128          211 LALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSELRF  287 (449)
Q Consensus       211 l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~l~~  287 (449)
                      .+|.....+.+.+.+.......           ..+||+||+||||+.+|++|....   ..+++.++|..+........
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~-----------~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~   70 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAE-----------CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAE   70 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCC-----------SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHhCCC-----------CCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHH
Confidence            4666677777777776655433           469999999999999999999876   35788999988765544444


Q ss_pred             HHHc-----------------CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhc-CccccCC-----
Q 013128          288 LLLT-----------------MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFID-GLWSCCG-----  344 (449)
Q Consensus       288 ~~~~-----------------~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ld-g~~~~~~-----  344 (449)
                      +|..                 ..+.+.|||||||.+..                  .....|++.++ +.....+     
T Consensus        71 lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~------------------~~Q~~L~~~l~~~~~~~~~~~~~~  132 (247)
T d1ny5a2          71 LFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSL------------------EAQAKLLRVIESGKFYRLGGRKEI  132 (247)
T ss_dssp             HHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCH------------------HHHHHHHHHHHHSEECCBTCCSBE
T ss_pred             hcCcccCCcCCcccccCCHHHccCCCEEEEeChHhCCH------------------HHHHHHHHHHHhCCEEECCCCCce
Confidence            4422                 12356899999998843                  12233555553 1111101     


Q ss_pred             -CCeEEEEEcCCC-------CCCCccccCCCcc-ceEEEeCCCC--HHHHHHHHHHHhCcC-------CCCCHHHHHHHH
Q 013128          345 -EGRIIVFTTNHK-------EKLDPALLRPGRM-DMHLHMSYCN--TSVFKQLAFNYLGIS-------HHYLFEQIEELI  406 (449)
Q Consensus       345 -~~~iiI~tTN~~-------~~ld~aLlrpgR~-d~~i~l~~p~--~~~r~~l~~~~l~~~-------~~~l~~~i~~l~  406 (449)
                       ..+-||++|+.+       ..+++.|+.  |+ ...|.+|+..  .++...|+..++...       ...+.++....+
T Consensus       133 ~~~~RlI~~s~~~l~~l~~~~~f~~~L~~--~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L  210 (247)
T d1ny5a2         133 EVNVRILAATNRNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELL  210 (247)
T ss_dssp             ECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHH
T ss_pred             ecCeEEEEecCCCHHHHHHcCCCcHHHHh--hcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHH
Confidence             123456666543       134444444  43 3468888874  366777777766531       122445555555


Q ss_pred             HccCCCH
Q 013128          407 KEVNVTP  413 (449)
Q Consensus       407 ~~~~~tp  413 (449)
                      ....|..
T Consensus       211 ~~~~WPG  217 (247)
T d1ny5a2         211 LSYPWYG  217 (247)
T ss_dssp             HHSCCTT
T ss_pred             HhCCCCC
Confidence            5555553

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.90  E-value=4.9e-10  Score=104.47  Aligned_cols=61  Identities=25%  Similarity=0.493  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          215 SELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       215 ~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      .+.+..+.+.+..+.....     +...|++||||||||||||++|+++|++++.+++.++.+.+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~-----~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~   69 (273)
T d1gvnb_           9 KQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFK   69 (273)
T ss_dssp             HHHHHHHHHHHHHHHTTCC-----CCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHH
T ss_pred             HHHHHHHHHHHHHHHhccc-----CCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHH
Confidence            3445555556655555432     556688999999999999999999999999999999987663

>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=98.33  E-value=2.2e-05  Score=73.20  Aligned_cols=185  Identities=14%  Similarity=0.085  Sum_probs=100.1

Q ss_pred             cccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcC------Cc-EEEEecccccCh
Q 013128          210 TLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLK------FD-IYDLDLSAVQSN  282 (449)
Q Consensus       210 ~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~------~~-~~~l~~s~~~~~  282 (449)
                      ++.|.+...++|++.+...-...          .+.+.|||+.|+|||+||+.++++..      ++ ++-+..+...+.
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~~~----------~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~   90 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCDLD----------SFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPK   90 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTTSS----------SEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTT
T ss_pred             ceeCcHHHHHHHHHHHHhccCCC----------ceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCH
Confidence            35678888888888775432211          34578999999999999999998742      11 233443332221


Q ss_pred             HHH------------------------------HHH-HHc--CCCCceEEeeccchhhhcccccchhhhhccchhhHHHH
Q 013128          283 SEL------------------------------RFL-LLT--MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTL  329 (449)
Q Consensus       283 ~~l------------------------------~~~-~~~--~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~l  329 (449)
                      ..+                              ... +..  ..++++|+|||++....                     
T Consensus        91 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~---------------------  149 (277)
T d2a5yb3          91 STFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEET---------------------  149 (277)
T ss_dssp             HHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHH---------------------
T ss_pred             HHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhh---------------------
Confidence            111                              111 111  23678999999975311                     


Q ss_pred             HHHHHHhcCccccCCCCeEEEEEcCCCCCCCccccCCCccceEEEeCCCCHHHHHHHHHHHhCcCCC-CCHH-HHHHHHH
Q 013128          330 SGLLNFIDGLWSCCGEGRIIVFTTNHKEKLDPALLRPGRMDMHLHMSYCNTSVFKQLAFNYLGISHH-YLFE-QIEELIK  407 (449)
Q Consensus       330 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR~d~~i~l~~p~~~~r~~l~~~~l~~~~~-~l~~-~i~~l~~  407 (449)
                         +..+..     ... -||.||...+-.. .+..  +. ..+.+..++.++-.+|+..+...... +..+ ...++++
T Consensus       150 ---~~~~~~-----~~s-rilvTTR~~~v~~-~~~~--~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~  216 (277)
T d2a5yb3         150 ---IRWAQE-----LRL-RCLVTTRDVEISN-AASQ--TC-EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIE  216 (277)
T ss_dssp             ---HHHHHH-----TTC-EEEEEESBGGGGG-GCCS--CE-EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHH
T ss_pred             ---hhhhcc-----cCc-eEEEEeehHHHHH-hcCC--CC-ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHH
Confidence               111111     112 3555665442211 1211  21 35789999999999999876543321 1122 2355666


Q ss_pred             ccCCCHHHHHHHH--hcCCCHHHHHHHHHHHHHH
Q 013128          408 EVNVTPAEVAGEL--MKSTNAEVSLNGLVKFLHA  439 (449)
Q Consensus       408 ~~~~tpa~i~~~l--~~~~~~~~al~~l~~~l~~  439 (449)
                      ..+=.|--+.-+-  ++.. ....+..+...|+.
T Consensus       217 ~c~GlPLAl~~ig~~l~~k-~~~~~~~~~~~L~~  249 (277)
T d2a5yb3         217 LSSGNPATLMMFFKSCEPK-TFEKMAQLNNKLES  249 (277)
T ss_dssp             HHTTCHHHHHHHHTTCCSS-SHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHhccC-CHHHHHHHHHHHhc
Confidence            6666664432211  1222 34455666666654

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=98.26  E-value=5e-07  Score=80.11  Aligned_cols=112  Identities=21%  Similarity=0.230  Sum_probs=69.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccchhhhcccccchhhh
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDCSVKLQNRESSEVQ  318 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~l~~~~~~~~~~~~  318 (449)
                      |+|.++.++|||||+||||+++.++++.++-.++...      ++.....+......-|+++||+-....          
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~~------N~~s~F~Lq~l~~~kv~l~dD~t~~~~----------  112 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFV------NSTSHFWLEPLTDTKVAMLDDATTTCW----------  112 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCC------CSSSCGGGGGGTTCSSEEEEEECHHHH----------
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEecc------CCCCCcccccccCCeEEEEeccccchH----------
Confidence            5677889999999999999999999999975443221      112234556666778999999854321          


Q ss_pred             hccchhhHHHHH-HHHHHhcCcccc--C--CC-----CeEEEEEcCCC---CCCCccccCCCccceEEEeCC
Q 013128          319 ATNQEENKVTLS-GLLNFIDGLWSC--C--GE-----GRIIVFTTNHK---EKLDPALLRPGRMDMHLHMSY  377 (449)
Q Consensus       319 ~~~~~~~~~~ls-~LL~~ldg~~~~--~--~~-----~~iiI~tTN~~---~~ld~aLlrpgR~d~~i~l~~  377 (449)
                              .... -+-+.+||-.-+  +  ..     ..-+|+|||..   +.-.++|.+  |+ ..++|+.
T Consensus       113 --------~~~d~~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~~~d~~~~L~s--Ri-~~f~F~~  173 (205)
T d1tuea_         113 --------TYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RI-TVFEFPN  173 (205)
T ss_dssp             --------HHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SC-EEEECCS
T ss_pred             --------HHHHHHHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCCccccchhhhh--eE-EEEECCC
Confidence                    0111 134556652110  0  00     12356788864   233467888  88 5677764

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=98.21  E-value=3.2e-07  Score=77.46  Aligned_cols=33  Identities=45%  Similarity=0.771  Sum_probs=29.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++.|+|.|||||||||+++++|..|++++++.+
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~id~~   34 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   34 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            467999999999999999999999999988654

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.15  E-value=4e-06  Score=72.15  Aligned_cols=25  Identities=28%  Similarity=0.623  Sum_probs=22.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      ++|.||||||||||+++++..+..+
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            7899999999999999999998653

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.03  E-value=1.1e-06  Score=75.70  Aligned_cols=34  Identities=18%  Similarity=0.103  Sum_probs=30.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .+.|+|.|||||||||||++||+.++.+++..+.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~~   40 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYG   40 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeeeh
Confidence            4679999999999999999999999998876543

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=98.03  E-value=1e-06  Score=75.28  Aligned_cols=30  Identities=30%  Similarity=0.535  Sum_probs=27.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .++|.|||||||||+|+++|..++++++++
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~~   35 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYINV   35 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEec
Confidence            578999999999999999999999998864

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=97.97  E-value=1.6e-06  Score=74.46  Aligned_cols=31  Identities=35%  Similarity=0.523  Sum_probs=28.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +++|.||||+||||+++++|..+|+++++++
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEecC
Confidence            5888999999999999999999999999864

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=97.93  E-value=2.1e-06  Score=74.05  Aligned_cols=32  Identities=22%  Similarity=0.447  Sum_probs=29.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +.++|.|||||||||+++.+|+.+|+++++.|
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~D   34 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEehh
Confidence            56888999999999999999999999999764

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.91  E-value=1.8e-06  Score=73.93  Aligned_cols=35  Identities=31%  Similarity=0.395  Sum_probs=31.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLS  277 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s  277 (449)
                      ++-++|.|||||||||+++++|+.++.+++.++..
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d   38 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSD   38 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHH
Confidence            35688999999999999999999999999988754

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.91  E-value=2.5e-06  Score=73.27  Aligned_cols=30  Identities=37%  Similarity=0.588  Sum_probs=27.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++|.|+|||||||+++.+|..++++++++|
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~fiD~D   33 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            556699999999999999999999999765

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.90  E-value=4.2e-06  Score=71.42  Aligned_cols=34  Identities=21%  Similarity=0.327  Sum_probs=30.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      ++-|+|.||||+||||+|+++|+.++..++.++.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEeec
Confidence            4679999999999999999999999998888764

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.80  E-value=4.8e-06  Score=71.00  Aligned_cols=33  Identities=36%  Similarity=0.551  Sum_probs=28.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      ++-++|.|||||||||+++++|..++...+..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d   38 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   38 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechh
Confidence            456889999999999999999999998776544

>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=97.76  E-value=6.8e-06  Score=69.73  Aligned_cols=29  Identities=38%  Similarity=0.661  Sum_probs=25.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      +-++|.|||||||||+|+++|.+++..++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            46899999999999999999999987654

>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=97.73  E-value=1.1e-05  Score=68.82  Aligned_cols=29  Identities=34%  Similarity=0.480  Sum_probs=25.2

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      |.+..|+|.||||+||||+++.+|..++.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            33455999999999999999999999974

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=6.9e-06  Score=70.32  Aligned_cols=24  Identities=46%  Similarity=0.807  Sum_probs=22.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++++|+||||||||+|+++++..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            679999999999999999999998

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.65  E-value=1.3e-05  Score=70.31  Aligned_cols=32  Identities=19%  Similarity=0.325  Sum_probs=28.0

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .|.-|+|.||||+||||+|+.||.++|+..+.
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            35678999999999999999999999986654

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.59  E-value=1.9e-05  Score=68.13  Aligned_cols=29  Identities=21%  Similarity=0.360  Sum_probs=26.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      |+|.||||+||||+|+.||.++|+..+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            78999999999999999999999887754

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.57  E-value=1e-05  Score=70.71  Aligned_cols=31  Identities=13%  Similarity=0.301  Sum_probs=27.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      |-.++|.|||||||||+|+.||+.+|+..+.
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~~~~is   33 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQLAHIS   33 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            4468999999999999999999999988754

>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=97.55  E-value=1.8e-05  Score=68.45  Aligned_cols=30  Identities=33%  Similarity=0.571  Sum_probs=26.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      .++|.|||||||||+++.||+.+|+..+.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g~~~i~~   31 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLGIPQIST   31 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            378899999999999999999999887764

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=97.55  E-value=2.6e-05  Score=68.03  Aligned_cols=30  Identities=27%  Similarity=0.443  Sum_probs=26.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      -++|.|||||||||+|+.||.++|+..+..
T Consensus         5 riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            367789999999999999999999877654

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.50  E-value=6.3e-05  Score=69.73  Aligned_cols=59  Identities=19%  Similarity=0.281  Sum_probs=42.2

Q ss_pred             CCCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHcCCCCceEEeeccch
Q 013128          240 RAWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLTMPSRSMLVIEDIDC  305 (449)
Q Consensus       240 ~~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~~~~~~Il~iDeiD~  305 (449)
                      .+....++|+|||+||||+++.+|++.+|.- ..++-+.  +    ..-++......++++||.+.
T Consensus       101 ~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~-~~~~~~~--~----~f~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         101 FGKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTN--E----NFPFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             STTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTC--S----SCTTGGGSSCSEEEECSCCE
T ss_pred             CCccEEEEEEcCCCCCHHHHHHHHHHHhcch-hhccccC--C----CccccccCCCEEEEEeCCCc
Confidence            4567789999999999999999999999653 2222111  1    12345566788999999764

>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=97.50  E-value=0.00013  Score=65.55  Aligned_cols=37  Identities=24%  Similarity=0.216  Sum_probs=29.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |++.+.-++|+||||+|||+++..+|...   +..+..++
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            56677789999999999999999999886   44455554

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.47  E-value=3.6e-05  Score=67.43  Aligned_cols=31  Identities=19%  Similarity=0.366  Sum_probs=27.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ..++|.||||+||||+|+.||+++|...+..
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            4588899999999999999999998877654

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=97.46  E-value=3.5e-05  Score=66.71  Aligned_cols=29  Identities=21%  Similarity=0.343  Sum_probs=26.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      |+|.||||+||||+|+.||..+++..+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            78899999999999999999999987764

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=97.45  E-value=3.9e-05  Score=67.25  Aligned_cols=29  Identities=17%  Similarity=0.472  Sum_probs=25.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.||..+|+..++.
T Consensus         9 IiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           9 AAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            77889999999999999999999877644

>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=97.44  E-value=0.00026  Score=65.44  Aligned_cols=118  Identities=19%  Similarity=0.217  Sum_probs=65.9

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hH---HHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NS---ELRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~---~l~~~~~~  291 (449)
                      |++.++-+.++||||||||++|..+|...   +..++++|...-.+                     ..   ++...+.+
T Consensus        53 Gip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~  132 (268)
T d1xp8a1          53 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  132 (268)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHh
Confidence            55666779999999999999998888776   56666666443211                     11   12233444


Q ss_pred             CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCCC
Q 013128          292 MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEKL  359 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l  359 (449)
                      .....+|++|-+..+.+..+-.+... ..........++.++..+-.+..  ..++.+|+|.+-.+.+
T Consensus       133 ~~~~~liIiDSi~al~~r~e~~~~~~-~~~~~~~a~~l~~~lr~l~~~~~--~~~~~vi~tNQv~~~~  197 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALTPRAEIEGDMG-DSLPGLQARLMSQALRKLTAILS--KTGTAAIFINQVREKI  197 (268)
T ss_dssp             TTCCSEEEEECTTTCCCSTTC---------CCHHHHHHHHHHHHHHHHHT--TTCCEEEEEEEC----
T ss_pred             cCCCcEEEEecccccccHHHHccccc-chhHHHHHHHHHHHHHHHHhhhh--hcCCeEEEEeEEeecc
Confidence            56788999999998875322211100 00112334455666665554433  2445666664443443

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.44  E-value=3.6e-05  Score=67.44  Aligned_cols=32  Identities=16%  Similarity=0.370  Sum_probs=27.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++-++|.||||+||||+|+.||..+|+..++.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            45688999999999999999999998866543

>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=97.43  E-value=2.9e-05  Score=66.03  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=22.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .|+|.|+||+||||+++++|..|+.
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3788899999999999999999854

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.41  E-value=4.4e-05  Score=66.08  Aligned_cols=29  Identities=24%  Similarity=0.511  Sum_probs=25.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||+++.||.++|...+..
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            67889999999999999999999876655

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=97.41  E-value=4.2e-05  Score=67.77  Aligned_cols=29  Identities=38%  Similarity=0.661  Sum_probs=26.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      -|.+.|||||||+|+++.||+++|++.++
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~iS   33 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLLD   33 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            57888999999999999999999987754

>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=97.39  E-value=3.3e-05  Score=66.75  Aligned_cols=62  Identities=16%  Similarity=0.142  Sum_probs=39.1

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEecccccChHHHHHHHHc-CCCCceEEeeccc
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQSNSELRFLLLT-MPSRSMLVIEDID  304 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~~~~~l~~~~~~-~~~~~Il~iDeiD  304 (449)
                      +.|.-++|.|+|||||||+|+.++...++..+  +...+.+...+...+.. ......+++|...
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~~i--~~D~~~~~~~~~~~~~~~l~~g~~vIiD~t~   74 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHV--NRDTLGSWQRCVSSCQAALRQGKRVVIDNTN   74 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCEEE--EHHHHCSHHHHHHHHHHHHHTTCCEEEESCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCEEE--chHHHHHHHHHHHHHHHHHHCCCCceeeCcC
Confidence            34567999999999999999999988886554  44444443333322222 1234455566443

>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=97.38  E-value=0.0002  Score=66.20  Aligned_cols=112  Identities=17%  Similarity=0.212  Sum_probs=63.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccCh---------------------H---HHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSN---------------------S---ELRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~---------------------~---~l~~~~~~  291 (449)
                      |++.++-..|+||||||||++|..+|...   +..++.+|...-.+.                     .   ++...+..
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            67777889999999999999987666554   566666664432111                     1   12223444


Q ss_pred             CCCCceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEc
Q 013128          292 MPSRSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTT  353 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  353 (449)
                      ...+.+|+||-+..+.+..+-... ............++.++..+-.+...  ..+.+|+|.
T Consensus       136 ~~~~~liIiDSi~al~~~~E~e~~-~~~~~~~~~a~~l~~~l~~l~~~~~~--~~~~vi~~N  194 (269)
T d1mo6a1         136 SGALDIVVIDSVAALVPRAELEGE-MGDSHVGLQARLMSQALRKMTGALNN--SGTTAIFIN  194 (269)
T ss_dssp             TTCEEEEEEECSTTCCCHHHHC--------CCHHHHHHHHHHHHHHHHHHH--HTCEEEEEE
T ss_pred             cCCCCEEEEecccccccHHHhccc-cccchHHHHHHHHHHHHHHHHHHHhh--cCchhhhhh
Confidence            567889999999988742221111 00001122345566666655444332  345666664

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=9.8e-06  Score=70.48  Aligned_cols=27  Identities=26%  Similarity=0.310  Sum_probs=23.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      .|+|.|+||+||||+|+++|..++..+
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~~   47 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCHG   47 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            477899999999999999999986543

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.37  E-value=5.1e-05  Score=66.20  Aligned_cols=30  Identities=20%  Similarity=0.391  Sum_probs=26.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .-|+|.||||+||||.|+.||+++|+..+.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g~~~i~   31 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYGYTHLS   31 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCceEc
Confidence            347899999999999999999999886654

>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=97.36  E-value=0.00017  Score=66.63  Aligned_cols=70  Identities=16%  Similarity=0.205  Sum_probs=47.0

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccC---------------------hHH---HHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQS---------------------NSE---LRFLLLT  291 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~---------------------~~~---l~~~~~~  291 (449)
                      |++..+-+.|+||||||||+++-.+|...   +..++++|...-.+                     ..+   +...+.+
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~  129 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  129 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHh
Confidence            56666779999999999999998888776   55566665432211                     111   1122333


Q ss_pred             CCCCceEEeeccchhhh
Q 013128          292 MPSRSMLVIEDIDCSVK  308 (449)
Q Consensus       292 ~~~~~Il~iDeiD~l~~  308 (449)
                      ...+.+|+||-+..+.+
T Consensus       130 ~~~~~liViDSi~al~~  146 (263)
T d1u94a1         130 SGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEECcccccc
Confidence            45678999999988763

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.32  E-value=5.6e-05  Score=65.15  Aligned_cols=29  Identities=17%  Similarity=0.285  Sum_probs=26.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      ++|.||||+||||.++.||+++++..+..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            67899999999999999999999877654

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.31  E-value=5.5e-05  Score=62.95  Aligned_cols=24  Identities=29%  Similarity=0.405  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +-|+|.||||+||||+|+.++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            458899999999999999987664

>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=97.29  E-value=0.0005  Score=61.58  Aligned_cols=29  Identities=21%  Similarity=0.126  Sum_probs=25.8

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++..+-++|+||||||||+++..+|...
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            67777889999999999999999998754

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.25  E-value=7.9e-05  Score=66.20  Aligned_cols=28  Identities=29%  Similarity=0.552  Sum_probs=25.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      +.+-||||+||||+|+.||.++|+++++
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            4567999999999999999999998765

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.21  E-value=0.00095  Score=59.21  Aligned_cols=37  Identities=22%  Similarity=0.222  Sum_probs=28.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      |.-++|.||+|+||||.+.-||..+   +..+.-+.+...
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   48 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTF   48 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            4568899999999999999999877   455555554443

>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=97.17  E-value=0.00038  Score=61.94  Aligned_cols=28  Identities=32%  Similarity=0.256  Sum_probs=24.6

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |++..+-++|+||||||||+++..+|..
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            5777788999999999999999888754

>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=97.16  E-value=0.00073  Score=60.53  Aligned_cols=29  Identities=24%  Similarity=0.323  Sum_probs=25.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |.+..+-++|+||||||||+++..+|...
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            56667779999999999999999988765

>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=97.09  E-value=0.00068  Score=60.06  Aligned_cols=36  Identities=22%  Similarity=0.217  Sum_probs=27.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      ++.++|.||+|+||||.+.-+|.++   |..+.-+.+..
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt   44 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDT   44 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEecc
Confidence            4668899999999999999999887   44555554443

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.08  E-value=0.00079  Score=59.86  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=25.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |.-++|.||+|+||||.+.-+|.++   +..+--+.
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit   46 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA   46 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEe
Confidence            4558899999999999999999877   44444443

>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=97.06  E-value=0.00084  Score=54.69  Aligned_cols=35  Identities=26%  Similarity=0.338  Sum_probs=28.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSA  278 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~  278 (449)
                      +..+|.+|+|+|||.++-.++.+.+..++.+-...
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~   43 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSV   43 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChH
Confidence            56799999999999999887878887777665443

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.06  E-value=0.00012  Score=62.47  Aligned_cols=26  Identities=19%  Similarity=0.364  Sum_probs=23.2

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +-|+|.|||||||||+++.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~   27 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRK   27 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            45889999999999999999998853

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.03  E-value=0.00023  Score=59.78  Aligned_cols=31  Identities=19%  Similarity=0.165  Sum_probs=25.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      -+.+.|+||||||||++.|++++   |..+..+.
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEec
Confidence            47899999999999999999987   55555443

>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=96.98  E-value=0.00086  Score=61.19  Aligned_cols=27  Identities=33%  Similarity=0.322  Sum_probs=22.3

Q ss_pred             CCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          241 AWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       241 ~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      .+..-.+|+|+||+|||+++..+|..+
T Consensus        27 ~pg~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          27 VAGTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            334568899999999999999888764

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.96  E-value=0.0018  Score=58.40  Aligned_cols=98  Identities=17%  Similarity=0.178  Sum_probs=58.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc-----CC------------c-E-EEEecc-cccC--------hHHHHHHHHcCCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL-----KF------------D-I-YDLDLS-AVQS--------NSELRFLLLTMPS  294 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l-----~~------------~-~-~~l~~s-~~~~--------~~~l~~~~~~~~~  294 (449)
                      .+.++|.||..+|||++++++|--.     |.            + + ..+... ++..        -.++..++....+
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~  120 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE  120 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCT
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhccc
Confidence            4679999999999999999988655     21            1 1 112111 1111        1456677888889


Q ss_pred             CceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCCC
Q 013128          295 RSMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKEK  358 (449)
Q Consensus       295 ~~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~  358 (449)
                      +++++|||+-.-.             +..+.......++..+..     .....+|+||...+.
T Consensus       121 ~sLvliDE~~~gT-------------~~~eg~~l~~a~l~~l~~-----~~~~~~i~tTH~~~l  166 (234)
T d1wb9a2         121 YSLVLMDEIGRGT-------------STYDGLSLAWACAENLAN-----KIKALTLFATHYFEL  166 (234)
T ss_dssp             TEEEEEESCCCCS-------------SSSHHHHHHHHHHHHHHH-----TTCCEEEEECSCGGG
T ss_pred             ccEEeecccccCC-------------ChhhhhHHHHHhhhhhhc-----cccceEEEecchHHH
Confidence            9999999997522             112223334445554421     123467777776543

>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=96.95  E-value=0.00029  Score=61.46  Aligned_cols=32  Identities=16%  Similarity=0.321  Sum_probs=25.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK---FDIYDLD  275 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~  275 (449)
                      --++|.|+||+||||+|++||.+++   .+...++
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~   37 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFN   37 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEc
Confidence            4588999999999999999999884   4444443

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.94  E-value=0.0047  Score=50.65  Aligned_cols=22  Identities=18%  Similarity=0.321  Sum_probs=19.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++|.|+||+|||+|+..++..-
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            6899999999999999998654

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.00023  Score=61.78  Aligned_cols=29  Identities=21%  Similarity=0.190  Sum_probs=25.5

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |+++.+-++|+||||+|||+++..+|...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            56677789999999999999999998765

>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=96.85  E-value=0.0022  Score=56.67  Aligned_cols=36  Identities=19%  Similarity=0.178  Sum_probs=27.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      +-++|.||+|+||||.+.-||..+   +..+.-+.+...
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~   49 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQ   49 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            347889999999999999999887   555555554443

>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=96.83  E-value=0.0021  Score=62.64  Aligned_cols=87  Identities=16%  Similarity=0.286  Sum_probs=56.4

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcc-eEEeCCCCCCHHHHHHHHHHHcC---CcEEEEec----
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRG-YLLYGPPGTGKSSLIAAMANQLK---FDIYDLDL----  276 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg-~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~~----  276 (449)
                      +.++++|...+++.+.+.+.+    ..           ++| +|+.||+|+||||+..++.++++   .+++.+.-    
T Consensus       134 ~~~l~~LG~~~~~~~~l~~l~----~~-----------~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~  198 (401)
T d1p9ra_         134 RLDLHSLGMTAHNHDNFRRLI----KR-----------PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEF  198 (401)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHH----TS-----------SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCS
T ss_pred             chhhhhhcccHHHHHHHHHHH----hh-----------hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCccc
Confidence            346889998888776665433    21           345 78889999999999999999984   45665530    


Q ss_pred             --ccc-------cChHHHHHHHHc--CCCCceEEeeccchh
Q 013128          277 --SAV-------QSNSELRFLLLT--MPSRSMLVIEDIDCS  306 (449)
Q Consensus       277 --s~~-------~~~~~l~~~~~~--~~~~~Il~iDeiD~l  306 (449)
                        ...       .........+..  ...|-||+|.||...
T Consensus       199 ~~~~~~q~~v~~~~~~~~~~~l~~~lR~dPDvi~igEiRd~  239 (401)
T d1p9ra_         199 DIDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEIRDL  239 (401)
T ss_dssp             CCSSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCCCSH
T ss_pred             ccCCCCeeeecCCcCCCHHHHHHHHHhhcCCEEEecCcCCh
Confidence              000       011122222222  247999999999754

>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=96.78  E-value=0.0018  Score=54.68  Aligned_cols=88  Identities=20%  Similarity=0.222  Sum_probs=53.9

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHcCC--------------------cEE
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQLKF--------------------DIY  272 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l~~--------------------~~~  272 (449)
                      .+++.-.++-+.+...+...      ...++.-++|.|+=|+|||++++++++.+|.                    .++
T Consensus         9 ~~e~~t~~lg~~la~~l~~~------~~~~g~ii~L~G~LGaGKTtfvr~~~~~lg~~~~V~SPTF~l~~~Y~~~~~~i~   82 (158)
T d1htwa_           9 PDEFSMLRFGKKFAEILLKL------HTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIY   82 (158)
T ss_dssp             CSHHHHHHHHHHHHHHHHHH------CCSSCEEEEEECSTTSSHHHHHHHHHHHTTCCSCCCCCTTTCEEEEEETTEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHhc------cCCCCeEEEEecCCCccHHHHHHHHHhhcccccccCCCceEEEEeeccCCceEE
Confidence            34444555555555444211      1112234889999999999999999999963                    355


Q ss_pred             EEecccccChHHHHHH-H-HcCCCCceEEeeccchh
Q 013128          273 DLDLSAVQSNSELRFL-L-LTMPSRSMLVIEDIDCS  306 (449)
Q Consensus       273 ~l~~s~~~~~~~l~~~-~-~~~~~~~Il~iDeiD~l  306 (449)
                      .+|+-.+.+..++..+ + ......+|++||=-+.+
T Consensus        83 H~DlYRl~~~~El~~lg~~e~~~~~~i~~IEWpe~~  118 (158)
T d1htwa_          83 HFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKG  118 (158)
T ss_dssp             EEECTTCSCTTHHHHSTHHHHHSSSCEEEEESGGGG
T ss_pred             EEEEeccCChhhhhhCCchhHhccCCEEEEECchhh
Confidence            5666666665555432 1 11245678888865544

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=96.75  E-value=0.0014  Score=52.75  Aligned_cols=25  Identities=20%  Similarity=0.207  Sum_probs=18.1

Q ss_pred             CcceEEeCCCCCCHHHHHH-HHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIA-AMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~-aiA~~l  267 (449)
                      ++.++|++|||+|||..+- ++....
T Consensus         7 ~~~~il~~~tGsGKT~~~~~~~~~~~   32 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRFLPQILAEC   32 (140)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             CCcEEEEcCCCCChhHHHHHHHHHHh
Confidence            4678999999999996553 444433

>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=96.74  E-value=0.0027  Score=57.85  Aligned_cols=26  Identities=27%  Similarity=0.359  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||+|+|||||++.|+..+.
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            45589999999999999999998774

>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=96.63  E-value=0.00032  Score=59.88  Aligned_cols=25  Identities=32%  Similarity=0.456  Sum_probs=22.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      -++|.|+||+||||+++.+|..++.
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4688999999999999999999854

>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=96.63  E-value=0.0045  Score=55.88  Aligned_cols=26  Identities=23%  Similarity=0.258  Sum_probs=23.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+-|.||+|+|||||+++++..+.
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            44589999999999999999999884

>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=96.61  E-value=0.00056  Score=60.63  Aligned_cols=37  Identities=30%  Similarity=0.434  Sum_probs=29.6

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEecccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDLSAV  279 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~s~~  279 (449)
                      +..|+|.|.||+||||++++++..+    +.+++.++...+
T Consensus        24 g~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~i   64 (208)
T d1m7ga_          24 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNI   64 (208)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHH
Confidence            3458899999999999999999866    567777765544

>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=96.60  E-value=0.00072  Score=58.51  Aligned_cols=28  Identities=32%  Similarity=0.555  Sum_probs=24.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      |.|+|.||+|+|||+|++.++++..-.+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~   29 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSF   29 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcce
Confidence            5689999999999999999999986444

>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=96.59  E-value=0.0028  Score=56.08  Aligned_cols=34  Identities=24%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      |.-++|.||+|+||||.+.-||..+   +..+--+.+
T Consensus        12 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~   48 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGA   48 (211)
T ss_dssp             SEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEEC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEe
Confidence            4558889999999999999999887   344444433

>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=96.59  E-value=0.0049  Score=56.04  Aligned_cols=26  Identities=23%  Similarity=0.411  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+-|.||+|+|||||++.|+..+.
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcccC
Confidence            44589999999999999999999874

>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=96.54  E-value=0.0031  Score=53.07  Aligned_cols=23  Identities=13%  Similarity=0.359  Sum_probs=20.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .-++|.|.||+|||+|+.++.+.
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999875

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=96.53  E-value=0.0013  Score=55.18  Aligned_cols=23  Identities=17%  Similarity=0.398  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+++.|+||+|||+|++.+.+.-
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~   26 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGED   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            38999999999999999987643

>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=96.52  E-value=0.0023  Score=60.52  Aligned_cols=26  Identities=19%  Similarity=0.488  Sum_probs=23.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++++|+.||+|+|||++.+|++++..
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~  191 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIP  191 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcc
Confidence            46899999999999999999999984

>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=96.50  E-value=0.00085  Score=58.32  Aligned_cols=28  Identities=32%  Similarity=0.509  Sum_probs=24.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      |.|+|.||+|+|||++++.++...+-.+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            3588999999999999999999986544

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.46  E-value=0.0034  Score=56.02  Aligned_cols=95  Identities=16%  Similarity=0.206  Sum_probs=56.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc-----CC------------cE--EEEecc-cccC--------hHHHHHHHHcCCCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL-----KF------------DI--YDLDLS-AVQS--------NSELRFLLLTMPSR  295 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l-----~~------------~~--~~l~~s-~~~~--------~~~l~~~~~~~~~~  295 (449)
                      +.++|.||...|||++++++|-..     |.            +-  ..+... ++..        -.++..++.....+
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~  115 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATEN  115 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTT
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCC
Confidence            468999999999999999887655     21            11  112111 1111        14566778888899


Q ss_pred             ceEEeeccchhhhcccccchhhhhccchhhHHHHHHHHHHhcCccccCCCCeEEEEEcCCCC
Q 013128          296 SMLVIEDIDCSVKLQNRESSEVQATNQEENKVTLSGLLNFIDGLWSCCGEGRIIVFTTNHKE  357 (449)
Q Consensus       296 ~Il~iDeiD~l~~~~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  357 (449)
                      ++++|||+-.-.             +..+.......++..+-..      +..+++||.+.+
T Consensus       116 sLvliDE~~~gT-------------~~~eg~ala~aile~L~~~------~~~~i~tTH~~e  158 (224)
T d1ewqa2         116 SLVLLDEVGRGT-------------SSLDGVAIATAVAEALHER------RAYTLFATHYFE  158 (224)
T ss_dssp             EEEEEESTTTTS-------------CHHHHHHHHHHHHHHHHHH------TCEEEEECCCHH
T ss_pred             cEEeecccccCc-------------chhhhcchHHHHHHHHhhc------CcceEEeeechh
Confidence            999999997521             1122233344455555321      236778887754

>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=96.36  E-value=0.0012  Score=56.67  Aligned_cols=30  Identities=17%  Similarity=0.348  Sum_probs=23.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcC---CcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLK---FDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~---~~~~~l~  275 (449)
                      |-+.||+|+||||+|+.++..++   .....+.
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~   57 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLREQGISVCVFH   57 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccccccceecc
Confidence            55899999999999999999874   3444444

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.35  E-value=0.0012  Score=58.23  Aligned_cols=37  Identities=22%  Similarity=0.150  Sum_probs=27.3

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEe
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLD  275 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~  275 (449)
                      |++++.-++|+||||+|||+++..+|...    +..++.++
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            56677779999999999999997665432    44555554

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.26  E-value=0.0079  Score=52.16  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |.|+|.|+||+|||+|+.++.+.
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            47999999999999999999874

>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=96.25  E-value=0.0058  Score=55.59  Aligned_cols=38  Identities=21%  Similarity=0.123  Sum_probs=28.2

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc----CCcEEEEec
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL----KFDIYDLDL  276 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l----~~~~~~l~~  276 (449)
                      |..++.-++|.|+||+|||+++..+|..+    +.++..+++
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            44445568999999999999988888542    666666653

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.17  E-value=0.0045  Score=51.82  Aligned_cols=21  Identities=33%  Similarity=0.719  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||+|++.+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999864

>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=96.13  E-value=0.0095  Score=49.69  Aligned_cols=21  Identities=29%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|+..+.+.
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999875

>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=96.11  E-value=0.0044  Score=52.08  Aligned_cols=22  Identities=32%  Similarity=0.489  Sum_probs=19.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +++.|.+|+|||+|+..+.+.-
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999998543

>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=96.07  E-value=0.0024  Score=61.25  Aligned_cols=38  Identities=26%  Similarity=0.302  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ..++++..+...+.                .+-.+|.||||||||+++..+...
T Consensus       149 ~~~~Q~~A~~~al~----------------~~~~vI~G~pGTGKTt~i~~~l~~  186 (359)
T d1w36d1         149 EINWQKVAAAVALT----------------RRISVISGGPGTGKTTTVAKLLAA  186 (359)
T ss_dssp             SCCHHHHHHHHHHT----------------BSEEEEECCTTSTHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHc----------------CCeEEEEcCCCCCceehHHHHHHH
Confidence            45667776665441                346889999999999998655433

>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=96.05  E-value=0.0017  Score=55.68  Aligned_cols=25  Identities=28%  Similarity=0.592  Sum_probs=22.6

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +-++|.||+|+|||++++.++.+..
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            4688999999999999999999874

>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=96.05  E-value=0.0028  Score=53.22  Aligned_cols=31  Identities=13%  Similarity=0.247  Sum_probs=25.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      -+-+.|++|+|||||+..++.+|   |..+..+.
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            35689999999999999999987   55665553

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.04  E-value=0.0027  Score=53.73  Aligned_cols=21  Identities=33%  Similarity=0.773  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|+||||||+|+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999998865

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.03  E-value=0.0012  Score=58.54  Aligned_cols=29  Identities=21%  Similarity=0.240  Sum_probs=25.1

Q ss_pred             cCCCCcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          239 GRAWKRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       239 g~~~~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      |++...-++|+||||+|||+++..+|..+
T Consensus        30 Gl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          30 GLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            46666779999999999999999999766

>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=95.98  E-value=0.013  Score=47.78  Aligned_cols=21  Identities=29%  Similarity=0.569  Sum_probs=19.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||+|+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999874

>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=95.94  E-value=0.013  Score=48.99  Aligned_cols=22  Identities=32%  Similarity=0.572  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+++.|+||+|||+|+..+.+.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3999999999999999988653

>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=95.93  E-value=0.01  Score=49.71  Aligned_cols=21  Identities=29%  Similarity=0.491  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|+..+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>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=95.79  E-value=0.019  Score=47.58  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|++|+|||+|+..+...-
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~~   26 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASGQ   26 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            37889999999999999987643

>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=95.78  E-value=0.003  Score=54.22  Aligned_cols=32  Identities=25%  Similarity=0.366  Sum_probs=26.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .+|+||.||+|+|||++|.++... |..++.=|
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~lv~DD   45 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHRLIADD   45 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCEEEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEEecC
Confidence            578999999999999999998875 77666444

>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=95.78  E-value=0.0072  Score=50.98  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=19.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|++.+.+.
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998764

>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=95.72  E-value=0.0095  Score=49.71  Aligned_cols=21  Identities=29%  Similarity=0.529  Sum_probs=19.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|+..+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999874

>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=95.66  E-value=0.0076  Score=50.56  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=19.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|+..+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999999864

>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=95.60  E-value=0.0031  Score=55.17  Aligned_cols=26  Identities=27%  Similarity=0.240  Sum_probs=22.6

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      -|-|.||+|+||||+++.++..++..
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~~   29 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQN   29 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchh
Confidence            35588999999999999999998753

>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=95.59  E-value=0.004  Score=54.83  Aligned_cols=30  Identities=23%  Similarity=0.196  Sum_probs=24.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |.|.||.|+||||+++.+++.|   |.+++.+.
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4556999999999999999987   56666553

>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=95.57  E-value=0.014  Score=48.87  Aligned_cols=21  Identities=43%  Similarity=0.697  Sum_probs=18.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            688999999999999988754

>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=95.53  E-value=0.012  Score=49.41  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.||+|||+|+..+.+.
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999998763

>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=95.51  E-value=0.018  Score=48.45  Aligned_cols=21  Identities=38%  Similarity=0.683  Sum_probs=19.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|+..+.+.
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998863

>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=95.50  E-value=0.0053  Score=51.63  Aligned_cols=21  Identities=29%  Similarity=0.575  Sum_probs=19.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|++.+++.
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999873

>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=95.50  E-value=0.015  Score=53.59  Aligned_cols=35  Identities=26%  Similarity=0.327  Sum_probs=27.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc------CCcEEEEeccccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL------KFDIYDLDLSAVQ  280 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l------~~~~~~l~~s~~~  280 (449)
                      +-|.|++|||||||+..|...+      +..+..+++.++.
T Consensus        30 IGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY   70 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFY   70 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGB
T ss_pred             EEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCC
Confidence            4478999999999999988776      3456667777764

>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=95.45  E-value=0.016  Score=48.55  Aligned_cols=20  Identities=35%  Similarity=0.662  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~  265 (449)
                      ++|.|+||+|||+|+..+.+
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999875

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.44  E-value=0.014  Score=51.89  Aligned_cols=24  Identities=33%  Similarity=0.440  Sum_probs=18.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++.+++.+|+|+|||..+...+-.
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~   81 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLF   81 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHHH
Confidence            467999999999999766554443

>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=95.41  E-value=0.015  Score=48.37  Aligned_cols=22  Identities=27%  Similarity=0.549  Sum_probs=19.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++|.|.+|+|||+|++.+...-
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7899999999999999988653

>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=95.39  E-value=0.013  Score=48.79  Aligned_cols=21  Identities=33%  Similarity=0.521  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|++.+.+.
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=95.38  E-value=0.0094  Score=49.50  Aligned_cols=21  Identities=29%  Similarity=0.509  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|.+|+|||+|++.+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            688999999999999998853

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.36  E-value=0.0064  Score=53.69  Aligned_cols=30  Identities=20%  Similarity=0.519  Sum_probs=24.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc--CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL--KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l--~~~~~~l~  275 (449)
                      +++.||+|+|||||+.++..++  +.....++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn   34 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   34 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEe
Confidence            6789999999999999999876  34455554

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.29  E-value=0.049  Score=47.79  Aligned_cols=52  Identities=17%  Similarity=0.142  Sum_probs=33.3

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCcceEEeCCCCCCHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~rg~LL~GPpGtGKT~la  260 (449)
                      .+|+++...+.+.+.+.+.   -+..+...+...++   .++.+++..|+|||||...
T Consensus        12 ~sF~~l~L~~~l~~~L~~~---g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYAY---GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhh
Confidence            3799999888887777432   12222222222211   1467999999999999754

>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=95.26  E-value=0.0079  Score=50.60  Aligned_cols=21  Identities=38%  Similarity=0.736  Sum_probs=19.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.||+|||+|+..+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998753

>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=95.25  E-value=0.0043  Score=53.26  Aligned_cols=29  Identities=28%  Similarity=0.414  Sum_probs=24.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDL  274 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l  274 (449)
                      -+-|.|++|+||||+|+.+ .+.|++++..
T Consensus         5 IIgitG~~gSGKstva~~l-~~~g~~~~~~   33 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALL-RSWGYPVLDL   33 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHH-HHTTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCeEEEc
Confidence            3558899999999999988 5689888754

>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=95.23  E-value=0.0051  Score=52.38  Aligned_cols=30  Identities=23%  Similarity=0.365  Sum_probs=24.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      .+|+||.||+|+|||+++.++... |..++.
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~~li~   44 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GHRLVA   44 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEEe
Confidence            579999999999999999888776 655543

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.23  E-value=0.12  Score=44.49  Aligned_cols=51  Identities=25%  Similarity=0.239  Sum_probs=30.5

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHHH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~la  260 (449)
                      +|+++...+++.+.+.+.  . +..+.-.+...+   -.++.+++.+|+|+|||..-
T Consensus         2 sF~~l~L~~~l~~~L~~~--g-~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay   55 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEA--G-FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAF   55 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHT--T-CCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHH
T ss_pred             ChHHcCCCHHHHHHHHHC--C-CCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhh
Confidence            688888888777766542  1 111211111111   01467999999999999543

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=95.22  E-value=0.0031  Score=53.30  Aligned_cols=23  Identities=17%  Similarity=0.326  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|+||+|||+|++.+++.-
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999987543

>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=95.22  E-value=0.0072  Score=51.70  Aligned_cols=26  Identities=15%  Similarity=0.436  Sum_probs=22.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      ++.++|.||+|+|||+|++.++....
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCC
Confidence            45789999999999999999998763

>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=95.20  E-value=0.037  Score=46.20  Aligned_cols=21  Identities=38%  Similarity=0.596  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|+||+|||+|+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            889999999999999988764

>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=95.16  E-value=0.005  Score=50.79  Aligned_cols=22  Identities=23%  Similarity=0.469  Sum_probs=19.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|+||+|||||++++.+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999999875

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=95.16  E-value=0.033  Score=50.26  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=21.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +-.++|.|.||+||||++.+|.+.-
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CcEEEEECCCCCcHHHHHHHHhCCC
Confidence            3469999999999999999998753

>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=95.09  E-value=0.0057  Score=52.43  Aligned_cols=32  Identities=31%  Similarity=0.352  Sum_probs=26.2

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      .+|+||.||+|+|||+++.++... |..++.=|
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~lvaDD   46 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLFVGDD   46 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEEEEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCceecCC
Confidence            578999999999999999888764 66666444

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.08  E-value=0.21  Score=43.02  Aligned_cols=52  Identities=25%  Similarity=0.156  Sum_probs=31.2

Q ss_pred             CCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHH
Q 013128          205 PMTFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSL  259 (449)
Q Consensus       205 p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~l  259 (449)
                      ..+|+++...+++.+.+.+.  . +..+.-.+...+   -.++.+++..|+|||||..
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~--g-~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTla   56 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEM--G-WEKPSPIQEESIPIALSGRDILARAKNGTGKSGA   56 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTT--T-CCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHH
T ss_pred             CCChhccCcCHHHHHHHHHC--C-CCCCCHHHHHHHHHHHcCCCEEeeccCccccccc
Confidence            45788888887776666432  1 112222222111   1246799999999999954

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.07  E-value=0.018  Score=49.71  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=15.5

Q ss_pred             CcceEEeCCCCCCHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la  260 (449)
                      .+.+++.+|+|+|||..+
T Consensus        40 ~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             CSCEEEECSSHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHH
Confidence            356899999999999876

>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=95.07  E-value=0.011  Score=49.36  Aligned_cols=21  Identities=29%  Similarity=0.545  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|+..+.+.
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999988764

>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=95.02  E-value=0.0077  Score=50.24  Aligned_cols=21  Identities=38%  Similarity=0.657  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|+||+|||+|+..+++.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998874

>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=94.98  E-value=0.011  Score=49.44  Aligned_cols=21  Identities=33%  Similarity=0.596  Sum_probs=18.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|+..+.+.
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
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=94.97  E-value=0.0068  Score=52.27  Aligned_cols=25  Identities=24%  Similarity=0.561  Sum_probs=21.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ...++|.|+||+|||||+.++.+.-
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3478999999999999999998763

>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=94.94  E-value=0.019  Score=48.06  Aligned_cols=21  Identities=29%  Similarity=0.483  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|+..+++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999998874

>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=94.93  E-value=0.0092  Score=52.26  Aligned_cols=25  Identities=40%  Similarity=0.616  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +-++|.||+|+|||+|++.++....
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            3478999999999999999999875

>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=94.87  E-value=0.017  Score=54.30  Aligned_cols=36  Identities=28%  Similarity=0.432  Sum_probs=26.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---C--CcEEEEecccccC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---K--FDIYDLDLSAVQS  281 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~--~~~~~l~~s~~~~  281 (449)
                      |=+.||||+|||||+.+++..+   |  .-++.+|+++-.+
T Consensus        57 IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~   97 (327)
T d2p67a1          57 LGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVT   97 (327)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC----
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeee
Confidence            6689999999999999999876   2  4466777665543

>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=94.85  E-value=0.015  Score=54.11  Aligned_cols=36  Identities=14%  Similarity=0.082  Sum_probs=28.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC-----CcEEEEeccccc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK-----FDIYDLDLSAVQ  280 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~-----~~~~~l~~s~~~  280 (449)
                      -|-+.|++|+||||+|+.++..+.     ..+..+.+.++.
T Consensus        82 iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~  122 (308)
T d1sq5a_          82 IISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFL  122 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             EEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeE
Confidence            466889999999999999999884     456666666664

>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=94.81  E-value=0.0062  Score=51.70  Aligned_cols=23  Identities=22%  Similarity=0.440  Sum_probs=19.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      .--++|.|+||+|||+|++.+..
T Consensus        17 ~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          17 ELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            34599999999999999998753

>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=94.81  E-value=0.0068  Score=55.53  Aligned_cols=18  Identities=28%  Similarity=0.510  Sum_probs=15.0

Q ss_pred             cceEEeCCCCCCHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIA  261 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~  261 (449)
                      ..+|+.||||||||+++-
T Consensus        15 ~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             SEEEECCCTTSCHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHH
Confidence            458999999999998654

>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=94.79  E-value=0.011  Score=50.83  Aligned_cols=21  Identities=38%  Similarity=0.681  Sum_probs=19.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|+..+.+.
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999998864

>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=94.78  E-value=0.007  Score=50.71  Aligned_cols=21  Identities=19%  Similarity=0.509  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||||+.++...
T Consensus        16 I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          16 LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            999999999999999998653

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.69  E-value=0.18  Score=44.11  Aligned_cols=53  Identities=25%  Similarity=0.276  Sum_probs=34.0

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCcceEEeCCCCCCHHHH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKRGYLLYGPPGTGKSSL  259 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~rg~LL~GPpGtGKT~l  259 (449)
                      ...+|+++...+++.+.+.+.  .| ..+.-.+...+|   .++.++...|+|||||..
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~~--g~-~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTla   70 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYAY--GF-EKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT   70 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHH--TC-CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CCCCHHHCCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhh
Confidence            345899999988887777542  22 222222222111   246799999999999964

>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=94.59  E-value=0.0067  Score=50.90  Aligned_cols=22  Identities=32%  Similarity=0.610  Sum_probs=19.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .|.|.|+||+|||||++++.+.
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999753

>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=94.57  E-value=0.006  Score=53.34  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=22.7

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+.|.||.|+|||||.+.|++.+.
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcccc
Confidence            34478999999999999999999873

>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=94.56  E-value=0.0093  Score=52.11  Aligned_cols=29  Identities=38%  Similarity=0.558  Sum_probs=24.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +-|.|++|+|||++++.+. .+|+++++.|
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~vidaD   34 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINVIDAD   34 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEEEEHH
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcEEEch
Confidence            4589999999999999875 7898887654

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.52  E-value=0.055  Score=46.97  Aligned_cols=57  Identities=14%  Similarity=0.123  Sum_probs=33.3

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC----CCCcceEEeCCCCCCHHHHHHHHHHH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGR----AWKRGYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~----~~~rg~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +|+++...+++.+.+.+.  . +..+.-.+...+    ..+..+++..|+|+|||...-..+.+
T Consensus         5 sf~~l~l~~~l~~~l~~~--g-~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~   65 (208)
T d1hv8a1           5 NFNELNLSDNILNAIRNK--G-FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE   65 (208)
T ss_dssp             CGGGSSCCHHHHHHHHHH--T-CCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CHHHcCCCHHHHHHHHHC--C-CCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccc
Confidence            688887777776665431  1 112211122111    11347999999999999877555444

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.51  E-value=0.0091  Score=52.01  Aligned_cols=29  Identities=28%  Similarity=0.412  Sum_probs=24.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      +-|.|++||||||+++.+. ++|+++++.|
T Consensus         5 IgITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            3479999999999999886 6899988765

>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=94.46  E-value=0.015  Score=50.21  Aligned_cols=30  Identities=20%  Similarity=0.381  Sum_probs=25.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc---CCcEEEEe
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL---KFDIYDLD  275 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~  275 (449)
                      |.+.|+.|+||||+++.+++.+   |.+++.+.
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            5678999999999999999987   66776654

>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=94.40  E-value=0.0065  Score=52.14  Aligned_cols=29  Identities=17%  Similarity=0.158  Sum_probs=24.9

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      -|.+.|+.|+||||+++.|+++++...+.
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~~~   39 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDICLL   39 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEE
Confidence            47788999999999999999999765543

>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=94.37  E-value=0.01  Score=49.33  Aligned_cols=21  Identities=29%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||+|+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988863

>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=94.37  E-value=0.03  Score=52.42  Aligned_cols=34  Identities=35%  Similarity=0.516  Sum_probs=26.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc-----CCcEEEEecccc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL-----KFDIYDLDLSAV  279 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l-----~~~~~~l~~s~~  279 (449)
                      +=+.||||+|||||+.+++.++     +.-++.+|.++-
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~   92 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSST   92 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGG
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccH
Confidence            5589999999999999999875     345666776554

>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=94.33  E-value=0.0065  Score=51.37  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .|+|.|+||+|||||+.++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999864

>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=94.29  E-value=0.013  Score=52.00  Aligned_cols=28  Identities=36%  Similarity=0.504  Sum_probs=22.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcE
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDI  271 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~  271 (449)
                      +...|.|++|+|||||+.++........
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~~~~~T  123 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPGLKLRV  123 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCCC-
T ss_pred             CeEEEECCCCCCHHHHHHhhcchhhhhc
Confidence            4678999999999999999987655443

>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=94.27  E-value=0.011  Score=49.37  Aligned_cols=21  Identities=29%  Similarity=0.657  Sum_probs=19.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|++.+.+.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999874

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.20  E-value=0.011  Score=52.89  Aligned_cols=27  Identities=30%  Similarity=0.463  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+-|.||.|||||||++.|+..+..
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~Gl~~p   52 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAGLETI   52 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCCCC
Confidence            345889999999999999999998743

>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=94.10  E-value=0.014  Score=49.11  Aligned_cols=20  Identities=30%  Similarity=0.615  Sum_probs=8.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~  265 (449)
                      ++|.|.||||||+|++++.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78899999999999998875

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=94.05  E-value=0.012  Score=52.80  Aligned_cols=27  Identities=26%  Similarity=0.395  Sum_probs=23.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+-|.||+|+|||||++.|+..+..
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl~~p   58 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGLEEP   58 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCC
Confidence            345789999999999999999998854

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.05  E-value=0.011  Score=51.48  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=21.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -|.+.|++|+||||+++.+++.|
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47788999999999999999987

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.04  E-value=0.01  Score=53.04  Aligned_cols=27  Identities=26%  Similarity=0.362  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +-.+-|.||+|||||||++.|+.....
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl~~p   57 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCLDKP   57 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCcchhhHhccCCCCC
Confidence            345889999999999999999997754

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.97  E-value=0.02  Score=50.19  Aligned_cols=31  Identities=23%  Similarity=0.187  Sum_probs=26.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcCCcEEEEe
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLKFDIYDLD  275 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~~~~~~l~  275 (449)
                      -|.+.|+-|+||||+++.+++.|....+.+.
T Consensus         5 ~I~iEG~DGsGKST~~~~L~~~L~~~~~~~~   35 (214)
T d1tmka_           5 LILIEGLDRTGKTTQCNILYKKLQPNCKLLK   35 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTTSEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhCCEEEE
Confidence            3678899999999999999999987666554

>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=93.95  E-value=0.012  Score=52.77  Aligned_cols=24  Identities=38%  Similarity=0.639  Sum_probs=21.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +-|.||.|+|||||++.|+..+..
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~~p   50 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEECCCCChHHHHHHHHHcCCCC
Confidence            447899999999999999998854

>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=93.90  E-value=0.014  Score=49.03  Aligned_cols=21  Identities=33%  Similarity=0.640  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|+||+|||+|+..+.+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=93.88  E-value=0.011  Score=50.16  Aligned_cols=21  Identities=24%  Similarity=0.537  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||+|++.+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999998853

>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=93.87  E-value=0.017  Score=49.18  Aligned_cols=21  Identities=29%  Similarity=0.513  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|+..+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            889999999999999998864

>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=93.84  E-value=0.011  Score=48.77  Aligned_cols=21  Identities=43%  Similarity=0.727  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|+||+|||||+.++.+.
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999754

>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=93.81  E-value=0.016  Score=49.17  Aligned_cols=21  Identities=33%  Similarity=0.669  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|.||||||+|+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>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=93.79  E-value=0.012  Score=54.28  Aligned_cols=26  Identities=27%  Similarity=0.484  Sum_probs=23.0

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+-|.||.|+|||||+++|+..+.
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCCc
Confidence            34488999999999999999999884

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.76  E-value=0.016  Score=48.21  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=19.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|+..+.+.
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>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=93.74  E-value=0.015  Score=53.65  Aligned_cols=23  Identities=22%  Similarity=0.420  Sum_probs=17.0

Q ss_pred             cceEEeCCCCCCHHHHHH-HHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIA-AMANQ  266 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~-aiA~~  266 (449)
                      ..+|+.||||||||+++- .+|..
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~l   48 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYL   48 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHH
Confidence            458999999999997654 34443

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.73  E-value=0.017  Score=47.85  Aligned_cols=21  Identities=19%  Similarity=0.362  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|+..+.+.
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999864

>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=93.72  E-value=0.011  Score=50.75  Aligned_cols=21  Identities=38%  Similarity=0.515  Sum_probs=19.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~  265 (449)
                      -+.|.|+||+|||||+.++.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            389999999999999999985

>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=93.68  E-value=0.012  Score=52.92  Aligned_cols=26  Identities=23%  Similarity=0.428  Sum_probs=22.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      +.-+-|.||+|+|||||++.|+..+.
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~gl~~   53 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLERFYQ   53 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhC
Confidence            44588999999999999999999883

>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=93.65  E-value=0.02  Score=50.57  Aligned_cols=30  Identities=17%  Similarity=0.145  Sum_probs=25.9

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCCcEE
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKFDIY  272 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~~~~  272 (449)
                      |+=|.+.|+-|+||||+++.|+++++...+
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            456889999999999999999999976544

>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=93.54  E-value=0.014  Score=52.83  Aligned_cols=27  Identities=33%  Similarity=0.438  Sum_probs=23.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+-|.||+|+|||||++.|+..+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~gl~~p   66 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQNLYQP   66 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcccCC
Confidence            445899999999999999999998843

>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=93.50  E-value=0.015  Score=52.19  Aligned_cols=25  Identities=28%  Similarity=0.502  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+-|.||.|+|||||+++|+....
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHhcCCC
Confidence            4478999999999999999999874

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.48  E-value=0.18  Score=45.39  Aligned_cols=62  Identities=18%  Similarity=0.156  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~  284 (449)
                      +.+++++.+.+...+....          .+..-||+|..|+|||-++-..+...   |+.+..+-.+.+.....
T Consensus        84 LT~~Q~~ai~ei~~d~~~~----------~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh  148 (264)
T d1gm5a3          84 LTNAQKRAHQEIRNDMISE----------KPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQH  148 (264)
T ss_dssp             CCHHHHHHHHHHHHHHHSS----------SCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHH
T ss_pred             CCchHHHHHHHHHHHhhcc----------CcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHH
Confidence            4567777666655544432          25678999999999999876665443   77787777776655443

>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=93.47  E-value=0.019  Score=47.88  Aligned_cols=21  Identities=29%  Similarity=0.597  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|++.+.+.
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998763

>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=93.47  E-value=0.016  Score=48.17  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|++|+|||+|+..+.+.
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999998864

>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=93.34  E-value=0.013  Score=52.23  Aligned_cols=26  Identities=23%  Similarity=0.459  Sum_probs=23.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      --+-|.||.|+|||||+++|+..+..
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl~~p   52 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGFHVP   52 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCcCC
Confidence            34889999999999999999998854

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.34  E-value=0.017  Score=48.59  Aligned_cols=22  Identities=27%  Similarity=0.431  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .|.|.|.||+|||||++++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999865

>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=93.22  E-value=0.015  Score=52.11  Aligned_cols=26  Identities=31%  Similarity=0.388  Sum_probs=22.7

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-+-|.||+|||||||++.|+.....
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~~p   57 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLERP   57 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCccc
Confidence            44789999999999999999998754

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.12  E-value=0.077  Score=45.83  Aligned_cols=31  Identities=23%  Similarity=0.204  Sum_probs=25.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEEEec
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYDLDL  276 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~  276 (449)
                      .+|.+|+|+|||.++-+++.+++...+.+-.
T Consensus        88 ~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          88 GCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             cEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            4678899999999999999999877665543

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.11  E-value=0.019  Score=50.81  Aligned_cols=28  Identities=18%  Similarity=0.241  Sum_probs=23.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCCcEEE
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKFDIYD  273 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~~~~~  273 (449)
                      |-|.|+.||||||+|+.+++.+|+.+++
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~i~   31 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVKYQ   31 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeEEc
Confidence            5689999999999999999988865543

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.05  E-value=0.02  Score=47.86  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=19.7

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .|.|.|.||+|||||+.++.+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3889999999999999999863

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.98  E-value=0.021  Score=47.96  Aligned_cols=23  Identities=17%  Similarity=0.338  Sum_probs=20.0

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+++.|++|+|||+|+..+.+.-
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47889999999999999988753

>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=92.85  E-value=0.0092  Score=49.16  Aligned_cols=21  Identities=33%  Similarity=0.695  Sum_probs=19.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +.|.|.||+|||||+.++.+.
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            689999999999999999876

>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=92.76  E-value=0.013  Score=51.61  Aligned_cols=27  Identities=15%  Similarity=0.151  Sum_probs=23.5

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFD  270 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~  270 (449)
                      +-|.+-||-|+||||+++.|++.+...
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~~~   29 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCEDW   29 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTTE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhcC
Confidence            347899999999999999999999543

>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=92.73  E-value=0.028  Score=47.10  Aligned_cols=21  Identities=38%  Similarity=0.556  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|++|+|||+|+..++..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>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=92.67  E-value=0.028  Score=47.54  Aligned_cols=22  Identities=18%  Similarity=0.392  Sum_probs=19.8

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -++|.|.+|+|||+|++.+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998864

>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=92.64  E-value=0.016  Score=52.11  Aligned_cols=25  Identities=24%  Similarity=0.515  Sum_probs=22.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+-|.||+|||||||++.|+....
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~~   56 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLDV   56 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCcC
Confidence            3488999999999999999999873

>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=92.54  E-value=0.026  Score=47.54  Aligned_cols=22  Identities=36%  Similarity=0.594  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+.+.|++|+|||||+.++.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3788999999999999999864

>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=92.42  E-value=0.019  Score=48.07  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=19.8

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      ..-|.|.|+|++|||||+++|.+
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34599999999999999998854

>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=92.37  E-value=0.015  Score=48.83  Aligned_cols=21  Identities=29%  Similarity=0.509  Sum_probs=17.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      +++.|++|+|||+|+..+++.
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999987654

>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=92.34  E-value=0.028  Score=50.89  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=22.0

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      .-+-|.||.|+|||||+++|+..+.
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~Gl~~   53 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINFLEK   53 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCcc
Confidence            3478999999999999999998764

>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=92.26  E-value=0.07  Score=48.18  Aligned_cols=36  Identities=22%  Similarity=0.220  Sum_probs=30.8

Q ss_pred             CCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          242 WKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       242 ~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      .++-+++.|.=|+||||++.++|..+   |..+.-+|+.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            36788899999999999999999888   7787777765

>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=92.21  E-value=0.024  Score=50.75  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=23.4

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+-|.||.|+|||||+++|+..+..
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~~p   58 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLVRA   58 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCC
Confidence            344789999999999999999998854

>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=92.20  E-value=0.031  Score=47.23  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|.+|+|||+|+..+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988874

>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=92.04  E-value=0.03  Score=50.04  Aligned_cols=27  Identities=26%  Similarity=0.456  Sum_probs=23.1

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +.-+-|.||.|+|||||.++|+..+..
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~~p   54 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLIKP   54 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            334679999999999999999999853

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=91.90  E-value=0.049  Score=52.36  Aligned_cols=35  Identities=31%  Similarity=0.350  Sum_probs=27.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      .+++++.|++|+|||+++..+...+   +..++.+|..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4789999999999999987766554   6677777653

>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=91.89  E-value=0.029  Score=47.35  Aligned_cols=20  Identities=35%  Similarity=0.556  Sum_probs=17.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~  265 (449)
                      |-|.|+||+|||||+.++.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999999854

>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=91.82  E-value=0.036  Score=47.18  Aligned_cols=22  Identities=18%  Similarity=0.377  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++|.|++|+|||+|+..+...-
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999887643

>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=91.78  E-value=0.04  Score=50.59  Aligned_cols=35  Identities=14%  Similarity=0.206  Sum_probs=24.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAV  279 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~  279 (449)
                      -|-+.|++|+||||+++++++.+   +.....++..++
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsf   43 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   43 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCC
Confidence            47789999999999999999877   455555555554

>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=91.50  E-value=0.016  Score=48.84  Aligned_cols=24  Identities=38%  Similarity=0.422  Sum_probs=21.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -.+|+||.|+|||+++.||.--+.
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc
Confidence            367899999999999999998774

>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=91.36  E-value=0.034  Score=46.70  Aligned_cols=21  Identities=52%  Similarity=0.640  Sum_probs=18.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      |.|.|.||+|||||+.++.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999753

>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=91.10  E-value=0.038  Score=49.89  Aligned_cols=26  Identities=42%  Similarity=0.630  Sum_probs=22.8

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      .-+-|.||.|+|||||+++|+..+..
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl~~p   56 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGFLKA   56 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCcHHHHHHHHHCCCcC
Confidence            34789999999999999999998843

>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=90.58  E-value=0.17  Score=45.24  Aligned_cols=36  Identities=31%  Similarity=0.416  Sum_probs=29.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEeccc
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSA  278 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~  278 (449)
                      .+-+++.|.=|+||||++..+|..+   |..+..+|+.-
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp   58 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDP   58 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence            4567888999999999988888777   77888877763

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.21  E-value=0.078  Score=44.53  Aligned_cols=23  Identities=30%  Similarity=0.316  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -+++.|++|+|||+|+..+.+.-
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48999999999999999887753

>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=90.21  E-value=0.067  Score=45.22  Aligned_cols=18  Identities=39%  Similarity=0.654  Sum_probs=17.3

Q ss_pred             eEEeCCCCCCHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAM  263 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~ai  263 (449)
                      ++|.|.+|+|||+|+..+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            789999999999999998

>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=90.21  E-value=0.41  Score=43.23  Aligned_cols=22  Identities=36%  Similarity=0.634  Sum_probs=20.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      ++|.|++|||||+|+..+++..
T Consensus        71 ~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          71 IGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEeeCCCCCCHHHHHHHHHHHH
Confidence            9999999999999999998774

>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=90.17  E-value=0.075  Score=48.71  Aligned_cols=23  Identities=30%  Similarity=0.590  Sum_probs=21.1

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -.+|.||+|||||+|+..+++..
T Consensus        45 r~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          45 RGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             eeeEeCCCCCCHHHHHHHHHHHH
Confidence            39999999999999999999866

>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=90.15  E-value=0.1  Score=44.62  Aligned_cols=33  Identities=15%  Similarity=0.281  Sum_probs=27.3

Q ss_pred             cceEEeCC-CCCCHHHHHHHHHHHc---CCcEEEEec
Q 013128          244 RGYLLYGP-PGTGKSSLIAAMANQL---KFDIYDLDL  276 (449)
Q Consensus       244 rg~LL~GP-pGtGKT~la~aiA~~l---~~~~~~l~~  276 (449)
                      +-|++.|- +|+|||+++..||..+   |+.+..++.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            35788898 6999999999999888   777777764

>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=90.14  E-value=0.058  Score=47.83  Aligned_cols=24  Identities=46%  Similarity=0.616  Sum_probs=20.9

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      --+-|.||.|+|||||.++|+...
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            347899999999999999999844

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=90.13  E-value=0.32  Score=42.92  Aligned_cols=62  Identities=15%  Similarity=0.147  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecccccChHH
Q 013128          213 LDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLSAVQSNSE  284 (449)
Q Consensus       213 g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s~~~~~~~  284 (449)
                      ..+++++.+.+.......          +.+...||+|..|+|||.++-..+...   |..+..+-.........
T Consensus        56 lt~~Q~~~~~~i~~~~~~----------~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~  120 (233)
T d2eyqa3          56 TTPDQAQAINAVLSDMCQ----------PLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQH  120 (233)
T ss_dssp             CCHHHHHHHHHHHHHHHS----------SSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHhc----------cCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHH
Confidence            345666555444433332          225678999999999999876555543   67777666555544433

>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=89.96  E-value=0.027  Score=50.11  Aligned_cols=26  Identities=35%  Similarity=0.604  Sum_probs=19.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      +..+|.|++|+|||||+.++......
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~~  123 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELGL  123 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC----
T ss_pred             ceEEEECCCCccHHHHHHhhccHhHh
Confidence            44678899999999999999765543

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=89.02  E-value=1.4  Score=35.16  Aligned_cols=61  Identities=15%  Similarity=0.223  Sum_probs=37.6

Q ss_pred             eEEeCCCCCCHHH-HHHHHHH--HcCCcEEEEecccc--------------------cChHHHHHHHHcC---CCCceEE
Q 013128          246 YLLYGPPGTGKSS-LIAAMAN--QLKFDIYDLDLSAV--------------------QSNSELRFLLLTM---PSRSMLV  299 (449)
Q Consensus       246 ~LL~GPpGtGKT~-la~aiA~--~l~~~~~~l~~s~~--------------------~~~~~l~~~~~~~---~~~~Il~  299 (449)
                      -+++||=.+|||+ |++.+-+  ..+..++.+..+.-                    ....++...+...   ....+|+
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~   84 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   84 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEE
Confidence            4689999999999 6666633  34667665543211                    1123333333332   2567999


Q ss_pred             eeccchh
Q 013128          300 IEDIDCS  306 (449)
Q Consensus       300 iDeiD~l  306 (449)
                      |||+.-+
T Consensus        85 IDE~QFf   91 (139)
T d2b8ta1          85 IDEVQFF   91 (139)
T ss_dssp             ECSGGGS
T ss_pred             echhhhc
Confidence            9999865

>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=88.87  E-value=0.1  Score=45.53  Aligned_cols=22  Identities=32%  Similarity=0.472  Sum_probs=19.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      -+||.|++|+|||+|++.+...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999988543

>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=88.44  E-value=0.095  Score=49.04  Aligned_cols=24  Identities=33%  Similarity=0.231  Sum_probs=21.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      |.|-|+-|+||||+++.++++++.
T Consensus         9 I~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           9 IYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEECCccCCHHHHHHHHHHHhcc
Confidence            678899999999999999999853

>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=88.07  E-value=0.094  Score=46.01  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=20.4

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|..|+|||||++.+.+..
T Consensus         5 v~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEEeeCCCCCHHHHHHHHHhcC
Confidence            47899999999999999998864

>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=87.93  E-value=0.12  Score=43.45  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=20.2

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      -++|.|..|+|||+|+..+...-
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37999999999999999997654

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.91  E-value=0.1  Score=47.41  Aligned_cols=23  Identities=35%  Similarity=0.576  Sum_probs=20.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -+|+||-|+|||++..||+-.++
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg   49 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFG   49 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhC
Confidence            58999999999999999977654

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.36  E-value=0.12  Score=48.07  Aligned_cols=53  Identities=15%  Similarity=0.325  Sum_probs=31.6

Q ss_pred             CCCCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHH
Q 013128          204 HPMTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIA  261 (449)
Q Consensus       204 ~p~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~  261 (449)
                      ++.+||.+.+.+...+++.+.+..++-..     +-......++-||+.|+|||+.+-
T Consensus        42 ~~f~FD~vf~~~~~q~~vf~~~~~~lv~~-----~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          42 KPYAFDRVFQSSTSQEQVYNDCAKKIVKD-----VLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             EEEECSEEECTTCCHHHHHHHHTHHHHHH-----HHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             ceeECCEEECCCCCHHHHHHHHHHHHHHH-----HHcCCCcceeeecccCCCCceecc
Confidence            34567777766555555554443322111     111124568999999999999873

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=87.34  E-value=0.16  Score=42.86  Aligned_cols=22  Identities=27%  Similarity=0.449  Sum_probs=17.3

Q ss_pred             cceEEeCCCCCCHHHHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      +..|+.+|+|+|||.++..++.
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHH
Confidence            4588999999999986665554

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.15  E-value=0.15  Score=48.02  Aligned_cols=23  Identities=35%  Similarity=0.605  Sum_probs=20.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -+|+||.|+|||+++.||+-.||
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~lg   50 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVLG   50 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            47999999999999999986664

>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=86.02  E-value=0.14  Score=47.77  Aligned_cols=24  Identities=21%  Similarity=0.369  Sum_probs=21.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      |.|-|+-|+||||+++.++++++.
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            678899999999999999999864

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.45  E-value=0.51  Score=40.39  Aligned_cols=50  Identities=22%  Similarity=0.270  Sum_probs=30.9

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcC---CCCcceEEeCCCCCCHHHH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGR---AWKRGYLLYGPPGTGKSSL  259 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~---~~~rg~LL~GPpGtGKT~l  259 (449)
                      +|+++...+++.+.+.+.  .| ..+.-.+...+   -.++.+++..|+|||||..
T Consensus         2 ~F~dl~L~~~l~~~l~~~--g~-~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDC--GF-EHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHT--TC-CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             CccccCcCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHcCCCeEEEeccccccccc
Confidence            688888888777766532  11 22222222111   1246799999999999864

>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=85.04  E-value=0.43  Score=43.12  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHc
Q 013128          246 YLLYGPPGTGKSSLIAAMANQL  267 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l  267 (449)
                      +++.|++|+|||+++..++...
T Consensus        70 ~~Ifg~~g~GKt~l~~~~~~~~   91 (276)
T d1fx0a3          70 ELIIGDRQTGKTAVATDTILNQ   91 (276)
T ss_dssp             CBEEESSSSSHHHHHHHHHHTC
T ss_pred             EeeccCCCCChHHHHHHHHhhh
Confidence            8899999999999997665544

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=84.90  E-value=1.1  Score=42.64  Aligned_cols=37  Identities=22%  Similarity=0.256  Sum_probs=32.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcCCcEEEEeccccc
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLKFDIYDLDLSAVQ  280 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~~~~~~l~~s~~~  280 (449)
                      +..+|.|-+|+|||.++++++...+.+++.+..+...
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~~   68 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTL   68 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHHH
T ss_pred             CcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHHH
Confidence            4588999999999999999999999999888665543

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=84.77  E-value=0.27  Score=46.09  Aligned_cols=50  Identities=22%  Similarity=0.201  Sum_probs=28.8

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la  260 (449)
                      .+||.+.+.+...+.|.+.+..++-.     .+-..+...++-||++|+|||+++
T Consensus        48 f~FD~vf~~~~~q~~vy~~~~~plv~-----~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          48 FTFDRVFDMSCKQSDIFDFSIKPTVD-----DILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHH-----HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             EECCeEcCCCCCHHHHHHHHHHHHHH-----HhhccCceeEEecccCCCCcceee
Confidence            45777766555455555443322221     111112346899999999999875

>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=84.63  E-value=0.33  Score=43.09  Aligned_cols=33  Identities=24%  Similarity=0.340  Sum_probs=26.3

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      .|-++|.=|+||||++..+|..|   |..+.-+|+.
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D   38 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecC
Confidence            45678989999999999888887   6777766654

>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=84.51  E-value=0.24  Score=41.19  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHH
Q 013128          246 YLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~  266 (449)
                      ++|.|..|+|||+|++.+...
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999987543

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.32  E-value=0.4  Score=45.73  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=20.5

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHH
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMAN  265 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~  265 (449)
                      +-.|.+.|.||+|||||+.++.+
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            34699999999999999999975

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=83.19  E-value=0.23  Score=46.22  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHHcCC
Q 013128          246 YLLYGPPGTGKSSLIAAMANQLKF  269 (449)
Q Consensus       246 ~LL~GPpGtGKT~la~aiA~~l~~  269 (449)
                      |.|-|+=|+||||+++.+++.++.
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l~~   30 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALGSR   30 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC----
T ss_pred             EEEECCcCCCHHHHHHHHHHHhCC
Confidence            678899999999999999998854

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=83.08  E-value=0.39  Score=44.68  Aligned_cols=49  Identities=12%  Similarity=0.329  Sum_probs=29.1

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la  260 (449)
                      .+||.+.+.+...+++.+.+...+..      +-......++-||..|+|||+.+
T Consensus        52 f~FD~vf~~~~~q~~vy~~v~~~v~~------~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          52 FKFDKIFDQQDTNVDVFKEVGQLVQS------SLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             EEESEEECTTCCHHHHHHHHHHHHGG------GGGTCCEEEEEECCTTSSHHHHH
T ss_pred             eecCeEeCCCCCHHHHHHHhhhhhcc------hhcccccceeeeeccCCcccccc
Confidence            34666666555555566554432221      11112346888999999999876

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.97  E-value=0.75  Score=39.50  Aligned_cols=52  Identities=19%  Similarity=0.226  Sum_probs=32.5

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCcceEEeCCCCCCHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKRGYLLYGPPGTGKSSLI  260 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~rg~LL~GPpGtGKT~la  260 (449)
                      .+|+++...+++.+.+.+.  . +..+.-.+...++   .++.+++.+|+|||||...
T Consensus        10 ~sF~~l~l~~~l~~~L~~~--g-~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_          10 YKFDDMELDENLLRGVFGY--G-FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             CCGGGGTCCHHHHHHHHHH--T-CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             cChhhCCCCHHHHHHHHHC--C-CCCCCHHHHHHHHHHHcCCCEEeecccccchhhhh
Confidence            4699998888777776531  1 2222222222111   2467999999999999753

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=82.50  E-value=0.29  Score=40.77  Aligned_cols=22  Identities=18%  Similarity=0.360  Sum_probs=19.5

Q ss_pred             ceEEeCCCCCCHHHHHHHHHHH
Q 013128          245 GYLLYGPPGTGKSSLIAAMANQ  266 (449)
Q Consensus       245 g~LL~GPpGtGKT~la~aiA~~  266 (449)
                      .+-+.|+|++|||||+.++.+.
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            4789999999999999999853

>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=82.19  E-value=0.34  Score=43.64  Aligned_cols=25  Identities=32%  Similarity=0.481  Sum_probs=22.1

Q ss_pred             cceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          244 RGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      |++-+.|+.|+|||||+.+|....|
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~g   27 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKTG   27 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHcC
Confidence            6788999999999999999976654

>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=81.87  E-value=0.63  Score=39.80  Aligned_cols=32  Identities=28%  Similarity=0.416  Sum_probs=25.0

Q ss_pred             eEEe-CCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          246 YLLY-GPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       246 ~LL~-GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      |.+. |-.|+|||+++..+|..+   |..+.-+|+.
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            3444 779999999999988887   6777777654

>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=81.77  E-value=0.34  Score=43.87  Aligned_cols=26  Identities=12%  Similarity=0.029  Sum_probs=23.3

Q ss_pred             CcceEEeCCCCCCHHHHHHHHHHHcC
Q 013128          243 KRGYLLYGPPGTGKSSLIAAMANQLK  268 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~la~aiA~~l~  268 (449)
                      -|++-+.|..|+|||||+.+|....+
T Consensus         6 iRni~i~gh~~~GKTtL~e~ll~~~g   31 (276)
T d2bv3a2           6 LRNIGIAAHIDAGKTTTTERILYYTG   31 (276)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcC
Confidence            47899999999999999999987764

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=81.77  E-value=0.56  Score=39.83  Aligned_cols=50  Identities=14%  Similarity=0.100  Sum_probs=28.9

Q ss_pred             CcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCC---CCcceEEeCCCCCCHHHH
Q 013128          207 TFKTLALDSELKREITEDLENFMNGKEYYTRIGRA---WKRGYLLYGPPGTGKSSL  259 (449)
Q Consensus       207 ~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~---~~rg~LL~GPpGtGKT~l  259 (449)
                      +|+++...+.+.+.+.+.  .| ..+.-.++..++   .++.+++..|+|||||..
T Consensus         2 ~F~~l~L~~~l~~~l~~~--g~-~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTla   54 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTL--RF-YKPTEIQERIIPGALRGESMVGQSQTGTGKTHA   54 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHT--TC-CSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHH
T ss_pred             ccccCCcCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHCCCCeEeeccccccccee
Confidence            577777777776665431  11 122112221111   146799999999999973

>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=81.37  E-value=0.7  Score=39.51  Aligned_cols=34  Identities=26%  Similarity=0.352  Sum_probs=26.6

Q ss_pred             cceEEe-CCCCCCHHHHHHHHHHHc---CCcEEEEecc
Q 013128          244 RGYLLY-GPPGTGKSSLIAAMANQL---KFDIYDLDLS  277 (449)
Q Consensus       244 rg~LL~-GPpGtGKT~la~aiA~~l---~~~~~~l~~s  277 (449)
                      +-|-++ +-.|+|||+++..+|..+   |.++.-+|+.
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            345566 558999999999999887   7788877764

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=81.22  E-value=0.23  Score=45.80  Aligned_cols=19  Identities=32%  Similarity=0.566  Sum_probs=15.9

Q ss_pred             cceEEeCCCCCCHHHHHHH
Q 013128          244 RGYLLYGPPGTGKSSLIAA  262 (449)
Q Consensus       244 rg~LL~GPpGtGKT~la~a  262 (449)
                      ..-|++|.+|||||||...
T Consensus        15 ~valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          15 DVAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             CEEEEEECTTSCHHHHTCB
T ss_pred             CEEEEEccCCCCccccccC
Confidence            3479999999999998753

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=80.47  E-value=0.36  Score=43.23  Aligned_cols=16  Identities=38%  Similarity=0.524  Sum_probs=14.5

Q ss_pred             CcceEEeCCCCCCHHH
Q 013128          243 KRGYLLYGPPGTGKSS  258 (449)
Q Consensus       243 ~rg~LL~GPpGtGKT~  258 (449)
                      ++..|+.+|+|+|||+
T Consensus         9 ~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TCEEEECCCTTSSTTT
T ss_pred             CCcEEEEECCCCCHHH
Confidence            5779999999999995

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=80.42  E-value=0.36  Score=44.71  Aligned_cols=52  Identities=17%  Similarity=0.177  Sum_probs=29.6

Q ss_pred             CCcccccCCHHHHHHHHHHHHHHHcChhHHhhhcCCCCcceEEeCCCCCCHHHHHH
Q 013128          206 MTFKTLALDSELKREITEDLENFMNGKEYYTRIGRAWKRGYLLYGPPGTGKSSLIA  261 (449)
Q Consensus       206 ~~f~~l~g~~~~k~~i~~~l~~~~~~~~~~~~~g~~~~rg~LL~GPpGtGKT~la~  261 (449)
                      .+||.+.+.+...+++.+.+..++-..- +. -|  ....++-||..|+|||+..-
T Consensus        52 F~fD~Vf~~~~~q~~vy~~~~~plv~~~-~~-~G--~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          52 FIVDKVFDDTVDNFTVYENTIKPLIIDL-YE-NG--CVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHHHH-HH-HC--CEEEEEEECCTTSSHHHHHH
T ss_pred             EeCCeecCCCCCHHHHHHHHHHHHHHHH-Hh-cC--CCeEEEeeeccccccceeee
Confidence            4566666655555555554433322110 00 01  13458999999999999863