Citrus Sinensis ID: 044214

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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-----
Protein Sequence
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGIE
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHHHccccEEEEccccHHHHcccccHHHHHHHHHHHHHccccccccHHHHHHHHcccEEEEEEcccccHHHHHHHHccccccccccEEEEEcccHHHHHHccccccccccccccHHHHHHHHHHHccccccEEHHHHHHHHHHHHHcccccHHHHHHHHHccccccccHHHHHEEccccccccHHHHHHHHHHccccccccHHHHcccccEEEccccEEEccHHHHHHHHHHHHccccccccccccccEEEEEEEccccEEEEEcHHHHcccccccEEEEcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccHHHHHHHHHHHHHHHccHHHHHHHHccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHccccccccccEEEEEEccHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccccEEHHHHHHHHHHHHHcccHHHHHHEEEccccccHHHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHccEEEEccccEEEHHHHHHHHHHHHHHcccccccccEEEEccccEEEEccccccEEEcHHHHHHccccEEEEEEcccccccccEEEEccccccccccccEEEEcc
Coil and Loop (DISEMBL)
KRESELINEVVNHILKRLdevfrprdnknqlvGVESTVEEIESLLGveskgvyalgiwgiggigkTTIARAIFDkisgdfdgscflenvreesqipgglSCLRQKLLSNllkdknvmpyidlnfrrlGHMKVLIVFDDVTCFSQLESLmgsldwltpvSRIILTTRNKQVLRNWRVNafkrnhpdvgneklsSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVAcffqgehvdpvmkffnasgfypeirisvlvdkpliaICSYKKIRMRDLLQELGGeivrkesinpgnrkqgqkIEDICLDMSKVIEICLntstftkmpklrflkfysssfngenkckisylqdpgfagvklnnfgie
Flexible Loop (DISEMBL)
kreselinEVVNHilkrldevfrprdnknqlvgveSTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNllkdknvmPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLmgsldwltPVSRIILttrnkqvlrnwrvnafkrnhpdvgneKLSSNVMKYAQGVPLALKVLVWESAISKLqrilhpsiLEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEivrkesinpgnrkqgqkIEDICLDMSKVIEICLNtstftkmpklRFLKFYSSSFNGENKCKISYlqdpgfagvklnnfgie
Low Complexity Region (SEG)
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALgiwgiggigKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGIE
Disordered region (IsUnstruct)
******INEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVR*************KIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNF***
Disordered Region (DISOPRED)
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGI*
Disordered Region (DISEMBL)
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGIE
Disordered Region (DISPRO)
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGIE
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQDPGFAGVKLNNFGIE
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	385	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.909	0.305	0.347	3e-53
O82500	1095	Putative disease resistan	no	no	0.901	0.316	0.348	6e-50
Q9FL92	1372	Probable WRKY transcripti	no	no	0.776	0.217	0.351	1e-49
Q9FH83	1288	Probable WRKY transcripti	no	no	0.833	0.249	0.331	2e-46
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.890	0.212	0.319	2e-41
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.937	0.190	0.316	1e-40
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.818	0.242	0.313	1e-36
Q9T048	985	Disease resistance protei	no	no	0.6	0.234	0.252	7e-10
Q9C646	899	Probable disease resistan	no	no	0.579	0.248	0.263	2e-07
Q9FJB5	901	Disease resistance RPP8-l	no	no	0.610	0.260	0.247	1e-06

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

 Score =  209 bits (532), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 140/403 (34%), Positives = 223/403 (55%), Gaps = 53/403 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           K +++ I ++V+ I  +L ++         +VG+++ +E+IESLL +   GV  +GIWG+
Sbjct: 160 KTDADCIRQIVDQISSKLCKI--SLSYLQNIVGIDTHLEKIESLLEIGINGVRIMGIWGM 217

Query: 61  GGIGKTTIARAIFDKISG------DFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDK 114
           GG+GKTTIARAIFD + G       FDG+CFL++++E  +   G+  L+  LLS LL++K
Sbjct: 218 GGVGKTTIARAIFDTLLGRMDSSYQFDGACFLKDIKENKR---GMHSLQNALLSELLREK 274

Query: 115 -NVMPYIDLNFR---RLGHMKVLIVFDDVTCFSQ-LESLMGSLDWLTPVSRIILTTRNKQ 169
            N     D   +   RL   KVLIV DD+      LE L G LDW    SRII+TTR+K 
Sbjct: 275 ANYNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRDKH 334

Query: 170 VLRN------------------WRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-- 209
           ++                    ++ +AF +  P+   EKLS  V+ YA+G+PLALKV   
Sbjct: 335 LIEKNDIIYEVTALPDHESIQLFKQHAFGKEVPNENFEKLSLEVVNYAKGLPLALKVWGS 394

Query: 210 --------VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVM 261
                    W+SAI  ++   +  I++ LKISYD LE K++ +FLD+ACF +GE  D ++
Sbjct: 395 LLHNLRLTEWKSAIEHMKNNSYSGIIDKLKISYDGLEPKQQEMFLDIACFLRGEEKDYIL 454

Query: 262 KFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQK 321
           +   +     E  + +L+DK L+ I  Y +++M DL+Q++G  IV  +  +PG R +   
Sbjct: 455 QILESCHIGAEYGLRILIDKSLVFISEYNQVQMHDLIQDMGKYIVNFQK-DPGERSR--- 510

Query: 322 IEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKC 364
                L ++K +E  ++ +T T   +  ++  YSS+    N+ 
Sbjct: 511 -----LWLAKEVEEVMSNNTGTMAMEAIWVSSYSSTLRFSNQA 548

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

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

 Score =  198 bits (503), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 145/416 (34%), Positives = 216/416 (51%), Gaps = 69/416 (16%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           E+  I  +   +L++L+    P  + N LVG+E+ + ++ESLL +ES+GV  +GIWG  G
Sbjct: 158 EAYKITTISKDVLEKLNAT--PSRDFNDLVGMEAHIAKMESLLCLESQGVRIVGIWGPAG 215

Query: 63  IGKTTIARAIFDKISGDFDGSCFLENVREESQIPG----GLSC-LRQKLLSNLLKDKNVM 117
           +GKTTIARA++++   +F+ S F+ENVRE     G    GL   L+Q+ LS LL  K   
Sbjct: 216 VGKTTIARALYNQYHENFNLSIFMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQK--- 272

Query: 118 PYIDLNFRRLGHM-------KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQV 170
              DL  R LG +       KVLI+ DDV    QL++L     W    SRI++TT+NKQ+
Sbjct: 273 ---DLRVRHLGAIEERLKSQKVLIILDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQL 329

Query: 171 LRNWRVN--------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL- 209
           L +  +N                    AFK++ P    + L+      A  +PLAL+VL 
Sbjct: 330 LVSHDINHMYQVAYPSKQEALTIFCQHAFKQSSPSDDLKHLAIEFTTLAGHLPLALRVLG 389

Query: 210 ---------VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPV 260
                     WE ++  L+  L   + +VLK+ YD L D EK++FL +AC F G+H + +
Sbjct: 390 SFMRGKGKEEWEFSLPTLKSRLDGEVEKVLKVGYDGLHDHEKDLFLHIACIFSGQHENYL 449

Query: 261 MKFFNASG-FYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ 318
            +   A+   Y    + VL DK LI      +I M  LL++LG E+VRK+SI  PG R+ 
Sbjct: 450 KQMIIANNDTYVSFGLQVLADKSLIQKFENGRIEMHSLLRQLGKEVVRKQSIYEPGKRQF 509

Query: 319 GQKIEDIC----------------LDMSKVI-EICLNTSTFTKMPKLRFLKFYSSS 357
               ++ C                LDM ++  E+ ++  TF +M  L +LKFY SS
Sbjct: 510 LMNAKETCGVLSNNTGTGTVLGISLDMCEIKEELYISEKTFEEMRNLVYLKFYMSS 565

Arabidopsis thaliana (taxid: 3702)

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

 Score =  197 bits (501), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 119/339 (35%), Positives = 186/339 (54%), Gaps = 40/339 (11%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           +S+L+ E V  + ++L  + R        +G+ S + EIE ++  +   +  +GIWG+ G
Sbjct: 122 DSQLVKETVRDVYEKLFYMER--------IGIYSKLLEIEKMINKQPLDIRCVGIWGMPG 173

Query: 63  IGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDL 122
           IGKTT+A+A+FD++SG+FD  CF+E+  +  Q  G    L ++ L         +  + L
Sbjct: 174 IGKTTLAKAVFDQMSGEFDAHCFIEDYTKAIQEKGVYCLLEEQFLKENAGASGTVTKLSL 233

Query: 123 NFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN----- 177
              RL + +VL+V DDV     +ES +G  DW  P S II+T+++K V R  RVN     
Sbjct: 234 LRDRLNNKRVLVVLDDVRSPLVVESFLGGFDWFGPKSLIIITSKDKSVFRLCRVNQIYEV 293

Query: 178 ------------AFKRNHPDVGNEKL---SSNVMKYAQGVPLALKVL-----------VW 211
                       +   +  D+  + L   S  V+KYA G PLAL +              
Sbjct: 294 QGLNEKEALQLFSLCASIDDMAEQNLHEVSMKVIKYANGHPLALNLYGRELMGKKRPPEM 353

Query: 212 ESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYP 271
           E A  KL+       ++ +K SYD+L D+EKNIFLD+ACFFQGE+VD VM+     GF+P
Sbjct: 354 EIAFLKLKECPPAIFVDAIKSSYDTLNDREKNIFLDIACFFQGENVDYVMQLLEGCGFFP 413

Query: 272 EIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKES 310
            + I VLV+K L+ I S  ++RM +L+Q++G +I+ +E+
Sbjct: 414 HVGIDVLVEKSLVTI-SENRVRMHNLIQDVGRQIINRET 451

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  187 bits (474), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 129/389 (33%), Positives = 193/389 (49%), Gaps = 68/389 (17%)

Query: 32  VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVRE 91
           +G+ S + EIE+++  +  G+  +GIWG+ GIGKTT+A+A+FD++S  FD SCF+E+  +
Sbjct: 152 IGIYSKLLEIENMVNKQPIGIRCVGIWGMPGIGKTTLAKAVFDQMSSAFDASCFIEDYDK 211

Query: 92  ESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGS 151
                G    L ++LL     D  +M    L   RL   +VL+V DDV      ES +  
Sbjct: 212 SIHEKGLYCLLEEQLLPG--NDATIMKLSSLR-DRLNSKRVLVVLDDVRNALVGESFLEG 268

Query: 152 LDWLTPVSRIILTTRNKQVLRNWRVN---------------------AFKRNHPDVGNEK 190
            DWL P S II+T+R+KQV     +N                     + K +  +   ++
Sbjct: 269 FDWLGPGSLIIITSRDKQVFCLCGINQIYEVQGLNEKEARQLFLLSASIKEDMGEQNLQE 328

Query: 191 LSSNVMKYAQGVPLALKVL-----------VWESAISKLQRILHPSILEVLKISYDSLED 239
           LS  V+ YA G PLA+ V              E+A  KL+R     I++  K +YD+L D
Sbjct: 329 LSVRVINYANGNPLAISVYGRELKGKKKLSEMETAFLKLKRRPPFKIVDAFKSTYDTLSD 388

Query: 240 KEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQ 299
            EKNIFLD+ACFFQGE+V+ V++     GF+P + I VLVDK L+ I S  ++ +  L Q
Sbjct: 389 NEKNIFLDIACFFQGENVNYVIQLLEGCGFFPHVEIDVLVDKCLVTI-SENRVWLHKLTQ 447

Query: 300 ELGGEIVRKESINPGNRKQ-------------------------------GQKIEDICLD 328
           ++G EI+  E++    R++                                ++IE + LD
Sbjct: 448 DIGREIINGETVQIERRRRLWEPWSIKYLLEYNEHKANGEPKTTFKRAQGSEEIEGLFLD 507

Query: 329 MSKVIEICLNTSTFTKMPKLRFLKFYSSS 357
            S  +   L  S F  M  LR LK Y S+
Sbjct: 508 TSN-LRFDLQPSAFKNMLNLRLLKIYCSN 535

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  170 bits (431), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 133/416 (31%), Positives = 203/416 (48%), Gaps = 73/416 (17%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           +SEL+ E+V  +  +L    R        VG+ + + EIE LL  + + + ++GIWG+ G
Sbjct: 148 DSELVEEIVRDVYGKLYPAER--------VGIYARLLEIEKLLYKQHRDIRSIGIWGMPG 199

Query: 63  IGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM--PYI 120
           IGKTT+A+A+F+ +S D+D SCF+EN  +E+    GL  L ++ +  +LKD+  +   YI
Sbjct: 200 IGKTTLAKAVFNHMSTDYDASCFIENF-DEAFHKEGLHRLLKERIGKILKDEFDIESSYI 258

Query: 121 ---DLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN 177
               L+  +L   ++L+V DDV      ES +  LDW    S II+T+ +KQV    ++N
Sbjct: 259 MRPTLHRDKLYDKRILVVLDDVRDSLAAESFLKRLDWFGSGSLIIITSVDKQVFAFCQIN 318

Query: 178 --------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-------- 209
                                F  N P+  + KLS  V+ Y  G PLAL +         
Sbjct: 319 QIYTVQGLNVHEALQLFSQSVFGINEPEQNDRKLSMKVIDYVNGNPLALSIYGRELMGKK 378

Query: 210 -VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASG 268
              E+A  +L+      I +VLK +Y +L D EKNI LD+A FF+GE V+ VM+    S 
Sbjct: 379 SEMETAFFELKHCPPLKIQDVLKNAYSALSDNEKNIVLDIAFFFKGETVNYVMQLLEESH 438

Query: 269 FYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKE------------------- 309
           ++P + I VLVDK ++ I S   ++M +L+Q+   EI   E                   
Sbjct: 439 YFPRLAIDVLVDKCVLTI-SENTVQMNNLIQDTCQEIFNGEIETCTRMWEPSRIRYLLEY 497

Query: 310 ---------SINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS 356
                       P +    + IE I LD S V +  +    F  M  L+FLK Y+S
Sbjct: 498 DELEGSGETKAMPKSGLVAEHIESIFLDTSNV-KFDVKHDAFKNMFNLKFLKIYNS 552

Arabidopsis thaliana (taxid: 3702)

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

 Score =  167 bits (423), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 132/417 (31%), Positives = 206/417 (49%), Gaps = 56/417 (13%)

Query: 1    KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
            K ESELI+E+V   LK L        +K  ++G++  VEEI SLL +ES  V ++GIWG 
Sbjct: 791  KSESELIDEIVRDALKVLCSA-----DKVNMIGMDMQVEEILSLLCIESLDVRSIGIWGT 845

Query: 61   GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK-DKNVMPY 119
             GIGKTTIA  IF KIS  ++    L+++ +E ++ G    +R+  LS +L+ + +V+  
Sbjct: 846  VGIGKTTIAEEIFRKISVQYETCVVLKDLHKEVEVKGH-DAVRENFLSEVLEVEPHVIRI 904

Query: 120  IDLNF----RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWR 175
             D+       RL   ++L++ DDV  +  +++ +G+L++  P SRII+T+RN++V    +
Sbjct: 905  SDIKTSFLRSRLQRKRILVILDDVNDYRDVDTFLGTLNYFGPGSRIIMTSRNRRVFVLCK 964

Query: 176  VNAFKRNHP----------DVGN----------EKLSSNVMKYAQGVPLALKVLV----- 210
            ++      P          D G           + LS  ++K++ G P  L+ L      
Sbjct: 965  IDHVYEVKPLDIPKSLLLLDRGTCQIVLSPEVYKTLSLELVKFSNGNPQVLQFLSSIDRE 1024

Query: 211  WESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFY 270
            W     +++      I  + + S   L+D E+ IFLD+ACFF     D V    +  GF 
Sbjct: 1025 WNKLSQEVKTTSPIYIPGIFEKSCCGLDDNERGIFLDIACFFNRIDKDNVAMLLDGCGFS 1084

Query: 271  PEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESIN-PGNRKQ----------- 318
              +    LVDK L+ I  +  + M   +Q  G EIVR+ES + PG+R +           
Sbjct: 1085 AHVGFRGLVDKSLLTISQHNLVDMLSFIQATGREIVRQESADRPGDRSRLWNADYIRHVF 1144

Query: 319  -----GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQ 370
                    IE I LDM   ++   N + F KM  LR LK Y S    E K  +S+ Q
Sbjct: 1145 INDTGTSAIEGIFLDMLN-LKFDANPNVFEKMCNLRLLKLYCS--KAEEKHGVSFPQ 1198

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  154 bits (389), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 112/357 (31%), Positives = 182/357 (50%), Gaps = 42/357 (11%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYAL-GIWGIG 61
           E+ +I E+   +L++      P D+   LVG+E+ +E I+S+L +ESK    + GIWG  
Sbjct: 158 EAAMIEELAEDVLRK---TMTPSDDFGDLVGIENHIEAIKSVLCLESKEARIMVGIWGQS 214

Query: 62  GIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK-LLSNLLKDKNV-MPY 119
           GIGK+TI RA++ K+S  F    F+           G+    +K LLS +L  K++ + +
Sbjct: 215 GIGKSTIGRALYSKLSIQFHHRAFITYKSTSGSDVSGMKLRWEKELLSEILGQKDIKIEH 274

Query: 120 IDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN-- 177
             +  +RL   KVLI+ DDV     L++L+G  +W    SRII+ T+++Q+L+   ++  
Sbjct: 275 FGVVEQRLKQQKVLILLDDVDSLEFLKTLVGKAEWFGSGSRIIVITQDRQLLKAHEIDLI 334

Query: 178 ------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL---------- 209
                             AF ++ P    ++L+  V K A  +PL L VL          
Sbjct: 335 YEVEFPSEHLALTMLCRSAFGKDSPPDDFKELAFEVAKLAGNLPLGLSVLGSSLKGRTKE 394

Query: 210 VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGF 269
            W   + +L+  L+  I++ L++SYD L  K++++FL +AC F G  V  V      +  
Sbjct: 395 WWMEMMPRLRNGLNGDIMKTLRVSYDRLHQKDQDMFLYIACLFNGFEVSYVKDLLKDN-- 452

Query: 270 YPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQGQKIEDI 325
              +  ++L +K LI I     I M +LL++LG EI R +S  NPG R+     EDI
Sbjct: 453 ---VGFTMLTEKSLIRITPDGYIEMHNLLEKLGREIDRAKSKGNPGKRRFLTNFEDI 506

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score = 65.5 bits (158), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 80/317 (25%), Positives = 128/317 (40%), Gaps = 86/317 (27%)

Query: 31  LVGVESTVEEIESLLGVE-------------------SKGVYALGIWGIGGIGKTTIARA 71
           ++ VEST E +E + GV                    S+    +G+WG+GG+GKTT+ R 
Sbjct: 124 MLSVESTPERVEHVPGVSVVHQTMASNMLAKIRDGLTSEKAQKIGVWGMGGVGKTTLVRT 183

Query: 72  -----------------IFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDK 114
                            IF  +S +FD     + + E   I   +    +KL   +    
Sbjct: 184 LNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDIDTQMEESEEKLARRI---- 239

Query: 115 NVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNW 174
               Y+ L   R    K L++ DDV     L+ L          S++ILT+R  +V R+ 
Sbjct: 240 ----YVGLMKER----KFLLILDDVWKPIDLDLLGIPRTEENKGSKVILTSRFLEVCRSM 291

Query: 175 RVN---------------AFKRNHPDVGN----EKLSSNVMKYAQGVPLAL--------- 206
           + +                F +N  DV       K++  V +   G+PLA+         
Sbjct: 292 KTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRG 351

Query: 207 --KVLVWESAISKLQ------RILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVD 258
              V +W   +SKL       + +   I + LK+SYD LEDK K  FL  A F +   ++
Sbjct: 352 KKNVKLWNHVLSKLSKSVPWIKSIEEKIFQPLKLSYDFLEDKAKFCFLLCALFPEDYSIE 411

Query: 259 --PVMKFFNASGFYPEI 273
              V++++ A GF  E+
Sbjct: 412 VTEVVRYWMAEGFMEEL 428

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C646|RX24L_ARATH Probable disease resistance protein RXW24L OS=Arabidopsis thaliana GN=RXW24L PE=2 SV=1

 Score = 57.0 bits (136), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 77/292 (26%), Positives = 127/292 (43%), Gaps = 69/292 (23%)

Query: 25  RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIF--DKISGDFDG 82
           RD++N  VG+E+ V+++   L VE      + + G+GG+GKTT+AR +F  D +   FDG
Sbjct: 156 RDSENDFVGMEANVKKLVGYL-VEKDDYQIVSLTGMGGLGKTTLARQVFNHDVVKDRFDG 214

Query: 83  SCFLENVREESQIPGGLSCLRQKLLSNLLKDK-NVMPYIDLN---FRRLGHMKVLIVFDD 138
             ++   +E ++I    + L Q L S   KD+   M   DL+   FR L   K LIV DD
Sbjct: 215 FAWVSVSQEFTRISVWQTIL-QNLTSKERKDEIQNMKEADLHDDLFRLLESSKTLIVLDD 273

Query: 139 VTCFSQLESLMGSLDW--LTPV------SRIILTTRNKQVLR------------------ 172
           +             DW  + P+       +++LT+R + +                    
Sbjct: 274 I---------WKEEDWDLIKPIFPPKKGWKVLLTSRTESIAMRGDTTYISFKPKCLSIPD 324

Query: 173 NWRVN---AFKRNHP-----DVGNEKLSSNVMKYAQGVPLALKVL-----------VWE- 212
           +W +    A  R        D   E +   ++K+  G+ LA+KVL            W+ 
Sbjct: 325 SWTLFQSIAMPRKDTSEFKVDEEMENMGKKMIKHCGGLSLAVKVLGGLLAAKYTLHDWKR 384

Query: 213 ------SAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVD 258
                 S I +     + SI  VL +S++ L +  K+ FL +A F +   +D
Sbjct: 385 LSENIGSHIVERTSGNNSSIDHVLSVSFEELPNYLKHCFLYLAHFPEDHEID 436

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 78/315 (24%), Positives = 132/315 (41%), Gaps = 80/315 (25%)

Query: 24  PRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIF--DKISGDFD 81
           P  +++ LVGVE +VEE+   + VE   +  + I G+GGIGKTT+AR IF  D +   FD
Sbjct: 156 PNSSESDLVGVEQSVEELVGPM-VEIDNIQVVSISGMGGIGKTTLARQIFHHDLVRRHFD 214

Query: 82  GSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLN------FRRLGHMKVLIV 135
           G  ++   ++ +Q       + Q++L  L      +  +D        F+ L   + L+V
Sbjct: 215 GFAWVCVSQQFTQ-----KHVWQRILQELRPHDGEILQMDEYTIQGKLFQLLETGRYLVV 269

Query: 136 FDDVTCFSQLESLMGSLDW-----LTPVSR---IILTTRNKQV----------------- 170
            DDV             DW     + P  R   ++LT+RN+ V                 
Sbjct: 270 LDDV---------WKEEDWDRIKEVFPRKRGWKMLLTSRNEGVGLHADPTCLSFRARILN 320

Query: 171 -LRNWRVNAFKRNHPDVGN------EKLSSNVMKYAQGVPLALKV----LVWESAISKLQ 219
              +W++  F+R  P          E +   ++ Y  G+PLA+KV    L  +   S+ +
Sbjct: 321 PKESWKL--FERIVPRRNETEYEEMEAIGKEMVTYCGGLPLAVKVLGGLLANKHTASEWK 378

Query: 220 RILH-----------------PSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVD--PV 260
           R+                    S+  +L +SY+ L    K+ FL +A F +   +    +
Sbjct: 379 RVSENIGAQIVGKSCLDDNSLNSVYRILSLSYEDLPTDLKHCFLYLAHFPEDYKIKTRTL 438

Query: 261 MKFFNASGFYPEIRI 275
             ++ A G Y  + I
Sbjct: 439 YSYWAAEGIYDGLTI 453

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	385
255537139	1137	leucine-rich repeat-containing protein,	0.924	0.313	0.420	3e-71
255564976	944	TMV resistance protein N, putative [Rici	0.914	0.372	0.435	4e-70
359486071	1261	PREDICTED: TMV resistance protein N-like	0.929	0.283	0.393	2e-67
356577113	1344	PREDICTED: putative disease resistance p	0.914	0.261	0.396	3e-67
356502071	694	PREDICTED: TMV resistance protein N-like	0.903	0.501	0.404	4e-67
359486073	1296	PREDICTED: TMV resistance protein N-like	0.929	0.276	0.390	3e-66
255573549	908	ATP binding protein, putative [Ricinus c	0.909	0.385	0.398	5e-66
359495289	1133	PREDICTED: TMV resistance protein N-like	0.945	0.321	0.402	1e-65
356550897	970	PREDICTED: TMV resistance protein N-like	0.919	0.364	0.398	2e-64
359486075	1291	PREDICTED: TMV resistance protein N-like	0.922	0.274	0.383	7e-64

>gi|255537139|ref|XP_002509636.1| leucine-rich repeat-containing protein, putative [Ricinus communis] gi|223549535|gb|EEF51023.1| leucine-rich repeat-containing protein, putative [Ricinus communis]

 Score =  275 bits (703), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 172/409 (42%), Positives = 240/409 (58%), Gaps = 53/409 (12%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           ES+L++E+V + LK+L + +   D    +VGV+S +E+I+ LL + S  V  LGIWG+GG
Sbjct: 157 ESKLVDEIVMYTLKQLKQSYSS-DVVEGIVGVDSRIEQIKELLSIGSVDVRFLGIWGMGG 215

Query: 63  IGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV---MPY 119
           IGKTT+A A+F +I+  F+GSCFL NVR   +  GGL+ L+++LLS  L+ ++     P 
Sbjct: 216 IGKTTLAEAVFYQIAYQFEGSCFLANVRGNFEKNGGLARLQEELLSKTLEKRDFKIDTPN 275

Query: 120 IDLNF---RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN--- 173
           I  +F   + L H +VLIV DD     QL+ L+GS DW  P SRII+T+R+KQVL     
Sbjct: 276 IGYSFWVKQMLKHRRVLIVVDDANDSEQLDLLVGSHDWFGPGSRIIVTSRDKQVLTKIVD 335

Query: 174 ----------------WRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-------- 209
                           +    FK+         LS  V++YA+GVPLALKVL        
Sbjct: 336 DIYEVKELVHHEALQLFNQTTFKKKCVPEDYSYLSDLVIEYAKGVPLALKVLGSFLFGKS 395

Query: 210 --VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNAS 267
              WESA+ KL++  H +   VLKISYD L+ +EKNIFLD+ACFF+GE V+ V K  +  
Sbjct: 396 KTEWESALDKLKKAPHRATQNVLKISYDGLDAEEKNIFLDIACFFRGESVEMVTKILDGC 455

Query: 268 GFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQ--------- 318
           GF  +I + +LVDK LI I +  K+ M DLLQE+G EIV +ES  P  R +         
Sbjct: 456 GFSTKIGLCLLVDKSLITILN-DKVEMHDLLQEMGKEIVLQESKQPSQRTRLWNHEDILH 514

Query: 319 -------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNG 360
                   + IE +CL+ S + +I LN++ F +M  LRFLKFY S  +G
Sbjct: 515 VFSRNLGTETIEGMCLNTSMINKIELNSNAFGRMYNLRFLKFYQSYIHG 563

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  271 bits (693), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 176/404 (43%), Positives = 231/404 (57%), Gaps = 52/404 (12%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + ES+LI E+   ILK+L+ +    D+K  LVG+ S +++IE LL VE   V  LG+WG+
Sbjct: 163 RSESKLIQEIAEDILKKLNHMSSSTDSKG-LVGINSRIDKIELLLCVELADVRFLGLWGM 221

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYI 120
           GG GKTT A  +F++IS  FD  CFL NV EES+  G L  L+++L S LL   NV  Y 
Sbjct: 222 GGAGKTTTAEVVFNRISTQFDSCCFLANVNEESERYGLLK-LQRQLFSKLLGQDNV-NYA 279

Query: 121 DLNF--RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN----- 173
           +  F   RL H KVLIV DDV    QLE+L G  +W  P SRIILT+R+K VL+N     
Sbjct: 280 EGIFDKSRLKHRKVLIVLDDVNNLRQLENLAGEHNWFGPGSRIILTSRDKDVLKNKTDAI 339

Query: 174 --------------WRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL---------- 209
                         + +NAF++  P     KLS  V+ YA+G PL LKVL          
Sbjct: 340 YKIEDLDHHEALQLFSLNAFRQECPKADYMKLSKRVINYAKGNPLGLKVLGSFLYQRNIK 399

Query: 210 VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGF 269
            WESA+ KL+R  +  I  VLK+SYD L+D+EK+IFLDVACFF GE  D V +  N  GF
Sbjct: 400 EWESALHKLERSTNKEIQNVLKVSYDGLDDEEKDIFLDVACFFNGEDRDFVTRILNGCGF 459

Query: 270 YPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ---------- 318
             +I ISVLV K L+ I S   + + +LLQ++G  IVR+ES   PG R +          
Sbjct: 460 SADIAISVLVSKSLLTI-SNNTLAIHNLLQQMGWGIVRQESTKEPGRRSRLCTSEDVVHV 518

Query: 319 ------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS 356
                  + IE I LDMSK  ++ L+   F +M  LR LKF+ S
Sbjct: 519 LSKNTGTEAIEGIYLDMSKSRKVYLSPKAFERMHNLRLLKFHHS 562

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  262 bits (669), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 162/412 (39%), Positives = 239/412 (58%), Gaps = 54/412 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           K ESE+I E+V+ I K+L++      N   LVG+ S ++ + SLL + S  V  +GIWG+
Sbjct: 167 KHESEVIKEIVSKIWKKLNDA--SSCNMEALVGMASHIQNMVSLLRIGSDDVRMVGIWGM 224

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPY- 119
            GIGKTTIA A++ KI   F+G CFL NVRE+SQ     + ++ +LLS + ++ N+    
Sbjct: 225 AGIGKTTIAEAVYQKIRTRFEGCCFLSNVREKSQ-KNDPAVIQMELLSQIFEEGNLNTGV 283

Query: 120 ----IDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL---- 171
               I++  + L  M+VLIV DDV C  QLE L G+ +W +P SRII+TTR K +L    
Sbjct: 284 LSGGINVIEKTLHSMRVLIVLDDVDCPQQLEVLAGNHNWFSPGSRIIITTREKHLLDEKV 343

Query: 172 --------------RNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-------- 209
                         + +  +AFK   P     +L    + Y +G+PLALK+L        
Sbjct: 344 EIYVAKELNKDEARKLFYQHAFKYKPPVGDFVQLCDRALNYTKGIPLALKILGRFLYNRS 403

Query: 210 --VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNAS 267
              WES + KL+RI +  I +VL+IS+D L+D +K+IFLD+ACFF+G+  D V+K   + 
Sbjct: 404 KKEWESELEKLRRIPNKEIQDVLRISFDGLDDNQKDIFLDIACFFKGQDKDYVIKLLKSC 463

Query: 268 GFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ-------- 318
            F+PEI I  L+DK L+ I SY K+ M DL+QE+G EIVR+ESI +PG R +        
Sbjct: 464 DFFPEIEIRNLIDKSLVTI-SYNKLCMHDLIQEMGWEIVRQESIKDPGKRSRLWVNDDVI 522

Query: 319 --------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGEN 362
                    + +E + L++S + E+  + + FTKM KLR L+FY +   G +
Sbjct: 523 DMLTTNTGTEAVEGMVLNLSTLKELHFSVNVFTKMNKLRVLRFYDAQIWGSS 574

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356577113|ref|XP_003556672.1| PREDICTED: putative disease resistance protein At4g11170-like [Glycine max]

 Score =  262 bits (669), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 161/406 (39%), Positives = 236/406 (58%), Gaps = 54/406 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + E+ELI  +V  ++++L+ ++ P + K  LVG++  +  IESLL + SK V  +GIWG+
Sbjct: 191 RTENELIEGIVKDVMEKLNRIY-PTEVKETLVGIDQNIAPIESLLRIGSKEVRIIGIWGM 249

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM--- 117
           GG+GKTTIA A+F K+S  ++GSCFL NVREE +   GL  LR KL S +L+D   +   
Sbjct: 250 GGVGKTTIANALFTKLSSQYEGSCFLANVREEYE-NQGLGYLRNKLFSEVLEDDVNLHIS 308

Query: 118 -PYIDLNF--RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL--- 171
            P +   F  RRL   KVLIV DDV    +LE L    D L   S +I+TTR+K V+   
Sbjct: 309 TPKVRSTFVMRRLRQKKVLIVLDDVDDSKKLEYLAAQHDCLGSGSIVIVTTRDKHVISKG 368

Query: 172 ----------------RNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL------ 209
                           R + +NAF + +P+ G E LS  V+ +A G PLALKVL      
Sbjct: 369 VDETYEVKGLSLHHAVRLFSLNAFGKTYPEKGFEMLSKQVVDHANGNPLALKVLGSLLHS 428

Query: 210 ----VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFN 265
                W +A+ KL ++ +  I  VL+ SYD L+ ++KN+FLD+ACFF+GE+++ V++   
Sbjct: 429 RNEQQWANALRKLTKVPNAEIQNVLRWSYDGLDYEQKNMFLDIACFFRGENIENVIRLLE 488

Query: 266 ASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ------ 318
             GFYP I I +L +K L+      K+ M DL+QE+G EIV +ESI +PG R +      
Sbjct: 489 ICGFYPYIGIKILQEKSLVTFSDDGKVCMHDLIQEMGWEIVHRESIKDPGRRSRLWDPKE 548

Query: 319 ----------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFY 354
                        +E I LD+S++ ++ L+  TF++M  +RFLKFY
Sbjct: 549 VYDVLKNNRGTDAVEGIILDVSQISDLPLSYETFSRMINIRFLKFY 594

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502071|ref|XP_003519845.1| PREDICTED: TMV resistance protein N-like [Glycine max]

 Score =  261 bits (667), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 167/413 (40%), Positives = 244/413 (59%), Gaps = 65/413 (15%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           ES+L++ +V  I ++L + F PR++ N LVG++  +  I+SLL +ES  V  +GIWG+GG
Sbjct: 74  ESDLVHGIVEDIWEKLSK-FCPRES-NGLVGIDQNIARIQSLLLMESSEVLFVGIWGMGG 131

Query: 63  IGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMP---- 118
           IGKTTIARA+FDK S  +DG CFL NV+EE +   GLS LR+KL+S L + + +      
Sbjct: 132 IGKTTIARAVFDKFSSQYDGLCFL-NVKEELE-QHGLSLLREKLISELFEGEGLHTSGTS 189

Query: 119 ---YIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWR 175
              +++ + RR+G  KVL+V DDV    Q++ L+G        SR+I+T+R++ VL +  
Sbjct: 190 KARFLNSSIRRMGRKKVLVVLDDVNTSEQIKDLVGEPTCFGAGSRVIITSRDQNVLTSGG 249

Query: 176 V--------------------NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL------ 209
           V                    NAF  + P +G EKL+  V+K AQG+PLAL+VL      
Sbjct: 250 VHQIHEVKEMDSRDSLKLFCLNAFNESQPKMGYEKLTEEVVKIAQGIPLALRVLGADFRS 309

Query: 210 -----VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFF 264
                +WESA+SK+++  +  I  VL+ S+D LE+ EK  FLD+A FF+ +  D V+   
Sbjct: 310 RSTIDMWESALSKIKKYPNKKIQSVLRFSFDGLEELEKKAFLDIAFFFEEDSKDYVITQL 369

Query: 265 NASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNR------- 316
           +A GFY  + I VL  K LI I    +I+M DL +++G EIVR+ESI NPG R       
Sbjct: 370 DAWGFYGAVGIEVLQRKALITISKDNRIQMHDLTRQMGCEIVRQESITNPGRRSRLRDSE 429

Query: 317 --------KQG-QKIEDICLDMSKVIEICLNTST------FTKMPKLRFLKFY 354
                   +QG  ++E + +D+S+ I++ L  ST      F KMP+LRFLKFY
Sbjct: 430 EVYNVLRHEQGTDEVEAMQIDVSQAIDLRLELSTFKKFSNFKKMPRLRFLKFY 482

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  258 bits (659), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 161/412 (39%), Positives = 237/412 (57%), Gaps = 54/412 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + ESE I E+V+ I K L++      N   LVG++S ++++ SLL + S  V  +GIWG+
Sbjct: 172 EHESEFIKEIVSKIWKELNDA--SSCNMEALVGMDSHIQKMFSLLRIGSDDVRMVGIWGM 229

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPY- 119
            GIGKTTIA A++ KI   F+G CFL NVRE+SQ     + ++ KLLS + +  N+    
Sbjct: 230 AGIGKTTIAEAVYQKIRTQFEGCCFLSNVREKSQ-NNDPAVIQMKLLSQIFEKGNLNTGL 288

Query: 120 ----IDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL---- 171
               I++  + L  M+VLIV DDV C  QLE L G+ +W  P SRII+TTR K +L    
Sbjct: 289 LSGGINVIEKTLHSMRVLIVLDDVDCPQQLEVLAGNHNWFGPGSRIIITTREKHLLDEKV 348

Query: 172 --------------RNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-------- 209
                         + +  +AFK   P     +L    + Y +G+PLALK+L        
Sbjct: 349 EIYIVKELNKDEARKLFYQHAFKYKPPAGDFVQLCDRALNYTKGIPLALKILGRFLYNRS 408

Query: 210 --VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNAS 267
              WES + KL+RI +  I +VL+IS+D L+D +K+IFLD+ACFF+G+  D V+K   + 
Sbjct: 409 KKEWESELEKLRRIPNNEIQDVLRISFDGLDDNQKDIFLDIACFFKGQDKDYVIKLLKSC 468

Query: 268 GFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ-------- 318
            F+PEI I  L+DK L+ I SY K+ M DL+Q++G EIVR+ESI +PG R +        
Sbjct: 469 DFFPEIGIRNLIDKSLVTI-SYNKLCMHDLIQKMGWEIVRQESIKDPGKRSRLWVNDDVI 527

Query: 319 --------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGEN 362
                    + +E + L++S + E+  + + FTKM KLR L+FY +   G +
Sbjct: 528 DMLTTNTGTEAVEGMVLNLSTLKELHFSVNVFTKMNKLRVLRFYDAQIWGSS 579

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573549|ref|XP_002527699.1| ATP binding protein, putative [Ricinus communis] gi|223532930|gb|EEF34698.1| ATP binding protein, putative [Ricinus communis]

 Score =  258 bits (658), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 162/407 (39%), Positives = 248/407 (60%), Gaps = 57/407 (14%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + ES +IN++VN+ILKRL ++     N + L+G++S V+++E+LL + S     +GIWG+
Sbjct: 159 RPESLVINDIVNYILKRLHQL---SSNLDGLIGMDSHVKQLETLLCLGSFDNRTVGIWGM 215

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMP-Y 119
           GGIGKTTIAR IF+K+SG F+  CFL N+RE+    G L+ L+++ L  +   +N+    
Sbjct: 216 GGIGKTTIARVIFNKMSGSFENRCFLGNIREKIGKTGLLN-LQREFLCEISGGENISADT 274

Query: 120 IDLN----FRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWR 175
           +D+      +RL + KVL+V DDV     L SL G L+   P SRII+T+R+KQVL+   
Sbjct: 275 VDVMSSFIIKRLRNKKVLVVLDDVDNLMDLSSLTGGLNLFGPGSRIIVTSRDKQVLQYCG 334

Query: 176 VN--------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL------ 209
           V+                    AF+++ P      LS+ V++YA+G+PLALK+       
Sbjct: 335 VDSIYEVKGLNNHESLQLFSHYAFEQSLPTEAYWNLSNRVLQYAKGLPLALKICGSHLCT 394

Query: 210 ----VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFN 265
                WES + +L+  L+  + EVL+ISY  L+D +K+IFLD+ACFF+G+ +D V +   
Sbjct: 395 RSIEQWESILHRLESPLNSEVQEVLQISYYGLDDLDKDIFLDIACFFRGQGIDHVKEILY 454

Query: 266 ASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNR-------- 316
            SGFY +I I+ L+ K LI+I S K++ M +L+QE+G EIVR+ESI  PG+R        
Sbjct: 455 DSGFYADIGIARLIGKSLISI-SDKRLEMHNLVQEMGWEIVRQESIYEPGSRSRLWNHEE 513

Query: 317 --------KQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYS 355
                   K    +  I LD+SK+ ++CL++ +FT+M  L+FLKFY+
Sbjct: 514 IYHVLTSNKGTGAVRGINLDLSKIHKLCLSSDSFTRMGNLKFLKFYT 560

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495289|ref|XP_002276927.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  256 bits (655), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 169/420 (40%), Positives = 240/420 (57%), Gaps = 56/420 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQ-LVGVESTVEEIESLLGVESKGVYALGIWG 59
           K E  LI  +  +I  +L    R  +  +Q LVG+ES++ EI+SLL  ES  V  +GIWG
Sbjct: 192 KHEPMLIKGIATYIWNKL--FSRSSNYADQNLVGIESSIREIKSLLFTESLDVRMVGIWG 249

Query: 60  IGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPY 119
           +GGIGKTT+ARA++++IS  F+  CFLENV +  +    LS L++K LS LL+D+N+   
Sbjct: 250 MGGIGKTTLARAVYNQISHQFEACCFLENVSDYLEKQDFLS-LQKKYLSQLLEDENLNTK 308

Query: 120 IDLNFRRL-GHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN- 177
             ++ + L    KVLIV DDV     LE L+G   W    SRII+TTRNKQ+L    VN 
Sbjct: 309 GCISIKALLCSKKVLIVIDDVNNSKILEDLIGKHGWFGIGSRIIITTRNKQLLVTHGVNE 368

Query: 178 -------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL--------- 209
                              AFK+ HP     +LS  ++ YAQG+PLAL+VL         
Sbjct: 369 VYQAEKLNDDNAVELFSRYAFKKAHPIDDYVELSQCIVVYAQGLPLALRVLGSFLFDKSK 428

Query: 210 -VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASG 268
             WES + KL++I    I +VL++S+D LED E++IFLD+ACFFQG   D VM+ F + G
Sbjct: 429 RQWESQLDKLKKIPKKEIQDVLRVSFDGLEDNERDIFLDIACFFQGHDKDYVMEIFRSCG 488

Query: 269 FYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ--------- 318
           F+P+I I VL++K LI++    K+ M +LLQ++G EIVR+ S   PG R +         
Sbjct: 489 FFPDIGIRVLIEKSLISVVE-NKLMMHNLLQKMGREIVREASPKEPGKRSRLWIHDDVNH 547

Query: 319 -------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSF---NGENKCKISY 368
                   +++E I LD+S + EI      F  M +LR LK Y+ +F   +   KCK+ +
Sbjct: 548 VLTKKTGTEEVEGISLDLSSLKEINFTNEAFAPMNRLRLLKVYTLNFLMDSKREKCKVHF 607

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  252 bits (644), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 163/409 (39%), Positives = 230/409 (56%), Gaps = 55/409 (13%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + ESE + ++V  +L++L    R  +++ +LVGVE   E+IESLL + S  V  LGIWG+
Sbjct: 162 RTESEFLKDIVKDVLRKLAP--RYPNHRKELVGVEENYEKIESLLKIGSSKVRILGIWGM 219

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM--- 117
           GGIGKTT+A A++DK+S +F+G CFL NVREES    G   LR KL S LL+++N+    
Sbjct: 220 GGIGKTTLASALYDKLSPEFEGCCFLANVREESD-KHGFKALRNKLFSELLENENLCFDA 278

Query: 118 -PYIDLNF--RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQV---- 170
             ++  +F   RLG  KV IV DDV    QLE+L+   D+L   SR+I+TTRNKQ+    
Sbjct: 279 SSFLVSHFVLSRLGRKKVFIVLDDVDTSEQLENLIEDFDFLGLGSRVIVTTRNKQIFSQV 338

Query: 171 --------------LRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL------- 209
                         L+ + ++ F+   P  G E LS + + Y +G+PLALKVL       
Sbjct: 339 DKIYKVKELSIHHSLKLFCLSVFREKQPKHGYEDLSRSAISYCKGIPLALKVLGASLRSR 398

Query: 210 ---VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNA 266
               WE  + KLQ+  +  I  VLK+SYD L+  +K IFLD+ACF +G+  D V     A
Sbjct: 399 SKQAWECELRKLQKFPNMEIHNVLKLSYDGLDYSQKEIFLDIACFLRGKQRDHVTSILEA 458

Query: 267 SGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNR--------- 316
             F     I VL+DK LI I    +I M DL+QE+G +IV +E I +PG R         
Sbjct: 459 FDFPAASGIEVLLDKALITISGGIQIEMHDLIQEMGWKIVHQEHIKDPGRRSRLWKHEEV 518

Query: 317 -------KQGQKIEDICLDMSKVIE-ICLNTSTFTKMPKLRFLKFYSSS 357
                  K  + +E + LD+SK+ E + L+     KM  +RFLK +S S
Sbjct: 519 HDVLKYNKGTEVVEGVILDLSKLTEDLYLSFDFLAKMTNVRFLKIHSWS 567

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  250 bits (639), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 159/415 (38%), Positives = 233/415 (56%), Gaps = 60/415 (14%)

Query: 1   KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGI 60
           + ES++I E+V+ I   L++      N   LVG++S ++ + SLL + S  V  +GIWG+
Sbjct: 167 RHESKVIKEIVSKIWNELNDA--SSCNMEALVGMDSHIQNMVSLLCIGSDDVRMVGIWGM 224

Query: 61  GGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYI 120
            GIGKTTIA A++ KI   F+G CFL NVRE+SQ     + ++ +LLS +  + N+   I
Sbjct: 225 AGIGKTTIAEAVYQKICTQFEGCCFLSNVREKSQ-KNDPAVIQMELLSQVFWEGNLNTRI 283

Query: 121 DLNFRR--------LGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL- 171
              F R        L  M+VLIV DDV    QLE L G+ +W  P SRII+TTR K +L 
Sbjct: 284 ---FNRGINAIKKTLHSMRVLIVLDDVDRPQQLEVLAGNHNWFGPGSRIIITTREKHLLD 340

Query: 172 -----------------RNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL----- 209
                            R +  +AFK   P     +L    + Y +G+PLALK+L     
Sbjct: 341 EKVEIYEVKELNKDEARRLFYQHAFKYKPPAGDFVQLCDRALNYTKGIPLALKILGRFLY 400

Query: 210 -----VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFF 264
                 WES + KL+RI +  I +VL+IS+D L+D +K+IF D+ACFF+G+  D V+K  
Sbjct: 401 NRSKKEWESELEKLRRIPNKEIQDVLRISFDGLDDNQKDIFFDIACFFKGQDKDYVIKLL 460

Query: 265 NASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESI-NPGNRKQ----- 318
            +  F+PEI I  L+DK L+ I SY K+ M DL+QE+G EIVR+ES+ +PG R +     
Sbjct: 461 KSCDFFPEIGIRNLIDKSLVTI-SYNKLCMHDLIQEMGWEIVRQESMKDPGKRSRLWVND 519

Query: 319 -----------GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGEN 362
                       + +E + L++S + E+  + + FTKM KLR L+FY +   G +
Sbjct: 520 DVIDMLTTNTGTEAVEGMVLNLSTLKELHFSVNVFTKMNKLRVLRFYDAQIWGSS 574

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	385
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.470	0.158	0.335	6.3e-45
TAIR|locus:2175991	1294	AT5G17680 [Arabidopsis thalian	0.457	0.136	0.352	5.9e-44
TAIR|locus:2118106	1219	AT4G12010 [Arabidopsis thalian	0.431	0.136	0.371	8.2e-40
TAIR|locus:2155347	1372	TTR1 "TOLERANT TO TOBACCO RING	0.311	0.087	0.431	1.8e-39
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.449	0.157	0.364	7.7e-39
TAIR|locus:2158485	1288	RRS1 "RESISTANT TO RALSTONIA S	0.335	0.100	0.397	4.7e-37
TAIR|locus:2122199	1607	AT4G36140 [Arabidopsis thalian	0.363	0.087	0.384	1.8e-35
TAIR|locus:2823395	1004	AT1G63860 [Arabidopsis thalian	0.901	0.345	0.299	3.6e-34
TAIR|locus:2153368	697	AT5G45210 [Arabidopsis thalian	0.488	0.269	0.306	1.6e-33
TAIR|locus:2195478	1031	AT1G63870 [Arabidopsis thalian	0.485	0.181	0.319	2.2e-33

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

 Score = 277 (102.6 bits), Expect = 6.3e-45, Sum P(2) = 6.3e-45
 Identities = 67/200 (33%), Positives = 115/200 (57%)

Query:   174 WRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKV---LV-------WESAISKLQRILH 223
             ++ +AF +  P+   EKLS  V+ YA+G+PLALKV   L+       W+SAI  ++   +
Sbjct:   357 FKQHAFGKEVPNENFEKLSLEVVNYAKGLPLALKVWGSLLHNLRLTEWKSAIEHMKNNSY 416

Query:   224 PSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPL 283
               I++ LKISYD LE K++ +FLD+ACF +GE  D +++   +     E  + +L+DK L
Sbjct:   417 SGIIDKLKISYDGLEPKQQEMFLDIACFLRGEEKDYILQILESCHIGAEYGLRILIDKSL 476

Query:   284 IAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDICLDMSKVIEICLNTSTFT 343
             + I  Y +++M DL+Q++G  IV  +  +PG R +        L ++K +E  ++ +T T
Sbjct:   477 VFISEYNQVQMHDLIQDMGKYIVNFQK-DPGERSR--------LWLAKEVEEVMSNNTGT 527

Query:   344 KMPKLRFLKFYSSSFNGENK 363
                +  ++  YSS+    N+
Sbjct:   528 MAMEAIWVSSYSSTLRFSNQ 547

GO:0005515 "protein binding" evidence=IPI

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

 Score = 296 (109.3 bits), Expect = 5.9e-44, Sum P(2) = 5.9e-44
 Identities = 72/204 (35%), Positives = 118/204 (57%)

Query:   187 GNEKLSSNVMKYAQGVPLALKVL----------VWESAISKLQRILHPSILEVLKISYDS 236
             G E+LS   + YA G+PLAL+VL           WES +++L+   H  I+EVL++SYD 
Sbjct:   366 GFEELSVQAVNYASGLPLALRVLGSFLYRRSQIEWESTLARLKTYPHSDIMEVLRVSYDG 425

Query:   237 LEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRD 296
             L+++EK IFL ++CF+  + VD V K  +  G+  EI I++L +K LI + S   +++ D
Sbjct:   426 LDEQEKAIFLYISCFYNMKQVDYVRKLLDLCGYAAEIGITILTEKSLI-VESNGCVKIHD 484

Query:   297 LLQELGGEIVRKESIN-PGNR---------------KQG-QKIEDICLDMSKVIEICLNT 339
             LL+++G E+VR++++N P  R                 G Q +E I L++S++ E+  + 
Sbjct:   485 LLEQMGRELVRQQAVNNPAQRLLLWDPEDICHLLSENSGTQLVEGISLNLSEISEVFASD 544

Query:   340 STFTKMPKLRFLKFYSSSFNGENK 363
               F  +  L+ L FY  SF+GE +
Sbjct:   545 RAFEGLSNLKLLNFYDLSFDGETR 568

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 250 (93.1 bits), Expect = 8.2e-40, Sum P(2) = 8.2e-40
 Identities = 65/175 (37%), Positives = 99/175 (56%)

Query:     3 ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKG-VYALXXXXXX 61
             E++L++E+     K+L+++  P  N+  LVG+ES ++ +E LL  E    V+ +      
Sbjct:   161 EAKLVDEIAVDTFKKLNDL-APSGNEG-LVGIESRLKNLEKLLSWEDLDTVHIIGIVGMV 218

Query:    62 XXXKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYID 121
                KTT+A  ++ ++ G FDGSCFL N+RE S    GL  L QKL S +L D+++     
Sbjct:   219 GIGKTTLADCLYGRMRGQFDGSCFLTNIRENSG-RSGLESLLQKLFSTVLNDRDLEIGAP 277

Query:   122 LN----F-RRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL 171
              N    F RRL   ++LIV DDV    Q+  LMG   W    SRII+TTR+ +++
Sbjct:   278 GNAHERFERRLKSKRLLIVLDDVNDEKQIRYLMGHCKWYQGGSRIIITTRDSKLI 332

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

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

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

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

TAIR|locus:2155347 TTR1 "TOLERANT TO TOBACCO RINGSPOT NEPOVIRUS 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 258 (95.9 bits), Expect = 1.8e-39, Sum P(3) = 1.8e-39
 Identities = 57/132 (43%), Positives = 85/132 (64%)

Query:   190 KLSSNVMKYAQGVPLALKV----LV-------WESAISKLQRILHPSILEVLKISYDSLE 238
             ++S  V+KYA G PLAL +    L+        E A  KL+       ++ +K SYD+L 
Sbjct:   321 EVSMKVIKYANGHPLALNLYGRELMGKKRPPEMEIAFLKLKECPPAIFVDAIKSSYDTLN 380

Query:   239 DKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLL 298
             D+EKNIFLD+ACFFQGE+VD VM+     GF+P + I VLV+K L+ I S  ++RM +L+
Sbjct:   381 DREKNIFLDIACFFQGENVDYVMQLLEGCGFFPHVGIDVLVEKSLVTI-SENRVRMHNLI 439

Query:   299 QELGGEIVRKES 310
             Q++G +I+ +E+
Sbjct:   440 QDVGRQIINRET 451

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006952 "defense response" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009615 "response to virus" evidence=IMP

GO:0009626 "plant-type hypersensitive response" evidence=IMP

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

 Score = 244 (91.0 bits), Expect = 7.7e-39, Sum P(3) = 7.7e-39
 Identities = 66/181 (36%), Positives = 104/181 (57%)

Query:     3 ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALXXXXXXX 62
             E+  I  +   +L++L+    P  + N LVG+E+ + ++ESLL +ES+GV  +       
Sbjct:   158 EAYKITTISKDVLEKLNAT--PSRDFNDLVGMEAHIAKMESLLCLESQGVRIVGIWGPAG 215

Query:    63 XXKTTIARAIFDKISGDFDGSCFLENVREESQIPG----GLSC-LRQKLLSNLLKDKNV- 116
               KTTIARA++++   +F+ S F+ENVRE     G    GL   L+Q+ LS LL  K++ 
Sbjct:   216 VGKTTIARALYNQYHENFNLSIFMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQKDLR 275

Query:   117 MPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRV 176
             + ++     RL   KVLI+ DDV    QL++L     W    SRI++TT+NKQ+L +  +
Sbjct:   276 VRHLGAIEERLKSQKVLIILDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQLLVSHDI 335

Query:   177 N 177
             N
Sbjct:   336 N 336

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0010193 "response to ozone" evidence=IEP

TAIR|locus:2158485 RRS1 "RESISTANT TO RALSTONIA SOLANACEARUM 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 4.7e-37, Sum P(3) = 4.7e-37
 Identities = 56/141 (39%), Positives = 85/141 (60%)

Query:   189 EKLSSNVMKYAQGVPLAL-----------KVLVWESAISKLQRILHPSILEVLKISYDSL 237
             ++LS  V+ YA G PLA+           K+   E+A  KL+R     I++  K +YD+L
Sbjct:   327 QELSVRVINYANGNPLAISVYGRELKGKKKLSEMETAFLKLKRRPPFKIVDAFKSTYDTL 386

Query:   238 EDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDL 297
              D EKNIFLD+ACFFQGE+V+ V++     GF+P + I VLVDK L+ I S  ++ +  L
Sbjct:   387 SDNEKNIFLDIACFFQGENVNYVIQLLEGCGFFPHVEIDVLVDKCLVTI-SENRVWLHKL 445

Query:   298 LQELGGEIVRKESINPGNRKQ 318
              Q++G EI+  E++    R++
Sbjct:   446 TQDIGREIINGETVQIERRRR 466

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IMP;TAS

GO:0003677 "DNA binding" evidence=IDA

GO:0008219 "cell death" evidence=IMP

TAIR|locus:2122199 AT4G36140 [Arabidopsis thaliana (taxid:3702)]

 Score = 246 (91.7 bits), Expect = 1.8e-35, Sum P(3) = 1.8e-35
 Identities = 58/151 (38%), Positives = 90/151 (59%)

Query:   178 AFKRNHPDVGNEKLSSNVMKYAQGVPLAL----KVLV------WESAISKLQRILHPSIL 227
             AF+R+  +    +LS  V+ YA G PLAL    +VL        E+   KL++     I 
Sbjct:   751 AFRRDINEQNLLELSLKVIDYASGNPLALSFYCRVLKGKELSEMETTFFKLKQRTPYKIF 810

Query:   228 EVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAIC 287
             ++ K SY++L+D EKNIFLD+ACFF GE+VD VM+     GF+P + I VLV+  L+ I 
Sbjct:   811 DLFKSSYETLDDNEKNIFLDIACFFSGENVDYVMRLLEGCGFFPHVGIDVLVENCLVTI- 869

Query:   288 SYKKIRMRDLLQELGGEIVRKESINPGNRKQ 318
             S  +++M  ++Q+ G EI+  E++    R++
Sbjct:   870 SENRVKMHRIIQDFGREIIDGETVQIERRRR 900

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2823395 AT1G63860 [Arabidopsis thaliana (taxid:3702)]

 Score = 382 (139.5 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 117/391 (29%), Positives = 198/391 (50%)

Query:     3 ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALXXXXXXX 62
             E++ I ++   +  +L+    P  + + +VG+E+ + E+ESLL ++  GV  +       
Sbjct:   161 EAKRIEKIARDVSNKLNAT--PCRDFDGMVGLEAHLTEMESLLDLDYDGVKMVGISGPAG 218

Query:    63 XXKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLR--QKLLSNLLKDKNV-MPY 119
               KTTIA+A+  + S  F  +CF++N+R  S +  GL  LR  ++ LSN+L    + + +
Sbjct:   219 IGKTTIAKALQSRFSNRFQLTCFVDNLRG-SYL-SGLDELRLQEQFLSNVLNQDGIRINH 276

Query:   120 IDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN-WRVNA 178
               +   RL  ++VLI+ DDV    QLE+L     W  P SRI++TT NK++L+  W+   
Sbjct:   277 SGVIEERLCKLRVLIILDDVDHIKQLEALANKTTWFGPRSRIVVTTENKELLQQEWK--- 333

Query:   179 FKRNHPDVGNEKLSSNVMKYAQGVPLALKVLV----------WESAISKLQRILHPSILE 228
                ++P  G + L+  V +    +PL L ++           WE  I  L+  +   I E
Sbjct:   334 ---SYPQKGFQWLALRVTQLCGKLPLGLCMVGSSLRGKNEEGWEEVICSLENNIDRDIEE 390

Query:   229 VLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIR-ISVLVDKPLIAIC 287
             VL++ Y+SL+D EK +FL +A FF  ++V  V + F A G     R + +L ++ LI I 
Sbjct:   391 VLRVGYESLDDNEKTLFLHIAIFFNNQYVHLVERLF-ADGDLDFKRALKILENRSLIEIS 449

Query:   288 SYKKIRMRDLLQELGGEIVRKESINPGNRKQGQKIEDIC----------------LDMSK 331
                +I M  LLQ++G + ++K+   P  R+      +IC                 D+S 
Sbjct:   450 FSSRIVMHRLLQQVGKKAIQKQE--PLKRQILMDAREICYVLENDTDTRYVSAILFDISG 507

Query:   332 VIEICLNTSTFTKMPKLRFLKFYSSSFNGEN 362
             + E+ +    F +M  LRFL  Y S  +G +
Sbjct:   508 IDEVYIREGAFRRMSNLRFLTVYKSKDDGND 538

GO:0005622 "intracellular" evidence=IEA

GO:0006952 "defense response" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2153368 AT5G45210 [Arabidopsis thaliana (taxid:3702)]

 Score = 228 (85.3 bits), Expect = 1.6e-33, Sum P(2) = 1.6e-33
 Identities = 66/215 (30%), Positives = 103/215 (47%)

Query:   168 KQVLRNWRVNAFKRNHP-DVGNEKLSSNVMKYAQGVPLAL-----------KVLVWESAI 215
             ++ +R +   AF +  P D     +S  V +YA G P AL           K    E   
Sbjct:   325 EEAVRLFARTAFHKEGPSDAKLMDVSKKVARYAGGNPKALCFYGRELEKKKKPEEMEEEF 384

Query:   216 SKLQRILHPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRI 275
              K+++     IL + + SYD+L D E++IFLD+ACFF GE  D VM+     GF+P + I
Sbjct:   385 EKMRQCPPQEILSLFRSSYDALNDNERSIFLDIACFFNGEPCDDVMRILEGCGFFPHVGI 444

Query:   276 SVLVDKPLIAICSYKKIRMRDLLQELGGEIV-----RKESINPG--------NRKQGQK- 321
               L ++ L+ I   K++ M+  +Q+   E +     R+    P         ++ +G + 
Sbjct:   445 DRLAERSLLTISKEKRVEMQGFIQDAAREFINQTSRRRRHWEPSRIRLLLENDKSKGNEV 504

Query:   322 IEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS 356
             IE I LD +K +   +N   F  M  LR LK YS+
Sbjct:   505 IEGIFLDTTK-LTFDVNPMAFENMYNLRLLKIYST 538

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2195478 AT1G63870 [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 2.2e-33, Sum P(2) = 2.2e-33
 Identities = 69/216 (31%), Positives = 105/216 (48%)

Query:   178 AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL----------VWESAISKLQRIL-HPSI 226
             AF++     G EKL+  V K    +PL L+VL           WE  I +L+ IL H  I
Sbjct:   358 AFRKTTLSHGFEKLARRVTKLCGNLPLGLRVLGSSLRGKNEEEWEEVIRRLETILDHQDI 417

Query:   227 LEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAI 286
              EVL++ Y SL + E+++FL +A FF     D V   F  +    +  + +L DK LI I
Sbjct:   418 EEVLRVGYGSLHENEQSLFLHIAVFFNYTDGDLVKAMFTDNNLDIKHGLKILADKSLINI 477

Query:   287 CSYKKIRMRDLLQELGGEIVRKESINPGNRK---------------QGQK-IEDICLDMS 330
              + ++I +  LLQ+ G + V KE   P   K                G K +  I  D+S
Sbjct:   478 SNNREIVIHKLLQQFGRQAVHKEE--PWKHKILIHAPEICDVLEYATGTKAMSGISFDIS 535

Query:   331 KVIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKI 366
              V E+ ++  +F ++P LRFLK + S  +G ++  I
Sbjct:   536 GVDEVVISGKSFKRIPNLRFLKVFKSRDDGNDRVHI 571

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	385
PLN03210	1153	PLN03210, PLN03210, Resistant to P	2e-57
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-21

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

 Score =  202 bits (514), Expect = 2e-57
 Identities = 132/419 (31%), Positives = 207/419 (49%), Gaps = 61/419 (14%)

Query: 3   ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGG 62
           E+++I E+ N +L +L+    P ++    VG+E  + ++ SLL +ES+ V  +GIWG  G
Sbjct: 160 EAKMIEEIANDVLGKLN--LTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSG 217

Query: 63  IGKTTIARAIFDKISGDFDGSCFLEN--VREESQIPGGLSC--------LRQKLLSNLLK 112
           IGKTTIARA+F ++S  F  S F++   + +  +I    +         L++  LS +L 
Sbjct: 218 IGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILD 277

Query: 113 DKNV-MPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL 171
            K++ + ++     RL H KVLI  DD+     L++L G   W    SRII+ T++K  L
Sbjct: 278 KKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFL 337

Query: 172 RNWRVN--------------------AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-- 209
           R   ++                    AFK+N P  G  +L+S V   A  +PL L VL  
Sbjct: 338 RAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGS 397

Query: 210 --------VWESAISKLQRILHPSILEVLKISYDSLED-KEKNIFLDVACFFQGEHVDPV 260
                    W   + +L+  L   I + L++SYD L + K+K IF  +AC F GE V+ +
Sbjct: 398 YLRGRDKEDWMDMLPRLRNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVNDI 457

Query: 261 MKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQ 320
                 S     I +  LVDK LI +     + M  LLQE+G EIVR +S  PG R+   
Sbjct: 458 KLLLANSDLDVNIGLKNLVDKSLIHV-REDIVEMHSLLQEMGKEIVRAQSNEPGEREFLV 516

Query: 321 KIEDIC----------------LDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNGENK 363
             +DIC                LD+ ++ E+ ++ + F  M  L FLKFY+  ++ + +
Sbjct: 517 DAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFLKFYTKKWDQKKE 575

syringae 6; Provisional. Length = 1153

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

 Score = 92.8 bits (231), Expect = 2e-21
 Identities = 68/291 (23%), Positives = 118/291 (40%), Gaps = 55/291 (18%)

Query: 34  VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK--ISGDFDGSCFLENVRE 91
            E  +E +   L   S  +  +GI G+GG+GKTT+A+ I++   + G FD   ++   + 
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 92  --ESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLM 149
             E ++   +      L  +   +KN           L   + L+V DDV   +  + + 
Sbjct: 61  YTEFRLQKDI-LQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIG 119

Query: 150 GSLDWLTPVSRIILTTRNKQVL------------------RNWRV---NAFKRNHP---- 184
                    SR+I+TTR++ V                    +W +     F++  P    
Sbjct: 120 VPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPE 179

Query: 185 --DVGNEKLSSNVMKYAQGVPLALKVL-----------VWESAISKLQRILHP-----SI 226
             +V  E     +++  +G+PLALKVL            WE  + +L   L        +
Sbjct: 180 LEEVAKE-----IVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNEV 234

Query: 227 LEVLKISYDSLEDKEKNIFLDVACFFQGE--HVDPVMKFFNASGFYPEIRI 275
           L +L +SYD+L    K  FL +A F +      + ++K + A GF     I
Sbjct: 235 LSILSLSYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIAEGFVIPSDI 285

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	385
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PRK04841	903	transcriptional regulator MalT; Provisional	99.65
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.43
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.39
COG3899	849	Predicted ATPase [General function prediction only	99.35
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.31
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.3
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.3
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.1
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.09
COG3903	414	Predicted ATPase [General function prediction only	98.96
PF05729	166	NACHT: NACHT domain	98.95
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.86
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.83
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.79
PF13173	128	AAA_14: AAA domain	98.74
PTZ00202	550	tuzin; Provisional	98.7
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.69
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.68
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.62
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.58
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.58
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.56
PRK13342	413	recombination factor protein RarA; Reviewed	98.54
PLN03025	319	replication factor C subunit; Provisional	98.51
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.47
PRK06893	229	DNA replication initiation factor; Validated	98.46
PRK12402	337	replication factor C small subunit 2; Reviewed	98.43
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.4
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.4
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.38
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.38
PRK09376	416	rho transcription termination factor Rho; Provisio	98.36
PRK04195	482	replication factor C large subunit; Provisional	98.34
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.34
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.33
KOG2028	554	consensus ATPase related to the helicase subunit o	98.32
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.31
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.3
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.29
cd01128	249	rho_factor Transcription termination factor rho is	98.28
PF00004	132	AAA: ATPase family associated with various cellula	98.28
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.28
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.27
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.27
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.27
PRK08116	268	hypothetical protein; Validated	98.26
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.24
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.23
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.23
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.22
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.22
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.22
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.22
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.19
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.18
PRK08727	233	hypothetical protein; Validated	98.18
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.17
PF14516	331	AAA_35: AAA-like domain	98.17
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.17
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.16
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.16
CHL00095	821	clpC Clp protease ATP binding subunit	98.16
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.15
PRK13341	725	recombination factor protein RarA/unknown domain f	98.15
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.15
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.14
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.13
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.12
PRK10865	857	protein disaggregation chaperone; Provisional	98.11
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.11
TIGR00767	415	rho transcription termination factor Rho. Members	98.1
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.1
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.09
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.08
PHA02544	316	44 clamp loader, small subunit; Provisional	98.08
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.08
PRK08084	235	DNA replication initiation factor; Provisional	98.06
PRK05642	234	DNA replication initiation factor; Validated	98.04
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.02
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.0
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.99
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.99
PRK12377	248	putative replication protein; Provisional	97.98
PRK08181	269	transposase; Validated	97.98
smart00382	148	AAA ATPases associated with a variety of cellular	97.97
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.96
PRK07952	244	DNA replication protein DnaC; Validated	97.96
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.92
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.91
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.9
PRK10536	262	hypothetical protein; Provisional	97.9
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.9
PRK06921	266	hypothetical protein; Provisional	97.9
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.9
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.89
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.89
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.89
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.87
PRK09183	259	transposase/IS protein; Provisional	97.87
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.86
PRK06526	254	transposase; Provisional	97.83
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.83
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.82
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.8
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.79
CHL00181	287	cbbX CbbX; Provisional	97.78
PRK06835	329	DNA replication protein DnaC; Validated	97.78
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.76
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.76
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.75
PRK12608	380	transcription termination factor Rho; Provisional	97.75
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.75
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.75
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.74
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.74
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.74
PRK08939	306	primosomal protein DnaI; Reviewed	97.73
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.73
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.73
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.73
PRK09087	226	hypothetical protein; Validated	97.72
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.71
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.71
CHL00095	821	clpC Clp protease ATP binding subunit	97.71
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.71
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.7
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.7
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.7
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.69
PRK12422	445	chromosomal replication initiation protein; Provis	97.69
PRK10865	857	protein disaggregation chaperone; Provisional	97.68
CHL00176	638	ftsH cell division protein; Validated	97.67
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.66
PRK08118	167	topology modulation protein; Reviewed	97.66
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.66
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.65
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.64
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.64
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.63
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.63
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.62
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.61
PRK06620	214	hypothetical protein; Validated	97.61
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.61
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.61
PHA00729	226	NTP-binding motif containing protein	97.6
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.58
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.56
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.55
PRK14974	336	cell division protein FtsY; Provisional	97.54
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.53
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.5
PRK06696	223	uridine kinase; Validated	97.49
PRK04296	190	thymidine kinase; Provisional	97.49
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.48
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.47
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.47
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.46
PRK07261	171	topology modulation protein; Provisional	97.45
PRK07667	193	uridine kinase; Provisional	97.45
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.45
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.44
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.44
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.42
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	97.41
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.41
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.4
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.4
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.38
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.37
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.36
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.36
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.35
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.31
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.28
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.28
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.28
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.28
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.26
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.26
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.24
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.24
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.24
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.23
PRK05541	176	adenylylsulfate kinase; Provisional	97.22
PRK06762	166	hypothetical protein; Provisional	97.21
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.2
PRK13695	174	putative NTPase; Provisional	97.2
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.19
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.19
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.18
PRK10867	433	signal recognition particle protein; Provisional	97.18
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	97.14
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.13
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	97.13
CHL00195	489	ycf46 Ycf46; Provisional	97.1
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.1
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.08
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	97.07
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.06
TIGR00959	428	ffh signal recognition particle protein. This mode	97.05
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	97.05
PRK06067	234	flagellar accessory protein FlaH; Validated	97.04
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.04
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.03
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.02
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	97.02
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	97.01
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.01
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.01
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.0
PTZ00301	210	uridine kinase; Provisional	96.98
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.96
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.96
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.96
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.93
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.93
PRK15455	644	PrkA family serine protein kinase; Provisional	96.93
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.92
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.91
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.91
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.89
PRK13531	498	regulatory ATPase RavA; Provisional	96.88
PRK06547	172	hypothetical protein; Provisional	96.88
PRK08233	182	hypothetical protein; Provisional	96.88
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.87
PRK05480	209	uridine/cytidine kinase; Provisional	96.87
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.87
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.86
PRK04040	188	adenylate kinase; Provisional	96.86
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.86
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.86
PRK11823	446	DNA repair protein RadA; Provisional	96.85
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.84
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.83
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	96.83
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.82
PRK06217	183	hypothetical protein; Validated	96.81
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.81
PRK03839	180	putative kinase; Provisional	96.8
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	96.8
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.8
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.78
PRK05439	311	pantothenate kinase; Provisional	96.78
PF07726	131	AAA_3: ATPase family associated with various cellu	96.76
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.75
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.75
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.75
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.75
KOG0736	953	consensus Peroxisome assembly factor 2 containing	96.75
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.75
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.75
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.74
PRK00625	173	shikimate kinase; Provisional	96.74
PRK14528	186	adenylate kinase; Provisional	96.74
PRK00131	175	aroK shikimate kinase; Reviewed	96.73
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.73
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.72
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.72
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.71
PRK00889	175	adenylylsulfate kinase; Provisional	96.7
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.69
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.68
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.68
PRK09354	349	recA recombinase A; Provisional	96.67
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	96.67
PRK13765	637	ATP-dependent protease Lon; Provisional	96.67
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.66
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.66
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	96.64
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.63
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.63
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.63
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.62
PRK03846	198	adenylylsulfate kinase; Provisional	96.62
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.61
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.61
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.6
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	96.6
PRK10416	318	signal recognition particle-docking protein FtsY;	96.59
PRK05917	290	DNA polymerase III subunit delta'; Validated	96.58
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.58
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.56
PRK13947	171	shikimate kinase; Provisional	96.56
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.56
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.55
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.55
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.54
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.53
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	96.52
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.51
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.51
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	96.5
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.49
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.49
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	96.48
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.47
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.47
cd03246	173	ABCC_Protease_Secretion This family represents the	96.47
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.46
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.46
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.46
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.45
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.45
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.44
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.43
PRK12678	672	transcription termination factor Rho; Provisional	96.43
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.43
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	96.41
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.4
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	96.4
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	96.39
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.37
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.36
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.36
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.36
PRK14738	206	gmk guanylate kinase; Provisional	96.35
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.35
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.35
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	96.34
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	96.34
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.34
PRK04132	846	replication factor C small subunit; Provisional	96.34
PTZ00088	229	adenylate kinase 1; Provisional	96.34
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.33
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.33
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	96.32
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	96.32
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.32
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.31
PRK15453	290	phosphoribulokinase; Provisional	96.31
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.31
PRK13949	169	shikimate kinase; Provisional	96.31
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.31
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.3
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.29
PRK13948	182	shikimate kinase; Provisional	96.29
PRK08506	472	replicative DNA helicase; Provisional	96.29
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	96.29
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.28
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.27
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	96.27
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.27
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	96.27
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.26
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.26
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	96.26
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.25
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.25
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.25
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.25
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	96.24
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.24
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	96.23
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	96.22
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	96.22
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	96.22
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.21
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	96.21
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	96.2
PLN02924	220	thymidylate kinase	96.18
PRK09435	332	membrane ATPase/protein kinase; Provisional	96.18
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	96.18
COG0714	329	MoxR-like ATPases [General function prediction onl	96.17
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.16
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.16
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.16
PRK13975	196	thymidylate kinase; Provisional	96.16
PHA02244	383	ATPase-like protein	96.16
PRK13946	184	shikimate kinase; Provisional	96.15
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.14
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.14
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	96.13
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	96.12
PRK14530	215	adenylate kinase; Provisional	96.11
PTZ00494	664	tuzin-like protein; Provisional	96.1
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	96.1
PTZ00035	337	Rad51 protein; Provisional	96.1
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	96.1
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	96.1
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.1
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	96.09
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.09
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	96.08
PRK14529	223	adenylate kinase; Provisional	96.07
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.07
PRK13768	253	GTPase; Provisional	96.07
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	96.07
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	96.07
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	96.06
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.06
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	96.05
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	96.05
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	96.05
PRK05973	237	replicative DNA helicase; Provisional	96.04
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	96.03
PLN02674	244	adenylate kinase	96.03
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.03
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	96.01
PRK05057	172	aroK shikimate kinase I; Reviewed	96.01
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.0
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.0
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.0
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.98
) 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	95.97
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.96
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	95.96
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	95.96
PRK14527	191	adenylate kinase; Provisional	95.95
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	95.95
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.95
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.95
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	95.95
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.94
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	95.94
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	95.93
PRK14737	186	gmk guanylate kinase; Provisional	95.93
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.9
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	95.9
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.9
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.88
TIGR01287	275	nifH nitrogenase iron protein. This model describe	95.88
PRK04182	180	cytidylate kinase; Provisional	95.88
PLN02200	234	adenylate kinase family protein	95.88
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	95.87
KOG4252	246	consensus GTP-binding protein [Signal transduction	95.87
PRK03731	171	aroL shikimate kinase II; Reviewed	95.87
PF13245	76	AAA_19: Part of AAA domain	95.86
COG0488	530	Uup ATPase components of ABC transporters with dup	95.86
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.86
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.86
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.86
PRK06761	282	hypothetical protein; Provisional	95.86
PRK00300	205	gmk guanylate kinase; Provisional	95.86
cd03116	159	MobB Molybdenum is an essential trace element in t	95.85
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.85
PRK08149	428	ATP synthase SpaL; Validated	95.84
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.84
CHL00206	2281	ycf2 Ycf2; Provisional	95.84
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	95.84
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.83
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	95.83
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	95.82
PLN02348	395	phosphoribulokinase	95.81
PRK04328	249	hypothetical protein; Provisional	95.8
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.8
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	95.8
PRK13230	279	nitrogenase reductase-like protein; Reviewed	95.79
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.78
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	95.77
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	95.77
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	95.77
COG2074	299	2-phosphoglycerate kinase [Carbohydrate transport	95.76
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	95.76
cd02117	212	NifH_like This family contains the NifH (iron prot	95.76
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	95.76
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.75
COG4133	209	CcmA ABC-type transport system involved in cytochr	95.74
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	95.73
cd02034	116	CooC The accessory protein CooC, which contains a	95.73
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.72
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.72
PRK04220	301	2-phosphoglycerate kinase; Provisional	95.71
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.7
PLN02318	656	phosphoribulokinase/uridine kinase	95.7
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.69
PRK14532	188	adenylate kinase; Provisional	95.69
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	95.69
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.68
PRK10436	462	hypothetical protein; Provisional	95.68
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.67
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.66
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.66
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	95.66
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	95.65
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	95.64
PRK14531	183	adenylate kinase; Provisional	95.64
PRK12338	319	hypothetical protein; Provisional	95.63
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	95.63
cd03114	148	ArgK-like The function of this protein family is u	95.63
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	95.62
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	95.61
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.61
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.6
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.6
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.6
PHA02530	300	pseT polynucleotide kinase; Provisional	95.6
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.59
cd02040	270	NifH NifH gene encodes component II (iron protein)	95.56
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.56
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	95.56
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	95.55
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	95.55
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	95.55
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.55
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.54

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.9e-57  Score=459.46  Aligned_cols=342  Identities=26%  Similarity=0.363  Sum_probs=285.6

Q ss_pred             cccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH---hhCCCCceEEEeeccccccCCCChHHHHHHHHH
Q 044214           32 VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK---ISGDFDGSCFLENVREESQIPGGLSCLRQKLLS  108 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~---~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~  108 (385)
                      ||.+..++++.+.|..++  ..+++|+||||+||||||++++++   ++.+|+.++|+.    +|+. ++...++.+|+.
T Consensus       161 VG~e~~~~kl~~~L~~d~--~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~----VSk~-f~~~~iq~~Il~  233 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLMEDD--VGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVV----VSKE-FTTRKIQQTILE  233 (889)
T ss_pred             ccHHHHHHHHHHHhccCC--CCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEE----Eccc-ccHHhHHHHHHH
Confidence            999999999999999543  389999999999999999999983   678999999999    6666 999999999999


Q ss_pred             HHhCCCC---C---CchHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHhh-ccc-----
Q 044214          109 NLLKDKN---V---MPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN-WRV-----  176 (385)
Q Consensus       109 ~l~~~~~---~---~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~-~~~-----  176 (385)
                      .++....   +   .+.+..+.+.|++||++|||||||+..+|+.+..+++....||+|++|||+..|+.. +++     
T Consensus       234 ~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~  313 (889)
T KOG4658|consen  234 RLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIE  313 (889)
T ss_pred             HhccCCcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCcccc
Confidence            8877444   1   177888999999999999999999999999999999988889999999999999988 554     


Q ss_pred             ---------------eecccC-CCCCCchHHHHHHHHHhCCCccchhHH-----------hHHHHHHHhhhc-------c
Q 044214          177 ---------------NAFKRN-HPDVGNEKLSSNVMKYAQGVPLALKVL-----------VWESAISKLQRI-------L  222 (385)
Q Consensus       177 ---------------~~~~~~-~~~~~~~~~~~~i~~~~~GlPLal~~~-----------~w~~~l~~l~~~-------~  222 (385)
                                     .+|... ...+..+++|++++++|+|+|||+.++           +|+.+.+.+...       .
T Consensus       314 v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~  393 (889)
T KOG4658|consen  314 VECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGM  393 (889)
T ss_pred             ccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCch
Confidence                           333332 222347999999999999999999999           799999988664       1


Q ss_pred             CcccchhhhhccccCchhhhhhhhhccccCCC--ccHHHHHHHHHHcCCc------------hhhhHHHhhcCCceeEec
Q 044214          223 HPSILEVLKISYDSLEDKEKNIFLDVACFFQG--EHVDPVMKFFNASGFY------------PEIRISVLVDKPLIAICS  288 (385)
Q Consensus       223 ~~~~~~~l~~sy~~L~~~~k~~~~~la~fp~~--~~~~~l~~~~~~~g~~------------~~~~l~~L~~~sLi~~~~  288 (385)
                      .+.+..++..||+.||++.|.||+|||.||++  ++.+.|+.+|+++|++            +..++.+|++++|+....
T Consensus       394 ~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~  473 (889)
T KOG4658|consen  394 EESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEER  473 (889)
T ss_pred             hhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcc
Confidence            25688999999999999999999999999999  7899999999999976            345799999999999764


Q ss_pred             C----CcEEeCHHHHHHHHHHHh-----hcc--CCCCCccc-----------------------------cCCeeEEEee
Q 044214          289 Y----KKIRMRDLLQELGGEIVR-----KES--INPGNRKQ-----------------------------GQKIEDICLD  328 (385)
Q Consensus       289 ~----~~~~mH~lv~~~a~~~~~-----~e~--~~~~~~~~-----------------------------~~~~r~l~l~  328 (385)
                      .    ..|.|||+||++|..++.     +++  ...+...+                             ..+++++.+.
T Consensus       474 ~~~~~~~~kmHDvvRe~al~ias~~~~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~~~~~~~~~~~~L~tLll~  553 (889)
T KOG4658|consen  474 DEGRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKIEHIAGSSENPKLRTLLLQ  553 (889)
T ss_pred             cccceeEEEeeHHHHHHHHHHhccccccccceEEECCcCccccccccchhheeEEEEeccchhhccCCCCCCccceEEEe
Confidence            2    469999999999999999     443  11110000                             2234444444


Q ss_pred             cCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          329 MSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ........++..+|.+|+.||||||++|    +||.+|+  .|||||++++|.++.||
T Consensus       554 ~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP  611 (889)
T KOG4658|consen  554 RNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLP  611 (889)
T ss_pred             ecchhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccc
Confidence            3321134567778999999999999977    8999999  99999999999999999

>PLN03210 Resistant to P

Probab=100.00  E-value=1.4e-53  Score=454.34  Aligned_cols=381  Identities=35%  Similarity=0.570  Sum_probs=325.2

Q ss_pred             CcHhHHHHHHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214            1 KRESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus         1 ~~e~~~i~~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ++|+++|++|+++|++++..  +++...+.+|||+++++++..+|..+.+++++|+|+||||+||||||+++|+++..+|
T Consensus       158 ~~E~~~i~~Iv~~v~~~l~~--~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F  235 (1153)
T PLN03210        158 PNEAKMIEEIANDVLGKLNL--TPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSRQF  235 (1153)
T ss_pred             CCHHHHHHHHHHHHHHhhcc--ccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhhcC
Confidence            36999999999999999998  8888889999999999999999987777899999999999999999999999999999


Q ss_pred             CceEEEeec--ccc---cc-----CCCChHHHHHHHHHHHhCCCC-CCchHHHHHHHhCCceEEEEEeCCCChhhhhHhh
Q 044214           81 DGSCFLENV--REE---SQ-----IPGGLSCLRQKLLSNLLKDKN-VMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLM  149 (385)
Q Consensus        81 ~~~~w~~~~--~~~---~~-----~~~~~~~l~~~ll~~l~~~~~-~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~  149 (385)
                      ++.+|+...  ...   ..     .......++.+++..+..... .......+++.+.++|+||||||||+..+|+.+.
T Consensus       236 ~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~  315 (1153)
T PLN03210        236 QSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALA  315 (1153)
T ss_pred             CeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCHHHHHHHH
Confidence            999888531  110   00     001123455666666654432 2233467888999999999999999999999998


Q ss_pred             ccCCCCCCCcEEEEEeccHHHHhhccc--------------------eecccCCCCCCchHHHHHHHHHhCCCccchhHH
Q 044214          150 GSLDWLTPVSRIILTTRNKQVLRNWRV--------------------NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL  209 (385)
Q Consensus       150 ~~~~~~~~gs~ilvTtR~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~i~~~~~GlPLal~~~  209 (385)
                      ....+.++|++||||||++.++..+++                    ++|....+++.+.+++++|+++|+|+||||+++
T Consensus       316 ~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vl  395 (1153)
T PLN03210        316 GQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVL  395 (1153)
T ss_pred             hhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            877788899999999999998865432                    667666666678899999999999999999998


Q ss_pred             ----------hHHHHHHHhhhccCcccchhhhhccccCch-hhhhhhhhccccCCCccHHHHHHHHHHcCCchhhhHHHh
Q 044214          210 ----------VWESAISKLQRILHPSILEVLKISYDSLED-KEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVL  278 (385)
Q Consensus       210 ----------~w~~~l~~l~~~~~~~~~~~l~~sy~~L~~-~~k~~~~~la~fp~~~~~~~l~~~~~~~g~~~~~~l~~L  278 (385)
                                +|+..+++++.....++..++++||+.|++ .+|.||+++|+|+.+.+.+.+..++...++.++..++.|
T Consensus       396 gs~L~~k~~~~W~~~l~~L~~~~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~~v~~~l~~~~~~~~~~l~~L  475 (1153)
T PLN03210        396 GSYLRGRDKEDWMDMLPRLRNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVNDIKLLLANSDLDVNIGLKNL  475 (1153)
T ss_pred             HHHHcCCCHHHHHHHHHHHHhCccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHHHHHHHHHhcCCCchhChHHH
Confidence                      899999999988788899999999999987 599999999999999888888888888888888889999


Q ss_pred             hcCCceeEecCCcEEeCHHHHHHHHHHHhhccCCCCCccc----------------cCCeeEEEeecCCceeeeeCcccc
Q 044214          279 VDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQ----------------GQKIEDICLDMSKVIEICLNTSTF  342 (385)
Q Consensus       279 ~~~sLi~~~~~~~~~mH~lv~~~a~~~~~~e~~~~~~~~~----------------~~~~r~l~l~~~~~~~~~~~~~~~  342 (385)
                      +++|||+.. .+++.|||++|++|+++++++..++++++|                +.++++|+++.+......+....|
T Consensus       476 ~~ksLi~~~-~~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF  554 (1153)
T PLN03210        476 VDKSLIHVR-EDIVEMHSLLQEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAF  554 (1153)
T ss_pred             HhcCCEEEc-CCeEEhhhHHHHHHHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHH
Confidence            999999987 678999999999999999998777888876                567899999999887888999999


Q ss_pred             CCCCCCcEEEecCc----------ccCCCCC---CCeeEEEcCCCCCCCCC-CCCC
Q 044214          343 TKMPKLRFLKFYSS----------SFNGENK---CKISYLQDPGFAGVKLN-NFGI  384 (385)
Q Consensus       343 ~~~~~LrvL~l~~~----------~lp~~i~---~~LryL~l~~~~~~~lP-~~~~  384 (385)
                      .+|++|++|.+.+.          .+|+++.   .+||+|+|.+++++.+| +|.+
T Consensus       555 ~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f~~  610 (1153)
T PLN03210        555 KGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLRCMPSNFRP  610 (1153)
T ss_pred             hcCccccEEEEecccccccccceeecCcchhhcCcccEEEEecCCCCCCCCCcCCc
Confidence            99999999999642          5888887   68999999999999999 6654

syringae 6; Provisional

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

Probab=100.00  E-value=8.3e-39  Score=293.94  Aligned_cols=234  Identities=30%  Similarity=0.450  Sum_probs=184.4

Q ss_pred             cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH--hhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           34 VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK--ISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        34 R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~--~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      ||.++++|.+.|...+++.++|+|+||||+||||||.+++++  ++.+|+.++|+.    .+.. .+...++..++..+.
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~----~~~~-~~~~~~~~~i~~~l~   75 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVS----LSKN-PSLEQLLEQILRQLG   75 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEE----EES--SCCHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccc----cccc-ccccccccccccccc
Confidence            789999999999975588999999999999999999999987  889999999998    3333 666889999999998


Q ss_pred             CCCCC-----C--chHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHhhccc--------
Q 044214          112 KDKNV-----M--PYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRV--------  176 (385)
Q Consensus       112 ~~~~~-----~--~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~~--------  176 (385)
                      ....+     .  +....+.+.|+++++||||||||+...|+.+...++....|++||||||+..++.....        
T Consensus        76 ~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~  155 (287)
T PF00931_consen   76 EPDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELE  155 (287)
T ss_dssp             CC-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECS
T ss_pred             ccccccccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccc
Confidence            77321     1  77889999999999999999999999998888777766779999999999987765441        


Q ss_pred             -------------eecccC-CCCCCchHHHHHHHHHhCCCccchhHH-----------hHHHHHHHhhhcc------Ccc
Q 044214          177 -------------NAFKRN-HPDVGNEKLSSNVMKYAQGVPLALKVL-----------VWESAISKLQRIL------HPS  225 (385)
Q Consensus       177 -------------~~~~~~-~~~~~~~~~~~~i~~~~~GlPLal~~~-----------~w~~~l~~l~~~~------~~~  225 (385)
                                   .++... ......++.+++|++.|+|+||||+++           +|...++.+....      ...
T Consensus       156 ~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~  235 (287)
T PF00931_consen  156 PLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRS  235 (287)
T ss_dssp             S--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence                         212222 223456788999999999999999998           7988888866543      356


Q ss_pred             cchhhhhccccCchhhhhhhhhccccCCC--ccHHHHHHHHHHcCCchh
Q 044214          226 ILEVLKISYDSLEDKEKNIFLDVACFFQG--EHVDPVMKFFNASGFYPE  272 (385)
Q Consensus       226 ~~~~l~~sy~~L~~~~k~~~~~la~fp~~--~~~~~l~~~~~~~g~~~~  272 (385)
                      +..++..||+.|+++.|.||.+||+||.+  ++.+.++++|.++|++..
T Consensus       236 ~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~  284 (287)
T PF00931_consen  236 VFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISS  284 (287)
T ss_dssp             HHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC-
T ss_pred             ccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCcc
Confidence            89999999999999999999999999988  789999999999998754

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.65  E-value=9e-15  Score=155.07  Aligned_cols=267  Identities=14%  Similarity=0.143  Sum_probs=168.7

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      .||..++.+|-|+..++.|..     ....+++.|+|++|.||||++.++.++    ++.++|++ .....   .+...+
T Consensus         8 ~~p~~~~~~~~R~rl~~~l~~-----~~~~~~~~v~apaG~GKTtl~~~~~~~----~~~~~w~~-l~~~d---~~~~~f   74 (903)
T PRK04841          8 SRPVRLHNTVVRERLLAKLSG-----ANNYRLVLVTSPAGYGKTTLISQWAAG----KNNLGWYS-LDESD---NQPERF   74 (903)
T ss_pred             CCCCCccccCcchHHHHHHhc-----ccCCCeEEEECCCCCCHHHHHHHHHHh----CCCeEEEe-cCccc---CCHHHH
Confidence            567788899999977777653     335679999999999999999998864    23688997 43221   445566


Q ss_pred             HHHHHHHHhCCCCC--------------C---chHHHHHHHhC--CceEEEEEeCCCCh---h---hhhHhhccCCCCCC
Q 044214          103 RQKLLSNLLKDKNV--------------M---PYIDLNFRRLG--HMKVLIVFDDVTCF---S---QLESLMGSLDWLTP  157 (385)
Q Consensus       103 ~~~ll~~l~~~~~~--------------~---~~~~~l~~~l~--~k~~LlVlDdv~~~---~---~~~~l~~~~~~~~~  157 (385)
                      +..++..+......              .   .....+...+.  +.+++|||||+...   .   .+..+....   .+
T Consensus        75 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~---~~  151 (903)
T PRK04841         75 ASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQ---PE  151 (903)
T ss_pred             HHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhC---CC
Confidence            66666666421110              0   11222333332  68999999999532   1   233333332   35


Q ss_pred             CcEEEEEeccHHHH--hhc---------cce--ecc---------cCCCCCCchHHHHHHHHHhCCCccchhHH--hHHH
Q 044214          158 VSRIILTTRNKQVL--RNW---------RVN--AFK---------RNHPDVGNEKLSSNVMKYAQGVPLALKVL--VWES  213 (385)
Q Consensus       158 gs~ilvTtR~~~~~--~~~---------~~~--~~~---------~~~~~~~~~~~~~~i~~~~~GlPLal~~~--~w~~  213 (385)
                      +.++|||||...-.  ...         +..  .|.         .........+.+.++++.|+|+|+++..+  .+..
T Consensus       152 ~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~  231 (903)
T PRK04841        152 NLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIEAAESSRLCDDVEGWATALQLIALSARQ  231 (903)
T ss_pred             CeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCCHHHHHHHHHHhCChHHHHHHHHHHHhh
Confidence            67888999974211  010         000  121         11222234567889999999999999876  2111


Q ss_pred             H-------HHHhhhccCcccchhhhhc-cccCchhhhhhhhhccccCCCccHHHHHHHHHHcCCchhhhHHHhhcCCcee
Q 044214          214 A-------ISKLQRILHPSILEVLKIS-YDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIA  285 (385)
Q Consensus       214 ~-------l~~l~~~~~~~~~~~l~~s-y~~L~~~~k~~~~~la~fp~~~~~~~l~~~~~~~g~~~~~~l~~L~~~sLi~  285 (385)
                      .       ...+.......+...+.-. ++.||++.+.++...|+++ .++.+.+..+...  -.....+++|.+.+++.
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~-~~~~~l~~~l~~~--~~~~~~L~~l~~~~l~~  308 (903)
T PRK04841        232 NNSSLHDSARRLAGINASHLSDYLVEEVLDNVDLETRHFLLRCSVLR-SMNDALIVRVTGE--ENGQMRLEELERQGLFI  308 (903)
T ss_pred             CCCchhhhhHhhcCCCchhHHHHHHHHHHhcCCHHHHHHHHHhcccc-cCCHHHHHHHcCC--CcHHHHHHHHHHCCCee
Confidence            0       0111111123455554433 8999999999999999986 6776665555432  23567899999999965


Q ss_pred             E-ec-C-CcEEeCHHHHHHHHHHHhh
Q 044214          286 I-CS-Y-KKIRMRDLLQELGGEIVRK  308 (385)
Q Consensus       286 ~-~~-~-~~~~mH~lv~~~a~~~~~~  308 (385)
                      . .+ + .+|+.|+++++++++....
T Consensus       309 ~~~~~~~~~yr~H~L~r~~l~~~l~~  334 (903)
T PRK04841        309 QRMDDSGEWFRYHPLFASFLRHRCQW  334 (903)
T ss_pred             EeecCCCCEEehhHHHHHHHHHHHHh
Confidence            3 32 2 3699999999999987643

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.43  E-value=5.9e-12  Score=124.47  Aligned_cols=270  Identities=13%  Similarity=0.134  Sum_probs=170.0

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      .+|..+...|-|...++.|..     ..+.+.+.|..++|.|||||+.+... ....-..+.|++.-.+.    .+...+
T Consensus        13 ~~P~~~~~~v~R~rL~~~L~~-----~~~~RL~li~APAGfGKttl~aq~~~-~~~~~~~v~Wlslde~d----ndp~rF   82 (894)
T COG2909          13 VRPVRPDNYVVRPRLLDRLRR-----ANDYRLILISAPAGFGKTTLLAQWRE-LAADGAAVAWLSLDESD----NDPARF   82 (894)
T ss_pred             CCCCCcccccccHHHHHHHhc-----CCCceEEEEeCCCCCcHHHHHHHHHH-hcCcccceeEeecCCcc----CCHHHH
Confidence            567778888989877776654     44678999999999999999999988 44455678999833222    667777


Q ss_pred             HHHHHHHHhCCCCCC-----------------chHHHHHHHhC--CceEEEEEeCCC---Ch---hhhhHhhccCCCCCC
Q 044214          103 RQKLLSNLLKDKNVM-----------------PYIDLNFRRLG--HMKVLIVFDDVT---CF---SQLESLMGSLDWLTP  157 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~-----------------~~~~~l~~~l~--~k~~LlVlDdv~---~~---~~~~~l~~~~~~~~~  157 (385)
                      ...++..+....+..                 .....+..-+.  .+++.+||||..   +.   ..++.+....|   +
T Consensus        83 ~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P---~  159 (894)
T COG2909          83 LSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAP---E  159 (894)
T ss_pred             HHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCC---C
Confidence            788877776443321                 22333333333  478999999984   22   23455554443   6


Q ss_pred             CcEEEEEeccHHHHhhccc---------------------eec-ccCCCCCCchHHHHHHHHHhCCCccchhHH-hHH--
Q 044214          158 VSRIILTTRNKQVLRNWRV---------------------NAF-KRNHPDVGNEKLSSNVMKYAQGVPLALKVL-VWE--  212 (385)
Q Consensus       158 gs~ilvTtR~~~~~~~~~~---------------------~~~-~~~~~~~~~~~~~~~i~~~~~GlPLal~~~-~w~--  212 (385)
                      +-.+++|||+..-......                     ..| ......+....-++.+.+.++|.+-|+.++ -|-  
T Consensus       160 ~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld~~~~~~L~~~teGW~~al~L~aLa~~~  239 (894)
T COG2909         160 NLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLDAADLKALYDRTEGWAAALQLIALALRN  239 (894)
T ss_pred             CeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCChHHHHHHHhhcccHHHHHHHHHHHccC
Confidence            7889999998633222111                     111 122223344555677777777777777765 111  


Q ss_pred             -----HHHHHhhhccCcccc-hhhhhccccCchhhhhhhhhccccCCCccHHHHHHHHHHcCCchhhhHHHhhcCCceeE
Q 044214          213 -----SAISKLQRILHPSIL-EVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAI  286 (385)
Q Consensus       213 -----~~l~~l~~~~~~~~~-~~l~~sy~~L~~~~k~~~~~la~fp~~~~~~~l~~~~~~~g~~~~~~l~~L~~~sLi~~  286 (385)
                           .....+... .+.+. -...--++.||++.|..+..+|+++. +.-+...++...+  .....+++|.+++|+-.
T Consensus       240 ~~~~~q~~~~LsG~-~~~l~dYL~eeVld~Lp~~l~~FLl~~svl~~-f~~eL~~~Ltg~~--ng~amLe~L~~~gLFl~  315 (894)
T COG2909         240 NTSAEQSLRGLSGA-ASHLSDYLVEEVLDRLPPELRDFLLQTSVLSR-FNDELCNALTGEE--NGQAMLEELERRGLFLQ  315 (894)
T ss_pred             CCcHHHHhhhccch-HHHHHHHHHHHHHhcCCHHHHHHHHHHHhHHH-hhHHHHHHHhcCC--cHHHHHHHHHhCCCcee
Confidence                 111111100 01121 22334578999999999999999954 3333333332221  24456999999999773


Q ss_pred             --ec-CCcEEeCHHHHHHHHHHHhhc
Q 044214          287 --CS-YKKIRMRDLLQELGGEIVRKE  309 (385)
Q Consensus       287 --~~-~~~~~mH~lv~~~a~~~~~~e  309 (385)
                        ++ .+.|+.|.+..+|.+.....+
T Consensus       316 ~Ldd~~~WfryH~LFaeFL~~r~~~~  341 (894)
T COG2909         316 RLDDEGQWFRYHHLFAEFLRQRLQRE  341 (894)
T ss_pred             eecCCCceeehhHHHHHHHHhhhccc
Confidence              22 567999999999999877664

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.39  E-value=2.9e-11  Score=116.18  Aligned_cols=259  Identities=16%  Similarity=0.163  Sum_probs=144.2

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCC--CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC--ceEEEeeccccccCCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVE--SKGVYALGIWGIGGIGKTTIARAIFDKISGDFD--GSCFLENVREESQIPGG   98 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~--~~~w~~~~~~~~~~~~~   98 (385)
                      .+...|+.|+||++++++|...+...  ......+.|+|++|+|||++++.+++++.....  ..+++. ....    .+
T Consensus        24 ~~~~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in-~~~~----~~   98 (394)
T PRK00411         24 EPDYVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYIN-CQID----RT   98 (394)
T ss_pred             CCCCcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEE-CCcC----CC
Confidence            55567788999999999999988531  234456789999999999999999998765542  233333 2222    45


Q ss_pred             hHHHHHHHHHHHhCC-CC--CC---chHHHHHHHhC--CceEEEEEeCCCChh------hhhHhhccCCCCCCCcE--EE
Q 044214           99 LSCLRQKLLSNLLKD-KN--VM---PYIDLNFRRLG--HMKVLIVFDDVTCFS------QLESLMGSLDWLTPVSR--II  162 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~-~~--~~---~~~~~l~~~l~--~k~~LlVlDdv~~~~------~~~~l~~~~~~~~~gs~--il  162 (385)
                      ...++..++.++... .+  ..   +....+.+.+.  +++.+||||+++...      .+..+....... ++++  +|
T Consensus        99 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~-~~~~v~vI  177 (394)
T PRK00411         99 RYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEY-PGARIGVI  177 (394)
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhcc-CCCeEEEE
Confidence            667888888888652 21  11   44555566654  467999999997542      344444332211 2323  56


Q ss_pred             EEeccHHHHhhccc--------------------------eecccC-CCCCCchHHHHHHHHHh----CCCccchhHH--
Q 044214          163 LTTRNKQVLRNWRV--------------------------NAFKRN-HPDVGNEKLSSNVMKYA----QGVPLALKVL--  209 (385)
Q Consensus       163 vTtR~~~~~~~~~~--------------------------~~~~~~-~~~~~~~~~~~~i~~~~----~GlPLal~~~--  209 (385)
                      .++...++......                          ..+... ......++.++.+++.+    |..+.|+.++  
T Consensus       178 ~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~  257 (394)
T PRK00411        178 GISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRR  257 (394)
T ss_pred             EEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            66554433222110                          000000 01112234445555554    3455666654  


Q ss_pred             hHHHHHHHhhh-ccCccc--------chhhhhccccCchhhhhhhhhccccC----CCccHHHHHHH----HHHcCCc--
Q 044214          210 VWESAISKLQR-ILHPSI--------LEVLKISYDSLEDKEKNIFLDVACFF----QGEHVDPVMKF----FNASGFY--  270 (385)
Q Consensus       210 ~w~~~l~~l~~-~~~~~~--------~~~l~~sy~~L~~~~k~~~~~la~fp----~~~~~~~l~~~----~~~~g~~--  270 (385)
                      .+.....+-.. ...+.+        ...+.-.+..||.++|..+..++...    ..+....+...    ....|..  
T Consensus       258 a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~~~  337 (394)
T PRK00411        258 AGLIAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYEPR  337 (394)
T ss_pred             HHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCCcC
Confidence            11111111000 000111        22334568899999998887766442    22444444332    1222332  


Q ss_pred             ----hhhhHHHhhcCCceeEe
Q 044214          271 ----PEIRISVLVDKPLIAIC  287 (385)
Q Consensus       271 ----~~~~l~~L~~~sLi~~~  287 (385)
                          ...+++.|.+.|||+..
T Consensus       338 ~~~~~~~~l~~L~~~glI~~~  358 (394)
T PRK00411        338 THTRFYEYINKLDMLGIINTR  358 (394)
T ss_pred             cHHHHHHHHHHHHhcCCeEEE
Confidence                23579999999999964

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.35  E-value=4.8e-12  Score=130.83  Aligned_cols=275  Identities=15%  Similarity=0.242  Sum_probs=159.1

Q ss_pred             CccccchhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEee----ccccccCCCChHHHHH
Q 044214           30 QLVGVESTVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLEN----VREESQIPGGLSCLRQ  104 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~----~~~~~~~~~~~~~l~~  104 (385)
                      .++||+.+++.|...+.. ..+...++.+.|.+|||||+|+++|.+.+.+.+.  .++..    ....+.- ..+.+.++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~--~~i~~~f~q~~~~ipl-~~lvq~~r   77 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRG--YFIKGKFDQFERNIPL-SPLVQAFR   77 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhccce--eeeHhhcccccCCCch-HHHHHHHH
Confidence            379999999999998875 3345679999999999999999999997755421  11110    1111111 23333344


Q ss_pred             HHHHHHhCCCCCC--------------------------------------------------chHHHHHHHh-CCceEE
Q 044214          105 KLLSNLLKDKNVM--------------------------------------------------PYIDLNFRRL-GHMKVL  133 (385)
Q Consensus       105 ~ll~~l~~~~~~~--------------------------------------------------~~~~~l~~~l-~~k~~L  133 (385)
                      +++.++.......                                                  .....+.... +.++.+
T Consensus        78 ~l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plV  157 (849)
T COG3899          78 DLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLV  157 (849)
T ss_pred             HHHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeE
Confidence            4444332211100                                                  0111122222 346999


Q ss_pred             EEEeCC-CChhh----hhHhhccCCC-CCCCcEEEE--EeccH--HHHhhc-cc------------------eecccCCC
Q 044214          134 IVFDDV-TCFSQ----LESLMGSLDW-LTPVSRIIL--TTRNK--QVLRNW-RV------------------NAFKRNHP  184 (385)
Q Consensus       134 lVlDdv-~~~~~----~~~l~~~~~~-~~~gs~ilv--TtR~~--~~~~~~-~~------------------~~~~~~~~  184 (385)
                      +|+||+ |-...    ++.++....- .-....|..  |.+..  .+.... ..                  ..+.  +.
T Consensus       158 i~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~--~~  235 (849)
T COG3899         158 IVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLG--CT  235 (849)
T ss_pred             EEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhC--Cc
Confidence            999999 64433    2333322210 000112222  22211  000000 00                  1111  11


Q ss_pred             CCCchHHHHHHHHHhCCCccchhHH-----------------hHHHHHHHhhhcc-CcccchhhhhccccCchhhhhhhh
Q 044214          185 DVGNEKLSSNVMKYAQGVPLALKVL-----------------VWESAISKLQRIL-HPSILEVLKISYDSLEDKEKNIFL  246 (385)
Q Consensus       185 ~~~~~~~~~~i~~~~~GlPLal~~~-----------------~w~~~l~~l~~~~-~~~~~~~l~~sy~~L~~~~k~~~~  246 (385)
                      .....+..+.|+++..|+|+.+..+                 .|......+.... .+++.+.+....+.||...|.++.
T Consensus       236 ~~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l~~rl~kL~~~t~~Vl~  315 (849)
T COG3899         236 KLLPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLK  315 (849)
T ss_pred             ccccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHHHHHHhcCCHHHHHHHH
Confidence            2345678999999999999999987                 3333333322211 133555788899999999999999


Q ss_pred             hccccCCCccHHHHHHHHHHcCCchhhhHHHhhcCCceeEec--------CC---cEEeCHHHHHHHHHHHhhc
Q 044214          247 DVACFFQGEHVDPVMKFFNASGFYPEIRISVLVDKPLIAICS--------YK---KIRMRDLLQELGGEIVRKE  309 (385)
Q Consensus       247 ~la~fp~~~~~~~l~~~~~~~g~~~~~~l~~L~~~sLi~~~~--------~~---~~~mH~lv~~~a~~~~~~e  309 (385)
                      ..||+...|+.+.|..++..........+......++|.+..        ..   +-+.|+++|+.|-....++
T Consensus       316 ~AA~iG~~F~l~~La~l~~~~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~F~H~~vqqaaY~~i~~~  389 (849)
T COG3899         316 AAACIGNRFDLDTLAALAEDSPALEAAALLDALQEGLILPLSETYRFGSNVDIATYKFLHDRVQQAAYNLIPES  389 (849)
T ss_pred             HHHHhCccCCHHHHHHHHhhchHHHHHHHHHHhHhhceeccccccccccccchhhHHhhHHHHHHHHhccCchh
Confidence            999999999999999998864443333444445555555421        11   2278999999997654443

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.31  E-value=1.3e-11  Score=114.40  Aligned_cols=248  Identities=16%  Similarity=0.182  Sum_probs=136.2

Q ss_pred             CCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           29 NQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      .+|||+++.+++|..++..   .......+.++|++|+|||+||+.+++.+...+.   ... ....    .....+ ..
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~---~~~-~~~~----~~~~~l-~~   74 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLK---ITS-GPAL----EKPGDL-AA   74 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEE---Eec-cchh----cCchhH-HH
Confidence            4699999999999988862   1233556889999999999999999998754321   111 1111    111111 11


Q ss_pred             HHHHHhCCCC----CC-----chHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHH----h
Q 044214          106 LLSNLLKDKN----VM-----PYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL----R  172 (385)
Q Consensus       106 ll~~l~~~~~----~~-----~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~----~  172 (385)
                      .+..+....-    +.     ...+.+...+.+.+..+|+|+..+...+...      ..+.+-|..||+...+.    .
T Consensus        75 ~l~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~------~~~~~li~~t~~~~~l~~~l~s  148 (305)
T TIGR00635        75 ILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLD------LPPFTLVGATTRAGMLTSPLRD  148 (305)
T ss_pred             HHHhcccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeec------CCCeEEEEecCCccccCHHHHh
Confidence            1222211110    00     1222333334444444444443333322111      11244455666653221    1


Q ss_pred             hccc-eeccc---------------CCCCCCchHHHHHHHHHhCCCccchhHH---hHHHHHHHhhhc-cC----cccch
Q 044214          173 NWRV-NAFKR---------------NHPDVGNEKLSSNVMKYAQGVPLALKVL---VWESAISKLQRI-LH----PSILE  228 (385)
Q Consensus       173 ~~~~-~~~~~---------------~~~~~~~~~~~~~i~~~~~GlPLal~~~---~w~~~l~~l~~~-~~----~~~~~  228 (385)
                      .+.. ..|..               .......++.+..|++.|+|.|-.+..+   .|.... ..... ..    .....
T Consensus       149 R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~-~~~~~~it~~~v~~~l~  227 (305)
T TIGR00635       149 RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQ-VRGQKIINRDIALKALE  227 (305)
T ss_pred             hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHH-HcCCCCcCHHHHHHHHH
Confidence            2211 00100               1112234567889999999999766543   221110 01110 00    11222


Q ss_pred             hhhhccccCchhhhhhhh-hccccCCC-ccHHHHHHHHHHcCCchhhhHH-HhhcCCceeEecCCcE
Q 044214          229 VLKISYDSLEDKEKNIFL-DVACFFQG-EHVDPVMKFFNASGFYPEIRIS-VLVDKPLIAICSYKKI  292 (385)
Q Consensus       229 ~l~~sy~~L~~~~k~~~~-~la~fp~~-~~~~~l~~~~~~~g~~~~~~l~-~L~~~sLi~~~~~~~~  292 (385)
                      .+...|..|++..+..+. .++.+..+ +..+.+...+..+....+..++ .|++++||+....|++
T Consensus       228 ~l~~~~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g~~  294 (305)
T TIGR00635       228 MLMIDELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRI  294 (305)
T ss_pred             HhCCCCCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCchhh
Confidence            356778899998888777 44666544 7888888888887777888888 6999999986655553

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.30  E-value=2.8e-11  Score=113.08  Aligned_cols=239  Identities=18%  Similarity=0.215  Sum_probs=136.2

Q ss_pred             CCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      ..-.+|+|+++.++.+..++..   .......+.|+|++|+|||+||+.+++.+...+.   +.. ....    .. ...
T Consensus        22 ~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~---~~~-~~~~----~~-~~~   92 (328)
T PRK00080         22 KSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIR---ITS-GPAL----EK-PGD   92 (328)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeE---EEe-cccc----cC-hHH
Confidence            3557899999999999887752   2334567889999999999999999998754321   111 1111    11 111


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCChh--hhhHhhccCC-------------------CCCCCcEE
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFS--QLESLMGSLD-------------------WLTPVSRI  161 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~--~~~~l~~~~~-------------------~~~~gs~i  161 (385)
                      +..++..+                  ++..+|++|+++...  ..+.+...+.                   ...+.+-|
T Consensus        93 l~~~l~~l------------------~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li  154 (328)
T PRK00080         93 LAAILTNL------------------EEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLI  154 (328)
T ss_pred             HHHHHHhc------------------ccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEE
Confidence            11222221                  123456666664211  1111111000                   00123445


Q ss_pred             EEEeccHHHH----hhccc-------------eecc---cCCCCCCchHHHHHHHHHhCCCccchhHH---hHHHHHHH-
Q 044214          162 ILTTRNKQVL----RNWRV-------------NAFK---RNHPDVGNEKLSSNVMKYAQGVPLALKVL---VWESAISK-  217 (385)
Q Consensus       162 lvTtR~~~~~----~~~~~-------------~~~~---~~~~~~~~~~~~~~i~~~~~GlPLal~~~---~w~~~l~~-  217 (385)
                      ..|++...+.    ..++.             ..+.   ........++.+..|++.|+|.|-.+..+   .|...... 
T Consensus       155 ~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~  234 (328)
T PRK00080        155 GATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKG  234 (328)
T ss_pred             eecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcC
Confidence            5666643221    12211             0000   01112234567899999999999755544   22111110 


Q ss_pred             ---hhhccCcccchhhhhccccCchhhhhhhh-hccccCCC-ccHHHHHHHHHHcCCchhhhHH-HhhcCCceeEecCCc
Q 044214          218 ---LQRILHPSILEVLKISYDSLEDKEKNIFL-DVACFFQG-EHVDPVMKFFNASGFYPEIRIS-VLVDKPLIAICSYKK  291 (385)
Q Consensus       218 ---l~~~~~~~~~~~l~~sy~~L~~~~k~~~~-~la~fp~~-~~~~~l~~~~~~~g~~~~~~l~-~L~~~sLi~~~~~~~  291 (385)
                         +....-......+...+..|++..+..+. .+..|+.+ +..+.+...+..+....++.++ .|++.+||+....|+
T Consensus       235 ~~~I~~~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~gr  314 (328)
T PRK00080        235 DGVITKEIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGR  314 (328)
T ss_pred             CCCCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCchH
Confidence               00000022334567778899998888886 66777654 8889998888887777787888 999999998665554

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.30  E-value=5.6e-10  Score=106.11  Aligned_cols=115  Identities=16%  Similarity=0.272  Sum_probs=78.5

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC------ceEEEeecccccc
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD------GSCFLENVREESQ   94 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~------~~~w~~~~~~~~~   94 (385)
                      .+...|+.++||++++++|...|..  .......+.|+|++|+|||++++.+++++.+...      ..+|+. ....  
T Consensus         9 ~~~~~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in-~~~~--   85 (365)
T TIGR02928         9 EPDYVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVN-CQIL--   85 (365)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEE-CCCC--
Confidence            4455567899999999999998863  2234457899999999999999999987653322      234444 2222  


Q ss_pred             CCCChHHHHHHHHHHHhC---CCC--CC---chHHHHHHHhC--CceEEEEEeCCCCh
Q 044214           95 IPGGLSCLRQKLLSNLLK---DKN--VM---PYIDLNFRRLG--HMKVLIVFDDVTCF  142 (385)
Q Consensus        95 ~~~~~~~l~~~ll~~l~~---~~~--~~---~~~~~l~~~l~--~k~~LlVlDdv~~~  142 (385)
                        .+...++..++.++..   ..+  ..   +....+.+.+.  +++++||||+++..
T Consensus        86 --~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        86 --DTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             --CCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence              4556788888888742   111  11   33455555553  56899999999765

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.

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

Probab=99.10  E-value=5.8e-11  Score=105.29  Aligned_cols=55  Identities=18%  Similarity=0.370  Sum_probs=40.9

Q ss_pred             ccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           31 LVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |+||+.++++|.+++..  +..+.+.|+|+.|+|||+|++++.+..++.-..++|+.
T Consensus         1 F~gR~~el~~l~~~l~~--~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~   55 (234)
T PF01637_consen    1 FFGREKELEKLKELLES--GPSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYID   55 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHC
T ss_pred             CCCHHHHHHHHHHHHHh--hcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEe
Confidence            79999999999999984  34568999999999999999999998754333444444

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

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

Probab=99.09  E-value=5e-09  Score=95.22  Aligned_cols=151  Identities=16%  Similarity=0.156  Sum_probs=86.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC---chHHHHHHH--
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM---PYIDLNFRR--  126 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~---~~~~~l~~~--  126 (385)
                      ...+.|+|++|+||||+++.+++.+...-...+|+.     ... .+..+++..++..++......   .....+...  
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~-----~~~-~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~  116 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLV-----NTR-VDAEDLLRMVAADFGLETEGRDKAALLRELEDFLI  116 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeee-----CCC-CCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHH
Confidence            457899999999999999999987653211122322     112 456678888887776543322   222333322  


Q ss_pred             ---hCCceEEEEEeCCCChh--hhhHhh---ccCCCCCCCcEEEEEeccHHHHhhc------------c----c------
Q 044214          127 ---LGHMKVLIVFDDVTCFS--QLESLM---GSLDWLTPVSRIILTTRNKQVLRNW------------R----V------  176 (385)
Q Consensus       127 ---l~~k~~LlVlDdv~~~~--~~~~l~---~~~~~~~~gs~ilvTtR~~~~~~~~------------~----~------  176 (385)
                         ..+++.++|+||++...  .++.+.   ...........|++|.... .....            .    .      
T Consensus       117 ~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~  195 (269)
T TIGR03015       117 EQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDRE  195 (269)
T ss_pred             HHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHH
Confidence               26788999999997643  344433   2111122233455555432 11110            0    0      


Q ss_pred             -------eeccc---CCCCCCchHHHHHHHHHhCCCccchhHH
Q 044214          177 -------NAFKR---NHPDVGNEKLSSNVMKYAQGVPLALKVL  209 (385)
Q Consensus       177 -------~~~~~---~~~~~~~~~~~~~i~~~~~GlPLal~~~  209 (385)
                             ..+..   ........+.++.|++.++|.|..|..+
T Consensus       196 e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l  238 (269)
T TIGR03015       196 ETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINIL  238 (269)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHH
Confidence                   11111   1112244678899999999999998866

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.

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.96  E-value=7.9e-10  Score=101.78  Aligned_cols=253  Identities=19%  Similarity=0.238  Sum_probs=168.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC-CchHHHHHHHhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV-MPYIDLNFRRLGH  129 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~-~~~~~~l~~~l~~  129 (385)
                      ..+.+.++|.|||||||++..+.. +...|...+|+......    .+...+.-.+...++-+... ......+.....+
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~~~~~~v~~vdl~pi----tD~~~v~~~~ag~~gl~~~~g~~~~~~~~~~~~~   87 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AASEYADGVAFVDLAPI----TDPALVFPTLAGALGLHVQPGDSAVDTLVRRIGD   87 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-Hhhhcccceeeeecccc----CchhHhHHHHHhhcccccccchHHHHHHHHHHhh
Confidence            357899999999999999999999 88899888888766665    33444444444445444432 2556678888999


Q ss_pred             ceEEEEEeCCCChh-hhhHhhccCCCCCCCcEEEEEeccHHHHhhccc------eecc---------------cCCCCCC
Q 044214          130 MKVLIVFDDVTCFS-QLESLMGSLDWLTPVSRIILTTRNKQVLRNWRV------NAFK---------------RNHPDVG  187 (385)
Q Consensus       130 k~~LlVlDdv~~~~-~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~~------~~~~---------------~~~~~~~  187 (385)
                      ++.++|+||..+.. .-..+...+...++.-.++.|+|..........      ..+.               .-.-...
T Consensus        88 rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~  167 (414)
T COG3903          88 RRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDD  167 (414)
T ss_pred             hhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHHHhccceeecCC
Confidence            99999999996543 233333344434455678888887633222111      1111               0001113


Q ss_pred             chHHHHHHHHHhCCCccchhHH-------hHHHHHHHhhh-------c------cCcccchhhhhccccCchhhhhhhhh
Q 044214          188 NEKLSSNVMKYAQGVPLALKVL-------VWESAISKLQR-------I------LHPSILEVLKISYDSLEDKEKNIFLD  247 (385)
Q Consensus       188 ~~~~~~~i~~~~~GlPLal~~~-------~w~~~l~~l~~-------~------~~~~~~~~l~~sy~~L~~~~k~~~~~  247 (385)
                      ......+|.+...|.|++|..+       ....+.+.++.       .      ........+.+||.-|+..++-.|..
T Consensus       168 ~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe~~~~~r  247 (414)
T COG3903         168 NAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWERALFGR  247 (414)
T ss_pred             chHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHHHHHhcc
Confidence            3466789999999999999998       22222222221       1      12567889999999999999999999


Q ss_pred             ccccCCCccHHHHHHHHHHcCCc-------hhhhHHHhhcCCceeEec---CCcEEeCHHHHHHHHHHHhhcc
Q 044214          248 VACFFQGEHVDPVMKFFNASGFY-------PEIRISVLVDKPLIAICS---YKKIRMRDLLQELGGEIVRKES  310 (385)
Q Consensus       248 la~fp~~~~~~~l~~~~~~~g~~-------~~~~l~~L~~~sLi~~~~---~~~~~mH~lv~~~a~~~~~~e~  310 (385)
                      ++.|...|+.+  ...|.+-|-.       ....+..|++.+++...+   .-.|+.-+-++.|+.....+..
T Consensus       248 La~~~g~f~~~--l~~~~a~g~~~~~~~y~~~~a~~ll~~kslv~a~~~~~~a~~Rl~eT~r~YalaeL~r~~  318 (414)
T COG3903         248 LAVFVGGFDLG--LALAVAAGADVDVPRYLVLLALTLLVDKSLVVALDLLGRARYRLLETGRRYALAELHRSG  318 (414)
T ss_pred             hhhhhhhhccc--HHHHHhcCCccccchHHHHHHHHHHhhccchhhhhhhhHHHHHHHHHHHHHHHHHHHhhh
Confidence            99998888776  2233332222       334577899999988654   2247777777888877766554

>PF05729 NACHT: NACHT domain

Probab=98.95  E-value=4e-09  Score=88.25  Aligned_cols=114  Identities=24%  Similarity=0.325  Sum_probs=65.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC------CceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHH-
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF------DGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFR-  125 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f------~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~-  125 (385)
                      +++.|+|.+|+||||+++.++.++....      ...+|+. .+..... .....+...+.........  .....+.. 
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~l~~~l~~~~~~~~~--~~~~~~~~~   76 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS-LRDISDS-NNSRSLADLLFDQLPESIA--PIEELLQEL   76 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEe-ehhhhhc-cccchHHHHHHHhhccchh--hhHHHHHHH
Confidence            4789999999999999999998765443      3344444 4433322 2222333333333322221  11112222 


Q ss_pred             HhCCceEEEEEeCCCChhh---------hhHhhccCCC--CCCCcEEEEEeccHHH
Q 044214          126 RLGHMKVLIVFDDVTCFSQ---------LESLMGSLDW--LTPVSRIILTTRNKQV  170 (385)
Q Consensus       126 ~l~~k~~LlVlDdv~~~~~---------~~~l~~~~~~--~~~gs~ilvTtR~~~~  170 (385)
                      ....+++++|+|++++...         +..++..+..  ..++++++||+|....
T Consensus        77 ~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~  132 (166)
T PF05729_consen   77 LEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAF  132 (166)
T ss_pred             HHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChH
Confidence            2357899999999974332         2222222221  2468999999998765

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

Probab=98.86  E-value=4.2e-08  Score=79.92  Aligned_cols=123  Identities=20%  Similarity=0.157  Sum_probs=71.4

Q ss_pred             cccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           32 VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      +|++..++.+...+..  +..+.+.|+|.+|+|||++++.+++.....-..++++. ....    .............  
T Consensus         1 ~~~~~~~~~i~~~~~~--~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~-~~~~----~~~~~~~~~~~~~--   71 (151)
T cd00009           1 VGQEEAIEALREALEL--PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLN-ASDL----LEGLVVAELFGHF--   71 (151)
T ss_pred             CchHHHHHHHHHHHhC--CCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEe-hhhh----hhhhHHHHHhhhh--
Confidence            4788899999998873  24457889999999999999999998754334445554 2221    1111111000000  


Q ss_pred             CCCCCCchHHHHHHHhCCceEEEEEeCCCCh-----hhhhHhhccCCCC---CCCcEEEEEeccHH
Q 044214          112 KDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF-----SQLESLMGSLDWL---TPVSRIILTTRNKQ  169 (385)
Q Consensus       112 ~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-----~~~~~l~~~~~~~---~~gs~ilvTtR~~~  169 (385)
                            ............++.++|+||++..     ..+..........   ..+..||+||....
T Consensus        72 ------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 ------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                  0011112223456789999999853     2233333333221   35778888887643

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.

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

Probab=98.83  E-value=3e-09  Score=90.80  Aligned_cols=50  Identities=34%  Similarity=0.535  Sum_probs=35.3

Q ss_pred             CccccchhHHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           30 QLVGVESTVEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .|+||+++++++...+. ..+...+.+.|+|.+|+|||+|.++++.++...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            48999999999999994 234557899999999999999999999987665

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

Probab=98.79  E-value=3.8e-08  Score=90.38  Aligned_cols=147  Identities=22%  Similarity=0.364  Sum_probs=84.3

Q ss_pred             CCccccchhHH---HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           29 NQLVGVESTVE---EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        29 ~~~vGR~~~l~---~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      +++||-+..+.   -|.+++.  ++.+....+||++|+||||||+.++......|...--+.         .++.++..-
T Consensus        24 de~vGQ~HLlg~~~~lrr~v~--~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~---------~gvkdlr~i   92 (436)
T COG2256          24 DEVVGQEHLLGEGKPLRRAVE--AGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVT---------SGVKDLREI   92 (436)
T ss_pred             HHhcChHhhhCCCchHHHHHh--cCCCceeEEECCCCCCHHHHHHHHHHhhCCceEEecccc---------ccHHHHHHH
Confidence            45555554442   2333444  456666779999999999999999998777765321111         333333322


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEE--EeccHHH------Hhhcc
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIIL--TTRNKQV------LRNWR  175 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilv--TtR~~~~------~~~~~  175 (385)
                      + ..            .-.....+++.+|++|.|.  +..+-+.|++...   .|.-|+|  ||-++..      ...+.
T Consensus        93 ~-e~------------a~~~~~~gr~tiLflDEIHRfnK~QQD~lLp~vE---~G~iilIGATTENPsF~ln~ALlSR~~  156 (436)
T COG2256          93 I-EE------------ARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVE---NGTIILIGATTENPSFELNPALLSRAR  156 (436)
T ss_pred             H-HH------------HHHHHhcCCceEEEEehhhhcChhhhhhhhhhhc---CCeEEEEeccCCCCCeeecHHHhhhhh
Confidence            2 11            1123344889999999995  6667777877765   5766666  6666532      22222


Q ss_pred             ceecccCCCCCCchHHHHH-HHHHhCCCc
Q 044214          176 VNAFKRNHPDVGNEKLSSN-VMKYAQGVP  203 (385)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~-i~~~~~GlP  203 (385)
                      +..|..-... ++..+.++ +.....|++
T Consensus       157 vf~lk~L~~~-di~~~l~ra~~~~~rgl~  184 (436)
T COG2256         157 VFELKPLSSE-DIKKLLKRALLDEERGLG  184 (436)
T ss_pred             eeeeecCCHH-HHHHHHHHHHhhhhcCCC
Confidence            2333322222 33444444 555666666

>PF13173 AAA_14: AAA domain

Probab=98.74  E-value=6.1e-08  Score=77.56  Aligned_cols=101  Identities=18%  Similarity=0.219  Sum_probs=68.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      +++.|.|+.|+|||||+++++++.. .-...+++. ....        ........         +..+.+.+...+++.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi~-~~~~--------~~~~~~~~---------~~~~~~~~~~~~~~~   63 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL-PPENILYIN-FDDP--------RDRRLADP---------DLLEYFLELIKPGKK   63 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc-ccccceeec-cCCH--------HHHHHhhh---------hhHHHHHHhhccCCc
Confidence            5899999999999999999998765 334455554 2111        11000000         022233333444778


Q ss_pred             EEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          133 LIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       133 LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      +++||++....+|......+.+..++.+|++|+.+.....
T Consensus        64 ~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~  103 (128)
T PF13173_consen   64 YIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLS  103 (128)
T ss_pred             EEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHh
Confidence            9999999988888888877776666789999998876654

>PTZ00202 tuzin; Provisional

Probab=98.70  E-value=1.6e-07  Score=87.88  Aligned_cols=102  Identities=16%  Similarity=0.109  Sum_probs=72.6

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCC-CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVES-KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      |...+.|+||+.++++|...|...+ +.+++++|+|++|+|||||++.+.....    ...++.+.       .+..+++
T Consensus       258 Pa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~----~~qL~vNp-------rg~eElL  326 (550)
T PTZ00202        258 PAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----MPAVFVDV-------RGTEDTL  326 (550)
T ss_pred             CCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC----ceEEEECC-------CCHHHHH
Confidence            6667899999999999999997433 3456999999999999999999997653    22444433       3568999


Q ss_pred             HHHHHHHhCCCCCC--chHHHHHHHh-----C-CceEEEEEe
Q 044214          104 QKLLSNLLKDKNVM--PYIDLNFRRL-----G-HMKVLIVFD  137 (385)
Q Consensus       104 ~~ll~~l~~~~~~~--~~~~~l~~~l-----~-~k~~LlVlD  137 (385)
                      ..++..++.+....  ++...+.+.+     . +++.+||+-
T Consensus       327 r~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~  368 (550)
T PTZ00202        327 RSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLLVLK  368 (550)
T ss_pred             HHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            99999999643322  4444444433     2 556666653

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

Probab=98.69  E-value=8.8e-08  Score=76.85  Aligned_cols=109  Identities=20%  Similarity=0.220  Sum_probs=72.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-----CCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC-C---chHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-----FDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV-M---PYIDL  122 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-----f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~-~---~~~~~  122 (385)
                      .+.+.|+|.+|+|||+++.++++.....     -..++|+. ...   . .+...+...++..+...... .   +..+.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~-~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~   78 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVN-CPS---S-RTPRDFAQEILEALGLPLKSRQTSDELRSL   78 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEE-HHH---H-SSHHHHHHHHHHHHT-SSSSTS-HHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEE-eCC---C-CCHHHHHHHHHHHhCccccccCCHHHHHHH
Confidence            4689999999999999999999876432     34455665 322   2 57889999999999877665 2   55566


Q ss_pred             HHHHhCCc-eEEEEEeCCCCh---hhhhHhhccCCCCCCCcEEEEEecc
Q 044214          123 NFRRLGHM-KVLIVFDDVTCF---SQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       123 l~~~l~~k-~~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      +.+.+... ..+||+|+++..   ..++.+.....  ..+.++|+..+.
T Consensus        79 ~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   79 LIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            66666654 469999999654   33444433322  567777777654

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

Probab=98.68  E-value=7.5e-07  Score=83.72  Aligned_cols=114  Identities=17%  Similarity=0.217  Sum_probs=82.4

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc--eEEEeeccccccCCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG--SCFLENVREESQIPGG   98 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~--~~w~~~~~~~~~~~~~   98 (385)
                      .+...|+.+.+|+++++++...|..  ....+.-+.|+|.+|+|||+.++.+.+++.+....  .+.+. ....    ..
T Consensus        11 ~~~~iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yIN-c~~~----~t   85 (366)
T COG1474          11 LEDYIPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYIN-CLEL----RT   85 (366)
T ss_pred             CCCCCcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEe-eeeC----CC
Confidence            3455566699999999999988763  22233348999999999999999999988666433  45554 3333    67


Q ss_pred             hHHHHHHHHHHHhCCCC-CC---chHHHHHHHhC--CceEEEEEeCCCC
Q 044214           99 LSCLRQKLLSNLLKDKN-VM---PYIDLNFRRLG--HMKVLIVFDDVTC  141 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~-~~---~~~~~l~~~l~--~k~~LlVlDdv~~  141 (385)
                      ..+++..++++++.... ..   +....+.+.+.  ++.+++|||+++.
T Consensus        86 ~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~  134 (366)
T COG1474          86 PYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDA  134 (366)
T ss_pred             HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhh
Confidence            78889999998863332 11   55566666664  4889999999964

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.62  E-value=2.8e-06  Score=83.95  Aligned_cols=51  Identities=27%  Similarity=0.343  Sum_probs=42.1

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.++||-+..++.|.+++..+. -.+.+.++|..|+||||+|+.+++.+.
T Consensus        13 qtFddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLn   63 (700)
T PRK12323         13 RDFTTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLN   63 (700)
T ss_pred             CcHHHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            345789999999999999998422 345678999999999999999998764

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.58  E-value=3.1e-06  Score=84.86  Aligned_cols=51  Identities=27%  Similarity=0.326  Sum_probs=41.9

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-+++||.+..++.|.+++..+ .-.+.+.++|..|+||||+|+.+++.+.
T Consensus        13 qtFdEVIGQe~Vv~~L~~aL~~g-RL~HAyLFtGPpGvGKTTlAriLAKaLn   63 (830)
T PRK07003         13 KDFASLVGQEHVVRALTHALDGG-RLHHAYLFTGTRGVGKTTLSRIFAKALN   63 (830)
T ss_pred             CcHHHHcCcHHHHHHHHHHHhcC-CCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34478999999999999999843 2345678999999999999999998653

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

Probab=98.58  E-value=1.2e-07  Score=81.44  Aligned_cols=57  Identities=23%  Similarity=0.444  Sum_probs=39.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      |..-++|||-+..++.+.-++..   ..+....+.+||++|+||||||.-+++.....|.
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~   79 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVNFK   79 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--EE
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCCeE
Confidence            34568899999999887765542   2345778999999999999999999998876653

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.56  E-value=1.8e-06  Score=87.16  Aligned_cols=114  Identities=17%  Similarity=0.183  Sum_probs=74.1

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC-----CC--ceEEEeecccc
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGD-----FD--GSCFLENVREE   92 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-----f~--~~~w~~~~~~~   92 (385)
                      .+...|+.+.||++|+++|...|..   ++....++.|+|.+|.|||+.++.+.+++.+.     .+  .++++. ....
T Consensus       749 ~~DYVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYIN-Cm~L  827 (1164)
T PTZ00112        749 QLDVVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEIN-GMNV  827 (1164)
T ss_pred             CcccCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEe-CCcc
Confidence            3445568899999999999988863   23333577899999999999999999876321     22  234443 2222


Q ss_pred             ccCCCChHHHHHHHHHHHhCCCCC--C---chHHHHHHHhC---CceEEEEEeCCCC
Q 044214           93 SQIPGGLSCLRQKLLSNLLKDKNV--M---PYIDLNFRRLG---HMKVLIVFDDVTC  141 (385)
Q Consensus        93 ~~~~~~~~~l~~~ll~~l~~~~~~--~---~~~~~l~~~l~---~k~~LlVlDdv~~  141 (385)
                          .....++..|..++....+.  .   .....+...+.   ....+||||+++.
T Consensus       828 ----stp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~  880 (1164)
T PTZ00112        828 ----VHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDY  880 (1164)
T ss_pred             ----CCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhh
Confidence                45566777777777444332  1   33344444442   2346999999974

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.54  E-value=5.6e-07  Score=86.77  Aligned_cols=111  Identities=21%  Similarity=0.414  Sum_probs=66.9

Q ss_pred             CCCCCccccchhHHH---HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           26 DNKNQLVGVESTVEE---IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~---l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      ..-+++||++..+..   +.+++.  .+....+.|+|++|+||||||+.+++.....|.   .+...  .    .+... 
T Consensus         9 ~~l~d~vGq~~~v~~~~~L~~~i~--~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~---~l~a~--~----~~~~~-   76 (413)
T PRK13342          9 KTLDEVVGQEHLLGPGKPLRRMIE--AGRLSSMILWGPPGTGKTTLARIIAGATDAPFE---ALSAV--T----SGVKD-   76 (413)
T ss_pred             CCHHHhcCcHHHhCcchHHHHHHH--cCCCceEEEECCCCCCHHHHHHHHHHHhCCCEE---EEecc--c----ccHHH-
Confidence            344679999988766   777776  345567889999999999999999997654432   12111  0    11111 


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEE
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIIL  163 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilv  163 (385)
                      .+.++....            .....+++.+|++|+++..  .+.+.++..+.   .+..+++
T Consensus        77 ir~ii~~~~------------~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI  124 (413)
T PRK13342         77 LREVIEEAR------------QRRSAGRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLI  124 (413)
T ss_pred             HHHHHHHHH------------HhhhcCCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEE
Confidence            112221110            0112457789999999743  45566666554   2444444

>PLN03025 replication factor C subunit; Provisional

Probab=98.51  E-value=1.3e-06  Score=81.44  Aligned_cols=126  Identities=17%  Similarity=0.266  Sum_probs=70.8

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      ..-.+++|.++.++.|..++..  ++.+.+.++|++|+||||+|..+++.+.. .|...+.-.+.   +.. .+.. ..+
T Consensus        10 ~~l~~~~g~~~~~~~L~~~~~~--~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~---sd~-~~~~-~vr   82 (319)
T PLN03025         10 TKLDDIVGNEDAVSRLQVIARD--GNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNA---SDD-RGID-VVR   82 (319)
T ss_pred             CCHHHhcCcHHHHHHHHHHHhc--CCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecc---ccc-ccHH-HHH
Confidence            3446789999999999888773  34455789999999999999999997633 33322111111   111 1222 222


Q ss_pred             HHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEecc
Q 044214          105 KLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       105 ~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      ..+.........         .-.++.-++|+|+++..  .....+...+......+++++++..
T Consensus        83 ~~i~~~~~~~~~---------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~  138 (319)
T PLN03025         83 NKIKMFAQKKVT---------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNT  138 (319)
T ss_pred             HHHHHHHhcccc---------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCC
Confidence            222221111000         00245679999999743  3344444433333455667766643

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.47  E-value=3.6e-06  Score=78.42  Aligned_cols=50  Identities=34%  Similarity=0.410  Sum_probs=41.4

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-.+++|+++.++.+..++..  +..+.+.|+|.+|+||||+|+.+++.+..
T Consensus        15 ~~~~~~g~~~~~~~l~~~i~~--~~~~~~ll~G~~G~GKt~~~~~l~~~l~~   64 (319)
T PRK00440         15 TLDEIVGQEEIVERLKSYVKE--KNMPHLLFAGPPGTGKTTAALALARELYG   64 (319)
T ss_pred             cHHHhcCcHHHHHHHHHHHhC--CCCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence            336699999999999999974  33445799999999999999999997643

>PRK06893 DNA replication initiation factor; Validated

Probab=98.46  E-value=1.5e-06  Score=76.86  Aligned_cols=36  Identities=17%  Similarity=0.262  Sum_probs=29.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.+.|+|++|+|||.|++.+++........+.|+.
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~   74 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIP   74 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEee
Confidence            356899999999999999999998765555666776

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.43  E-value=1.6e-06  Score=81.42  Aligned_cols=50  Identities=24%  Similarity=0.350  Sum_probs=41.8

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-+.++|++..++.+..++..  +..+.+.++|++|+|||++|+.+++.+..
T Consensus        13 ~~~~~~g~~~~~~~L~~~~~~--~~~~~lll~Gp~GtGKT~la~~~~~~l~~   62 (337)
T PRK12402         13 LLEDILGQDEVVERLSRAVDS--PNLPHLLVQGPPGSGKTAAVRALARELYG   62 (337)
T ss_pred             cHHHhcCCHHHHHHHHHHHhC--CCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            346799999999999998874  34456889999999999999999987644

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.40  E-value=1.6e-05  Score=79.53  Aligned_cols=50  Identities=32%  Similarity=0.398  Sum_probs=41.8

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.++||.+..++.|.+++..+ .-.+.+.++|..|+||||+|+.+++.+
T Consensus        13 ~tFddIIGQe~vv~~L~~ai~~~-rl~Ha~Lf~GP~GvGKTTlAriLAk~L   62 (709)
T PRK08691         13 KTFADLVGQEHVVKALQNALDEG-RLHHAYLLTGTRGVGKTTIARILAKSL   62 (709)
T ss_pred             CCHHHHcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCcHHHHHHHHHHHh
Confidence            34478999999999999999842 224578999999999999999999865

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.40  E-value=6.7e-06  Score=77.92  Aligned_cols=51  Identities=27%  Similarity=0.349  Sum_probs=42.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.+.+.+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~~~~iiGq~~~~~~l~~~~~~~-~~~h~~L~~Gp~G~GKTtla~~la~~l~   63 (363)
T PRK14961         13 QYFRDIIGQKHIVTAISNGLSLG-RIHHAWLLSGTRGVGKTTIARLLAKSLN   63 (363)
T ss_pred             CchhhccChHHHHHHHHHHHHcC-CCCeEEEEecCCCCCHHHHHHHHHHHhc
Confidence            34477999999999999988743 2345779999999999999999998764

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.38  E-value=4.7e-06  Score=82.58  Aligned_cols=51  Identities=33%  Similarity=0.335  Sum_probs=42.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.++||.+...+.|.+++..+. -.+.+.++|+.|+||||+|+.+++.+.
T Consensus        12 ktFddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~Ln   62 (702)
T PRK14960         12 RNFNELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCLN   62 (702)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            345789999999999999998432 256789999999999999999998763

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.38  E-value=1.2e-05  Score=75.69  Aligned_cols=52  Identities=21%  Similarity=0.156  Sum_probs=43.0

Q ss_pred             CCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|....+++|.+...+.|.+.+..+ .-...+.++|+.|+||+++|..+++.+
T Consensus        14 ~P~~~~~iiGq~~~~~~L~~~~~~~-rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         14 HPRETTALFGHAAAEAALLDAYRSG-RLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             CCCchhhccChHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3556678999999999999988842 224568999999999999999999865

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.36  E-value=9.6e-07  Score=82.21  Aligned_cols=97  Identities=16%  Similarity=0.106  Sum_probs=63.2

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC--
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM--  117 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~--  117 (385)
                      +.+.+.+ -++-+..+|+|++|+||||||+.+++.+.. +|+..+|+..+++.   +..+.++++.+...+.....+.  
T Consensus       159 vID~l~P-IGkGQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER---~~EVtdiqrsIlg~vv~st~d~~~  234 (416)
T PRK09376        159 IIDLIAP-IGKGQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDER---PEEVTDMQRSVKGEVVASTFDEPA  234 (416)
T ss_pred             eeeeecc-cccCceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCc---hhHHHHHHHHhcCcEEEECCCCCH
Confidence            3444442 133457889999999999999999997644 79999999855542   1467788887764332222211  


Q ss_pred             --------chHHHHHHH-hCCceEEEEEeCCCC
Q 044214          118 --------PYIDLNFRR-LGHMKVLIVFDDVTC  141 (385)
Q Consensus       118 --------~~~~~l~~~-l~~k~~LlVlDdv~~  141 (385)
                              ...+....+ ..+++++|++|++..
T Consensus       235 ~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR  267 (416)
T PRK09376        235 ERHVQVAEMVIEKAKRLVEHGKDVVILLDSITR  267 (416)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEEChHH
Confidence                    111222222 367999999999953

>PRK04195 replication factor C large subunit; Provisional

Probab=98.34  E-value=2.5e-06  Score=83.91  Aligned_cols=51  Identities=27%  Similarity=0.438  Sum_probs=42.3

Q ss_pred             CCCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.+++|.+..++.+.+|+..  .....+.+.|+|++|+||||+|+.+++.+
T Consensus        11 ~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el   63 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY   63 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3446799999999999999873  11226789999999999999999999976

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.34  E-value=6.3e-06  Score=84.23  Aligned_cols=51  Identities=24%  Similarity=0.306  Sum_probs=42.0

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCC-eEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKG-VYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~-~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-.++||-+..++.|.+++..  ++ ...+.++|+.|+||||+|+.+++.+..
T Consensus        13 ~tFddIIGQe~Iv~~LknaI~~--~rl~HAyLFtGPpGtGKTTLARiLAk~Lnc   64 (944)
T PRK14949         13 ATFEQMVGQSHVLHALTNALTQ--QRLHHAYLFTGTRGVGKTSLARLFAKGLNC   64 (944)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHh--CCCCeEEEEECCCCCCHHHHHHHHHHhccC
Confidence            3447899999999999999873  34 445689999999999999999997643

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.33  E-value=1.9e-06  Score=76.10  Aligned_cols=58  Identities=19%  Similarity=0.302  Sum_probs=41.8

Q ss_pred             CCCccc--cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           28 KNQLVG--VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        28 ~~~~vG--R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -++|++  .+..++++.+++.  ......+.|+|.+|+|||+||+.++++........+++.
T Consensus        14 ~~~~~~~~~~~~~~~l~~~~~--~~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~   73 (226)
T TIGR03420        14 FDNFYAGGNAELLAALRQLAA--GKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP   73 (226)
T ss_pred             hcCcCcCCcHHHHHHHHHHHh--cCCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEe
Confidence            346663  4456777887765  234568999999999999999999997765544555554

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.

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

Probab=98.32  E-value=2.3e-06  Score=77.63  Aligned_cols=118  Identities=22%  Similarity=0.324  Sum_probs=70.9

Q ss_pred             CCccccchhHH---HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           29 NQLVGVESTVE---EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        29 ~~~vGR~~~l~---~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      .++||.+..+.   .|.+++.  .+....+.+||++|+||||||+.++..-+.+-  ..|+......... .++..++.+
T Consensus       138 ~dyvGQ~hlv~q~gllrs~ie--q~~ipSmIlWGppG~GKTtlArlia~tsk~~S--yrfvelSAt~a~t-~dvR~ife~  212 (554)
T KOG2028|consen  138 DDYVGQSHLVGQDGLLRSLIE--QNRIPSMILWGPPGTGKTTLARLIASTSKKHS--YRFVELSATNAKT-NDVRDIFEQ  212 (554)
T ss_pred             HHhcchhhhcCcchHHHHHHH--cCCCCceEEecCCCCchHHHHHHHHhhcCCCc--eEEEEEeccccch-HHHHHHHHH
Confidence            45666654443   2344444  45677888999999999999999998665542  4455421111111 233333222


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEE--EeccHH
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIIL--TTRNKQ  169 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilv--TtR~~~  169 (385)
                      --               -...+.++|.+|++|.|.  +..+-+.|++...   +|..++|  ||.++.
T Consensus       213 aq---------------~~~~l~krkTilFiDEiHRFNksQQD~fLP~VE---~G~I~lIGATTENPS  262 (554)
T KOG2028|consen  213 AQ---------------NEKSLTKRKTILFIDEIHRFNKSQQDTFLPHVE---NGDITLIGATTENPS  262 (554)
T ss_pred             HH---------------HHHhhhcceeEEEeHHhhhhhhhhhhcccceec---cCceEEEecccCCCc
Confidence            21               112456788999999994  5566666666654   5665555  666653

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.31  E-value=5.7e-05  Score=75.57  Aligned_cols=50  Identities=26%  Similarity=0.377  Sum_probs=41.3

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-+++||-+..++.|.+++..+ .-.+.+.++|..|+||||+|+.+++.+
T Consensus        13 ~~f~dviGQe~vv~~L~~~l~~~-rl~ha~Lf~Gp~GvGKTtlAr~lAk~L   62 (618)
T PRK14951         13 RSFSEMVGQEHVVQALTNALTQQ-RLHHAYLFTGTRGVGKTTVSRILAKSL   62 (618)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34578999999999999998843 234677999999999999999998865

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.30  E-value=5.9e-05  Score=74.30  Aligned_cols=50  Identities=24%  Similarity=0.285  Sum_probs=41.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.++||-+..++.|.+++..+ .-...+.++|+.|+||||+|+.+++.+
T Consensus        13 ~~f~divGq~~v~~~L~~~~~~~-~l~ha~Lf~Gp~G~GKTt~A~~lAk~l   62 (509)
T PRK14958         13 RCFQEVIGQAPVVRALSNALDQQ-YLHHAYLFTGTRGVGKTTISRILAKCL   62 (509)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhC-CCCeeEEEECCCCCCHHHHHHHHHHHh
Confidence            34477999999999999999842 234567899999999999999999865

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.29  E-value=3.4e-06  Score=80.06  Aligned_cols=56  Identities=21%  Similarity=0.365  Sum_probs=42.9

Q ss_pred             CCCCCCccccchhHHHHHHhhcCC-----------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVE-----------SKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ....+.+.|+++.++++.+.+...           -..++-+.|+|++|+|||++|+.+++.....|
T Consensus       118 ~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~  184 (364)
T TIGR01242       118 NVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATF  184 (364)
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCE
Confidence            334457899999999998876421           12355699999999999999999999775543

Many proteins may score above the trusted cutoff because an internal

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

Probab=98.28  E-value=2.2e-06  Score=76.26  Aligned_cols=88  Identities=16%  Similarity=0.112  Sum_probs=58.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHHHHHHH-----HhCCCCC-C----ch
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQKLLSN-----LLKDKNV-M----PY  119 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~-----l~~~~~~-~----~~  119 (385)
                      .-+.++|.|.+|+|||||++.+++.+.. +|+..+|+..+.+.   +.+..++++.+...     ...+... .    ..
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er---~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~   91 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDER---PEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMV   91 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCC---CccHHHHHHHhccEEEEecCCCCHHHHHHHHHHH
Confidence            3457899999999999999999997643 68999998854432   15788888888332     2221110 0    12


Q ss_pred             HHHHHHH-hCCceEEEEEeCCCC
Q 044214          120 IDLNFRR-LGHMKVLIVFDDVTC  141 (385)
Q Consensus       120 ~~~l~~~-l~~k~~LlVlDdv~~  141 (385)
                      ......+ -.++++++++|++..
T Consensus        92 ~~~a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          92 LEKAKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             HHHHHHHHHCCCCEEEEEECHHH
Confidence            2222222 347999999999954

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.

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

Probab=98.28  E-value=7.6e-06  Score=65.43  Aligned_cols=23  Identities=39%  Similarity=0.557  Sum_probs=21.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |.|+|++|+|||++|+.+++.+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLG   23 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTT
T ss_pred             CEEECcCCCCeeHHHHHHHhhcc
Confidence            57999999999999999999874

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 ....

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

Probab=98.28  E-value=1.5e-05  Score=82.34  Aligned_cols=49  Identities=27%  Similarity=0.309  Sum_probs=40.5

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++||+++++.+...|...  ...-+.++|.+|+|||++|..+++++..
T Consensus       181 l~~~igr~~ei~~~~~~L~~~--~~~n~lL~G~pG~GKT~l~~~la~~~~~  229 (731)
T TIGR02639       181 IDPLIGREDELERTIQVLCRR--KKNNPLLVGEPGVGKTAIAEGLALRIAE  229 (731)
T ss_pred             CCcccCcHHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            357999999999999988742  3335679999999999999999998643

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

Probab=98.27  E-value=6.8e-06  Score=75.20  Aligned_cols=111  Identities=24%  Similarity=0.318  Sum_probs=80.3

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCC-eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKG-VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~-~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      ...+.+.+|+.++..+..++...+.. +..|.|+|-+|.|||.+.+++.+....   ..+|++ ..+.    +....++.
T Consensus         3 ~l~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~---~~vw~n-~~ec----ft~~~lle   74 (438)
T KOG2543|consen    3 VLEPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL---ENVWLN-CVEC----FTYAILLE   74 (438)
T ss_pred             ccccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC---cceeee-hHHh----ccHHHHHH
Confidence            34678999999999999999865543 556699999999999999999987633   356886 4444    88899999


Q ss_pred             HHHHHHh-CCCCCC----------chHHHHHH--HhC--CceEEEEEeCCCChhh
Q 044214          105 KLLSNLL-KDKNVM----------PYIDLNFR--RLG--HMKVLIVFDDVTCFSQ  144 (385)
Q Consensus       105 ~ll~~l~-~~~~~~----------~~~~~l~~--~l~--~k~~LlVlDdv~~~~~  144 (385)
                      .|+.+.. .+.+..          +....+.+  ...  ++.++|||||++...+
T Consensus        75 ~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD  129 (438)
T KOG2543|consen   75 KILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRD  129 (438)
T ss_pred             HHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhc
Confidence            9999985 222211          22333333  122  4689999999975544

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.27  E-value=1.7e-05  Score=78.23  Aligned_cols=51  Identities=22%  Similarity=0.300  Sum_probs=41.6

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.|...+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~f~diiGq~~~v~~L~~~i~~~-rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~   63 (546)
T PRK14957         13 QSFAEVAGQQHALNSLVHALETQ-KVHHAYLFTGTRGVGKTTLGRLLAKCLN   63 (546)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34467999999999999998742 2345678999999999999999998654

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.27  E-value=1.6e-05  Score=77.25  Aligned_cols=50  Identities=26%  Similarity=0.303  Sum_probs=41.0

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.++||-+..++.|.+.+..+. -.+.+.++|+.|+||||+|+.+++.+
T Consensus        10 ~~f~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~L   59 (491)
T PRK14964         10 SSFKDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCL   59 (491)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHH
Confidence            445789999999999998887422 24578999999999999999998854

>PRK08116 hypothetical protein; Validated

Probab=98.26  E-value=8.3e-06  Score=73.72  Aligned_cols=102  Identities=22%  Similarity=0.243  Sum_probs=59.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      ..+.++|.+|+|||.||..+++.+..+...+++++           ...++..+.........  .....+.+.+.+-. 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~-----------~~~ll~~i~~~~~~~~~--~~~~~~~~~l~~~d-  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN-----------FPQLLNRIKSTYKSSGK--EDENEIIRSLVNAD-  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE-----------HHHHHHHHHHHHhcccc--ccHHHHHHHhcCCC-
Confidence            35889999999999999999998765544445554           23344444433322211  22334445555544 


Q ss_pred             EEEEeCCC--Chhhh--hHhhccCCC-CCCCcEEEEEeccH
Q 044214          133 LIVFDDVT--CFSQL--ESLMGSLDW-LTPVSRIILTTRNK  168 (385)
Q Consensus       133 LlVlDdv~--~~~~~--~~l~~~~~~-~~~gs~ilvTtR~~  168 (385)
                      ||||||+.  ....|  ..+...+.. ...+..+|+||...
T Consensus       181 lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        181 LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            89999993  22222  223222211 12456789998753

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.24  E-value=2.2e-05  Score=72.87  Aligned_cols=161  Identities=18%  Similarity=0.212  Sum_probs=92.8

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEeeccccccCCCChHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      .+++|-+...+.+.+.+..+ .-.+.+.++|+.|+||||+|+.+++.+..      +.+...|.. ..  ... ..+.+ 
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~-~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~-~~--~~~-i~v~~-   77 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKN-RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKP-IN--KKS-IGVDD-   77 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcC-CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecc-cc--CCC-CCHHH-
Confidence            45789888899999998742 23567799999999999999999996522      223223322 11  111 22222 


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEEEeccHHHH-----hhcc
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNKQVL-----RNWR  175 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~-----~~~~  175 (385)
                      .+++...+....            ..+++-++|+|+++  +...++.++..+..-.+++.+|++|.+.+..     ..+.
T Consensus        78 ir~~~~~~~~~p------------~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~  145 (313)
T PRK05564         78 IRNIIEEVNKKP------------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQ  145 (313)
T ss_pred             HHHHHHHHhcCc------------ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhce
Confidence            222222221111            12345566677764  5667888888877666788888888765322     1121


Q ss_pred             ceecccCCC-----------CCCchHHHHHHHHHhCCCccchh
Q 044214          176 VNAFKRNHP-----------DVGNEKLSSNVMKYAQGVPLALK  207 (385)
Q Consensus       176 ~~~~~~~~~-----------~~~~~~~~~~i~~~~~GlPLal~  207 (385)
                      ...|.....           .....+.++.++..++|.|.-+.
T Consensus       146 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        146 IYKLNRLSKEEIEKFISYKYNDIKEEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             eeeCCCcCHHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHH
Confidence            112211100           01223446678888899886544

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.23  E-value=1.5e-05  Score=76.77  Aligned_cols=52  Identities=21%  Similarity=0.273  Sum_probs=42.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-.+++|-+..+..|..++..+. -.+.+.++|+.|+||||+|+.+++.+..
T Consensus        15 ~~f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnc   66 (484)
T PRK14956         15 QFFRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNC   66 (484)
T ss_pred             CCHHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCc
Confidence            345779999999999999988432 2346899999999999999999987643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.23  E-value=2.3e-05  Score=76.32  Aligned_cols=51  Identities=27%  Similarity=0.268  Sum_probs=40.8

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-++++|.+...+.|...+..+. -.+.+.++|++|+||||+|+.+++.+.
T Consensus        11 ~~~~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~~l~   61 (472)
T PRK14962         11 KTFSEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAKSLN   61 (472)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            345779999988888888887322 235688999999999999999998653

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.22  E-value=2.2e-05  Score=76.88  Aligned_cols=51  Identities=29%  Similarity=0.308  Sum_probs=41.6

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.|...+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        18 ~~f~dliGq~~vv~~L~~ai~~~-ri~~a~Lf~Gp~G~GKTT~ArilAk~Ln   68 (507)
T PRK06645         18 SNFAELQGQEVLVKVLSYTILND-RLAGGYLLTGIRGVGKTTSARIIAKAVN   68 (507)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            34467899999999999877742 2346789999999999999999998763

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.22  E-value=2.9e-05  Score=76.89  Aligned_cols=51  Identities=29%  Similarity=0.388  Sum_probs=41.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.|.+++..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~f~divGq~~v~~~L~~~i~~~-~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~   63 (527)
T PRK14969         13 KSFSELVGQEHVVRALTNALEQQ-RLHHAYLFTGTRGVGKTTLARILAKSLN   63 (527)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcC-CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34477999999999999998842 2245678999999999999999998763

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.22  E-value=1.5e-05  Score=78.21  Aligned_cols=51  Identities=29%  Similarity=0.213  Sum_probs=41.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-++++|-+...+.|.+++..+. -.+.+.++|++|+||||+|+.+++.+.
T Consensus        11 ~~~~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~   61 (504)
T PRK14963         11 ITFDEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVN   61 (504)
T ss_pred             CCHHHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            344679999999999999888432 345679999999999999999998764

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.22  E-value=3.6e-05  Score=72.87  Aligned_cols=51  Identities=24%  Similarity=0.293  Sum_probs=41.9

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-..++|.+..++.+.+++..+. -.+.+.++|++|+|||++|+.+++.+.
T Consensus        11 ~~~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~   61 (355)
T TIGR02397        11 QTFEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALN   61 (355)
T ss_pred             CcHhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344678999999999999987422 345788999999999999999998763

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.

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

Probab=98.19  E-value=1.9e-05  Score=69.67  Aligned_cols=242  Identities=16%  Similarity=0.245  Sum_probs=128.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      |..-.+|||-++..++|.-.+..   .....-.|.++|++|.||||||.-+++.+...+.    +. .+..-..|.++..
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k----~t-sGp~leK~gDlaa   96 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLK----IT-SGPALEKPGDLAA   96 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeE----ec-ccccccChhhHHH
Confidence            44457899999888888776652   2234668999999999999999999998765543    22 1112111133332


Q ss_pred             HHHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh-hhhhHhh-ccCC--------CCCCCcE-----------
Q 044214          102 LRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF-SQLESLM-GSLD--------WLTPVSR-----------  160 (385)
Q Consensus       102 l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~-~~~~~l~-~~~~--------~~~~gs~-----------  160 (385)
                      ++..    +.                  ..=+|++|.+... ...++++ +...        ..+++++           
T Consensus        97 iLt~----Le------------------~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTL  154 (332)
T COG2255          97 ILTN----LE------------------EGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTL  154 (332)
T ss_pred             HHhc----CC------------------cCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeE
Confidence            2222    11                  2235667777421 1122221 2111        1233333           


Q ss_pred             EEEEeccHHHHhhcc----c---eec-------------ccCCCCCCchHHHHHHHHHhCCCccchh-HHhHHHHHHHhh
Q 044214          161 IILTTRNKQVLRNWR----V---NAF-------------KRNHPDVGNEKLSSNVMKYAQGVPLALK-VLVWESAISKLQ  219 (385)
Q Consensus       161 ilvTtR~~~~~~~~~----~---~~~-------------~~~~~~~~~~~~~~~i~~~~~GlPLal~-~~~w~~~l~~l~  219 (385)
                      |=.|||.-.+.....    .   .-|             ...-..+..++.+.+|+++..|-|--.. ++.|-.......
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V~  234 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVK  234 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHHh
Confidence            334777432222211    1   000             0011122345678899999999995333 223322222222


Q ss_pred             hccC------cccchhhhhccccCchhhhhhhhhccccC--CCccHHHHHHHHHHcCCchhhhHH-HhhcCCceeEecCC
Q 044214          220 RILH------PSILEVLKISYDSLEDKEKNIFLDVACFF--QGEHVDPVMKFFNASGFYPEIRIS-VLVDKPLIAICSYK  290 (385)
Q Consensus       220 ~~~~------~~~~~~l~~sy~~L~~~~k~~~~~la~fp--~~~~~~~l~~~~~~~g~~~~~~l~-~L~~~sLi~~~~~~  290 (385)
                      ....      ......+..-=..|+...+..+..+.-..  ..+-.+.+......+....++.++ -|++.|+|+....|
T Consensus       235 ~~~~I~~~ia~~aL~~L~Vd~~GLd~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~TiEdv~EPyLiq~gfi~RTpRG  314 (332)
T COG2255         235 GDGDIDRDIADKALKMLDVDELGLDEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRDTIEDVIEPYLIQQGFIQRTPRG  314 (332)
T ss_pred             cCCcccHHHHHHHHHHhCcccccccHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchhHHHHHHhHHHHHhchhhhCCCc
Confidence            1111      12333444444566666666665544333  226667777666655544555544 38999999988888


Q ss_pred             cEE
Q 044214          291 KIR  293 (385)
Q Consensus       291 ~~~  293 (385)
                      +.-
T Consensus       315 R~a  317 (332)
T COG2255         315 RIA  317 (332)
T ss_pred             cee
Confidence            753

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.18  E-value=3.7e-05  Score=80.32  Aligned_cols=51  Identities=16%  Similarity=0.280  Sum_probs=41.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-+.++||+.+++++...|...  ...-+.++|.+|+||||+|..+++++..
T Consensus       184 ~~ld~~iGr~~ei~~~i~~l~r~--~~~n~lLvG~pGvGKTal~~~La~~i~~  234 (852)
T TIGR03345       184 GKIDPVLGRDDEIRQMIDILLRR--RQNNPILTGEAGVGKTAVVEGLALRIAA  234 (852)
T ss_pred             CCCCcccCCHHHHHHHHHHHhcC--CcCceeEECCCCCCHHHHHHHHHHHHhh
Confidence            34467999999999999988742  3335669999999999999999998744

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.

>PRK08727 hypothetical protein; Validated

Probab=98.18  E-value=1.2e-05  Score=71.26  Aligned_cols=58  Identities=19%  Similarity=0.242  Sum_probs=38.6

Q ss_pred             CCCccccch-hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           28 KNQLVGVES-TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        28 ~~~~vGR~~-~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -++|++... .+..+.....  ......+.|+|.+|+|||.|++.+++...+....+.++.
T Consensus        18 f~~f~~~~~n~~~~~~~~~~--~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~   76 (233)
T PRK08727         18 FDSYIAAPDGLLAQLQALAA--GQSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP   76 (233)
T ss_pred             hhhccCCcHHHHHHHHHHHh--ccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            355666553 3444443332  122346999999999999999999998766555566665

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

Probab=98.17  E-value=4.8e-05  Score=68.55  Aligned_cols=110  Identities=15%  Similarity=0.135  Sum_probs=74.1

Q ss_pred             CCCCccccc---hhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC------ceEEEeeccccccCC
Q 044214           27 NKNQLVGVE---STVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD------GSCFLENVREESQIP   96 (385)
Q Consensus        27 ~~~~~vGR~---~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~------~~~w~~~~~~~~~~~   96 (385)
                      ..+..||-.   ..++.|.++|.. .....+-+.|+|.+|.|||++++++.......++      .++.+.    .... 
T Consensus        32 ~~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq----~P~~-  106 (302)
T PF05621_consen   32 RADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQ----MPPE-  106 (302)
T ss_pred             hcCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEe----cCCC-
Confidence            346778865   345566666664 3345678999999999999999999986533332      122222    2223 


Q ss_pred             CChHHHHHHHHHHHhCCCCCC----chHHHHHHHhCC-ceEEEEEeCCCC
Q 044214           97 GGLSCLRQKLLSNLLKDKNVM----PYIDLNFRRLGH-MKVLIVFDDVTC  141 (385)
Q Consensus        97 ~~~~~l~~~ll~~l~~~~~~~----~~~~~l~~~l~~-k~~LlVlDdv~~  141 (385)
                      ++...+...|+..++.+....    .........++. +.-+||+|++.+
T Consensus       107 p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~  156 (302)
T PF05621_consen  107 PDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHN  156 (302)
T ss_pred             CChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHH
Confidence            889999999999998876533    333334445544 556899999954

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

>PF14516 AAA_35: AAA-like domain

Probab=98.17  E-value=0.00044  Score=64.64  Aligned_cols=114  Identities=8%  Similarity=0.071  Sum_probs=72.5

Q ss_pred             CCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeecccccc-CCCChHHH
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQ-IPGGLSCL  102 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~-~~~~~~~l  102 (385)
                      .+...+.+|.|...-+++.+.+...   -..+.|.|+-.+|||+|..++.+..++.-...++++ ...... ...+...+
T Consensus         6 ~~~~~~~Yi~R~~~e~~~~~~i~~~---G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id-~~~~~~~~~~~~~~f   81 (331)
T PF14516_consen    6 LPLDSPFYIERPPAEQECYQEIVQP---GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYID-LQQLGSAIFSDLEQF   81 (331)
T ss_pred             CCCCCCcccCchHHHHHHHHHHhcC---CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEE-eecCCCcccCCHHHH
Confidence            3566678889996666777666631   238899999999999999999988755433444554 333222 21456666


Q ss_pred             HHHHHHHHhCCCC---C------------CchHHHHHHH-h--CCceEEEEEeCCCC
Q 044214          103 RQKLLSNLLKDKN---V------------MPYIDLNFRR-L--GHMKVLIVFDDVTC  141 (385)
Q Consensus       103 ~~~ll~~l~~~~~---~------------~~~~~~l~~~-l--~~k~~LlVlDdv~~  141 (385)
                      ++.++..+...-.   .            ......+.+. +  .+++.+|++|+++.
T Consensus        82 ~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~  138 (331)
T PF14516_consen   82 LRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDR  138 (331)
T ss_pred             HHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhh
Confidence            6666665543321   0            0222233332 2  25899999999973

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.17  E-value=0.00018  Score=71.38  Aligned_cols=51  Identities=29%  Similarity=0.279  Sum_probs=42.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|++..++.+.+.+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~F~dIIGQe~iv~~L~~aI~~~-rl~hA~Lf~GP~GvGKTTlA~~lAk~L~   63 (605)
T PRK05896         13 HNFKQIIGQELIKKILVNAILNN-KLTHAYIFSGPRGIGKTSIAKIFAKAIN   63 (605)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            34578999999999999998742 2346788999999999999999998763

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

Probab=98.16  E-value=1.5e-05  Score=69.56  Aligned_cols=56  Identities=18%  Similarity=0.383  Sum_probs=43.1

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+..-+.++|.+.+.+.|.+-...  ......-+.+||..|.|||++++++.+.+.+.
T Consensus        22 ~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   22 DPIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            355557899999999988774431  12345578899999999999999999987654

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.16  E-value=3.7e-05  Score=73.77  Aligned_cols=51  Identities=22%  Similarity=0.254  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+...+.|.+++..+. -...+.++|+.|+||||+|..+++.+.
T Consensus        13 ~~~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~   63 (397)
T PRK14955         13 KKFADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVN   63 (397)
T ss_pred             CcHhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhc
Confidence            345789999999999999888422 244588999999999999999998764

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.16  E-value=4.9e-05  Score=79.57  Aligned_cols=47  Identities=28%  Similarity=0.452  Sum_probs=39.7

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++||+++++++...|...  ...-+.++|.+|+|||++|..+++++.
T Consensus       179 ~~~igr~~ei~~~~~~L~r~--~~~n~lL~G~pGvGKTal~~~la~~i~  225 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRR--TKNNPILIGEPGVGKTAIAEGLAQRIV  225 (821)
T ss_pred             CCCCCcHHHHHHHHHHHccc--ccCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999842  233457999999999999999999764

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.15  E-value=2e-05  Score=69.70  Aligned_cols=59  Identities=17%  Similarity=0.317  Sum_probs=37.6

Q ss_pred             CCCcc-ccchhH-HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           28 KNQLV-GVESTV-EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        28 ~~~~v-GR~~~l-~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -++|+ |..... ..+.++... ......+.|+|.+|+|||+||+.+++.....-...+++.
T Consensus        17 ~d~f~~~~~~~~~~~l~~~~~~-~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~   77 (227)
T PRK08903         17 FDNFVAGENAELVARLRELAAG-PVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLD   77 (227)
T ss_pred             hcccccCCcHHHHHHHHHHHhc-cCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            35555 554444 444554442 233457889999999999999999997643333344444

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

Probab=98.15  E-value=8.9e-06  Score=82.97  Aligned_cols=53  Identities=26%  Similarity=0.441  Sum_probs=41.1

Q ss_pred             CCCCCccccchhHH---HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           26 DNKNQLVGVESTVE---EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        26 ~~~~~~vGR~~~l~---~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..-++|+|.+..+.   .+.+.+.  .+....+.++|++|+||||||+.+++.....|
T Consensus        25 ~tldd~vGQe~ii~~~~~L~~~i~--~~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f   80 (725)
T PRK13341         25 RTLEEFVGQDHILGEGRLLRRAIK--ADRVGSLILYGPPGVGKTTLARIIANHTRAHF   80 (725)
T ss_pred             CcHHHhcCcHHHhhhhHHHHHHHh--cCCCceEEEECCCCCCHHHHHHHHHHHhcCcc
Confidence            33467899998874   5666666  34556778999999999999999999776555

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.15  E-value=2.2e-05  Score=73.62  Aligned_cols=54  Identities=24%  Similarity=0.204  Sum_probs=44.9

Q ss_pred             CCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .|.....++|-+...+.+...+..+. -...+.|+|+.|+||||+|..+++.+-.
T Consensus        18 ~P~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~~Llc   71 (351)
T PRK09112         18 SPSENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLANHILS   71 (351)
T ss_pred             CCCchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHHHHcC
Confidence            45666789999999999999998432 3457899999999999999999997644

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.14  E-value=3.1e-05  Score=77.61  Aligned_cols=52  Identities=27%  Similarity=0.325  Sum_probs=42.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-.++||-+..++.|.+.+..+. -.+.+.++|..|+||||+|+.+++.+..
T Consensus        13 ~~f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c   64 (647)
T PRK07994         13 QTFAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNC   64 (647)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhh
Confidence            445789999999999999988432 2456789999999999999999986543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.13  E-value=1.6e-05  Score=75.93  Aligned_cols=53  Identities=19%  Similarity=0.330  Sum_probs=41.3

Q ss_pred             CCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...+.+.|+++.++++.+.+..           +-..++-|.++|++|+|||++|+.+++....
T Consensus       128 ~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~  191 (389)
T PRK03992        128 VTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNA  191 (389)
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCC
Confidence            3345688999999999887631           1134567999999999999999999997653

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.12  E-value=8.7e-05  Score=74.71  Aligned_cols=51  Identities=25%  Similarity=0.332  Sum_probs=41.8

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.|..++..+. -.+.+.++|..|+||||+|+.+++.+.
T Consensus        13 ~~~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~   63 (585)
T PRK14950         13 QTFAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVN   63 (585)
T ss_pred             CCHHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344789999999999999887432 345678999999999999999998764

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.11  E-value=3e-05  Score=81.24  Aligned_cols=49  Identities=18%  Similarity=0.299  Sum_probs=40.6

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++||+.+++++...|...  ...-+.++|.+|+|||++|..++.++..
T Consensus       177 l~~vigr~~ei~~~i~iL~r~--~~~n~lL~G~pGvGKT~l~~~la~~i~~  225 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRIIN  225 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcC--CcCceEEECCCCCCHHHHHHHHHHHhhc
Confidence            356999999999999988842  3335669999999999999999998743

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.11  E-value=0.0001  Score=63.05  Aligned_cols=37  Identities=22%  Similarity=0.234  Sum_probs=27.6

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+.+.+.. ..-...+.++|+.|+|||++|+.+.+.+.
T Consensus         3 ~l~~~i~~-~~~~~~~L~~G~~G~gkt~~a~~~~~~l~   39 (188)
T TIGR00678         3 QLKRALEK-GRLAHAYLFAGPEGVGKELLALALAKALL   39 (188)
T ss_pred             HHHHHHHc-CCCCeEEEEECCCCCCHHHHHHHHHHHHc
Confidence            34555542 12246789999999999999999998764

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.

>TIGR00767 rho transcription termination factor Rho

Probab=98.10  E-value=1.1e-05  Score=75.59  Aligned_cols=88  Identities=16%  Similarity=0.121  Sum_probs=60.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC----------chH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM----------PYI  120 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~----------~~~  120 (385)
                      -+.++|+|.+|+|||||++.+++.+... |+..+|+..+++.   +..+.++++.+...+.....+.          ...
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER---~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDER---PEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCC---CccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            4579999999999999999999977554 9999999855332   2678888888855443222211          111


Q ss_pred             HHHHHH-hCCceEEEEEeCCCCh
Q 044214          121 DLNFRR-LGHMKVLIVFDDVTCF  142 (385)
Q Consensus       121 ~~l~~~-l~~k~~LlVlDdv~~~  142 (385)
                      +..... -.+++++|++|++...
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHH
Confidence            122222 3579999999999643

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

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.10  E-value=4.7e-05  Score=72.46  Aligned_cols=49  Identities=27%  Similarity=0.304  Sum_probs=40.2

Q ss_pred             CCccccchhHHHHHHhhcCCCC--------CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESK--------GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~--------~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++++|-+..++.|.+++..+.+        -.+.+.++|++|+|||++|+.+++.+-
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~   61 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQ   61 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            4688999999999999885321        356789999999999999999998653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.09  E-value=4.2e-05  Score=74.19  Aligned_cols=94  Identities=15%  Similarity=0.182  Sum_probs=54.5

Q ss_pred             ccccchhHH--HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC--ceEEEeeccccccCCCChHHHHHHH
Q 044214           31 LVGVESTVE--EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD--GSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        31 ~vGR~~~l~--~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~--~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      ++|-.....  ...+.... .+....+.|+|.+|+|||.|++.+++.+...++  .++|++           ..++...+
T Consensus       108 v~g~~n~~a~~~~~~~~~~-~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~-----------~~~f~~~~  175 (440)
T PRK14088        108 VVGPGNSFAYHAALEVAKN-PGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT-----------SEKFLNDL  175 (440)
T ss_pred             ccCCchHHHHHHHHHHHhC-cCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHH
Confidence            347544432  33333332 223446999999999999999999998766543  233443           22344444


Q ss_pred             HHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCC
Q 044214          107 LSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTC  141 (385)
Q Consensus       107 l~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~  141 (385)
                      ...+...     ....+.+.+..+.-+|++||++.
T Consensus       176 ~~~~~~~-----~~~~f~~~~~~~~dvLlIDDi~~  205 (440)
T PRK14088        176 VDSMKEG-----KLNEFREKYRKKVDVLLIDDVQF  205 (440)
T ss_pred             HHHHhcc-----cHHHHHHHHHhcCCEEEEechhh
Confidence            4443221     12334444444556899999963

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.08  E-value=0.00026  Score=70.92  Aligned_cols=52  Identities=25%  Similarity=0.362  Sum_probs=42.9

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-.+++|.+..++.|.+.+..+. -...+.++|+.|+||||+|+.+++.+..
T Consensus        21 ~~f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c   72 (598)
T PRK09111         21 QTFDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARALNY   72 (598)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhhCc
Confidence            345789999999999999998432 3457889999999999999999997643

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.08  E-value=2e-05  Score=73.31  Aligned_cols=51  Identities=20%  Similarity=0.199  Sum_probs=42.1

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+...+.+..++..+ .-..++.++|++|+|||++|+.+++...
T Consensus        18 ~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lll~G~~G~GKT~la~~l~~~~~   68 (316)
T PHA02544         18 STIDECILPAADKETFKSIVKKG-RIPNMLLHSPSPGTGKTTVAKALCNEVG   68 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcC-CCCeEEEeeCcCCCCHHHHHHHHHHHhC
Confidence            44577999999999999998742 2356777899999999999999998764

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.08  E-value=7.4e-05  Score=71.08  Aligned_cols=51  Identities=27%  Similarity=0.326  Sum_probs=42.3

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+...+.+.+.+..+ .-.+.+.++|++|+|||++|+.+++.+.
T Consensus        14 ~~~~~iig~~~~~~~l~~~i~~~-~~~~~~L~~G~~G~GKt~~a~~la~~l~   64 (367)
T PRK14970         14 QTFDDVVGQSHITNTLLNAIENN-HLAQALLFCGPRGVGKTTCARILARKIN   64 (367)
T ss_pred             CcHHhcCCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34477899999999999999842 2346888999999999999999998764

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.06  E-value=2.5e-05  Score=69.32  Aligned_cols=57  Identities=14%  Similarity=0.246  Sum_probs=37.3

Q ss_pred             CCcc-ccc-hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           29 NQLV-GVE-STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        29 ~~~v-GR~-~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+ |-. ..+..+.++...  ...+.+.|+|++|+|||+|++.+++........+.++.
T Consensus        22 d~f~~~~n~~a~~~l~~~~~~--~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~   80 (235)
T PRK08084         22 ASFYPGDNDSLLAALQNALRQ--EHSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVP   80 (235)
T ss_pred             cccccCccHHHHHHHHHHHhC--CCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            3454 633 334445554432  23357899999999999999999997765544455554

>PRK05642 DNA replication initiation factor; Validated

Probab=98.04  E-value=3.2e-05  Score=68.55  Aligned_cols=35  Identities=17%  Similarity=0.435  Sum_probs=28.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+.|+|..|+|||.|++.+++.+...-..++|++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~   80 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLP   80 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEee
Confidence            57899999999999999999987765445566665

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

Probab=98.02  E-value=2.3e-05  Score=68.73  Aligned_cols=120  Identities=20%  Similarity=0.303  Sum_probs=67.0

Q ss_pred             CccccchhHH-HHHHhh-cCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc--eEEEeeccccccCCCChHHHHHH
Q 044214           30 QLVGVESTVE-EIESLL-GVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG--SCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        30 ~~vGR~~~l~-~l~~~L-~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~--~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      .++|-..+.. .....+ .........+.|+|..|+|||.|.+++++.+.+..+.  +++++           ..++...
T Consensus        10 fv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~-----------~~~f~~~   78 (219)
T PF00308_consen   10 FVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS-----------AEEFIRE   78 (219)
T ss_dssp             S--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE-----------HHHHHHH
T ss_pred             CCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec-----------HHHHHHH
Confidence            3457544432 333333 3323334568899999999999999999987654332  33433           3344444


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh---hhhh----HhhccCCCCCCCcEEEEEeccH
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF---SQLE----SLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~~~----~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      +...+..     .....+++.+++-. +|++||++..   ..|+    .+...+.  ..|.+||+|++..
T Consensus        79 ~~~~~~~-----~~~~~~~~~~~~~D-lL~iDDi~~l~~~~~~q~~lf~l~n~~~--~~~k~li~ts~~~  140 (219)
T PF00308_consen   79 FADALRD-----GEIEEFKDRLRSAD-LLIIDDIQFLAGKQRTQEELFHLFNRLI--ESGKQLILTSDRP  140 (219)
T ss_dssp             HHHHHHT-----TSHHHHHHHHCTSS-EEEEETGGGGTTHHHHHHHHHHHHHHHH--HTTSEEEEEESS-
T ss_pred             HHHHHHc-----ccchhhhhhhhcCC-EEEEecchhhcCchHHHHHHHHHHHHHH--hhCCeEEEEeCCC
Confidence            5444433     23345566666443 6789999642   2222    2222222  2466899999653

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.00  E-value=2.8e-05  Score=70.28  Aligned_cols=48  Identities=29%  Similarity=0.374  Sum_probs=33.8

Q ss_pred             CccccchhHHHHHHhhc-------------CCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           30 QLVGVESTVEEIESLLG-------------VESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~-------------~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++|.+...+++.+...             ...+....+.++|++|+||||+|+.+++.+.
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~   67 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFK   67 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHH
Confidence            37787766666553321             0123456788999999999999999998753

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.

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

Probab=97.99  E-value=0.0002  Score=63.94  Aligned_cols=125  Identities=17%  Similarity=0.200  Sum_probs=77.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh--CCCCceEEEeeccccccCCCChHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS--GDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~--~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      |....+++|-+..+..|.+.+..  ...+....+|++|.|||+-|+.++.++-  +-|++++--.+.+....    .. +
T Consensus        32 Pkt~de~~gQe~vV~~L~~a~~~--~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderG----is-v  104 (346)
T KOG0989|consen   32 PKTFDELAGQEHVVQVLKNALLR--RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERG----IS-V  104 (346)
T ss_pred             CCcHHhhcchHHHHHHHHHHHhh--cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccc----cc-c
Confidence            34457799999999999999884  5667889999999999999999998763  34666655333333211    11 0


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHh---C---Cce-EEEEEeCCCC--hhhhhHhhccCCCCCCCcEE-EEEec
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRL---G---HMK-VLIVFDDVTC--FSQLESLMGSLDWLTPVSRI-ILTTR  166 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l---~---~k~-~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~i-lvTtR  166 (385)
                      .        ..  +......+....   .   .++ -.+|||+++.  .+.|..+...........+. +||+-
T Consensus       105 v--------r~--Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcny  168 (346)
T KOG0989|consen  105 V--------RE--KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNY  168 (346)
T ss_pred             h--------hh--hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCC
Confidence            0        00  000111111111   0   122 4789999975  46688888777765556555 44443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.99  E-value=5.7e-05  Score=79.36  Aligned_cols=49  Identities=18%  Similarity=0.314  Sum_probs=40.3

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++||+.+++++...|...  ...-+.++|.+|+|||++|..+++++..
T Consensus       172 ~~~~igr~~ei~~~~~~l~r~--~~~n~lL~G~pGvGKT~l~~~la~~i~~  220 (852)
T TIGR03346       172 LDPVIGRDEEIRRTIQVLSRR--TKNNPVLIGEPGVGKTAIVEGLAQRIVN  220 (852)
T ss_pred             CCcCCCcHHHHHHHHHHHhcC--CCCceEEEcCCCCCHHHHHHHHHHHHhc
Confidence            356999999999999998743  2334568999999999999999998754

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.

>PRK12377 putative replication protein; Provisional

Probab=97.98  E-value=2.8e-05  Score=69.15  Aligned_cols=72  Identities=17%  Similarity=0.170  Sum_probs=45.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      ...+.++|.+|+|||.||.++++.+......+++++           ..++...+-......    .....+.+.+ .+.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~-----------~~~l~~~l~~~~~~~----~~~~~~l~~l-~~~  164 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVT-----------VPDVMSRLHESYDNG----QSGEKFLQEL-CKV  164 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEE-----------HHHHHHHHHHHHhcc----chHHHHHHHh-cCC
Confidence            357899999999999999999998876655566665           223333333322111    1112233333 345


Q ss_pred             EEEEEeCC
Q 044214          132 VLIVFDDV  139 (385)
Q Consensus       132 ~LlVlDdv  139 (385)
                      =||||||+
T Consensus       165 dLLiIDDl  172 (248)
T PRK12377        165 DLLVLDEI  172 (248)
T ss_pred             CEEEEcCC
Confidence            68999999

>PRK08181 transposase; Validated

Probab=97.98  E-value=5e-05  Score=68.38  Aligned_cols=99  Identities=20%  Similarity=0.170  Sum_probs=54.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      .-+.++|++|+|||.||..+++........+.|+.           ..++...+.....    +.. .....+.+. +.=
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~-----------~~~L~~~l~~a~~----~~~-~~~~l~~l~-~~d  169 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR-----------TTDLVQKLQVARR----ELQ-LESAIAKLD-KFD  169 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeee-----------HHHHHHHHHHHHh----CCc-HHHHHHHHh-cCC
Confidence            35899999999999999999997765544455554           2334444432211    111 112222332 334


Q ss_pred             EEEEeCCCC----hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          133 LIVFDDVTC----FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       133 LlVlDdv~~----~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ||||||+..    ......++..+.....+..+||||...
T Consensus       170 LLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        170 LLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             EEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            999999942    111122332222111123588888754

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.97  E-value=4.1e-05  Score=61.49  Aligned_cols=35  Identities=31%  Similarity=0.418  Sum_probs=27.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+.|+|++|+||||+|+.++..+......++++.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~   37 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYID   37 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEEC
Confidence            47899999999999999999997766543444554

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.

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

Probab=97.96  E-value=0.00016  Score=69.22  Aligned_cols=223  Identities=15%  Similarity=0.116  Sum_probs=121.2

Q ss_pred             hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCC
Q 044214           36 STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKN  115 (385)
Q Consensus        36 ~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~  115 (385)
                      .-+.++.+.+...  .. ++.|.|+-++||||+++.+.....+.   .+++........    -..+ .+.+.       
T Consensus        24 ~~~~~l~~~~~~~--~~-i~~i~GpR~~GKTtll~~l~~~~~~~---~iy~~~~d~~~~----~~~l-~d~~~-------   85 (398)
T COG1373          24 KLLPRLIKKLDLR--PF-IILILGPRQVGKTTLLKLLIKGLLEE---IIYINFDDLRLD----RIEL-LDLLR-------   85 (398)
T ss_pred             hhhHHHHhhcccC--Cc-EEEEECCccccHHHHHHHHHhhCCcc---eEEEEecchhcc----hhhH-HHHHH-------
Confidence            4445555555422  22 99999999999999997777665544   555552222211    1111 11111       


Q ss_pred             CCchHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHhhccceecccC-----CCCCCchH
Q 044214          116 VMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVNAFKRN-----HPDVGNEK  190 (385)
Q Consensus       116 ~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~~~~~~~~-----~~~~~~~~  190 (385)
                            .+...-..++..++||.|.....|...+..+.+.++. +|++|+-+...........+...     -.+-.+.+
T Consensus        86 ------~~~~~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~E  158 (398)
T COG1373          86 ------AYIELKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFRE  158 (398)
T ss_pred             ------HHHHhhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHH
Confidence                  1111111277899999999999999999888876666 88888877655443322111110     00111222


Q ss_pred             H---------------HHHHHHHhCCCccchhHHhHHHHHHH-hhhccCcccchhhhhcc-ccCchhhhhhhhhcccc-C
Q 044214          191 L---------------SSNVMKYAQGVPLALKVLVWESAISK-LQRILHPSILEVLKISY-DSLEDKEKNIFLDVACF-F  252 (385)
Q Consensus       191 ~---------------~~~i~~~~~GlPLal~~~~w~~~l~~-l~~~~~~~~~~~l~~sy-~~L~~~~k~~~~~la~f-p  252 (385)
                      .               .-+-.-.+||.|.++..-.-+..+.. +......   ++....- ... +..+..+.+++-. +
T Consensus       159 fl~~~~~~~~~~~~~~~f~~Yl~~GGfP~~v~~~~~~~~~~~~~~~~~~~---Di~~~~~~~~~-~~~k~i~~~l~~~~g  234 (398)
T COG1373         159 FLKLKGEEIEPSKLELLFEKYLETGGFPESVKADLSEKKLKEYLDTILKR---DIIERGKIENA-DLMKRILRFLASNIG  234 (398)
T ss_pred             HHhhcccccchhHHHHHHHHHHHhCCCcHHHhCcchhhHHHHHHHHHHHH---HHHHHcCcccH-HHHHHHHHHHHhhcC
Confidence            2               22233457999988874310000001 1110001   1111111 111 3556666655555 5


Q ss_pred             CCccHHHHHHHHH-HcCCchhhhHHHhhcCCceeEe
Q 044214          253 QGEHVDPVMKFFN-ASGFYPEIRISVLVDKPLIAIC  287 (385)
Q Consensus       253 ~~~~~~~l~~~~~-~~g~~~~~~l~~L~~~sLi~~~  287 (385)
                      +.++.+.+.+.+. -+.-....+++-|.+.-++...
T Consensus       235 ~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~~  270 (398)
T COG1373         235 SPISYSSLARELKGISKDTIRKYLSYLEDAFLLFLV  270 (398)
T ss_pred             CccCHHHHHHHHhccchHHHHHHHHHHHHhhheEEe
Confidence            5689999999884 4444466788888888887743

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.96  E-value=7.3e-05  Score=66.33  Aligned_cols=88  Identities=13%  Similarity=0.150  Sum_probs=50.9

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM  117 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~  117 (385)
                      +..+.+....-......+.++|.+|+|||+||..+++.+......+++++           +.++...+-..... . + 
T Consensus        85 l~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it-----------~~~l~~~l~~~~~~-~-~-  150 (244)
T PRK07952         85 LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT-----------VADIMSAMKDTFSN-S-E-  150 (244)
T ss_pred             HHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE-----------HHHHHHHHHHHHhh-c-c-
Confidence            44444444432223457899999999999999999998765545555554           23333333322211 1 1 


Q ss_pred             chHHHHHHHhCCceEEEEEeCCC
Q 044214          118 PYIDLNFRRLGHMKVLIVFDDVT  140 (385)
Q Consensus       118 ~~~~~l~~~l~~k~~LlVlDdv~  140 (385)
                      .....+.+.+.+ .=+||+||+.
T Consensus       151 ~~~~~~l~~l~~-~dlLvIDDig  172 (244)
T PRK07952        151 TSEEQLLNDLSN-VDLLVIDEIG  172 (244)
T ss_pred             ccHHHHHHHhcc-CCEEEEeCCC
Confidence            122234444553 4478889994

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.92  E-value=5.4e-05  Score=73.53  Aligned_cols=122  Identities=16%  Similarity=0.262  Sum_probs=64.9

Q ss_pred             ccccchh--HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC--ceEEEeeccccccCCCChHHHHHHH
Q 044214           31 LVGVEST--VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD--GSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        31 ~vGR~~~--l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~--~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      ++|....  ......+..........+.|+|..|+|||.|++++++.+.....  .+++++           ..++...+
T Consensus       118 v~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~-----------~~~f~~~~  186 (450)
T PRK14087        118 VIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS-----------GDEFARKA  186 (450)
T ss_pred             cCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHH
Confidence            4565543  23333333322223356889999999999999999997654332  223332           23455555


Q ss_pred             HHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh----hhhhHhhccCCC-CCCCcEEEEEecc
Q 044214          107 LSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF----SQLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       107 l~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----~~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      ...+....   .....+.+.++. .-+||+||+...    ...+.+...+.. ...|..||+|+..
T Consensus       187 ~~~l~~~~---~~~~~~~~~~~~-~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~  248 (450)
T PRK14087        187 VDILQKTH---KEIEQFKNEICQ-NDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDK  248 (450)
T ss_pred             HHHHHHhh---hHHHHHHHHhcc-CCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCC
Confidence            55443211   223344444543 347888999532    122333322211 1234578888754

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.91  E-value=0.00038  Score=68.28  Aligned_cols=51  Identities=25%  Similarity=0.283  Sum_probs=41.6

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-..++|-+..++.|.+++..+. -.+.+.++|+.|+||||+|+.++..+.
T Consensus        13 ~~f~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~L~   63 (486)
T PRK14953         13 KFFKEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKVLN   63 (486)
T ss_pred             CcHHHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344679999999999999998432 345678899999999999999998753

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.90  E-value=0.00027  Score=68.74  Aligned_cols=51  Identities=25%  Similarity=0.389  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+..++.|.+++..+. -.+.+.++|+.|+||||+|+.+++.+.
T Consensus        14 ~~~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~l~   64 (451)
T PRK06305         14 QTFSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKALN   64 (451)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            345789999999999999997321 245688999999999999999998763

>PRK10536 hypothetical protein; Provisional

Probab=97.90  E-value=0.00011  Score=65.04  Aligned_cols=132  Identities=14%  Similarity=0.213  Sum_probs=74.7

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH-h-hCCCCceEEEeecccccc----CCCChHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK-I-SGDFDGSCFLENVREESQ----IPGGLSCL  102 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~-~-~~~f~~~~w~~~~~~~~~----~~~~~~~l  102 (385)
                      ..+.+|......+..++..  .  ..|.+.|.+|+|||+||.+++.+ + .+.|...+.....-....    .|.+..+-
T Consensus        55 ~~i~p~n~~Q~~~l~al~~--~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~~~eK  130 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES--K--QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIAEK  130 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc--C--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCCHHHH
Confidence            4567788888888888873  2  38999999999999999999874 4 445554443321111100    11222221


Q ss_pred             HHHHHHH----HhCCCCCCchHHHH------------HHHhCCce---EEEEEeCCCC--hhhhhHhhccCCCCCCCcEE
Q 044214          103 RQKLLSN----LLKDKNVMPYIDLN------------FRRLGHMK---VLIVFDDVTC--FSQLESLMGSLDWLTPVSRI  161 (385)
Q Consensus       103 ~~~ll~~----l~~~~~~~~~~~~l------------~~~l~~k~---~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~i  161 (385)
                      ..-.+..    +..-.. ....+.+            ..+++++.   -++|+|.+.+  ..+...++...   +.+|++
T Consensus       131 ~~p~~~pi~D~L~~~~~-~~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~ltR~---g~~sk~  206 (262)
T PRK10536        131 FAPYFRPVYDVLVRRLG-ASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFLTRL---GENVTV  206 (262)
T ss_pred             HHHHHHHHHHHHHHHhC-hHHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHHhhc---CCCCEE
Confidence            1111111    111000 0111111            12455655   4999999964  45566666554   589999


Q ss_pred             EEEeccH
Q 044214          162 ILTTRNK  168 (385)
Q Consensus       162 lvTtR~~  168 (385)
                      |+|--..
T Consensus       207 v~~GD~~  213 (262)
T PRK10536        207 IVNGDIT  213 (262)
T ss_pred             EEeCChh
Confidence            9987543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.90  E-value=6.9e-05  Score=73.22  Aligned_cols=120  Identities=17%  Similarity=0.211  Sum_probs=63.9

Q ss_pred             ccccchh--HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc--eEEEeeccccccCCCChHHHHHHH
Q 044214           31 LVGVEST--VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG--SCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        31 ~vGR~~~--l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~--~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      .+|....  ......+..........+.|+|.+|+|||.|++.+++.+...++.  ++++.           ...+...+
T Consensus       125 v~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~-----------~~~~~~~~  193 (450)
T PRK00149        125 VVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVT-----------SEKFTNDF  193 (450)
T ss_pred             ccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHH
Confidence            4465543  233444433322234568999999999999999999988766533  33333           22333334


Q ss_pred             HHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh---h-hhhHhhccCCC-CCCCcEEEEEecc
Q 044214          107 LSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF---S-QLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       107 l~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~-~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      ...+..     .....+.+.+++ .-+|+|||++..   . ..+.++..+.. ...|..+++||..
T Consensus       194 ~~~~~~-----~~~~~~~~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~  253 (450)
T PRK00149        194 VNALRN-----NTMEEFKEKYRS-VDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDR  253 (450)
T ss_pred             HHHHHc-----CcHHHHHHHHhc-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCC
Confidence            333322     122344444443 448899999532   1 12223221110 1234557777764

>PRK06921 hypothetical protein; Provisional

Probab=97.90  E-value=3.5e-05  Score=69.57  Aligned_cols=36  Identities=17%  Similarity=0.212  Sum_probs=29.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      ...+.++|.+|+|||.||.++++.+..+ ...++++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            4578999999999999999999987655 45566665

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.90  E-value=0.00027  Score=69.46  Aligned_cols=50  Identities=26%  Similarity=0.315  Sum_probs=41.1

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.+++|-+...+.|...+..+ .-.+++.++|+.|+||||+|+.+++.+
T Consensus        11 ~~fdeiiGqe~v~~~L~~~I~~g-rl~hayLf~Gp~G~GKTt~Ar~LAk~L   60 (535)
T PRK08451         11 KHFDELIGQESVSKTLSLALDNN-RLAHAYLFSGLRGSGKTSSARIFARAL   60 (535)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcC-CCCeeEEEECCCCCcHHHHHHHHHHHh
Confidence            34477999999999999998743 234567899999999999999999875

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.89  E-value=0.00015  Score=72.31  Aligned_cols=51  Identities=27%  Similarity=0.281  Sum_probs=41.8

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+..++.|.+++..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        10 ~~f~eivGq~~i~~~L~~~i~~~-r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~   60 (584)
T PRK14952         10 ATFAEVVGQEHVTEPLSSALDAG-RINHAYLFSGPRGCGKTSSARILARSLN   60 (584)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34478999999999999999842 2344678999999999999999998764

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.89  E-value=5e-05  Score=74.20  Aligned_cols=55  Identities=24%  Similarity=0.381  Sum_probs=41.9

Q ss_pred             CCCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...-..+.|.+..++++.+.+..           +-..++-+.++|++|+|||++|+.+++.+...
T Consensus       178 ~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~  243 (512)
T TIGR03689       178 DVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQR  243 (512)
T ss_pred             CCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccc
Confidence            33446688899999998887531           11235678999999999999999999987554

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.89  E-value=0.00011  Score=76.16  Aligned_cols=51  Identities=24%  Similarity=0.268  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.++||.+..++.|.+++..+ .-.+.+.++|..|+||||+|+.+++.+.
T Consensus        12 ~~f~eiiGqe~v~~~L~~~i~~~-ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~   62 (824)
T PRK07764         12 ATFAEVIGQEHVTEPLSTALDSG-RINHAYLFSGPRGCGKTSSARILARSLN   62 (824)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhC-CCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            34467999999999999999842 2235688999999999999999998764

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

Probab=97.87  E-value=3.4e-05  Score=73.51  Aligned_cols=100  Identities=19%  Similarity=0.194  Sum_probs=62.4

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC--CCCceEEEeeccccccCCCChHHHHHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG--DFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~--~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      .++++.++.++.+...|...    +.+.++|++|+|||++|+.+++.+..  .|..+.|+.    ..+. .+..++....
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~Vt----FHps-ySYeDFI~G~  245 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQ----FHQS-YSYEDFIQGY  245 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEe----eccc-ccHHHHhccc
Confidence            45778888999999888732    36788999999999999999997743  455666666    2222 4444333211


Q ss_pred             HHHHhCCCCCC-----chHHHHHHHhC--CceEEEEEeCCCC
Q 044214          107 LSNLLKDKNVM-----PYIDLNFRRLG--HMKVLIVFDDVTC  141 (385)
Q Consensus       107 l~~l~~~~~~~-----~~~~~l~~~l~--~k~~LlVlDdv~~  141 (385)
                          .+.....     -..+.+.....  +++++||+|+++.
T Consensus       246 ----rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINR  283 (459)
T PRK11331        246 ----RPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINR  283 (459)
T ss_pred             ----CCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhc
Confidence                1111111     11222222222  4689999999964

>PRK09183 transposase/IS protein; Provisional

Probab=97.87  E-value=6.1e-05  Score=67.75  Aligned_cols=34  Identities=24%  Similarity=0.151  Sum_probs=25.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ..+.|+|++|+|||+||..++.........+.++
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~  136 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFT  136 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            4678999999999999999988654333333344

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

Probab=97.86  E-value=0.00026  Score=72.83  Aligned_cols=46  Identities=28%  Similarity=0.350  Sum_probs=38.6

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.++||+.+++++...|....  ..-+.++|.+|+|||++|+.+++++
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~--~~n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHHHH
Confidence            469999999999999888522  2345689999999999999999875

>PRK06526 transposase; Provisional

Probab=97.83  E-value=2.7e-05  Score=69.66  Aligned_cols=33  Identities=21%  Similarity=0.130  Sum_probs=25.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCF   85 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w   85 (385)
                      .-+.|+|++|+|||+||..+.......-..+.|
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f  131 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF  131 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCchhh
Confidence            468999999999999999999876443333334

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

Probab=97.83  E-value=2.3e-05  Score=66.28  Aligned_cols=36  Identities=28%  Similarity=0.258  Sum_probs=26.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..-+.++|.+|+|||.||..+++.+..+-..+.|+.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~   82 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFIT   82 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEee
Confidence            356899999999999999999987654444456665

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.82  E-value=0.00012  Score=70.53  Aligned_cols=120  Identities=18%  Similarity=0.246  Sum_probs=63.0

Q ss_pred             ccccchhHH--HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC--ceEEEeeccccccCCCChHHHHHHH
Q 044214           31 LVGVESTVE--EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD--GSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        31 ~vGR~~~l~--~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~--~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      ++|.+....  .+..+..........+.|+|.+|+|||.|++.+++.+.+..+  .++++.           ...+...+
T Consensus       113 i~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~-----------~~~~~~~~  181 (405)
T TIGR00362       113 VVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS-----------SEKFTNDF  181 (405)
T ss_pred             ccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE-----------HHHHHHHH
Confidence            457655432  233333322222456889999999999999999998766543  233443           12333334


Q ss_pred             HHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCChh----hhhHhhccCCC-CCCCcEEEEEecc
Q 044214          107 LSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFS----QLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       107 l~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      ...+...     ....+.+.+++ .-+|+|||++...    ..+.++..+.. ...+..+|+|+..
T Consensus       182 ~~~~~~~-----~~~~~~~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       182 VNALRNN-----KMEEFKEKYRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             HHHHHcC-----CHHHHHHHHHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence            4433321     12334444443 3478899996321    11223222211 1234567777754

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).

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.80  E-value=0.00012  Score=74.06  Aligned_cols=49  Identities=24%  Similarity=0.363  Sum_probs=40.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-+.++|++..+..+.+.+.  ......+.|+|++|+||||+|+.+++..
T Consensus       151 ~~~~~iiGqs~~~~~l~~~ia--~~~~~~vlL~Gp~GtGKTTLAr~i~~~~  199 (615)
T TIGR02903       151 RAFSEIVGQERAIKALLAKVA--SPFPQHIILYGPPGVGKTTAARLALEEA  199 (615)
T ss_pred             CcHHhceeCcHHHHHHHHHHh--cCCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            344679999999999888776  3345579999999999999999998755

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=0.0007  Score=67.68  Aligned_cols=50  Identities=20%  Similarity=0.225  Sum_probs=41.9

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.+++|.+...+.|.+++..+. -.+.+.++|+.|+|||++|+.+++.+
T Consensus        13 ~~f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAkal   62 (559)
T PRK05563         13 QTFEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAKAV   62 (559)
T ss_pred             CcHHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            445789999999999999998432 34567889999999999999999865

>CHL00181 cbbX CbbX; Provisional

Probab=97.78  E-value=0.00053  Score=62.64  Aligned_cols=25  Identities=32%  Similarity=0.408  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+.++|.+|+|||++|+.+++...
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~   84 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILY   84 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH
Confidence            4588999999999999999998653

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.78  E-value=6.8e-05  Score=69.57  Aligned_cols=35  Identities=20%  Similarity=0.245  Sum_probs=28.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .-+.++|.+|+|||.||..+++.+...-..+++++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t  218 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRT  218 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEE
Confidence            56999999999999999999998765545566665

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.76  E-value=0.00068  Score=67.63  Aligned_cols=51  Identities=29%  Similarity=0.307  Sum_probs=42.3

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..+++|..++..+ .-.+.+.++|+.|+||||+|+.+++.+-
T Consensus        13 ~~f~diiGqe~iv~~L~~~i~~~-~i~hayLf~Gp~G~GKTt~Ar~lAk~L~   63 (563)
T PRK06647         13 RDFNSLEGQDFVVETLKHSIESN-KIANAYIFSGPRGVGKTSSARAFARCLN   63 (563)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            34578999999999999999842 2345788999999999999999998753

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

Probab=97.76  E-value=0.00022  Score=68.08  Aligned_cols=56  Identities=20%  Similarity=0.325  Sum_probs=41.8

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      |...-.++.|.+...+++.+.+..           +-..++-+.++|++|+|||+||+.+++.....
T Consensus       140 p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~  206 (398)
T PTZ00454        140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAT  206 (398)
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC
Confidence            334445688999888888876531           11346789999999999999999999876443

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

Probab=97.75  E-value=0.00023  Score=67.08  Aligned_cols=124  Identities=17%  Similarity=0.257  Sum_probs=82.8

Q ss_pred             HHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc--eEE
Q 044214           10 VVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG--SCF   85 (385)
Q Consensus        10 i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~--~~w   85 (385)
                      +.+.....+..    ...+..++||+.+++.+.+++..  ..+....+-|.|.+|.|||.+...++.+.......  ++.
T Consensus       135 ~~~~~~~~l~~----t~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~  210 (529)
T KOG2227|consen  135 ISEQRSESLLN----TAPPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVY  210 (529)
T ss_pred             HHHHHHHHHHh----cCCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEE
Confidence            44445555554    34567899999999999999874  34556788899999999999999999877655433  345


Q ss_pred             EeeccccccCCCChHHHHHHHHHHH----hCCCCCCchHHHHHHHhCC--ceEEEEEeCCCCh
Q 044214           86 LENVREESQIPGGLSCLRQKLLSNL----LKDKNVMPYIDLNFRRLGH--MKVLIVFDDVTCF  142 (385)
Q Consensus        86 ~~~~~~~~~~~~~~~~l~~~ll~~l----~~~~~~~~~~~~l~~~l~~--k~~LlVlDdv~~~  142 (385)
                      +.+.. .    ....+++..|...+    .....+.+....+......  ..+|+|+|.++..
T Consensus       211 inc~s-l----~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L  268 (529)
T KOG2227|consen  211 INCTS-L----TEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHL  268 (529)
T ss_pred             Eeecc-c----cchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHH
Confidence            54221 1    44556666666665    2333233455555555544  3699999999753

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.75  E-value=0.00017  Score=67.29  Aligned_cols=99  Identities=15%  Similarity=0.127  Sum_probs=63.0

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC-Cce-EEEeeccccccCCCChHHHHHHHHHHHhCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF-DGS-CFLENVREESQIPGGLSCLRQKLLSNLLKDKN  115 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~-~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~  115 (385)
                      ..++.+.+.+- ++-+.+.|+|.+|+|||||++.+++.+.... +.. +|+. +.   ..+....++++.+...+.....
T Consensus       120 ~~RvID~l~Pi-GkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~l-Ig---ER~~EV~df~~~i~~~Vvast~  194 (380)
T PRK12608        120 SMRVVDLVAPI-GKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLL-ID---ERPEEVTDMRRSVKGEVYASTF  194 (380)
T ss_pred             hHhhhhheeec-CCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEE-ec---CCCCCHHHHHHHHhhhEEeecC
Confidence            34466666642 2335679999999999999999999876554 333 3443 33   2336788888888776665432


Q ss_pred             CC------c---hHHHHHHHh--CCceEEEEEeCCCC
Q 044214          116 VM------P---YIDLNFRRL--GHMKVLIVFDDVTC  141 (385)
Q Consensus       116 ~~------~---~~~~l~~~l--~~k~~LlVlDdv~~  141 (385)
                      +.      .   ....+.+++  .+++++||+|++..
T Consensus       195 de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr  231 (380)
T PRK12608        195 DRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTR  231 (380)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHH
Confidence            11      1   111222222  47999999999953

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

Probab=97.75  E-value=0.00023  Score=73.77  Aligned_cols=114  Identities=15%  Similarity=0.187  Sum_probs=65.0

Q ss_pred             CCCccccchhHHHHHHhhcC------CCC-CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChH
Q 044214           28 KNQLVGVESTVEEIESLLGV------ESK-GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLS  100 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~------~~~-~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~  100 (385)
                      ...++|-+..++.+.+.+..      ..+ ...++.++|++|+|||.||+.+++.+..   ..+.+. ..+.... ....
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~---~~~~~d-~se~~~~-~~~~  527 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGV---HLERFD-MSEYMEK-HTVS  527 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcC---CeEEEe-Cchhhhc-ccHH
Confidence            35688999999988887652      112 2346889999999999999999987632   233333 2221111 1111


Q ss_pred             HHHHHHHHHHhCCCC--CCchHHHHHHHhCC-ceEEEEEeCCC--ChhhhhHhhccCC
Q 044214          101 CLRQKLLSNLLKDKN--VMPYIDLNFRRLGH-MKVLIVFDDVT--CFSQLESLMGSLD  153 (385)
Q Consensus       101 ~l~~~ll~~l~~~~~--~~~~~~~l~~~l~~-k~~LlVlDdv~--~~~~~~~l~~~~~  153 (385)
                      .+       ++.+..  ..+....+.+.++. ...+++||+++  +.+.+..|+..+.
T Consensus       528 ~l-------ig~~~gyvg~~~~~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld  578 (731)
T TIGR02639       528 RL-------IGAPPGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMD  578 (731)
T ss_pred             HH-------hcCCCCCcccchhhHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhc
Confidence            11       111111  11222334444443 34699999997  4455566655543

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

Probab=97.75  E-value=0.00012  Score=65.67  Aligned_cols=73  Identities=25%  Similarity=0.237  Sum_probs=45.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      +..-+.++|.+|+|||.||.++.+.+...--.+.|+.           ..++..++.......    .....+.+.+.. 
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~-----------~~el~~~Lk~~~~~~----~~~~~l~~~l~~-  167 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFIT-----------APDLLSKLKAAFDEG----RLEEKLLRELKK-  167 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEE-----------HHHHHHHHHHHHhcC----chHHHHHHHhhc-
Confidence            4456889999999999999999998874434455554           234444444433321    222233333332 


Q ss_pred             eEEEEEeCC
Q 044214          131 KVLIVFDDV  139 (385)
Q Consensus       131 ~~LlVlDdv  139 (385)
                      -=||||||+
T Consensus       168 ~dlLIiDDl  176 (254)
T COG1484         168 VDLLIIDDI  176 (254)
T ss_pred             CCEEEEecc
Confidence            248899999

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

Probab=97.74  E-value=0.00025  Score=64.75  Aligned_cols=124  Identities=18%  Similarity=0.360  Sum_probs=77.5

Q ss_pred             CCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCC
Q 044214           29 NQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPG   97 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~   97 (385)
                      ...=|-++.+++|.+....           +=+.++-|.+||++|.|||-||++++++....|     +..++       
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtF-----Irvvg-------  218 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATF-----IRVVG-------  218 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceE-----EEecc-------
Confidence            4455788889888887642           124577899999999999999999999765443     33111       


Q ss_pred             ChHHHHHHHHHHHhCCCCCCchHHHHHHHhC-CceEEEEEeCCCCh----------------hhhhHhhccCCCCC--CC
Q 044214           98 GLSCLRQKLLSNLLKDKNVMPYIDLNFRRLG-HMKVLIVFDDVTCF----------------SQLESLMGSLDWLT--PV  158 (385)
Q Consensus        98 ~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~-~k~~LlVlDdv~~~----------------~~~~~l~~~~~~~~--~g  158 (385)
                            .++.....++..  .+...+.+.-+ ..++.|++|.++..                ..+-+|+..+..+.  .+
T Consensus       219 ------SElVqKYiGEGa--RlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~n  290 (406)
T COG1222         219 ------SELVQKYIGEGA--RLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGN  290 (406)
T ss_pred             ------HHHHHHHhccch--HHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCC
Confidence                  122233323222  44444555544 47899999999621                11445555555443  35


Q ss_pred             cEEEEEeccHHHHh
Q 044214          159 SRIILTTRNKQVLR  172 (385)
Q Consensus       159 s~ilvTtR~~~~~~  172 (385)
                      -+||..|...+.+.
T Consensus       291 vKVI~ATNR~D~LD  304 (406)
T COG1222         291 VKVIMATNRPDILD  304 (406)
T ss_pred             eEEEEecCCccccC
Confidence            68888887665544

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.74  E-value=6.1e-05  Score=75.52  Aligned_cols=53  Identities=23%  Similarity=0.324  Sum_probs=42.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCC---CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVES---KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~---~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |..-++++|-+..++++..++....   ...+++.|+|++|+||||+++.++..+.
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~  135 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELG  135 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4455779999999999999987422   3346799999999999999999998653

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

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.74  E-value=0.00041  Score=64.14  Aligned_cols=47  Identities=17%  Similarity=0.258  Sum_probs=39.7

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|.+...+.+.+.+..+ .-.+...++|+.|+||+++|..+++.+
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~-rl~ha~Lf~G~~G~Gk~~~A~~~a~~l   50 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQN-RIAPAYLFAGPEGVGRKLAALCFIEGL   50 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhC-CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999998842 225789999999999999999999865

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.73  E-value=0.0002  Score=65.92  Aligned_cols=118  Identities=14%  Similarity=0.205  Sum_probs=66.0

Q ss_pred             ccchhHHHHHHhhcCCC--CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHH
Q 044214           33 GVESTVEEIESLLGVES--KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~--~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l  110 (385)
                      +|....+...+++..-.  ...+-+.|+|..|+|||.||.++++.+...-..+.|+.           ...+...+....
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~-----------~~~l~~~lk~~~  203 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLH-----------FPEFIRELKNSI  203 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE-----------HHHHHHHHHHHH
Confidence            44444555555555211  13457899999999999999999998765544455665           123444443333


Q ss_pred             hCCCCCCchHHHHHHHhCCceEEEEEeCCC--Chhhhh--HhhccC-CCC-CCCcEEEEEecc
Q 044214          111 LKDKNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLE--SLMGSL-DWL-TPVSRIILTTRN  167 (385)
Q Consensus       111 ~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~--~l~~~~-~~~-~~gs~ilvTtR~  167 (385)
                      ...    . .....+.+. +.=||||||+-  ....|.  .++..+ ... ..+..+|+||--
T Consensus       204 ~~~----~-~~~~l~~l~-~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        204 SDG----S-VKEKIDAVK-EAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             hcC----c-HHHHHHHhc-CCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            211    1 122233333 44589999993  334443  243332 111 234567888864

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

Probab=97.73  E-value=0.0002  Score=61.43  Aligned_cols=48  Identities=29%  Similarity=0.317  Sum_probs=40.6

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+.||-++.++.+.-.-.  +++++-+.|.||+|+||||-+..+++.+-
T Consensus        26 l~dIVGNe~tv~rl~via~--~gnmP~liisGpPG~GKTTsi~~LAr~LL   73 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAK--EGNMPNLIISGPPGTGKTTSILCLARELL   73 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHH--cCCCCceEeeCCCCCchhhHHHHHHHHHh
Confidence            3568999999998887766  56678899999999999999999998753

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.73  E-value=0.00047  Score=64.31  Aligned_cols=124  Identities=19%  Similarity=0.157  Sum_probs=74.1

Q ss_pred             CccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC---------------------CceEEEee
Q 044214           30 QLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF---------------------DGSCFLEN   88 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f---------------------~~~~w~~~   88 (385)
                      .++|-+....++..+..........+.++|++|+||||+|..+++.+....                     +.+..+. 
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~-   80 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELN-   80 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEec-
Confidence            467777888888888774333344599999999999999999999765332                     2333332 


Q ss_pred             ccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEec
Q 044214           89 VREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus        89 ~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      ....... .-..+..+++.........            .++.-++++|+++..  +....++..+......+.+|++|.
T Consensus        81 ~s~~~~~-~i~~~~vr~~~~~~~~~~~------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470          81 PSDLRKI-DIIVEQVRELAEFLSESPL------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             ccccCCC-cchHHHHHHHHHHhccCCC------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcC
Confidence            1111000 0122233333332222110            356789999999754  445666666555567778877776


Q ss_pred             c
Q 044214          167 N  167 (385)
Q Consensus       167 ~  167 (385)
                      .
T Consensus       148 ~  148 (325)
T COG0470         148 D  148 (325)
T ss_pred             C
Confidence            4

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.73  E-value=0.00062  Score=69.02  Aligned_cols=50  Identities=22%  Similarity=0.355  Sum_probs=41.4

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-.+++|-+..++.|...+..+ .-.+.+.++|+.|+||||+|+.+++.+
T Consensus        15 ~~f~dIiGQe~~v~~L~~aI~~~-rl~HAYLF~GP~GtGKTt~AriLAk~L   64 (725)
T PRK07133         15 KTFDDIVGQDHIVQTLKNIIKSN-KISHAYLFSGPRGTGKTSVAKIFANAL   64 (725)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCcHHHHHHHHHHHh
Confidence            34467999999999999999842 235567899999999999999999865

>PRK09087 hypothetical protein; Validated

Probab=97.72  E-value=0.00031  Score=61.83  Aligned_cols=25  Identities=28%  Similarity=0.195  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.+.|+|.+|+|||+|++.+++..
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~   68 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKS   68 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhc
Confidence            3568999999999999999888753

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00036  Score=70.08  Aligned_cols=51  Identities=22%  Similarity=0.296  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|-+..++.|.+.+..+ .-...+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~f~eivGQe~i~~~L~~~i~~~-ri~ha~Lf~Gp~GvGKttlA~~lAk~L~   63 (620)
T PRK14954         13 SKFADITAQEHITHTIQNSLRMD-RVGHGYIFSGLRGVGKTTAARVFAKAVN   63 (620)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            34578999999999999988732 2245688999999999999999998763

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.71  E-value=0.0002  Score=71.04  Aligned_cols=96  Identities=19%  Similarity=0.278  Sum_probs=55.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC--ceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD--GSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~--~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      ..+.|+|..|+|||.|++.+++.+...+.  .++++.           ..++...+...+..     .....+++.+++-
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit-----------aeef~~el~~al~~-----~~~~~f~~~y~~~  378 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS-----------SEEFTNEFINSIRD-----GKGDSFRRRYREM  378 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee-----------HHHHHHHHHHHHHh-----ccHHHHHHHhhcC
Confidence            45899999999999999999998765432  233433           23333344333322     1123344444443


Q ss_pred             eEEEEEeCCCCh---hh----hhHhhccCCCCCCCcEEEEEecc
Q 044214          131 KVLIVFDDVTCF---SQ----LESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       131 ~~LlVlDdv~~~---~~----~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                       =+|||||+...   +.    +-.++..+.  ..|..|||||..
T Consensus       379 -DLLlIDDIq~l~gke~tqeeLF~l~N~l~--e~gk~IIITSd~  419 (617)
T PRK14086        379 -DILLVDDIQFLEDKESTQEEFFHTFNTLH--NANKQIVLSSDR  419 (617)
T ss_pred             -CEEEEehhccccCCHHHHHHHHHHHHHHH--hcCCCEEEecCC
Confidence             47888999532   11    222222222  235668888875

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.71  E-value=0.00013  Score=63.04  Aligned_cols=109  Identities=12%  Similarity=0.077  Sum_probs=64.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceEE
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVL  133 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~L  133 (385)
                      +|.|+|+.|+||||++..+...+.......++...-...... ...    ..+..+...........+.++..++..+=.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~-~~~----~~~i~q~~vg~~~~~~~~~i~~aLr~~pd~   77 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVH-ESK----RSLINQREVGLDTLSFENALKAALRQDPDV   77 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCccccc-cCc----cceeeecccCCCccCHHHHHHHHhcCCcCE
Confidence            789999999999999999888776554545444311100000 000    011111000011124566777888878889


Q ss_pred             EEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHH
Q 044214          134 IVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQV  170 (385)
Q Consensus       134 lVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~  170 (385)
                      +++|.+.+.+.+...+...   ..|..++.|+...+.
T Consensus        78 ii~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~  111 (198)
T cd01131          78 ILVGEMRDLETIRLALTAA---ETGHLVMSTLHTNSA  111 (198)
T ss_pred             EEEcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcH
Confidence            9999998777766555432   245567777765443

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

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.71  E-value=0.00024  Score=74.54  Aligned_cols=130  Identities=17%  Similarity=0.175  Sum_probs=74.1

Q ss_pred             CCccccchhHHHHHHhhcC------CCC-CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHH
Q 044214           29 NQLVGVESTVEEIESLLGV------ESK-GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~------~~~-~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      ..++|-+..++.+.+.+..      ..+ ....+.++|+.|+|||+||+.+++.+-..-...+-+. .++.... ..+..
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d-~s~~~~~-~~~~~  586 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLD-MSEYMEK-HTVSK  586 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEE-chhcccc-ccHHH
Confidence            5689999999999887652      112 2346779999999999999999987643322222232 2221111 11211


Q ss_pred             HHHHHHHHHhCCCC--CCchHHHHHHHhCCce-EEEEEeCCC--ChhhhhHhhccCCCC-----------CCCcEEEEEe
Q 044214          102 LRQKLLSNLLKDKN--VMPYIDLNFRRLGHMK-VLIVFDDVT--CFSQLESLMGSLDWL-----------TPVSRIILTT  165 (385)
Q Consensus       102 l~~~ll~~l~~~~~--~~~~~~~l~~~l~~k~-~LlVlDdv~--~~~~~~~l~~~~~~~-----------~~gs~ilvTt  165 (385)
                      +       ++.+..  ..+....+.+.++.++ .+++||+++  +.+.+..|+..+..+           ..++.+|+||
T Consensus       587 l-------~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Ts  659 (821)
T CHL00095        587 L-------IGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTS  659 (821)
T ss_pred             h-------cCCCCcccCcCccchHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeC
Confidence            1       111110  1122234455555555 589999996  445566666555432           1345677777


Q ss_pred             cc
Q 044214          166 RN  167 (385)
Q Consensus       166 R~  167 (385)
                      ..
T Consensus       660 n~  661 (821)
T CHL00095        660 NL  661 (821)
T ss_pred             Cc
Confidence            64

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00082  Score=67.83  Aligned_cols=52  Identities=25%  Similarity=0.254  Sum_probs=42.4

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-..++|.+...+.|..++..+. -.+.+.++|..|+||||+|+.+++.+..
T Consensus        13 ~~f~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c   64 (620)
T PRK14948         13 QRFDELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNC   64 (620)
T ss_pred             CcHhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcC
Confidence            344679999999999999988432 2357889999999999999999997643

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.70  E-value=0.00027  Score=74.32  Aligned_cols=130  Identities=18%  Similarity=0.212  Sum_probs=73.4

Q ss_pred             CCCccccchhHHHHHHhhcCC------CC-CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChH
Q 044214           28 KNQLVGVESTVEEIESLLGVE------SK-GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLS  100 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~------~~-~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~  100 (385)
                      ...++|.+..++.+...+...      .+ ...++.++|++|+|||++|+.+++.+...-...+.+. .++.... ... 
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d-~s~~~~~-~~~-  640 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRID-MSEYMEK-HSV-  640 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEe-chhhccc-chH-
Confidence            346899999999998887631      11 2457889999999999999999987644333333332 2211111 111 


Q ss_pred             HHHHHHHHHHhCCCCC---CchHHHHHHHhCCc-eEEEEEeCCC--ChhhhhHhhccCCCC-----------CCCcEEEE
Q 044214          101 CLRQKLLSNLLKDKNV---MPYIDLNFRRLGHM-KVLIVFDDVT--CFSQLESLMGSLDWL-----------TPVSRIIL  163 (385)
Q Consensus       101 ~l~~~ll~~l~~~~~~---~~~~~~l~~~l~~k-~~LlVlDdv~--~~~~~~~l~~~~~~~-----------~~gs~ilv  163 (385)
                             ..+.+..+.   .+....+...++.+ ..+|+||+++  +.+.+..|+..+...           -.++.||+
T Consensus       641 -------~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~  713 (852)
T TIGR03346       641 -------ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIM  713 (852)
T ss_pred             -------HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEE
Confidence                   112111111   11112333333333 3599999996  445566666555322           12344777


Q ss_pred             Eecc
Q 044214          164 TTRN  167 (385)
Q Consensus       164 TtR~  167 (385)
                      ||..
T Consensus       714 TSn~  717 (852)
T TIGR03346       714 TSNL  717 (852)
T ss_pred             eCCc
Confidence            8764

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.

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

Probab=97.70  E-value=0.00013  Score=70.20  Aligned_cols=54  Identities=26%  Similarity=0.429  Sum_probs=41.6

Q ss_pred             CCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           27 NKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      .-.++.|.+..++++.+.+..           +-...+-+.++|++|+|||++|+.+++.....|
T Consensus       181 ~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~f  245 (438)
T PTZ00361        181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATF  245 (438)
T ss_pred             CHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCE
Confidence            335678999999999887641           112355788999999999999999999876544

>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=97.70  E-value=9.1e-05  Score=65.08  Aligned_cols=36  Identities=25%  Similarity=0.460  Sum_probs=31.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEee
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLEN   88 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~   88 (385)
                      -.++|.|.+|+|||||...+.......|..+++++.
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEec
Confidence            357799999999999999999999999987777753

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

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.69  E-value=0.00042  Score=69.09  Aligned_cols=50  Identities=24%  Similarity=0.262  Sum_probs=40.8

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .-.+++|-+..++.|.+.+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        14 sf~dIiGQe~v~~~L~~ai~~~-ri~ha~Lf~GPpG~GKTtiArilAk~L~   63 (624)
T PRK14959         14 TFAEVAGQETVKAILSRAAQEN-RVAPAYLFSGTRGVGKTTIARIFAKALN   63 (624)
T ss_pred             CHHHhcCCHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHhcc
Confidence            4467899998888899888742 2256788999999999999999998763

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.69  E-value=0.00041  Score=67.28  Aligned_cols=99  Identities=14%  Similarity=0.203  Sum_probs=54.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      ...+.|+|..|+|||+|++.+++.+......++++.           ...+...+...+...     ....++..++. .
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~-----------~~~f~~~~~~~l~~~-----~~~~f~~~~~~-~  203 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVR-----------SELFTEHLVSAIRSG-----EMQRFRQFYRN-V  203 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEee-----------HHHHHHHHHHHHhcc-----hHHHHHHHccc-C
Confidence            356889999999999999999998765434444444           122333333333221     12334444443 4


Q ss_pred             EEEEEeCCCChh----hhhHhhccCCC-CCCCcEEEEEecc
Q 044214          132 VLIVFDDVTCFS----QLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       132 ~LlVlDdv~~~~----~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      -+|++||+....    ..+.++..+.. ...|..||+||..
T Consensus       204 dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~  244 (445)
T PRK12422        204 DALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTC  244 (445)
T ss_pred             CEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCC
Confidence            478889985321    12222222110 0135578888854

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.68  E-value=0.00027  Score=74.14  Aligned_cols=114  Identities=16%  Similarity=0.205  Sum_probs=64.7

Q ss_pred             CCccccchhHHHHHHhhcCC------CC-CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHH
Q 044214           29 NQLVGVESTVEEIESLLGVE------SK-GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~------~~-~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      ..++|.+..++.+...+...      .+ ...++.++|+.|+|||++|+.+++.+.......+.+. ..+...       
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id-~se~~~-------  639 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRID-MSEFME-------  639 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEE-hHHhhh-------
Confidence            46899999999888877521      12 2347889999999999999999986643333333333 211100       


Q ss_pred             HHHHHHHHHhCCCCCC---chHHHHHHHhCCc-eEEEEEeCCC--ChhhhhHhhccC
Q 044214          102 LRQKLLSNLLKDKNVM---PYIDLNFRRLGHM-KVLIVFDDVT--CFSQLESLMGSL  152 (385)
Q Consensus       102 l~~~ll~~l~~~~~~~---~~~~~l~~~l~~k-~~LlVlDdv~--~~~~~~~l~~~~  152 (385)
                        ......+.+..+..   +....+...++.+ .-+|+||+++  +...+..++..+
T Consensus       640 --~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll~il  694 (857)
T PRK10865        640 --KHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVL  694 (857)
T ss_pred             --hhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCCHHHHHHHHHHH
Confidence              11112222222111   1112233333333 3699999996  455566665544

>CHL00176 ftsH cell division protein; Validated

Probab=97.67  E-value=0.00024  Score=71.68  Aligned_cols=48  Identities=29%  Similarity=0.381  Sum_probs=35.7

Q ss_pred             CCccccchhHHHHHHhh---cCC-------CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLL---GVE-------SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L---~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|.++..+++.+.+   ...       ....+-|.++|++|+|||+||+.++...
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~  240 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA  240 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            56889887777666554   221       1224569999999999999999999865

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

Probab=97.66  E-value=8.4e-05  Score=60.18  Aligned_cols=22  Identities=36%  Similarity=0.480  Sum_probs=20.8

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|+|.+|+|||+||+.+++.+
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL   23 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999987

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.

>PRK08118 topology modulation protein; Reviewed

Probab=97.66  E-value=6.7e-05  Score=62.82  Aligned_cols=34  Identities=29%  Similarity=0.446  Sum_probs=27.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC---CCCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG---DFDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~---~f~~~~w~   86 (385)
                      +.|.|+|++|+||||||+.+++.+.-   +|+..+|-
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~   38 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK   38 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc
Confidence            36899999999999999999997643   36666654

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.66  E-value=0.0014  Score=61.61  Aligned_cols=37  Identities=24%  Similarity=0.340  Sum_probs=28.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++|+|+|.+|+||||++..++..+...-..+.++.
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~  276 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFIT  276 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEe
Confidence            4579999999999999999999987654433344444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.65  E-value=0.00035  Score=63.79  Aligned_cols=49  Identities=22%  Similarity=0.361  Sum_probs=32.8

Q ss_pred             CccccchhHHHHHHhhc---C---------C-CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLG---V---------E-SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~---~---------~-~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++|-++..+++.++..   .         . ......+.++|.+|+|||++|+.+++.+..
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~   84 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHR   84 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            36887766666554321   0         0 112236889999999999999999886543

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.64  E-value=0.0004  Score=72.70  Aligned_cols=51  Identities=24%  Similarity=0.382  Sum_probs=39.6

Q ss_pred             CCccccchhHHHHHHhhcC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLLGV-------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..++|-+..++.+.+.+..       ++....++.++|++|+|||.||+.+++.+-..
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~  623 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGG  623 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCC
Confidence            4689999999988887642       12234578999999999999999999876433

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.

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

Probab=97.64  E-value=0.00019  Score=64.38  Aligned_cols=89  Identities=18%  Similarity=0.201  Sum_probs=58.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC--------CCCCC-----
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK--------DKNVM-----  117 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~--------~~~~~-----  117 (385)
                      +-+.++|.|.+|+|||+|++.+++.++.+|+..+++..+++..   ..+.++...+...-..        ..++.     
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~---~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  144 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERT---REGNDLYHEMKESGVLSKTALVYGQMNEPPGARA  144 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCc---HHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            3467999999999999999999999887887777776554432   4456666666543111        11111     


Q ss_pred             ---chHHHHHHHh---CCceEEEEEeCCCCh
Q 044214          118 ---PYIDLNFRRL---GHMKVLIVFDDVTCF  142 (385)
Q Consensus       118 ---~~~~~l~~~l---~~k~~LlVlDdv~~~  142 (385)
                         ...-.+.+++   +++.+|+++||+...
T Consensus       145 ~~~~~a~~~AEyfr~~~g~~Vl~~~Dsltr~  175 (274)
T cd01133         145 RVALTGLTMAEYFRDEEGQDVLLFIDNIFRF  175 (274)
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEeChhHH
Confidence               1122233343   389999999999543

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

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.63  E-value=0.00096  Score=55.53  Aligned_cols=121  Identities=19%  Similarity=0.197  Sum_probs=68.4

Q ss_pred             ccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC--------------------CCCceEEEeecccc
Q 044214           33 GVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG--------------------DFDGSCFLENVREE   92 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~--------------------~f~~~~w~~~~~~~   92 (385)
                      |-+...+.|.+.+..+ .-+..+.++|..|+||+++|..+++.+-.                    ..+...|+..... 
T Consensus         1 gq~~~~~~L~~~~~~~-~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~-   78 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSG-RLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKK-   78 (162)
T ss_dssp             S-HHHHHHHHHHHHCT-C--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTS-
T ss_pred             CcHHHHHHHHHHHHcC-CcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccc-
Confidence            4556677777777732 23456899999999999999999986521                    2334444431111 


Q ss_pred             ccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccHH
Q 044214           93 SQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus        93 ~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      ... ..+.++. .+...+....            ..++.=++|+||++.  .+....|+..+..-..++.+|++|.+.+
T Consensus        79 ~~~-i~i~~ir-~i~~~~~~~~------------~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   79 KKS-IKIDQIR-EIIEFLSLSP------------SEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSS-BSHHHHH-HHHHHCTSS-------------TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             cch-hhHHHHH-HHHHHHHHHH------------hcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence            000 1222211 2222221111            124567899999974  4556777766655557888888887653

...

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.63  E-value=0.0013  Score=66.38  Aligned_cols=51  Identities=27%  Similarity=0.340  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+...+.|.+++..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        14 ~~f~~viGq~~~~~~L~~~i~~~-~l~hayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         14 STFESVVGQEALTTTLKNAIATN-KLAHAYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcC-CCCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            34478999999999999999842 2345688999999999999999998763

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

Probab=97.62  E-value=0.00046  Score=70.05  Aligned_cols=127  Identities=18%  Similarity=0.226  Sum_probs=81.8

Q ss_pred             CCccccchhHHHHHHhhcC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHH
Q 044214           29 NQLVGVESTVEEIESLLGV-------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      ...+|-+..+..+.+.+..       ++....+....|+.|||||-||++++..+-+.=+..+-+           ++.+
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~-----------DMSE  559 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRI-----------DMSE  559 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceee-----------chHH
Confidence            4689999999998887752       223356778899999999999999998764332333333           2222


Q ss_pred             HHH-HHHHHHhCCCCCC---chHHHHHHHhCCceE-EEEEeCCC--ChhhhhHhhccCCCC----C-------CCcEEEE
Q 044214          102 LRQ-KLLSNLLKDKNVM---PYIDLNFRRLGHMKV-LIVFDDVT--CFSQLESLMGSLDWL----T-------PVSRIIL  163 (385)
Q Consensus       102 l~~-~ll~~l~~~~~~~---~~~~~l~~~l~~k~~-LlVlDdv~--~~~~~~~l~~~~~~~----~-------~gs~ilv  163 (385)
                      ... .-.+.+.+..+..   +--..|-+..+.+|| +|.||.++  +++.++-|+..+.++    +       .++-||+
T Consensus       560 y~EkHsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIIm  639 (786)
T COG0542         560 YMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIM  639 (786)
T ss_pred             HHHHHHHHHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEE
Confidence            222 2234444444422   334556666777876 88999996  667777777766543    1       2455677


Q ss_pred             Eec
Q 044214          164 TTR  166 (385)
Q Consensus       164 TtR  166 (385)
                      ||.
T Consensus       640 TSN  642 (786)
T COG0542         640 TSN  642 (786)
T ss_pred             ecc
Confidence            775

>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=97.61  E-value=0.00048  Score=59.19  Aligned_cols=127  Identities=17%  Similarity=0.155  Sum_probs=61.5

Q ss_pred             cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH-h-hCCCCceEEEeeccccccC----CCChHH----HH
Q 044214           34 VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK-I-SGDFDGSCFLENVREESQI----PGGLSC----LR  103 (385)
Q Consensus        34 R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~-~-~~~f~~~~w~~~~~~~~~~----~~~~~~----l~  103 (385)
                      +..+-....+.|.    ...++.+.|++|.|||.||.+.+-+ + ..+|+..++....-+....    |.+..+    ..
T Consensus         5 ~~~~Q~~~~~al~----~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~   80 (205)
T PF02562_consen    5 KNEEQKFALDALL----NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYL   80 (205)
T ss_dssp             -SHHHHHHHHHHH----H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTT
T ss_pred             CCHHHHHHHHHHH----hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHH
Confidence            4445555555555    2348999999999999999998853 3 4678877777643221110    011100    01


Q ss_pred             HHHHHHHhCCCCCCchHHHHH----------HHhCCc---eEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          104 QKLLSNLLKDKNVMPYIDLNF----------RRLGHM---KVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~----------~~l~~k---~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      .-+...+..-... ...+.+.          .+++++   ..++|+|++.  +..++..++...   +.||+++++--..
T Consensus        81 ~p~~d~l~~~~~~-~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR~---g~~skii~~GD~~  156 (205)
T PF02562_consen   81 RPIYDALEELFGK-EKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTRI---GEGSKIIITGDPS  156 (205)
T ss_dssp             HHHHHHHTTTS-T-TCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB----TT-EEEEEE---
T ss_pred             HHHHHHHHHHhCh-HhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHccc---CCCcEEEEecCce
Confidence            1111111110000 1122222          134443   5799999994  567788887664   5899999987544

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK06620 hypothetical protein; Validated

Probab=97.61  E-value=0.00012  Score=63.82  Aligned_cols=50  Identities=16%  Similarity=0.082  Sum_probs=31.1

Q ss_pred             CCCCccccchh--HHHHHHhhcCCCCCe--EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           27 NKNQLVGVEST--VEEIESLLGVESKGV--YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        27 ~~~~~vGR~~~--l~~l~~~L~~~~~~~--~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+.++|-...  ...+.++-.....++  +.+.|+|++|+|||+|++.+++..
T Consensus        15 fd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~   68 (214)
T PRK06620         15 PDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLS   68 (214)
T ss_pred             chhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhcc
Confidence            33455666333  334444433111112  568999999999999999877654

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.61  E-value=0.00048  Score=60.74  Aligned_cols=47  Identities=21%  Similarity=0.274  Sum_probs=35.9

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |-+.|..+=..-.++.|+|.+|+|||++|.+++.........++|++
T Consensus        12 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361         12 LDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            44444433344679999999999999999999987755667788887

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.61  E-value=0.0012  Score=61.38  Aligned_cols=27  Identities=26%  Similarity=0.315  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+.+.++|+.|+|||++|..+++.+-
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~ll   47 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALL   47 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHc
Confidence            356788999999999999999998753

>PHA00729 NTP-binding motif containing protein

Probab=97.60  E-value=0.00032  Score=61.01  Aligned_cols=28  Identities=32%  Similarity=0.407  Sum_probs=24.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+...|.|+|.+|+||||||..+++++.
T Consensus        15 ~~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         15 NGFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3456799999999999999999998764

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.58  E-value=0.00091  Score=67.18  Aligned_cols=51  Identities=22%  Similarity=0.335  Sum_probs=41.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-.+++|.+...+.|.+.+..+ .-.+.+.++|+.|+||||+|+.+++.+.
T Consensus        13 ~~f~~iiGq~~v~~~L~~~i~~~-~~~hayLf~Gp~G~GKtt~A~~lak~l~   63 (576)
T PRK14965         13 QTFSDLTGQEHVSRTLQNAIDTG-RVAHAFLFTGARGVGKTSTARILAKALN   63 (576)
T ss_pred             CCHHHccCcHHHHHHHHHHHHcC-CCCeEEEEECCCCCCHHHHHHHHHHhhc
Confidence            34578999999999999998842 2245678999999999999999998753

>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=97.56  E-value=7.4e-05  Score=58.85  Aligned_cols=23  Identities=30%  Similarity=0.533  Sum_probs=21.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|.|++|+||||+|+.+++++
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999976

...

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.55  E-value=0.0019  Score=62.33  Aligned_cols=36  Identities=19%  Similarity=0.126  Sum_probs=28.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      .+.+|.++|.+|+||||.|..++..++..-..+..+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV  129 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLV  129 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEe
Confidence            467999999999999999999998776543333334

>PRK14974 cell division protein FtsY; Provisional

Probab=97.54  E-value=0.0022  Score=59.64  Aligned_cols=29  Identities=21%  Similarity=0.256  Sum_probs=25.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++.+|.++|++|+||||++..++..++..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~  167 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKN  167 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            46899999999999999999998876554

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.53  E-value=0.00045  Score=68.41  Aligned_cols=49  Identities=22%  Similarity=0.344  Sum_probs=35.4

Q ss_pred             CCccccchhHHHHHHhhc---C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLG---V-------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~---~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++++|-++..+++.+.+.   .       +....+-+.++|++|+|||+||+.+++...
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~  113 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAG  113 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcC
Confidence            457888877666655433   1       122345688999999999999999998653

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.

>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=97.50  E-value=0.0011  Score=57.05  Aligned_cols=56  Identities=14%  Similarity=0.090  Sum_probs=35.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      ++++.++|+.|+||||.+.+++.+.+.+-..+..++    .........+-++...+.++
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis----~D~~R~ga~eQL~~~a~~l~   56 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLKGKKVALIS----ADTYRIGAVEQLKTYAEILG   56 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE----ESTSSTHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhccccceeec----CCCCCccHHHHHHHHHHHhc
Confidence            468999999999999999999887655544455555    11111344444555555554

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 ....

>PRK06696 uridine kinase; Validated

Probab=97.49  E-value=0.00021  Score=62.89  Aligned_cols=46  Identities=22%  Similarity=0.258  Sum_probs=36.2

Q ss_pred             cchhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           34 VESTVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        34 R~~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      |++.+++|.+.+.. ..+.+.+|+|.|.+|+||||||+.+++.+...
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~   49 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKKR   49 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            55666777776643 34567899999999999999999999987544

>PRK04296 thymidine kinase; Provisional

Probab=97.49  E-value=0.00025  Score=60.70  Aligned_cols=108  Identities=15%  Similarity=0.032  Sum_probs=60.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC--C----chHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV--M----PYIDLNFRR  126 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~--~----~~~~~l~~~  126 (385)
                      .++.|+|..|.||||+|..++.+...+...++.+...  .... ....    .+.+.++.....  .    +....+.+ 
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~~--~d~~-~~~~----~i~~~lg~~~~~~~~~~~~~~~~~~~~-   74 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKPA--IDDR-YGEG----KVVSRIGLSREAIPVSSDTDIFELIEE-   74 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEecc--cccc-ccCC----cEecCCCCcccceEeCChHHHHHHHHh-
Confidence            4788999999999999999999876554444444210  0001 1111    222222211111  1    22333333 


Q ss_pred             hCCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccHHH
Q 044214          127 LGHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNKQV  170 (385)
Q Consensus       127 l~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~~~  170 (385)
                      ..++.-+||+|.+.-  .+++.++...+.  ..|..|++|.++.+.
T Consensus        75 ~~~~~dvviIDEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~~~  118 (190)
T PRK04296         75 EGEKIDCVLIDEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDTDF  118 (190)
T ss_pred             hCCCCCEEEEEccccCCHHHHHHHHHHHH--HcCCeEEEEecCccc
Confidence            233556899999953  343444544432  357789999998543

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

Probab=97.48  E-value=0.00057  Score=70.34  Aligned_cols=49  Identities=18%  Similarity=0.309  Sum_probs=38.9

Q ss_pred             CCccccchhHHHHHHhhcC------C-CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGV------E-SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~------~-~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..++|-++.++.+.+.+..      . ......+.++|++|+|||.+|+.++..+.
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~  513 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG  513 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4589999999988887762      1 12245789999999999999999998774

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.47  E-value=0.00082  Score=55.52  Aligned_cols=34  Identities=24%  Similarity=0.329  Sum_probs=27.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++.|+|.+|+|||+++..++......-..++|+.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            3689999999999999999987765545566665

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.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.47  E-value=0.00015  Score=58.75  Aligned_cols=39  Identities=28%  Similarity=0.386  Sum_probs=29.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCc-eEEEeecc
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDG-SCFLENVR   90 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~-~~w~~~~~   90 (385)
                      ..-|.|+|++|+||||+++.+++.+++. |.. .+|...++
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVR   45 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeee
Confidence            3468999999999999999999988766 653 34444343

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.46  E-value=0.00057  Score=70.99  Aligned_cols=52  Identities=19%  Similarity=0.335  Sum_probs=40.0

Q ss_pred             CCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           28 KNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      -+++.|.+..++++.+++..           +-...+.+.++|++|+|||+||+.+++.....
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~  239 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY  239 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCe
Confidence            34588999999998887631           11234678899999999999999999876443

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.

>PRK07261 topology modulation protein; Provisional

Probab=97.45  E-value=0.00025  Score=59.65  Aligned_cols=23  Identities=35%  Similarity=0.585  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|+|++|+||||||+++....
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            48899999999999999998764

>PRK07667 uridine kinase; Provisional

Probab=97.45  E-value=0.00033  Score=60.20  Aligned_cols=42  Identities=21%  Similarity=0.409  Sum_probs=33.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++.+.+.+....+...+|+|.|.+|+||||+|..+.+.+...
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~~~   44 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMKQE   44 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            455666666555566899999999999999999999977544

>cd01394 radB RadB

Probab=97.45  E-value=0.001  Score=58.31  Aligned_cols=48  Identities=23%  Similarity=0.352  Sum_probs=35.5

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|-.+|..+=..-.++.|+|.+|+||||+|.+++......-..++|++
T Consensus         7 ~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394           7 GLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             HHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            344445433345679999999999999999999987755555677775

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

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

Probab=97.44  E-value=0.0011  Score=57.42  Aligned_cols=99  Identities=19%  Similarity=0.297  Sum_probs=62.8

Q ss_pred             CCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHH
Q 044214           29 NQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      ..++|-+...+.|.+.-..  ..-..--|.+||.-|.|||+|++++.+.+.+.+-..+=++    .... .++       
T Consensus        60 ~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~----k~dl-~~L-------  127 (287)
T COG2607          60 ADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVD----KEDL-ATL-------  127 (287)
T ss_pred             HHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEc----HHHH-hhH-------
Confidence            4689988888887664331  1223446889999999999999999999887766533332    1010 111       


Q ss_pred             HHHHhCCCCCCchHHHHHHHh--CCceEEEEEeCCC---ChhhhhHhhccCC
Q 044214          107 LSNLLKDKNVMPYIDLNFRRL--GHMKVLIVFDDVT---CFSQLESLMGSLD  153 (385)
Q Consensus       107 l~~l~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~---~~~~~~~l~~~~~  153 (385)
                                    ..+.+.|  ...|+.|+.||+.   ..+....+...+.
T Consensus       128 --------------p~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~Le  165 (287)
T COG2607         128 --------------PDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALE  165 (287)
T ss_pred             --------------HHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhc
Confidence                          2223333  3578999999992   3344555554443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.44  E-value=0.00083  Score=58.47  Aligned_cols=38  Identities=18%  Similarity=0.216  Sum_probs=32.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..-+++.|+|.+|+|||++|.+++.........++|++
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~   47 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID   47 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            44679999999999999999999987765667788887

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

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.42  E-value=0.0062  Score=57.94  Aligned_cols=25  Identities=28%  Similarity=0.170  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+++++|++|+||||++.+++...
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999754

>smart00763 AAA_PrkA PrkA AAA domain

Probab=97.41  E-value=0.00015  Score=67.41  Aligned_cols=49  Identities=16%  Similarity=0.278  Sum_probs=41.4

Q ss_pred             CccccchhHHHHHHhhcCC----CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLGVE----SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++|.++.++++.+++...    +...+++.|+|++|+||||||..+++.+..
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            7999999999999988641    234678999999999999999999987643

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

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

Probab=97.41  E-value=0.0004  Score=62.50  Aligned_cols=79  Identities=19%  Similarity=0.200  Sum_probs=51.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh----hCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI----SGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRL  127 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~----~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l  127 (385)
                      -++|.++|++|.|||+|.+++++++    .++|.....+.         -+...++....+.-++...  ...+.+.+.+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liE---------inshsLFSKWFsESgKlV~--kmF~kI~ELv  245 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIE---------INSHSLFSKWFSESGKLVA--KMFQKIQELV  245 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEE---------EehhHHHHHHHhhhhhHHH--HHHHHHHHHH
Confidence            4789999999999999999999964    55676666665         2223344444333222111  4455666666


Q ss_pred             CCce--EEEEEeCCCC
Q 044214          128 GHMK--VLIVFDDVTC  141 (385)
Q Consensus       128 ~~k~--~LlVlDdv~~  141 (385)
                      +++.  +.+.+|.|.+
T Consensus       246 ~d~~~lVfvLIDEVES  261 (423)
T KOG0744|consen  246 EDRGNLVFVLIDEVES  261 (423)
T ss_pred             hCCCcEEEEEeHHHHH
Confidence            6655  4566888854

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

Probab=97.40  E-value=0.0013  Score=63.02  Aligned_cols=115  Identities=21%  Similarity=0.150  Sum_probs=65.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGH  129 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~  129 (385)
                      .....+.+.|++|+|||+||.+++.  ...|+.+-.++ ....    -++.+-.+-.           ..........+.
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~--~S~FPFvKiiS-pe~m----iG~sEsaKc~-----------~i~k~F~DAYkS  597 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIAL--SSDFPFVKIIS-PEDM----IGLSESAKCA-----------HIKKIFEDAYKS  597 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHh--hcCCCeEEEeC-hHHc----cCccHHHHHH-----------HHHHHHHHhhcC
Confidence            4466788999999999999999986  46788555444 1111    0110000000           111222333445


Q ss_pred             ceEEEEEeCCCChhhhh------------Hhh---ccCCCCCCCcEEEEEeccHHHHhhccc-eecccC
Q 044214          130 MKVLIVFDDVTCFSQLE------------SLM---GSLDWLTPVSRIILTTRNKQVLRNWRV-NAFKRN  182 (385)
Q Consensus       130 k~~LlVlDdv~~~~~~~------------~l~---~~~~~~~~gs~ilvTtR~~~~~~~~~~-~~~~~~  182 (385)
                      .--.||+||+...-+|-            .++   ...+..++.--|+-||-...++..|+. .+|...
T Consensus       598 ~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~  666 (744)
T KOG0741|consen  598 PLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSST  666 (744)
T ss_pred             cceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhhe
Confidence            56789999996443332            222   222323334445668888899988876 555543

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.40  E-value=7.9e-05  Score=47.08  Aligned_cols=38  Identities=11%  Similarity=0.051  Sum_probs=32.5

Q ss_pred             CCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCCCC
Q 044214          346 PKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNNFG  383 (385)
Q Consensus       346 ~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~~~  383 (385)
                      ++|++|+|+++   .+|..++  .+|++|++++|+++.+|.+.
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~~l~   43 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDISPLS   43 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEGGGT
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCcCCC
Confidence            47999999998   8888788  99999999999999988654

...

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

Probab=97.38  E-value=0.00039  Score=67.60  Aligned_cols=92  Identities=20%  Similarity=0.270  Sum_probs=58.7

Q ss_pred             CCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCC
Q 044214           29 NQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGG   98 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~   98 (385)
                      ..+=|.+..+.+|.+++..          +-..++-|.++|++|+|||.||++++.+..-.|     +.    ++.+   
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf-----~~----isAp---  257 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPF-----LS----ISAP---  257 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCce-----Ee----ecch---
Confidence            4577899999988887642          113367799999999999999999999765333     32    1111   


Q ss_pred             hHHHHHHHHHHHhCCCCCCchHHHH-HHHhCCceEEEEEeCCC
Q 044214           99 LSCLRQKLLSNLLKDKNVMPYIDLN-FRRLGHMKVLIVFDDVT  140 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~~~~~~~l-~~~l~~k~~LlVlDdv~  140 (385)
                            ++.+.+.++..  +.+..+ .+.-...++++++|+++
T Consensus       258 ------eivSGvSGESE--kkiRelF~~A~~~aPcivFiDeID  292 (802)
T KOG0733|consen  258 ------EIVSGVSGESE--KKIRELFDQAKSNAPCIVFIDEID  292 (802)
T ss_pred             ------hhhcccCcccH--HHHHHHHHHHhccCCeEEEeeccc
Confidence                  22222222221  222222 33345689999999996

>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=97.37  E-value=0.00042  Score=56.20  Aligned_cols=24  Identities=25%  Similarity=0.474  Sum_probs=21.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|.++|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            588999999999999999997644

...

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.36  E-value=0.0024  Score=66.46  Aligned_cols=51  Identities=20%  Similarity=0.326  Sum_probs=37.2

Q ss_pred             CCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+.|.+...++|.+.+..           +-...+-+.++|++|+|||++|+.+++.....
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~  514 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGAN  514 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCC
Confidence            4567877777777765531           11234568999999999999999999976543

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.

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

Probab=97.36  E-value=0.00074  Score=62.62  Aligned_cols=30  Identities=37%  Similarity=0.596  Sum_probs=26.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+..++|||++|+|||.+|+.+++...-.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~  175 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIE  175 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCC
Confidence            457889999999999999999999987654

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.35  E-value=0.0015  Score=61.73  Aligned_cols=100  Identities=17%  Similarity=0.154  Sum_probs=62.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      ....+.|||..|.|||-|++++.+......+....+.         .........+...+..     ...+.+++..  .
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y---------~~se~f~~~~v~a~~~-----~~~~~Fk~~y--~  175 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVY---------LTSEDFTNDFVKALRD-----NEMEKFKEKY--S  175 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEe---------ccHHHHHHHHHHHHHh-----hhHHHHHHhh--c
Confidence            4678999999999999999999998877776544444         2233333444443332     3345566666  3


Q ss_pred             eEEEEEeCCCC-------hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          131 KVLIVFDDVTC-------FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       131 ~~LlVlDdv~~-------~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      -=++++||++-       .+.+-.++..+.  ..|-.||+|++..
T Consensus       176 ~dlllIDDiq~l~gk~~~qeefFh~FN~l~--~~~kqIvltsdr~  218 (408)
T COG0593         176 LDLLLIDDIQFLAGKERTQEEFFHTFNALL--ENGKQIVLTSDRP  218 (408)
T ss_pred             cCeeeechHhHhcCChhHHHHHHHHHHHHH--hcCCEEEEEcCCC
Confidence            34888999952       122222233333  2344899999643

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

Probab=97.31  E-value=0.00012  Score=59.31  Aligned_cols=44  Identities=27%  Similarity=0.324  Sum_probs=32.0

Q ss_pred             cccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           32 VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ||....++++.+.+..-......|.|+|..|+||+++|+.+...
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~   44 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRY   44 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhh
Confidence            57777888887777642233446889999999999999988874

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.28  E-value=0.0079  Score=58.09  Aligned_cols=36  Identities=17%  Similarity=0.183  Sum_probs=27.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh--CCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS--GDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~--~~f~~~~w~~   87 (385)
                      .++++++|++|+||||++..++....  ..-..+..+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            35899999999999999999987664  3334455554

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

Probab=97.28  E-value=0.0026  Score=56.01  Aligned_cols=47  Identities=19%  Similarity=0.183  Sum_probs=33.7

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC------CceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF------DGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f------~~~~w~~   87 (385)
                      |-+.|..+=..-.++.|+|.+|+|||+||.+++.......      ..++|+.
T Consensus         8 lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~   60 (226)
T cd01393           8 LDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID   60 (226)
T ss_pred             HHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEe
Confidence            3334443334456999999999999999999987654444      5667776

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

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.28  E-value=0.0022  Score=56.91  Aligned_cols=45  Identities=20%  Similarity=0.229  Sum_probs=32.3

Q ss_pred             HhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEe
Q 044214           43 SLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLE   87 (385)
Q Consensus        43 ~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~   87 (385)
                      ..|..+-..-.++.|+|.+|+|||+||.+++......      -..++|++
T Consensus        10 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~   60 (235)
T cd01123          10 ELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID   60 (235)
T ss_pred             hhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEe
Confidence            3344333445799999999999999999998643222      36788887

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 .

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.28  E-value=0.0011  Score=60.13  Aligned_cols=80  Identities=19%  Similarity=0.280  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214            4 SELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV-------ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus         4 ~~~i~~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+..+++.+.+.+++..  ........+  ++...+.+.+.+..       ...+.++++++|++|+||||.+..++..+
T Consensus        21 ~~~~~~i~~~~~~~~~~--~~~~~~~~~--~~~~~e~l~~~~~~~~~~~~~~~~~~~vi~l~G~~G~GKTTt~akLA~~l   96 (272)
T TIGR00064        21 YEVVEKIIEALKKELKG--KKVKDAELL--KEILKEYLKEILKETDLELIVEENKPNVILFVGVNGVGKTTTIAKLANKL   96 (272)
T ss_pred             HHHHHHHHHHHHHHHhh--ccCCCHHHH--HHHHHHHHHHHHcccchhhcccCCCCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            34566677776655443  111111111  22223344444332       12346899999999999999999999877


Q ss_pred             hCCCCceEEEe
Q 044214           77 SGDFDGSCFLE   87 (385)
Q Consensus        77 ~~~f~~~~w~~   87 (385)
                      ...-..+.++.
T Consensus        97 ~~~g~~V~li~  107 (272)
T TIGR00064        97 KKQGKSVLLAA  107 (272)
T ss_pred             HhcCCEEEEEe
Confidence            65544455554

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.

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

Probab=97.26  E-value=0.0011  Score=64.70  Aligned_cols=100  Identities=22%  Similarity=0.382  Sum_probs=59.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHh-CCc
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRL-GHM  130 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~~k  130 (385)
                      +.-|.+||++|+|||-||+++++.-+-.|     ++ +...            +++....++..  ..+..+.++- ..-
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEag~NF-----is-VKGP------------ELlNkYVGESE--rAVR~vFqRAR~sa  604 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEAGANF-----IS-VKGP------------ELLNKYVGESE--RAVRQVFQRARASA  604 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhccCce-----Ee-ecCH------------HHHHHHhhhHH--HHHHHHHHHhhcCC
Confidence            56789999999999999999999866554     33 2221            23333322221  2333344433 357


Q ss_pred             eEEEEEeCCCC-------------hhhhhHhhccCCCC--CCCcEEEEEeccHHHH
Q 044214          131 KVLIVFDDVTC-------------FSQLESLMGSLDWL--TPVSRIILTTRNKQVL  171 (385)
Q Consensus       131 ~~LlVlDdv~~-------------~~~~~~l~~~~~~~--~~gs~ilvTtR~~~~~  171 (385)
                      +|+|++|.++.             ...+..|+..+...  ..|--||-.|..+++.
T Consensus       605 PCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiI  660 (802)
T KOG0733|consen  605 PCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDII  660 (802)
T ss_pred             CeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCccc
Confidence            99999999963             12245555555422  2355566666555543

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.26  E-value=0.001  Score=54.79  Aligned_cols=113  Identities=17%  Similarity=0.133  Sum_probs=61.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHH-----hCC-----CCCC-----
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNL-----LKD-----KNVM-----  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l-----~~~-----~~~~-----  117 (385)
                      .+|-|++-.|.||||+|...+-+...+-..+.++...... .. .+-..++..+ ..+     +..     .+..     
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~-~~-~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRALGHGYRVGVVQFLKGG-WK-YGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEEeCCC-Cc-cCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            3678888899999999999988765554445554433221 11 2333333332 000     000     0000     


Q ss_pred             --chHHHHHHHhCC-ceEEEEEeCCCC-----hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          118 --PYIDLNFRRLGH-MKVLIVFDDVTC-----FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       118 --~~~~~l~~~l~~-k~~LlVlDdv~~-----~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                        +.....++.+.. .-=|+|||++-.     .-..+.+...+.....+..||+|.|+.
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence              222333444433 456999999932     222334444444344677899999985

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=97.24  E-value=0.00052  Score=46.80  Aligned_cols=54  Identities=19%  Similarity=0.249  Sum_probs=43.5

Q ss_pred             CeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCC
Q 044214          321 KIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAG  376 (385)
Q Consensus       321 ~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~  376 (385)
                      +++.+.+..+.  -..+++..|.++++|++|+++++   .+|. .+.  .+|++|++++|++
T Consensus         2 ~L~~L~l~~n~--l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~l   61 (61)
T PF13855_consen    2 NLESLDLSNNK--LTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNNL   61 (61)
T ss_dssp             TESEEEETSST--ESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSSB
T ss_pred             cCcEEECCCCC--CCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCcC
Confidence            46677777664  45678899999999999999988   5554 555  8999999999875

...

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.24  E-value=0.0037  Score=56.79  Aligned_cols=185  Identities=18%  Similarity=0.187  Sum_probs=96.5

Q ss_pred             CCCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHH
Q 044214           27 NKNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      +-..++|-.++-..+..++.+  -.+...-+.|+|+.|.|||+|......+.++.-+...-+. .....   ..-.-.+.
T Consensus        22 ~~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~-Lng~~---~~dk~al~   97 (408)
T KOG2228|consen   22 PHINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVR-LNGEL---QTDKIALK   97 (408)
T ss_pred             CCcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEE-ECccc---hhhHHHHH
Confidence            446799999999999888863  1133446789999999999998877766332223333333 22111   11222344


Q ss_pred             HHHHHHhCCCC----CC----chHHHHHHHhCC------ceEEEEEeCCCCh----hh--hhHhhccC-CCCCCCcEEEE
Q 044214          105 KLLSNLLKDKN----VM----PYIDLNFRRLGH------MKVLIVFDDVTCF----SQ--LESLMGSL-DWLTPVSRIIL  163 (385)
Q Consensus       105 ~ll~~l~~~~~----~~----~~~~~l~~~l~~------k~~LlVlDdv~~~----~~--~~~l~~~~-~~~~~gs~ilv  163 (385)
                      .|.+++..+-.    ..    +....+...|+.      .+++.|+|.++-.    .+  +-.++..- ....|=|-|-+
T Consensus        98 ~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~  177 (408)
T KOG2228|consen   98 GITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGV  177 (408)
T ss_pred             HHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEe
Confidence            44444432221    11    445555555542      4688999888621    11  22222211 12345566778


Q ss_pred             EeccHHHHhhcc-c-eecc-------cCCCCCCchHHHHHHHHHhCCCccchhHHhHHHHHHH
Q 044214          164 TTRNKQVLRNWR-V-NAFK-------RNHPDVGNEKLSSNVMKYAQGVPLALKVLVWESAISK  217 (385)
Q Consensus       164 TtR~~~~~~~~~-~-~~~~-------~~~~~~~~~~~~~~i~~~~~GlPLal~~~~w~~~l~~  217 (385)
                      |||-.-.-.... + ..|.       ...+-+++..+.+++...-.|.|.++.  .|...+++
T Consensus       178 Ttrld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~v~~e~~~~~~--~wn~~~~~  238 (408)
T KOG2228|consen  178 TTRLDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLSVPAEFSDFAE--KWNRSVQE  238 (408)
T ss_pred             eccccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhcCCccCccHHH--HHHhhhhH
Confidence            998542211110 0 1121       122233445555555544456555444  77766555

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.24  E-value=0.011  Score=55.53  Aligned_cols=37  Identities=19%  Similarity=0.187  Sum_probs=28.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++++++|+.|+||||++..++......-..+.+++
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lIt  241 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFIT  241 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            4679999999999999999999986644434455555

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.23  E-value=0.0049  Score=58.51  Aligned_cols=27  Identities=22%  Similarity=0.199  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..++|.++|..|+||||.+..++..+.
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            467999999999999999999998664

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.22  E-value=0.00048  Score=58.23  Aligned_cols=37  Identities=32%  Similarity=0.661  Sum_probs=31.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+|.+.|++|+||||+|+.+++.+...+...+++.
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~   42 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLD   42 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            4468999999999999999999999887777777764

>PRK06762 hypothetical protein; Provisional

Probab=97.21  E-value=0.0012  Score=55.16  Aligned_cols=24  Identities=38%  Similarity=0.538  Sum_probs=22.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+|.|+|++|+||||+|+.+.+.+
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999999876

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.20  E-value=0.0011  Score=55.89  Aligned_cols=28  Identities=25%  Similarity=0.368  Sum_probs=24.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      +.|.++|.+|+||||+|+++++.++++-
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~i   29 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQEI   29 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHhh
Confidence            4688999999999999999999776543

>PRK13695 putative NTPase; Provisional

Probab=97.20  E-value=0.00084  Score=56.62  Aligned_cols=24  Identities=38%  Similarity=0.583  Sum_probs=21.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|+|+|.+|+|||||++.+++.++
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~   25 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLK   25 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999988765

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.19  E-value=0.0043  Score=58.00  Aligned_cols=46  Identities=20%  Similarity=0.172  Sum_probs=35.1

Q ss_pred             Cccc-cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           30 QLVG-VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        30 ~~vG-R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++| -+..++.+.+.+..+ .-.+...++|+.|+|||++|..+++.+
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~-~l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKN-RLSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcC-CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3566 566677787777632 235567999999999999999999865

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.19  E-value=0.0028  Score=59.96  Aligned_cols=94  Identities=15%  Similarity=0.175  Sum_probs=54.2

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC-
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM-  117 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~-  117 (385)
                      .++-+.|..+=..-.++.|.|.+|+|||||+.+++......-..++|++ ..      .....+... +..++....+. 
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs-~E------Es~~qi~~R-a~rlg~~~~~l~  140 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS-GE------ESPEQIKLR-ADRLGISTENLY  140 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE-CC------cCHHHHHHH-HHHcCCCcccEE
Confidence            3444444432234569999999999999999999987765545666765 21      222222221 23333222211 


Q ss_pred             ----chHHHHHHHhC-CceEEEEEeCCC
Q 044214          118 ----PYIDLNFRRLG-HMKVLIVFDDVT  140 (385)
Q Consensus       118 ----~~~~~l~~~l~-~k~~LlVlDdv~  140 (385)
                          ...+.+.+.+. .++-++|+|.+.
T Consensus       141 l~~e~~le~I~~~i~~~~~~lVVIDSIq  168 (372)
T cd01121         141 LLAETNLEDILASIEELKPDLVIIDSIQ  168 (372)
T ss_pred             EEccCcHHHHHHHHHhcCCcEEEEcchH
Confidence                22344444443 467789999983

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.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.18  E-value=0.0022  Score=55.22  Aligned_cols=113  Identities=19%  Similarity=0.170  Sum_probs=59.0

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM  117 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~  117 (385)
                      .+.+...+..   +-+++.|.|.+|.||||++..+.+.+...-..+++.. .         -......+....+...   
T Consensus         7 ~~a~~~~l~~---~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~a-p---------T~~Aa~~L~~~~~~~a---   70 (196)
T PF13604_consen    7 REAVRAILTS---GDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLA-P---------TNKAAKELREKTGIEA---   70 (196)
T ss_dssp             HHHHHHHHHC---TCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEE-S---------SHHHHHHHHHHHTS-E---
T ss_pred             HHHHHHHHhc---CCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEEC-C---------cHHHHHHHHHhhCcch---
Confidence            3444444542   2357889999999999999998886655433344443 1         1122223333332111   


Q ss_pred             chHHHHHHHh----------CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          118 PYIDLNFRRL----------GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       118 ~~~~~l~~~l----------~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..+..+....          ..+.-+||+|++..  ...+..++.....  .|+++|+.-=..
T Consensus        71 ~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~  131 (196)
T PF13604_consen   71 QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPN  131 (196)
T ss_dssp             EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TT
T ss_pred             hhHHHHHhcCCcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcc
Confidence            1111111111          12234999999964  4567777766552  577887766443

>PRK10867 signal recognition particle protein; Provisional

Probab=97.18  E-value=0.0046  Score=59.50  Aligned_cols=29  Identities=24%  Similarity=0.284  Sum_probs=25.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+.+|.++|.+|+||||.|..++..+...
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~  127 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            46899999999999999999998876554

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=97.14  E-value=0.006  Score=54.64  Aligned_cols=141  Identities=16%  Similarity=0.113  Sum_probs=89.4

Q ss_pred             HhHHHHHHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc
Q 044214            3 ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG   82 (385)
Q Consensus         3 e~~~i~~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~   82 (385)
                      +.+.++.-......+-+....+....+.|+|-.. .+++..++......-+.+.++|+.|+|||+-++.+++..    +.
T Consensus        46 ~~~~~~a~ia~~le~~~~q~~~~~~~~~~l~tkt-~r~~~~~~~~A~k~g~l~~vyg~~g~gKt~a~~~y~~s~----p~  120 (297)
T COG2842          46 DYATNEAKIAAFLEKKGVQAALEKLAPDFLETKT-VRRIFFRTRPASKTGSLVVVYGYAGLGKTQAAKNYAPSN----PN  120 (297)
T ss_pred             hHHHHHHHHHHHHcCCCcccccccccccccccch-hHhHhhhhhhhhhcCceEEEeccccchhHHHHHhhcccC----cc
Confidence            4555665566665554543355566788888654 333444444333334489999999999999999988742    33


Q ss_pred             eEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC--chHHHHHHHhCCceEEEEEeCCCC--hhhhhHhhccCC
Q 044214           83 SCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM--PYIDLNFRRLGHMKVLIVFDDVTC--FSQLESLMGSLD  153 (385)
Q Consensus        83 ~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~--~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~~~  153 (385)
                       .|...   .+.. +....+...+...........  +....+...+.+..-+++.|+.+.  ...++.+.....
T Consensus       121 -~~l~~---~~p~-~~a~~~i~~i~~~~~~~~~~~~~d~~~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d  190 (297)
T COG2842         121 -ALLIE---ADPS-YTALVLILIICAAAFGATDGTINDLTERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHD  190 (297)
T ss_pred             -ceeec---CChh-hHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHccCcceeeeehhhccChHHHHHHHHHHH
Confidence             33331   2333 566666666666665555432  677777788899999999999974  455666654444

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

Probab=97.13  E-value=0.00041  Score=55.03  Aligned_cols=22  Identities=50%  Similarity=0.856  Sum_probs=20.4

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |+|.|.+|+||||+|+++.++.
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            6899999999999999999874

...

>TIGR01817 nifA Nif-specific regulatory protein

Probab=97.13  E-value=0.0049  Score=61.71  Aligned_cols=51  Identities=20%  Similarity=0.296  Sum_probs=40.7

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .....++|....++++.+.+..-......|.|+|..|+|||++|+.+.+.-
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s  243 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLS  243 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhC
Confidence            345689999999999988776433334467899999999999999999853

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.10  E-value=0.0012  Score=64.73  Aligned_cols=50  Identities=20%  Similarity=0.203  Sum_probs=34.8

Q ss_pred             CCccccchhHHHHHHhh---cC-----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           29 NQLVGVESTVEEIESLL---GV-----ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L---~~-----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++.|.+...+.+....   ..     +-..++-|.++|++|+|||.+|+.+++...-
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~  285 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQL  285 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCC
Confidence            45777776665555421   10     1134567999999999999999999997643

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

Probab=97.10  E-value=0.0064  Score=61.59  Aligned_cols=126  Identities=20%  Similarity=0.263  Sum_probs=70.1

Q ss_pred             CCCCccccchhHH---HHHHhhcC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCC
Q 044214           27 NKNQLVGVESTVE---EIESLLGV-------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIP   96 (385)
Q Consensus        27 ~~~~~vGR~~~l~---~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~   96 (385)
                      .-.++.|-++..+   ++.+.|.+       +..-++=+.++|++|+|||-||++++..-     .+-|++    ++.. 
T Consensus       309 ~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA-----gVPF~s----vSGS-  378 (774)
T KOG0731|consen  309 KFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA-----GVPFFS----VSGS-  378 (774)
T ss_pred             ccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc-----CCceee----echH-
Confidence            3356788775555   45555653       22336779999999999999999999753     344554    2111 


Q ss_pred             CChHHHHHHHHHHHhCCCCCCchHHHHHHH-hCCceEEEEEeCCCCh-----------------hhhhHhhccCCCCCCC
Q 044214           97 GGLSCLRQKLLSNLLKDKNVMPYIDLNFRR-LGHMKVLIVFDDVTCF-----------------SQLESLMGSLDWLTPV  158 (385)
Q Consensus        97 ~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~-l~~k~~LlVlDdv~~~-----------------~~~~~l~~~~~~~~~g  158 (385)
                              +..........  ..+..+... =.+.++++.+|+++..                 ..+.+++.....+..+
T Consensus       379 --------EFvE~~~g~~a--srvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~  448 (774)
T KOG0731|consen  379 --------EFVEMFVGVGA--SRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETS  448 (774)
T ss_pred             --------HHHHHhcccch--HHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCC
Confidence                    11111111110  222222222 2457899999998521                 2266666666544444


Q ss_pred             cEE--EEEeccHHHHh
Q 044214          159 SRI--ILTTRNKQVLR  172 (385)
Q Consensus       159 s~i--lvTtR~~~~~~  172 (385)
                      ..|  +-+|...++..
T Consensus       449 ~~vi~~a~tnr~d~ld  464 (774)
T KOG0731|consen  449 KGVIVLAATNRPDILD  464 (774)
T ss_pred             CcEEEEeccCCccccC
Confidence            433  34555555543

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.08  E-value=0.0014  Score=61.69  Aligned_cols=108  Identities=12%  Similarity=0.080  Sum_probs=64.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      ..|.|.|+.|+||||+...+.+.+.......++.. -....   ..... ...+..+.............++..|+..+=
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~ti-Edp~E---~~~~~-~~~~i~q~evg~~~~~~~~~l~~~lr~~pd  197 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYINKNAAGHIITI-EDPIE---YVHRN-KRSLINQREVGLDTLSFANALRAALREDPD  197 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEE-cCChh---hhccC-ccceEEccccCCCCcCHHHHHHHhhccCCC
Confidence            58999999999999999999987766555555553 11000   00000 000000000001112566778888999999


Q ss_pred             EEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          133 LIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       133 LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      .|++|.+.+.+.+...+...   ..|..|+.|....
T Consensus       198 ~i~vgEird~~~~~~~l~aa---~tGh~v~~T~Ha~  230 (343)
T TIGR01420       198 VILIGEMRDLETVELALTAA---ETGHLVFGTLHTN  230 (343)
T ss_pred             EEEEeCCCCHHHHHHHHHHH---HcCCcEEEEEcCC
Confidence            99999998877766544432   2455566665543

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>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=97.07  E-value=0.00096  Score=54.68  Aligned_cols=36  Identities=28%  Similarity=0.374  Sum_probs=30.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+|-|+|.+|+||||||+++.+++.+.-..+.++.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFARGIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEec
Confidence            358999999999999999999999987777777775

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 ....

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.06  E-value=0.018  Score=53.33  Aligned_cols=164  Identities=15%  Similarity=0.159  Sum_probs=79.0

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC--Cce-----EEEeeccccccCCCChHHHHHHHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF--DGS-----CFLENVREESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f--~~~-----~w~~~~~~~~~~~~~~~~l~~~ll~~l  110 (385)
                      .+.+...+.. ..-...+.++|+.|+||+++|..+++.+-..-  .+.     -|+.    .... +++.-+... -..-
T Consensus        13 ~~~l~~~~~~-~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~----~g~H-PD~~~i~~~-p~~~   85 (319)
T PRK08769         13 YDQTVAALDA-GRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIA----AGTH-PDLQLVSFI-PNRT   85 (319)
T ss_pred             HHHHHHHHHc-CCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHh----cCCC-CCEEEEecC-CCcc
Confidence            4455555552 22345789999999999999999998652211  100     0000    0000 111000000 0000


Q ss_pred             hCC---CCCCchHHHHHHHhC-----CceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEeccH-HHHhhccc---
Q 044214          111 LKD---KNVMPYIDLNFRRLG-----HMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK-QVLRNWRV---  176 (385)
Q Consensus       111 ~~~---~~~~~~~~~l~~~l~-----~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~-~~~~~~~~---  176 (385)
                      +..   ...++.+..+.+.+.     +++-++|+|+++..  ..-..++..+..-..++.+|++|.+. .+......   
T Consensus        86 ~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq  165 (319)
T PRK08769         86 GDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQ  165 (319)
T ss_pred             cccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhhe
Confidence            000   001133333433332     45668999999743  44556665555444577676666543 33333222   


Q ss_pred             -eecccCCC---------CCCchHHHHHHHHHhCCCccchhH
Q 044214          177 -NAFKRNHP---------DVGNEKLSSNVMKYAQGVPLALKV  208 (385)
Q Consensus       177 -~~~~~~~~---------~~~~~~~~~~i~~~~~GlPLal~~  208 (385)
                       ..|.....         .......+..++..++|.|+....
T Consensus       166 ~i~~~~~~~~~~~~~L~~~~~~~~~a~~~~~l~~G~p~~A~~  207 (319)
T PRK08769        166 RLEFKLPPAHEALAWLLAQGVSERAAQEALDAARGHPGLAAQ  207 (319)
T ss_pred             EeeCCCcCHHHHHHHHHHcCCChHHHHHHHHHcCCCHHHHHH
Confidence             22221100         011233356788999999975543

>TIGR00959 ffh signal recognition particle protein

Probab=97.05  E-value=0.014  Score=56.23  Aligned_cols=27  Identities=22%  Similarity=0.225  Sum_probs=23.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++.++.++|.+|+||||.|..++..+.
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~  124 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLK  124 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            367999999999999999999998764

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.

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

Probab=97.05  E-value=0.0006  Score=58.63  Aligned_cols=26  Identities=35%  Similarity=0.538  Sum_probs=23.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +|+|.|.+|+||||+|+.+...+...
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTC
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCcc
Confidence            69999999999999999999988654

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

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.04  E-value=0.0045  Score=54.87  Aligned_cols=48  Identities=17%  Similarity=0.088  Sum_probs=34.3

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|-+.|..+=..-.++.|+|.+|+|||+||.+++.....+-..++|+.
T Consensus        13 ~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~   60 (234)
T PRK06067         13 ELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVIT   60 (234)
T ss_pred             HHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEE
Confidence            344445433345679999999999999999999765433445677776

>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=97.04  E-value=0.002  Score=52.46  Aligned_cols=102  Identities=18%  Similarity=0.175  Sum_probs=56.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      .+++|.|..|.|||||++.++.... ...+.+++.......-. +.              -.......-.+.+.+-.++-
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~-~~~G~i~~~~~~~i~~~-~~--------------lS~G~~~rv~laral~~~p~   90 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGELE-PDEGIVTWGSTVKIGYF-EQ--------------LSGGEKMRLALAKLLLENPN   90 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCCC-CCceEEEECCeEEEEEE-cc--------------CCHHHHHHHHHHHHHhcCCC
Confidence            5899999999999999999987543 23455555421111110 11              00011222234555556677


Q ss_pred             EEEEeCCC---ChhhhhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          133 LIVFDDVT---CFSQLESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       133 LlVlDdv~---~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      ++++|+..   +......+...+...  +..||++|.+.+...
T Consensus        91 illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~  131 (144)
T cd03221          91 LLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLD  131 (144)
T ss_pred             EEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHH
Confidence            89999983   333333333333222  246788887765543

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.03  E-value=0.0022  Score=57.41  Aligned_cols=26  Identities=27%  Similarity=0.532  Sum_probs=22.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +|.++|.+|+||||+|+++++.+...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~~   26 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSEK   26 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            37899999999999999999877543

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.02  E-value=0.0065  Score=60.34  Aligned_cols=131  Identities=15%  Similarity=0.177  Sum_probs=85.6

Q ss_pred             CCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhh-----C---CCCceEEEeeccccccC
Q 044214           27 NKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKIS-----G---DFDGSCFLENVREESQI   95 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~-----~---~f~~~~w~~~~~~~~~~   95 (385)
                      .+..+-+|+.+..+|.+.+..   .......+-|.|.+|.|||+.+..|.+.++     .   .|+ .+.+. .-..   
T Consensus       394 vp~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveIN-gm~l---  468 (767)
T KOG1514|consen  394 VPESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEIN-GLRL---  468 (767)
T ss_pred             ccccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEc-ceee---
Confidence            567788999999999988763   223345889999999999999999998543     1   243 22332 1112   


Q ss_pred             CCChHHHHHHHHHHHhCCCCCC-chHHHHHHHhC-----CceEEEEEeCCCC-----hhhhhHhhccCCCCCCCcEEEEE
Q 044214           96 PGGLSCLRQKLLSNLLKDKNVM-PYIDLNFRRLG-----HMKVLIVFDDVTC-----FSQLESLMGSLDWLTPVSRIILT  164 (385)
Q Consensus        96 ~~~~~~l~~~ll~~l~~~~~~~-~~~~~l~~~l~-----~k~~LlVlDdv~~-----~~~~~~l~~~~~~~~~gs~ilvT  164 (385)
                       ....++...|+..+.+....- ...+.+..+..     .+++++++|+++.     .+.+-.++.-.  ..++++++|-
T Consensus       469 -~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWp--t~~~sKLvvi  545 (767)
T KOG1514|consen  469 -ASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWP--TLKNSKLVVI  545 (767)
T ss_pred             -cCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCC--cCCCCceEEE
Confidence             667888888888887765522 44455555543     4679999999853     23344443221  2457776554


Q ss_pred             e
Q 044214          165 T  165 (385)
Q Consensus       165 t  165 (385)
                      +
T Consensus       546 ~  546 (767)
T KOG1514|consen  546 A  546 (767)
T ss_pred             E
Confidence            4

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.02  E-value=0.0066  Score=56.80  Aligned_cols=94  Identities=19%  Similarity=0.202  Sum_probs=56.6

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM  117 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~  117 (385)
                      ..++-+.|..+--.-.+|.|-|-+|||||||..+++.++.... .+.+++ ..      .+..++ +--...++-..++.
T Consensus        79 ~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~-~vLYVs-GE------ES~~Qi-klRA~RL~~~~~~l  149 (456)
T COG1066          79 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRG-KVLYVS-GE------ESLQQI-KLRADRLGLPTNNL  149 (456)
T ss_pred             hHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhcC-cEEEEe-CC------cCHHHH-HHHHHHhCCCccce
Confidence            3444444542222346899999999999999999999987766 677765 21      222222 22233344322322


Q ss_pred             -----chHHHHHHHh-CCceEEEEEeCCC
Q 044214          118 -----PYIDLNFRRL-GHMKVLIVFDDVT  140 (385)
Q Consensus       118 -----~~~~~l~~~l-~~k~~LlVlDdv~  140 (385)
                           ...+.+.+.+ ..++-++|+|-+.
T Consensus       150 ~l~aEt~~e~I~~~l~~~~p~lvVIDSIQ  178 (456)
T COG1066         150 YLLAETNLEDIIAELEQEKPDLVVIDSIQ  178 (456)
T ss_pred             EEehhcCHHHHHHHHHhcCCCEEEEeccc
Confidence                 3333444444 4688999999983

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

Probab=97.01  E-value=0.0036  Score=60.18  Aligned_cols=48  Identities=31%  Similarity=0.383  Sum_probs=34.7

Q ss_pred             CCccccch---hHHHHHHhhcCCC-------CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVES---TVEEIESLLGVES-------KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~---~l~~l~~~L~~~~-------~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.-|-|+   |++++.+.|.++.       .=++-|.++|++|.|||-||++++...
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc
Confidence            34566664   5566666776422       226789999999999999999999753

>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=97.01  E-value=0.0018  Score=58.40  Aligned_cols=35  Identities=17%  Similarity=0.149  Sum_probs=23.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.|.|+|.+|+||||+|+++...+.+.-..+.++.
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~   36 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEEKGKEVVIIS   36 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEc
Confidence            57999999999999999999997765323344443

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

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

Probab=97.01  E-value=0.00076  Score=66.98  Aligned_cols=53  Identities=26%  Similarity=0.360  Sum_probs=43.3

Q ss_pred             CCccccchhHHHHHHhhcC----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           29 NQLVGVESTVEEIESLLGV----ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      .+-+|-++..+++.+.|.-    ..-+-++++++|++|||||+|++.+++-+...|-
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rkfv  379 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFV  379 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEE
Confidence            4578999999999998862    2334579999999999999999999998876663

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=97.00  E-value=0.018  Score=56.33  Aligned_cols=131  Identities=20%  Similarity=0.225  Sum_probs=75.2

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHH
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      .-++++|-+.-...|...+..+. -.......|+-|+||||+|+-++.-+-..=.     ....     |.+-...-+.|
T Consensus        14 ~F~evvGQe~v~~~L~nal~~~r-i~hAYlfsG~RGvGKTt~Ari~AkalNC~~~-----~~~e-----PC~~C~~Ck~I   82 (515)
T COG2812          14 TFDDVVGQEHVVKTLSNALENGR-IAHAYLFSGPRGVGKTTIARILAKALNCENG-----PTAE-----PCGKCISCKEI   82 (515)
T ss_pred             cHHHhcccHHHHHHHHHHHHhCc-chhhhhhcCCCCcCchhHHHHHHHHhcCCCC-----CCCC-----cchhhhhhHhh
Confidence            34678999999999999998432 2456788999999999999999986522100     0000     01111111122


Q ss_pred             HHH-------HhCCCC-CCchHHHHHHHh-----CCceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          107 LSN-------LLKDKN-VMPYIDLNFRRL-----GHMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       107 l~~-------l~~~~~-~~~~~~~l~~~l-----~~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ...       +....+ .++-++.+.+..     +++.=+.|+|.|.  +...+..++..+..-...-..|+.|.+.
T Consensus        83 ~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~  159 (515)
T COG2812          83 NEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEP  159 (515)
T ss_pred             hcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCc
Confidence            111       000000 113333333333     2455688999996  4567888887776544555556655543

>PTZ00301 uridine kinase; Provisional

Probab=96.98  E-value=0.00075  Score=58.60  Aligned_cols=29  Identities=24%  Similarity=0.493  Sum_probs=24.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..+|+|.|.+|+||||||+.+.+++...+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~~~~   31 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELMAHC   31 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHHhhc
Confidence            46899999999999999999998775443

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

Probab=96.96  E-value=0.0021  Score=58.04  Aligned_cols=102  Identities=17%  Similarity=0.130  Sum_probs=61.3

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh-CCCC
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL-KDKN  115 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~-~~~~  115 (385)
                      .++.+..++..   ...+|.|.|..|+||||++..+.+.+...-..++.+.+..+.. . ...        .++. ....
T Consensus        68 ~~~~l~~~~~~---~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~-~-~~~--------~q~~v~~~~  134 (264)
T cd01129          68 NLEIFRKLLEK---PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ-I-PGI--------NQVQVNEKA  134 (264)
T ss_pred             HHHHHHHHHhc---CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec-C-CCc--------eEEEeCCcC
Confidence            33445555542   2347999999999999999999887644222333333222210 0 110        0110 0111


Q ss_pred             CCchHHHHHHHhCCceEEEEEeCCCChhhhhHhhcc
Q 044214          116 VMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGS  151 (385)
Q Consensus       116 ~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~  151 (385)
                      .......++..|+..+=.++++++.+.+....+...
T Consensus       135 ~~~~~~~l~~~lR~~PD~i~vgEiR~~e~a~~~~~a  170 (264)
T cd01129         135 GLTFARGLRAILRQDPDIIMVGEIRDAETAEIAVQA  170 (264)
T ss_pred             CcCHHHHHHHHhccCCCEEEeccCCCHHHHHHHHHH
Confidence            225677888888889999999999988876655544

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.96  E-value=0.0095  Score=48.78  Aligned_cols=24  Identities=42%  Similarity=0.624  Sum_probs=21.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|.|+|.+|+||||+|+.+...+.
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~   24 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLF   24 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999998764

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

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

Probab=96.96  E-value=0.0099  Score=52.29  Aligned_cols=121  Identities=18%  Similarity=0.383  Sum_probs=68.9

Q ss_pred             CccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCC
Q 044214           30 QLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGG   98 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~   98 (385)
                      ..=|-.+++++|.+....           +-+.++-|.++|++|.|||-+|++++++..     -+|+..++.       
T Consensus       178 dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtd-----acfirvigs-------  245 (435)
T KOG0729|consen  178 DVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTD-----ACFIRVIGS-------  245 (435)
T ss_pred             cccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccC-----ceEEeehhH-------
Confidence            345667777777765431           224567899999999999999999999753     334442211       


Q ss_pred             hHHHHHHHHHHHhCCCCCCchHHHHHHHhCC-ceEEEEEeCCCC-------------h---hhhhHhhccCCCCCC--Cc
Q 044214           99 LSCLRQKLLSNLLKDKNVMPYIDLNFRRLGH-MKVLIVFDDVTC-------------F---SQLESLMGSLDWLTP--VS  159 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~-k~~LlVlDdv~~-------------~---~~~~~l~~~~~~~~~--gs  159 (385)
                            ++.....++..  .....+.+..+. |-|+|++|.++.             .   ...-++..++..+.+  +-
T Consensus       246 ------elvqkyvgega--rmvrelf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgni  317 (435)
T KOG0729|consen  246 ------ELVQKYVGEGA--RMVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNI  317 (435)
T ss_pred             ------HHHHHHhhhhH--HHHHHHHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCe
Confidence                  12222222111  233344444444 668999998842             0   113344455554433  35


Q ss_pred             EEEEEeccHHH
Q 044214          160 RIILTTRNKQV  170 (385)
Q Consensus       160 ~ilvTtR~~~~  170 (385)
                      +|++.|..++.
T Consensus       318 kvlmatnrpdt  328 (435)
T KOG0729|consen  318 KVLMATNRPDT  328 (435)
T ss_pred             EEEeecCCCCC
Confidence            77877765443

>TIGR00763 lon ATP-dependent protease La

Probab=96.93  E-value=0.0013  Score=68.72  Aligned_cols=51  Identities=25%  Similarity=0.367  Sum_probs=39.5

Q ss_pred             CccccchhHHHHHHhhcC----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           30 QLVGVESTVEEIESLLGV----ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..+|.++..+++.+++..    +..+.+++.++|++|+|||++|+.+++.+...|
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~  375 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKF  375 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCe
Confidence            478888888888876541    222345799999999999999999999875544

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.

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

Probab=96.93  E-value=0.0058  Score=60.79  Aligned_cols=73  Identities=23%  Similarity=0.236  Sum_probs=47.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      ..-|.|.|..|+|||+||+++++.+... .-.+.+++ .... .. ..+..+++.+-             ..+...+.-.
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~-Cs~l-~~-~~~e~iQk~l~-------------~vfse~~~~~  494 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVS-CSTL-DG-SSLEKIQKFLN-------------NVFSEALWYA  494 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEe-chhc-cc-hhHHHHHHHHH-------------HHHHHHHhhC
Confidence            4578999999999999999999977543 33444444 2111 11 23444444332             2244556678


Q ss_pred             eEEEEEeCCC
Q 044214          131 KVLIVFDDVT  140 (385)
Q Consensus       131 ~~LlVlDdv~  140 (385)
                      +-++||||++
T Consensus       495 PSiIvLDdld  504 (952)
T KOG0735|consen  495 PSIIVLDDLD  504 (952)
T ss_pred             CcEEEEcchh
Confidence            8999999995

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.93  E-value=0.0011  Score=65.06  Aligned_cols=50  Identities=22%  Similarity=0.282  Sum_probs=41.3

Q ss_pred             CCccccchhHHHHHHhhc----CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           29 NQLVGVESTVEEIESLLG----VESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~----~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .+++|.++.++++.+.|.    .-..+.+++.++|++|+|||+||+.+++-+..
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            358999999999999883    22345679999999999999999999986543

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.92  E-value=0.0012  Score=56.73  Aligned_cols=30  Identities=33%  Similarity=0.544  Sum_probs=26.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .++.+|+|.|.+|+||||+|+.++..+...
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~~~~~   35 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHHhCcC
Confidence            456899999999999999999999988765

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.91  E-value=0.011  Score=55.77  Aligned_cols=83  Identities=16%  Similarity=0.121  Sum_probs=46.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCC--CceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC----chHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDF--DGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM----PYIDLNFR  125 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f--~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~----~~~~~l~~  125 (385)
                      ..+++++|+.|+||||++.+++.+....+  ..+.++. ....  . ....+-+....+.++.+....    +.. ....
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit-~D~~--R-~ga~EqL~~~a~~~gv~~~~~~~~~~l~-~~l~  211 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLT-TDSY--R-IGGHEQLRIFGKILGVPVHAVKDGGDLQ-LALA  211 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEe-cccc--c-ccHHHHHHHHHHHcCCceEecCCcccHH-HHHH
Confidence            46899999999999999999998754333  3445554 2111  1 233334444444443322211    222 2333


Q ss_pred             HhCCceEEEEEeCCC
Q 044214          126 RLGHMKVLIVFDDVT  140 (385)
Q Consensus       126 ~l~~k~~LlVlDdv~  140 (385)
                      .+.++ -++++|..-
T Consensus       212 ~l~~~-DlVLIDTaG  225 (374)
T PRK14722        212 ELRNK-HMVLIDTIG  225 (374)
T ss_pred             HhcCC-CEEEEcCCC
Confidence            44555 455699983

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.91  E-value=0.0014  Score=57.99  Aligned_cols=31  Identities=29%  Similarity=0.362  Sum_probs=26.9

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .++..+|+|.|.+|+|||||++.+...++..
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            4567899999999999999999999877654

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.89  E-value=0.024  Score=54.43  Aligned_cols=37  Identities=19%  Similarity=0.161  Sum_probs=28.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.+|.++|..|+||||++..++..++.+-..+..++
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~  135 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVC  135 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEc
Confidence            4689999999999999999999886654433344443

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.88  E-value=0.0024  Score=61.78  Aligned_cols=46  Identities=17%  Similarity=0.076  Sum_probs=39.0

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..++||++.++.+...+..+.    .|.|.|++|+|||+||+.+......
T Consensus        20 ~~i~gre~vI~lll~aalag~----hVLL~GpPGTGKT~LAraLa~~~~~   65 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFAFQN   65 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC----CEEEECCCChhHHHHHHHHHHHhcc
Confidence            469999999999988887432    5889999999999999999986543

>PRK06547 hypothetical protein; Provisional

Probab=96.88  E-value=0.0016  Score=54.64  Aligned_cols=28  Identities=36%  Similarity=0.438  Sum_probs=24.5

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .....+|+|.|.+|+||||+|..+++..
T Consensus        12 ~~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         12 GGGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             cCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3567799999999999999999999864

>PRK08233 hypothetical protein; Provisional

Probab=96.88  E-value=0.00089  Score=56.75  Aligned_cols=26  Identities=27%  Similarity=0.391  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|+|.|.+|+||||||..++..+.
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            36899999999999999999998764

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.87  E-value=0.0068  Score=50.55  Aligned_cols=114  Identities=16%  Similarity=0.093  Sum_probs=59.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHH---hCC-----CC-CC------
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNL---LKD-----KN-VM------  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l---~~~-----~~-~~------  117 (385)
                      ..|-|++-.|.||||.|...+-+...+--.+..+...... .. .+-...+..+.-.+   +..     .+ +.      
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~ra~~~g~~v~ivQFlKg~-~~-~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~   83 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALRALGHGKKVGVIQFIKGA-WP-NGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAK   83 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCC-cc-cChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHH
Confidence            4778888899999999999988765443334333222211 01 22222332220000   000     00 00      


Q ss_pred             chHHHHHHHhCC-ceEEEEEeCCC-----ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          118 PYIDLNFRRLGH-MKVLIVFDDVT-----CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       118 ~~~~~l~~~l~~-k~~LlVlDdv~-----~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      +.....++.+.. .-=|+|||.+.     ..-..+++...+....++..||+|-|+.
T Consensus        84 ~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        84 AAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            233344444444 44599999993     2222333333333344677899999975

Alternate name: corrinoid adenosyltransferase.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.87  E-value=0.0011  Score=57.74  Aligned_cols=27  Identities=41%  Similarity=0.647  Sum_probs=24.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+..+|+|.|.+|+||||||+.++..+
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            456799999999999999999999876

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.87  E-value=0.0077  Score=55.41  Aligned_cols=161  Identities=16%  Similarity=0.157  Sum_probs=82.6

Q ss_pred             ccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH-Hh--hCCCCceEEEeeccccccC----C----CChHH
Q 044214           33 GVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD-KI--SGDFDGSCFLENVREESQI----P----GGLSC  101 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~-~~--~~~f~~~~w~~~~~~~~~~----~----~~~~~  101 (385)
                      +|..+..--.++|.  ++.+..|.+.|.+|.|||.||.+..- ++  +..|..++-...+-...+.    |    ..+..
T Consensus       228 prn~eQ~~ALdlLl--d~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEeKm~P  305 (436)
T COG1875         228 PRNAEQRVALDLLL--DDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEEKMGP  305 (436)
T ss_pred             cccHHHHHHHHHhc--CCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhhhccc
Confidence            35555555555666  56788999999999999998887652 22  4456544433222111110    0    11222


Q ss_pred             HHHHHHHHH---hCCCC-CCchHHHH----------HHHhCCc---eEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEE
Q 044214          102 LRQKLLSNL---LKDKN-VMPYIDLN----------FRRLGHM---KVLIVFDDVTC--FSQLESLMGSLDWLTPVSRII  162 (385)
Q Consensus       102 l~~~ll~~l---~~~~~-~~~~~~~l----------~~~l~~k---~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~il  162 (385)
                      +.+.+...+   ..... .....+.+          ..+.+++   +-++|+|.+.+  ..++..+...   .+.|+||+
T Consensus       306 Wmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTpheikTiltR---~G~GsKIV  382 (436)
T COG1875         306 WMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPHELKTILTR---AGEGSKIV  382 (436)
T ss_pred             hHHHHHhHHHHHhcccccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHHHHHHHHHh---ccCCCEEE
Confidence            233332222   11111 11111111          1122332   46999999975  4556666544   47899999


Q ss_pred             EEeccHHHHhhccceecccCCCCCCchHHHHHHHHHhCCCccchhH
Q 044214          163 LTTRNKQVLRNWRVNAFKRNHPDVGNEKLSSNVMKYAQGVPLALKV  208 (385)
Q Consensus       163 vTtR~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~GlPLal~~  208 (385)
                      +|.--.++-..    .+..      ...-..-++++..|+|+.-.+
T Consensus       383 l~gd~aQiD~~----yl~~------~snGLtyvverfk~~~l~~hi  418 (436)
T COG1875         383 LTGDPAQIDTP----YLDE------TSNGLTYVVEKFKGHPLSAHI  418 (436)
T ss_pred             EcCCHHHcCCc----cccC------CCccHHHHHHHhcCCCceeEE
Confidence            88754332111    1111      111234567777888876543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.86  E-value=0.1  Score=48.35  Aligned_cols=150  Identities=15%  Similarity=0.124  Sum_probs=78.4

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC--------------------CCceEEEeeccccccCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD--------------------FDGSCFLENVREESQIPG   97 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~--------------------f~~~~w~~~~~~~~~~~~   97 (385)
                      .+.+.+.+.. ..-...+.++|+.|+||+++|..+++.+-..                    .+...|+..... ..   
T Consensus        12 ~~~l~~~~~~-~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~-~~---   86 (319)
T PRK06090         12 WQNWKAGLDA-GRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKE-GK---   86 (319)
T ss_pred             HHHHHHHHHc-CCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcC-CC---
Confidence            4455555552 2235688999999999999999999864211                    111222210000 00   


Q ss_pred             ChHHHHHHHHHHHhCCCCCCchHHHHHHHh-----CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH-H
Q 044214           98 GLSCLRQKLLSNLLKDKNVMPYIDLNFRRL-----GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK-Q  169 (385)
Q Consensus        98 ~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~-~  169 (385)
                                      .-.++.+..+.+.+     .++.-++|+|+++.  ......++..+.+-.+++.+|++|.+. .
T Consensus        87 ----------------~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~  150 (319)
T PRK06090         87 ----------------SITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKR  150 (319)
T ss_pred             ----------------cCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhh
Confidence                            00112333333333     23456889999974  455666666665545666666665543 4


Q ss_pred             HHhhccc----eecccCCCC--------CCchHHHHHHHHHhCCCccchhHH
Q 044214          170 VLRNWRV----NAFKRNHPD--------VGNEKLSSNVMKYAQGVPLALKVL  209 (385)
Q Consensus       170 ~~~~~~~----~~~~~~~~~--------~~~~~~~~~i~~~~~GlPLal~~~  209 (385)
                      +......    ..|......        .... .+..+++.++|.|+.....
T Consensus       151 lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~~~-~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        151 LLPTIVSRCQQWVVTPPSTAQAMQWLKGQGIT-VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             ChHHHHhcceeEeCCCCCHHHHHHHHHHcCCc-hHHHHHHHcCCCHHHHHHH
Confidence            4443332    122111000        0001 2456778889999866544

>PRK04040 adenylate kinase; Provisional

Probab=96.86  E-value=0.0012  Score=56.40  Aligned_cols=26  Identities=27%  Similarity=0.541  Sum_probs=23.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|+|+|++|+||||+++.+.+++.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            35899999999999999999999874

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.86  E-value=0.0063  Score=51.56  Aligned_cols=117  Identities=18%  Similarity=0.216  Sum_probs=62.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHH------HHHHHHhCCC------CCC--
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQ------KLLSNLLKDK------NVM--  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~------~ll~~l~~~~------~~~--  117 (385)
                      -.+++|.|..|.|||||++.++.... ...+.+++.. .....  .+......      +++..++-..      ...  
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~~-~~~G~v~~~g-~~~~~--~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLLK-PSSGEILLDG-KDLAS--LSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC-CCCcEEEECC-EECCc--CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            35899999999999999999987543 3455555541 11111  11111111      1222222111      011  


Q ss_pred             --chHHHHHHHhCCceEEEEEeCCC---ChhhhhHhhccCCCC-CC-CcEEEEEeccHHHHh
Q 044214          118 --PYIDLNFRRLGHMKVLIVFDDVT---CFSQLESLMGSLDWL-TP-VSRIILTTRNKQVLR  172 (385)
Q Consensus       118 --~~~~~l~~~l~~k~~LlVlDdv~---~~~~~~~l~~~~~~~-~~-gs~ilvTtR~~~~~~  172 (385)
                        ...-.+.+.+-..+-++++|+..   +....+.+...+... .. +..||++|.+.+...
T Consensus       101 G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~  162 (180)
T cd03214         101 GERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence              33334556666788899999983   233333333222211 12 567888888766543

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.86  E-value=0.0056  Score=51.79  Aligned_cols=115  Identities=17%  Similarity=0.090  Sum_probs=57.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeecccc--------------ccCCCChHHHHHHHHHHHhCCCC-CC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREE--------------SQIPGGLSCLRQKLLSNLLKDKN-VM  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~--------------~~~~~~~~~l~~~ll~~l~~~~~-~~  117 (385)
                      .+++|.|..|+|||||++.++..... ..+.+++... ..              .+. ..+..  ..+...+...-. ..
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~~~-~~G~i~~~g~-~~~~~~~~~~~~i~~~~q~-~~~~~--~tv~~~i~~~LS~G~  103 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGDLKP-QQGEITLDGV-PVSDLEKALSSLISVLNQR-PYLFD--TTLRNNLGRRFSGGE  103 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhccCCC-CCCEEEECCE-EHHHHHHHHHhhEEEEccC-Ceeec--ccHHHhhcccCCHHH
Confidence            48999999999999999999875422 2344444311 00              000 00000  011111100000 01


Q ss_pred             chHHHHHHHhCCceEEEEEeCCCC---hhhhhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          118 PYIDLNFRRLGHMKVLIVFDDVTC---FSQLESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       118 ~~~~~l~~~l~~k~~LlVlDdv~~---~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      ...-.+.+.+-.++=++++|+...   ....+.+...+.....+..||++|.+.+...
T Consensus       104 ~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  161 (178)
T cd03247         104 RQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIE  161 (178)
T ss_pred             HHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHH
Confidence            222345555667778899999842   2222222222221123567888888776654

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.85  E-value=0.0081  Score=58.47  Aligned_cols=95  Identities=16%  Similarity=0.200  Sum_probs=54.7

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM  117 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~  117 (385)
                      +..+-+.|..+=..-.++.|.|.+|+|||||+.+++......-..++|++ ..      .+...+... ++.++....+.
T Consensus        66 i~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs-~E------es~~qi~~r-a~rlg~~~~~l  137 (446)
T PRK11823         66 IGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVS-GE------ESASQIKLR-AERLGLPSDNL  137 (446)
T ss_pred             cHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE-cc------ccHHHHHHH-HHHcCCChhcE
Confidence            34444555433334569999999999999999999987754444567776 21      223333222 23333211111


Q ss_pred             -----chHHHHHHHhC-CceEEEEEeCCC
Q 044214          118 -----PYIDLNFRRLG-HMKVLIVFDDVT  140 (385)
Q Consensus       118 -----~~~~~l~~~l~-~k~~LlVlDdv~  140 (385)
                           ...+.+.+.++ .+.-++|+|.+.
T Consensus       138 ~~~~e~~l~~i~~~i~~~~~~lVVIDSIq  166 (446)
T PRK11823        138 YLLAETNLEAILATIEEEKPDLVVIDSIQ  166 (446)
T ss_pred             EEeCCCCHHHHHHHHHhhCCCEEEEechh
Confidence                 22334444443 366789999984

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.84  E-value=0.0055  Score=55.25  Aligned_cols=91  Identities=22%  Similarity=0.170  Sum_probs=56.0

Q ss_pred             hcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHH---HHHHHHHhCCCCCC----
Q 044214           45 LGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLR---QKLLSNLLKDKNVM----  117 (385)
Q Consensus        45 L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~---~~ll~~l~~~~~~~----  117 (385)
                      |..+=+.-+++=|+|+.|.||||+|.+++-..+..-...+|++.-..     .+...+.   ......+.-..+..    
T Consensus        53 LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~aq~~g~~a~fIDtE~~-----l~p~r~~~l~~~~~d~l~v~~~~~~e~q  127 (279)
T COG0468          53 LGGGLPRGRITEIYGPESSGKTTLALQLVANAQKPGGKAAFIDTEHA-----LDPERAKQLGVDLLDNLLVSQPDTGEQQ  127 (279)
T ss_pred             hcCCcccceEEEEecCCCcchhhHHHHHHHHhhcCCCeEEEEeCCCC-----CCHHHHHHHHHhhhcceeEecCCCHHHH
Confidence            33333556899999999999999999999877777778899973222     3333322   22112222222211    


Q ss_pred             -chHHHHHHHhCCceEEEEEeCCC
Q 044214          118 -PYIDLNFRRLGHMKVLIVFDDVT  140 (385)
Q Consensus       118 -~~~~~l~~~l~~k~~LlVlDdv~  140 (385)
                       +.++.+......+--|+|+|.+-
T Consensus       128 ~~i~~~~~~~~~~~i~LvVVDSva  151 (279)
T COG0468         128 LEIAEKLARSGAEKIDLLVVDSVA  151 (279)
T ss_pred             HHHHHHHHHhccCCCCEEEEecCc
Confidence             44444444544456799999983

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.83  E-value=0.01  Score=55.18  Aligned_cols=48  Identities=21%  Similarity=0.286  Sum_probs=33.5

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC------CceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF------DGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f------~~~~w~~   87 (385)
                      .+-+.|..+=..-.++-|+|.+|+|||+++.+++.......      ..++|++
T Consensus        90 ~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~  143 (317)
T PRK04301         90 ELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID  143 (317)
T ss_pred             HHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe
Confidence            34444443334567899999999999999999987543211      3677887

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=96.83  E-value=0.0032  Score=55.56  Aligned_cols=43  Identities=23%  Similarity=0.312  Sum_probs=32.0

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +..++.+.+....++..+|+|+|+||+|||||.-++...+.+.
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~   56 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRER   56 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhc
Confidence            3445555555545677899999999999999999999877654

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

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

Probab=96.82  E-value=0.0011  Score=46.55  Aligned_cols=23  Identities=30%  Similarity=0.572  Sum_probs=21.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|.|.+|+||||+|+.+.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999986

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.

>PRK06217 hypothetical protein; Validated

Probab=96.81  E-value=0.009  Score=50.77  Aligned_cols=24  Identities=29%  Similarity=0.533  Sum_probs=21.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.|.|.+|+||||+|+++.+.+.
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~   26 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLD   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            589999999999999999998763

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.81  E-value=0.017  Score=52.14  Aligned_cols=115  Identities=18%  Similarity=0.144  Sum_probs=66.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCC-----CC----chH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKN-----VM----PYI  120 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~-----~~----~~~  120 (385)
                      .+.+-++|.|..|+|||||.+.++..+... .+.+++. ...+... ....++...+ ..+ .+..     +.    ...
T Consensus       109 ~~~~~~~i~g~~g~GKttl~~~l~~~~~~~-~G~i~~~-g~~v~~~-d~~~ei~~~~-~~~-~q~~~~~r~~v~~~~~k~  183 (270)
T TIGR02858       109 NRVLNTLIISPPQCGKTTLLRDLARILSTG-ISQLGLR-GKKVGIV-DERSEIAGCV-NGV-PQHDVGIRTDVLDGCPKA  183 (270)
T ss_pred             CCeeEEEEEcCCCCCHHHHHHHHhCccCCC-CceEEEC-CEEeecc-hhHHHHHHHh-ccc-ccccccccccccccchHH
Confidence            345789999999999999999999866533 4445553 2222110 1112222111 111 1110     00    112


Q ss_pred             HHHHHHhC-CceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          121 DLNFRRLG-HMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       121 ~~l~~~l~-~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      .-+...+. ..+=++++|.+-..+.+..+...+.   .|..||+||.+..+..
T Consensus       184 ~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~  233 (270)
T TIGR02858       184 EGMMMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDVED  233 (270)
T ss_pred             HHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHHHH
Confidence            22333333 5788999999988777777766653   4778999998766543

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.

>PRK03839 putative kinase; Provisional

Probab=96.80  E-value=0.0011  Score=56.26  Aligned_cols=24  Identities=33%  Similarity=0.656  Sum_probs=21.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.|.|++|+||||+|+.+++++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999999763

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=96.80  E-value=0.0037  Score=56.57  Aligned_cols=34  Identities=18%  Similarity=0.256  Sum_probs=29.0

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG   82 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~   82 (385)
                      ..+..+|.|.|.+|+|||||+..+.+.+......
T Consensus       101 ~~~~~~v~l~G~pGsGKTTLl~~l~~~l~~~~~~  134 (290)
T PRK10463        101 ARKQLVLNLVSSPGSGKTTLLTETLMRLKDSVPC  134 (290)
T ss_pred             hcCCeEEEEECCCCCCHHHHHHHHHHHhccCCCE
Confidence            3568899999999999999999999988766543

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

Probab=96.80  E-value=0.02  Score=50.32  Aligned_cols=49  Identities=22%  Similarity=0.336  Sum_probs=37.5

Q ss_pred             CCccccchhHHH---HHHhhcCC----CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEE---IESLLGVE----SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~---l~~~L~~~----~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++.||.++...+   |.+.|.++    .--++-|..+|++|.|||-+|+++++..+
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~k  176 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAK  176 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccC
Confidence            568898877654   45566542    22377899999999999999999998654

>TIGR02012 tigrfam_recA protein RecA

Probab=96.78  E-value=0.0068  Score=55.92  Aligned_cols=49  Identities=20%  Similarity=0.222  Sum_probs=35.9

Q ss_pred             HHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           39 EEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        39 ~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..|-.+|. .+=+.-+++.|+|++|+||||||.+++......-..++|+.
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId   90 (321)
T TIGR02012        41 LSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   90 (321)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEc
Confidence            34444454 33345679999999999999999999887665556677775

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.

>PRK05439 pantothenate kinase; Provisional

Probab=96.78  E-value=0.004  Score=57.14  Aligned_cols=30  Identities=33%  Similarity=0.428  Sum_probs=25.7

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .+.+.+|+|.|.+|+||||+|+.+...+..
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~~l~~  112 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQALLSR  112 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            456789999999999999999999886653

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=96.76  E-value=0.0009  Score=52.51  Aligned_cols=28  Identities=32%  Similarity=0.535  Sum_probs=20.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCCCc
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDFDG   82 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f~~   82 (385)
                      |.|+|.+|+|||++|+.++..+...|..
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~f~R   29 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLSFKR   29 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT--EEE
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCceeE
Confidence            7899999999999999999988877754

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.75  E-value=0.0042  Score=55.80  Aligned_cols=48  Identities=19%  Similarity=0.250  Sum_probs=31.3

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh--hCC----CCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI--SGD----FDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~--~~~----f~~~~w~~   87 (385)
                      .|-+.|..+=..-.+.=|+|.+|+|||+|+.+++-.+  ...    -..++|++
T Consensus        26 ~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyid   79 (256)
T PF08423_consen   26 SLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYID   79 (256)
T ss_dssp             HHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEE
T ss_pred             HHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEe
Confidence            3444444222234589999999999999999987543  211    23477776

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.75  E-value=0.0064  Score=51.28  Aligned_cols=22  Identities=23%  Similarity=0.341  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|+|+.|+|||||.+.+..
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHhh
Confidence            5899999999999999998863

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.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.75  E-value=0.0078  Score=50.29  Aligned_cols=113  Identities=22%  Similarity=0.129  Sum_probs=58.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEee---ccccccCCC-ChHHHHHHHHHHHhCCCCCC----chHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLEN---VREESQIPG-GLSCLRQKLLSNLLKDKNVM----PYIDLNF  124 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~---~~~~~~~~~-~~~~l~~~ll~~l~~~~~~~----~~~~~l~  124 (385)
                      ..++|.|..|.|||||++.++..... ..+.+++..   +.-..+.+. ....+...+.-.   .....    ...-.+.
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~~~-~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~---~~~~LS~G~~~rv~la  103 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLWPW-GSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP---WDDVLSGGEQQRLAFA  103 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCC-CCceEEECCCceEEEECCCCccccccHHHHhhcc---CCCCCCHHHHHHHHHH
Confidence            48999999999999999999875432 233333321   111112101 111222322210   11111    3333455


Q ss_pred             HHhCCceEEEEEeCCC---ChhhhhHhhccCCCCCCCcEEEEEeccHHHH
Q 044214          125 RRLGHMKVLIVFDDVT---CFSQLESLMGSLDWLTPVSRIILTTRNKQVL  171 (385)
Q Consensus       125 ~~l~~k~~LlVlDdv~---~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~  171 (385)
                      +.+-.++=++++|+-.   +......+...+...  +..||++|.+....
T Consensus       104 ral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223         104 RLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             HHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            5566677888999983   223333333322222  35577788776554

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.75  E-value=0.0047  Score=57.66  Aligned_cols=48  Identities=23%  Similarity=0.196  Sum_probs=38.3

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ...++|+...+.++.+.+..-.....-|.|+|..|+||+++|+.+...
T Consensus         5 ~~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          5 KDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             cCccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            356999999999988877643333446889999999999999988753

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

Probab=96.75  E-value=0.0099  Score=59.70  Aligned_cols=93  Identities=24%  Similarity=0.362  Sum_probs=58.2

Q ss_pred             CCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCC
Q 044214           29 NQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGG   98 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~   98 (385)
                      ++.=|-++...+|.+.+..          +-.+..-|.+||++|.|||-+|++|+...+-     -|++ +...      
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL-----~FlS-VKGP------  739 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSL-----NFLS-VKGP------  739 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhcee-----eEEe-ecCH------
Confidence            4566677777777775542          1133557889999999999999999986432     2343 3221      


Q ss_pred             hHHHHHHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCCC
Q 044214           99 LSCLRQKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVTC  141 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~  141 (385)
                            +++....++.+  +....+.++- ..++|+|++|.+++
T Consensus       740 ------ELLNMYVGqSE--~NVR~VFerAR~A~PCVIFFDELDS  775 (953)
T KOG0736|consen  740 ------ELLNMYVGQSE--ENVREVFERARSAAPCVIFFDELDS  775 (953)
T ss_pred             ------HHHHHHhcchH--HHHHHHHHHhhccCCeEEEeccccc
Confidence                  23333333222  3334444443 45899999999975

>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=96.75  E-value=0.01  Score=49.84  Aligned_cols=34  Identities=21%  Similarity=0.243  Sum_probs=25.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++.++|++|+||||++..++..+.+.-..++.+.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~   35 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVA   35 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            6789999999999999999987765523333343

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.

>TIGR00416 sms DNA repair protein RadA

Probab=96.75  E-value=0.0098  Score=57.96  Aligned_cols=95  Identities=15%  Similarity=0.120  Sum_probs=54.1

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM  117 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~  117 (385)
                      +..|-+.|..+=..-.++.|.|.+|+|||||+.+++......-..++|++ ..      ....++... +..++-.....
T Consensus        80 i~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs-~E------Es~~qi~~r-a~rlg~~~~~l  151 (454)
T TIGR00416        80 FGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVS-GE------ESLQQIKMR-AIRLGLPEPNL  151 (454)
T ss_pred             cHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE-Cc------CCHHHHHHH-HHHcCCChHHe
Confidence            34455555433344579999999999999999999887654434567775 21      222222221 12222111111


Q ss_pred             -----chHHHHHHHhCC-ceEEEEEeCCC
Q 044214          118 -----PYIDLNFRRLGH-MKVLIVFDDVT  140 (385)
Q Consensus       118 -----~~~~~l~~~l~~-k~~LlVlDdv~  140 (385)
                           ...+.+.+.+.. +.-++|+|.+.
T Consensus       152 ~~~~e~~~~~I~~~i~~~~~~~vVIDSIq  180 (454)
T TIGR00416       152 YVLSETNWEQICANIEEENPQACVIDSIQ  180 (454)
T ss_pred             EEcCCCCHHHHHHHHHhcCCcEEEEecch
Confidence                 223444444433 66789999984

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)).

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

Probab=96.74  E-value=0.0033  Score=58.04  Aligned_cols=48  Identities=21%  Similarity=0.209  Sum_probs=35.8

Q ss_pred             HHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           40 EIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|-.+|. .+=+.-+++-|+|++|+||||||.+++......-..++|++
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          42 SLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             HHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            3444454 33345678999999999999999999887665666777886

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK00625 shikimate kinase; Provisional

Probab=96.74  E-value=0.0013  Score=55.31  Aligned_cols=24  Identities=25%  Similarity=0.447  Sum_probs=21.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.|+|++|+||||+++.+++++.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            378999999999999999998764

>PRK14528 adenylate kinase; Provisional

Probab=96.74  E-value=0.02  Score=48.79  Aligned_cols=24  Identities=25%  Similarity=0.389  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.|.|.|++|+||||+|+.+++.+
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999999998765

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.73  E-value=0.0014  Score=55.13  Aligned_cols=25  Identities=28%  Similarity=0.428  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...|.|+|++|+||||+|+.+++.+
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999999986

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

Probab=96.73  E-value=0.0022  Score=53.43  Aligned_cols=116  Identities=16%  Similarity=0.152  Sum_probs=59.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      .+++|.|..|+|||||.+.++.... ...+.+++.. .....  .+..+....-...+..-.......-.+.+.+-.++-
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~~-~~~G~v~~~g-~~~~~--~~~~~~~~~~i~~~~qLS~G~~qrl~laral~~~p~  102 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLYK-PDSGEILVDG-KEVSF--ASPRDARRAGIAMVYQLSVGERQMVEIARALARNAR  102 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC-CCCeEEEECC-EECCc--CCHHHHHhcCeEEEEecCHHHHHHHHHHHHHhcCCC
Confidence            4899999999999999999987543 3455566542 11111  111111110000000000011223345555666778


Q ss_pred             EEEEeCCC---ChhhhhHhhccCCCC-CCCcEEEEEeccHHHHh
Q 044214          133 LIVFDDVT---CFSQLESLMGSLDWL-TPVSRIILTTRNKQVLR  172 (385)
Q Consensus       133 LlVlDdv~---~~~~~~~l~~~~~~~-~~gs~ilvTtR~~~~~~  172 (385)
                      ++++|+..   +....+.+...+... ..|..||++|.+.....
T Consensus       103 illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~  146 (163)
T cd03216         103 LLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVF  146 (163)
T ss_pred             EEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            88999984   222223332222211 23667888888765443

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.

>TIGR00235 udk uridine kinase

Probab=96.72  E-value=0.0019  Score=56.21  Aligned_cols=28  Identities=39%  Similarity=0.611  Sum_probs=24.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +...+|+|+|.+|+||||||+.++..+.
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4567999999999999999999998654

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

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

Probab=96.72  E-value=0.0042  Score=55.06  Aligned_cols=122  Identities=20%  Similarity=0.164  Sum_probs=71.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccC-CCChHHHHHHHHHHHhCCCC-------CC---ch-
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQI-PGGLSCLRQKLLSNLLKDKN-------VM---PY-  119 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~-~~~~~~l~~~ll~~l~~~~~-------~~---~~-  119 (385)
                      -.+++|+|.+|+||||+++.+..-.... .+.+++. ..+.... .....+...+++..++....       +.   +. 
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L~~pt-~G~i~f~-g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQ  116 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGLEEPT-SGEILFE-GKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQ  116 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcCcCCC-CceEEEc-CcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhh
Confidence            3589999999999999999999855433 3344443 1111110 02334445566666553332       11   22 


Q ss_pred             HHHHHHHhCCceEEEEEeCCCCh------hhhhHhhccCCCCCCCcEEEEEeccHHHHhhccc
Q 044214          120 IDLNFRRLGHMKVLIVFDDVTCF------SQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRV  176 (385)
Q Consensus       120 ~~~l~~~l~~k~~LlVlDdv~~~------~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~~  176 (385)
                      .-.+.+.|.-++-++|.|..-+.      .+.-.++..+.. ..|...++.|.+-.+...+..
T Consensus       117 Ri~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~-~~~lt~lFIsHDL~vv~~isd  178 (268)
T COG4608         117 RIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQE-ELGLTYLFISHDLSVVRYISD  178 (268)
T ss_pred             hHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHH-HhCCeEEEEEEEHHhhhhhcc
Confidence            23466778889999999998432      222333322221 235567788888777766543

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.71  E-value=0.00098  Score=51.29  Aligned_cols=25  Identities=32%  Similarity=0.575  Sum_probs=21.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      |-|+|.+|+|||++|..++..+.++
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~   25 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKH   25 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHH
Confidence            4689999999999999999876544

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

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.70  E-value=0.0027  Score=53.53  Aligned_cols=35  Identities=34%  Similarity=0.323  Sum_probs=27.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ..+|+|+|++|+||||+|+.++..+...-..+.++
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            45899999999999999999999775432233444

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.69  E-value=0.014  Score=60.28  Aligned_cols=48  Identities=23%  Similarity=0.311  Sum_probs=38.1

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|+...+.++.+.+..-......|.|+|..|+|||++|+.+.+.-
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s  423 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS  423 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            469999999998877665322333478899999999999999998753

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.68  E-value=0.015  Score=56.85  Aligned_cols=28  Identities=21%  Similarity=0.299  Sum_probs=23.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+++|+|.+|+||||++..++..+..+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~  377 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQ  377 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            4799999999999999999998865443

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

Probab=96.68  E-value=0.075  Score=47.77  Aligned_cols=95  Identities=18%  Similarity=0.292  Sum_probs=59.8

Q ss_pred             CCCCCccccchhHHHHHHhhc---------C-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccC
Q 044214           26 DNKNQLVGVESTVEEIESLLG---------V-ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQI   95 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~---------~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~   95 (385)
                      ..=+..-|-+...+.|.+..-         . .....+-|.++|++|.||+.||++|+.....     -|++    +|..
T Consensus       130 VkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnS-----TFFS----vSSS  200 (439)
T KOG0739|consen  130 VKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANS-----TFFS----VSSS  200 (439)
T ss_pred             CchhhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCC-----ceEE----eehH
Confidence            334678899988888888542         1 2233678999999999999999999986432     2333    2221


Q ss_pred             CCChHHHHHHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCC
Q 044214           96 PGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVT  140 (385)
Q Consensus        96 ~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~  140 (385)
                           +    +.+.-.++..  .+...|.+.- ++|+-+|++|.++
T Consensus       201 -----D----LvSKWmGESE--kLVknLFemARe~kPSIIFiDEiD  235 (439)
T KOG0739|consen  201 -----D----LVSKWMGESE--KLVKNLFEMARENKPSIIFIDEID  235 (439)
T ss_pred             -----H----HHHHHhccHH--HHHHHHHHHHHhcCCcEEEeehhh
Confidence                 1    2222222111  3344444443 3689999999996

>PRK09354 recA recombinase A; Provisional

Probab=96.67  E-value=0.0079  Score=56.02  Aligned_cols=49  Identities=20%  Similarity=0.216  Sum_probs=37.2

Q ss_pred             HHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           39 EEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        39 ~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..|-.+|. .+=+.-+++-|+|++|+||||||.+++......-...+|+.
T Consensus        46 ~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId   95 (349)
T PRK09354         46 LALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   95 (349)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC
Confidence            34445555 33345679999999999999999999887666667778886

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=96.67  E-value=0.0094  Score=60.86  Aligned_cols=50  Identities=26%  Similarity=0.304  Sum_probs=33.3

Q ss_pred             CccccchhHHHHHHhhc---CC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           30 QLVGVESTVEEIESLLG---VE-------SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++.|.+...+++.+.+.   ..       ..-.+-|.|+|++|+|||++|+.+++.....
T Consensus       153 di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~  212 (644)
T PRK10733        153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP  212 (644)
T ss_pred             HHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            35666666555555332   10       0113459999999999999999999876543

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=96.67  E-value=0.0027  Score=64.07  Aligned_cols=78  Identities=18%  Similarity=0.186  Sum_probs=57.3

Q ss_pred             CCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHH
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      |+..-+.++|.++.++.|...+...    +.+.++|.+|+||||+|+.+++.+.. .++..+|..+.     . .....+
T Consensus        26 ~~~~~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~np-----~-~~~~~~   95 (637)
T PRK13765         26 PERLIDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPNP-----E-DPNNPK   95 (637)
T ss_pred             CcccHHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeCC-----C-cchHHH
Confidence            3445577999999999988877743    36889999999999999999987633 45778888742     1 455566


Q ss_pred             HHHHHHHHh
Q 044214          103 RQKLLSNLL  111 (385)
Q Consensus       103 ~~~ll~~l~  111 (385)
                      ++.+....+
T Consensus        96 ~~~v~~~~G  104 (637)
T PRK13765         96 IRTVPAGKG  104 (637)
T ss_pred             HHHHHHhcC
Confidence            666665443

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.66  E-value=0.0026  Score=50.70  Aligned_cols=40  Identities=15%  Similarity=0.182  Sum_probs=27.9

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +..++-+.|...-..-.+|.+.|.-|+|||||++.+++.+
T Consensus         7 ~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         7 AMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3444444443211223489999999999999999999865

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.

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.66  E-value=0.06  Score=47.35  Aligned_cols=112  Identities=15%  Similarity=0.114  Sum_probs=62.4

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      .....+..++.-...-+.+...-..-+++-.++.++|.-|.|||.+.+....-..+.=.+++.+.     ... .+...+
T Consensus        22 ~~~~~~~~~~~~a~h~e~l~~l~~~i~d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~-----~~~-~s~~~~   95 (269)
T COG3267          22 SWDIQPGLDYWAADHNEALLMLHAAIADGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVID-----KPT-LSDATL   95 (269)
T ss_pred             ccchhhhhhhhhhhhhHHHHHHHHHHhcCCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEec-----Ccc-hhHHHH
Confidence            33334444444444444333322222344568999999999999999955554333222232222     112 666777


Q ss_pred             HHHHHHHHhCCCCC-C-----chHHHHHHHh-CCce-EEEEEeCCC
Q 044214          103 RQKLLSNLLKDKNV-M-----PYIDLNFRRL-GHMK-VLIVFDDVT  140 (385)
Q Consensus       103 ~~~ll~~l~~~~~~-~-----~~~~~l~~~l-~~k~-~LlVlDdv~  140 (385)
                      ...++..+..+..- .     .....+.+.. ++++ ..+++|++.
T Consensus        96 ~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l~vdEah  141 (269)
T COG3267          96 LEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVLMVDEAH  141 (269)
T ss_pred             HHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeEEeehhHh
Confidence            88888887763321 1     2222333332 4566 999999995

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

Probab=96.64  E-value=0.0044  Score=55.51  Aligned_cols=64  Identities=20%  Similarity=0.180  Sum_probs=43.4

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      -.++...+....++..+|+|+|.||+|||||.-++..++.++-..+.-+ .+...|+  +.--.++.
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVl-AVDPSSp--~TGGsiLG  100 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVL-AVDPSSP--FTGGSILG  100 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEE-EECCCCC--CCCccccc
Confidence            3456666666677888999999999999999999998876654433333 2433333  44444443

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.63  E-value=0.0018  Score=55.13  Aligned_cols=26  Identities=31%  Similarity=0.250  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.++|+|.|++|+||||+|+.+++..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999999764

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.63  E-value=0.011  Score=53.92  Aligned_cols=37  Identities=16%  Similarity=0.178  Sum_probs=27.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC-C-CceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD-F-DGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f-~~~~w~~   87 (385)
                      +.++++|+|++|+||||++..++..+..+ - ..+..+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            35699999999999999999999866433 1 3344454

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=96.63  E-value=0.0026  Score=53.84  Aligned_cols=26  Identities=35%  Similarity=0.562  Sum_probs=22.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +|+|.|.+|+||||||..+...+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~~~   26 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRVN   26 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            58999999999999999999876543

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>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=96.62  E-value=0.0049  Score=52.02  Aligned_cols=104  Identities=15%  Similarity=0.052  Sum_probs=56.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEee--ccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLEN--VREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~--~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      .+++|.|..|+|||||++.++.... ...+.+++..  +....+. ..              -.......-.+.+.+-.+
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl~~-p~~G~i~~~g~~i~~~~q~-~~--------------LSgGq~qrv~laral~~~   89 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQLI-PNGDNDEWDGITPVYKPQY-ID--------------LSGGELQRVAIAAALLRN   89 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCC-CCCcEEEECCEEEEEEccc-CC--------------CCHHHHHHHHHHHHHhcC
Confidence            4899999999999999999887443 2344444431  1111111 11              000112233455556667


Q ss_pred             eEEEEEeCCC---ChhhhhH---hhccCCCCCCCcEEEEEeccHHHHhh
Q 044214          131 KVLIVFDDVT---CFSQLES---LMGSLDWLTPVSRIILTTRNKQVLRN  173 (385)
Q Consensus       131 ~~LlVlDdv~---~~~~~~~---l~~~~~~~~~gs~ilvTtR~~~~~~~  173 (385)
                      +-++++|+-.   +......   ++..+.. ..+..||++|.+......
T Consensus        90 p~lllLDEPts~LD~~~~~~l~~~l~~~~~-~~~~tiiivsH~~~~~~~  137 (177)
T cd03222          90 ATFYLFDEPSAYLDIEQRLNAARAIRRLSE-EGKKTALVVEHDLAVLDY  137 (177)
T ss_pred             CCEEEEECCcccCCHHHHHHHHHHHHHHHH-cCCCEEEEEECCHHHHHH
Confidence            7899999983   2222222   2222221 122567788877765553

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.62  E-value=0.0035  Score=54.06  Aligned_cols=38  Identities=24%  Similarity=0.256  Sum_probs=29.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++..+|+|+|.+|+||||||+.+...+...-...+++.
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~ld   59 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLD   59 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEEc
Confidence            45679999999999999999999997754433445553

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

Probab=96.61  E-value=0.0022  Score=63.62  Aligned_cols=53  Identities=28%  Similarity=0.371  Sum_probs=43.8

Q ss_pred             CCCccccchhHHHHHHhhc----CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           28 KNQLVGVESTVEEIESLLG----VESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~----~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      .++-+|.++..+++.+.+.    .++-+-+++..+|++|||||++|+.++..+..+|
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkF  466 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKF  466 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCce
Confidence            3467899999999998875    2445568999999999999999999999876655

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=96.61  E-value=0.0028  Score=55.09  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=49.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-------
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-------  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-------  117 (385)
                      +.++|.|.+|+|||+|+..+++....  +.++++. +++   .+..+.++.+++...-..+        .++.       
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~~~--d~~V~~~-iGe---r~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~   89 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQDA--DVVVYAL-IGE---RGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRA   89 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHCTT--TEEEEEE-ESE---CHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhcccc--cceeeee-ccc---cchhHHHHHHHHhhcccccccccccccchhhHHHHhhh
Confidence            47899999999999999999987643  3345554 221   1144556666554331111        1111       


Q ss_pred             -----chHHHHHHHhCCceEEEEEeCCC
Q 044214          118 -----PYIDLNFRRLGHMKVLIVFDDVT  140 (385)
Q Consensus       118 -----~~~~~l~~~l~~k~~LlVlDdv~  140 (385)
                           ..++.++.  .++++|+++||+.
T Consensus        90 ~~~a~t~AEyfrd--~G~dVlli~Dslt  115 (215)
T PF00006_consen   90 PYTALTIAEYFRD--QGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHHHHH--TTSEEEEEEETHH
T ss_pred             hccchhhhHHHhh--cCCceeehhhhhH
Confidence                 22333333  6899999999994

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.60  E-value=0.0086  Score=55.89  Aligned_cols=45  Identities=22%  Similarity=0.167  Sum_probs=35.0

Q ss_pred             ccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           31 LVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ++|+...++++.+.+..-...-..|.|+|..|+||+++|+.+.+.
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHh
Confidence            478888888877776643333456889999999999999998874

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

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=96.60  E-value=0.0043  Score=57.24  Aligned_cols=36  Identities=31%  Similarity=0.298  Sum_probs=29.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+++.+.|.|||||||+|.+.+-...+....+.-++
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g~kvLlvS   37 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVS   37 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcCCcEEEEE
Confidence            478999999999999999998887766665555554

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.59  E-value=0.0065  Score=56.29  Aligned_cols=36  Identities=19%  Similarity=0.283  Sum_probs=28.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      +..+++++|++|+||||++..++..++..-..+..+
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li  148 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLA  148 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEE
Confidence            468999999999999999999998776543333333

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=96.58  E-value=0.21  Score=45.41  Aligned_cols=145  Identities=11%  Similarity=0.047  Sum_probs=80.1

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC-------------CCCceEEEeeccccccCCCChHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG-------------DFDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-------------~f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      -++|...+..+ .-.....++|+.|+||+++|..++..+-.             ..+...|+...... .. -.+     
T Consensus         6 ~~~L~~~i~~~-rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~-~~-I~i-----   77 (290)
T PRK05917          6 WEALIQRVRDQ-KVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKG-RL-HSI-----   77 (290)
T ss_pred             HHHHHHHHHcC-CcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCC-Cc-CcH-----
Confidence            45566666632 23567889999999999999999986532             12333333211000 00 011     


Q ss_pred             HHHHHHhCCCCCCchHHHHHHHh-----CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEecc-HHHHhhcc-
Q 044214          105 KLLSNLLKDKNVMPYIDLNFRRL-----GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRN-KQVLRNWR-  175 (385)
Q Consensus       105 ~ll~~l~~~~~~~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~-~~~~~~~~-  175 (385)
                                   +.+..+.+.+     .++.-++|+|+++.  .+....++..+..-.+++.+|++|.+ ..+..... 
T Consensus        78 -------------dqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~S  144 (290)
T PRK05917         78 -------------ETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRS  144 (290)
T ss_pred             -------------HHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHh
Confidence                         2222333333     24556889999974  45667777666554456666666655 34433322 


Q ss_pred             ---ceecccCCCCCCchHHHHHHHHHhCCCc
Q 044214          176 ---VNAFKRNHPDVGNEKLSSNVMKYAQGVP  203 (385)
Q Consensus       176 ---~~~~~~~~~~~~~~~~~~~i~~~~~GlP  203 (385)
                         ...|.........++.+..++...+|.+
T Consensus       145 Rcq~~~~~~~~~~~i~~~~~~~l~~~~~g~~  175 (290)
T PRK05917        145 RSLSIHIPMEEKTLVSKEDIAYLIGYAQGKE  175 (290)
T ss_pred             cceEEEccchhccCCCHHHHHHHHHHhCCCh
Confidence               2333332222234566777888888855

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

Probab=96.58  E-value=0.0064  Score=60.64  Aligned_cols=73  Identities=21%  Similarity=0.273  Sum_probs=45.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhC-
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLG-  128 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~-  128 (385)
                      +.-++..++|++|.||||||.-++++.  -|. ++=+.    .|.. .....+-..|...+..+           ..+. 
T Consensus       324 P~kKilLL~GppGlGKTTLAHViAkqa--GYs-VvEIN----ASDe-Rt~~~v~~kI~~avq~~-----------s~l~a  384 (877)
T KOG1969|consen  324 PPKKILLLCGPPGLGKTTLAHVIAKQA--GYS-VVEIN----ASDE-RTAPMVKEKIENAVQNH-----------SVLDA  384 (877)
T ss_pred             CccceEEeecCCCCChhHHHHHHHHhc--Cce-EEEec----cccc-ccHHHHHHHHHHHHhhc-----------ccccc
Confidence            446799999999999999999999863  232 22332    2322 44444444444333222           2232 


Q ss_pred             -CceEEEEEeCCCC
Q 044214          129 -HMKVLIVFDDVTC  141 (385)
Q Consensus       129 -~k~~LlVlDdv~~  141 (385)
                       .++.-||+|.++-
T Consensus       385 dsrP~CLViDEIDG  398 (877)
T KOG1969|consen  385 DSRPVCLVIDEIDG  398 (877)
T ss_pred             CCCcceEEEecccC
Confidence             6788899999974

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.56  E-value=0.0025  Score=60.44  Aligned_cols=52  Identities=21%  Similarity=0.314  Sum_probs=39.8

Q ss_pred             CCccccchhHHHHHHhhcCC------------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLGVE------------SKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~------------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..++|.++..+.+...+...            ...++.|.++|++|+|||++|+.++..+...|
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~f   75 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   75 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeE
Confidence            45899998888886655421            11246789999999999999999999876544

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.

>PRK13947 shikimate kinase; Provisional

Probab=96.56  E-value=0.0019  Score=54.18  Aligned_cols=25  Identities=28%  Similarity=0.421  Sum_probs=22.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -|.|+|++|+||||+|+.+++++.-
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~   27 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSF   27 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            4889999999999999999998743

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.56  E-value=0.0097  Score=59.17  Aligned_cols=50  Identities=22%  Similarity=0.399  Sum_probs=41.5

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....++|+...++++.+.+..-......|.|+|..|+|||++|+.+.+.-
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s  234 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAAS  234 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            45779999999999988887534444578899999999999999999854

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.55  E-value=0.005  Score=55.55  Aligned_cols=38  Identities=18%  Similarity=0.112  Sum_probs=34.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.-+++.|+|.+|+|||++|.++......+...++|++
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            45679999999999999999999998877888899997

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.55  E-value=0.0023  Score=54.04  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=22.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++|.+.|++|+||||+|+.+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            4899999999999999999998753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=96.54  E-value=0.0085  Score=56.48  Aligned_cols=102  Identities=18%  Similarity=0.174  Sum_probs=59.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGH  129 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~  129 (385)
                      ..++-+-|||..|.|||.|+-.+|+.+...-..+             ........++-+.+.......+....+.+.+.+
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R-------------~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~  126 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRR-------------VHFHEFMLDVHSRLHQLRGQDDPLPQVADELAK  126 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCcccccc-------------ccccHHHHHHHHHHHHHhCCCccHHHHHHHHHh
Confidence            3467899999999999999999998653311111             111122222222222211222456667777788


Q ss_pred             ceEEEEEeCCC--Chh---hhhHhhccCCCCCCCcEEEEEec
Q 044214          130 MKVLIVFDDVT--CFS---QLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus       130 k~~LlVlDdv~--~~~---~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      +..||++|.+.  +..   .+..++..+-  ..|..++.||.
T Consensus       127 ~~~lLcfDEF~V~DiaDAmil~rLf~~l~--~~gvvlVaTSN  166 (362)
T PF03969_consen  127 ESRLLCFDEFQVTDIADAMILKRLFEALF--KRGVVLVATSN  166 (362)
T ss_pred             cCCEEEEeeeeccchhHHHHHHHHHHHHH--HCCCEEEecCC
Confidence            88899999983  332   2555555543  35654555553

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

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.53  E-value=0.031  Score=58.00  Aligned_cols=109  Identities=17%  Similarity=0.227  Sum_probs=71.7

Q ss_pred             CCccccchhHHHHHHhhcCCC------CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           29 NQLVGVESTVEEIESLLGVES------KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~------~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      ...+|-++.+..+.+.+....      .......+.|+.|+|||-||++++.-+-+..+..+-+.           +.+.
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriD-----------mse~  630 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLD-----------MSEF  630 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEec-----------hhhh
Confidence            457888888888888776311      13557789999999999999999998866655554443           2222


Q ss_pred             HHHHHHHHhCCCC---CCchHHHHHHHhCCce-EEEEEeCCCC--hhhhhHhhc
Q 044214          103 RQKLLSNLLKDKN---VMPYIDLNFRRLGHMK-VLIVFDDVTC--FSQLESLMG  150 (385)
Q Consensus       103 ~~~ll~~l~~~~~---~~~~~~~l~~~l~~k~-~LlVlDdv~~--~~~~~~l~~  150 (385)
                      ..  ...+.+..+   ..+....|-+.++.++ .+|+||||+.  ......+..
T Consensus       631 ~e--vskligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq  682 (898)
T KOG1051|consen  631 QE--VSKLIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQ  682 (898)
T ss_pred             hh--hhhccCCCcccccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHH
Confidence            22  233333322   2256667888888877 4778999973  444443333

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.52  E-value=0.0096  Score=57.58  Aligned_cols=46  Identities=22%  Similarity=0.318  Sum_probs=36.4

Q ss_pred             ccccchhHHHHHHhhc-----CCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           31 LVGVESTVEEIESLLG-----VESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~-----~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +-=-..-+.++..||.     ...-+.++..|+|++|+||||-.+.++..+
T Consensus        84 LAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel  134 (634)
T KOG1970|consen   84 LAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL  134 (634)
T ss_pred             HhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh
Confidence            3334456788888888     455667899999999999999999888753

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.51  E-value=0.019  Score=53.06  Aligned_cols=48  Identities=15%  Similarity=0.306  Sum_probs=32.3

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh------CCCCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS------GDFDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~------~~f~~~~w~~   87 (385)
                      .|-++|..+=..-+++-|+|.+|+|||+|+.+++-...      ..-..++|++
T Consensus        84 ~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYId  137 (313)
T TIGR02238        84 ALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID  137 (313)
T ss_pred             HHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEE
Confidence            34444543334467899999999999999998874321      1124677886

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.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.51  E-value=0.012  Score=49.31  Aligned_cols=57  Identities=11%  Similarity=0.070  Sum_probs=38.1

Q ss_pred             chHHHHHHHhCCceEEEEEeCC----CChhhhhH--hhccCCCCCCCcEEEEEeccHHHHhhccc
Q 044214          118 PYIDLNFRRLGHMKVLIVFDDV----TCFSQLES--LMGSLDWLTPVSRIILTTRNKQVLRNWRV  176 (385)
Q Consensus       118 ~~~~~l~~~l~~k~~LlVlDdv----~~~~~~~~--l~~~~~~~~~gs~ilvTtR~~~~~~~~~~  176 (385)
                      +..-.+.+.+-+++-+|+-|.-    +....|+-  ++..+  +..|..|+++|.+.++...+..
T Consensus       143 QQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeei--nr~GtTVl~ATHd~~lv~~~~~  205 (223)
T COG2884         143 QQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEI--NRLGTTVLMATHDLELVNRMRH  205 (223)
T ss_pred             HHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHH--hhcCcEEEEEeccHHHHHhccC
Confidence            3344566677788999999976    33333332  23333  2468999999999988877654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=96.50  E-value=0.0039  Score=62.10  Aligned_cols=47  Identities=23%  Similarity=0.429  Sum_probs=38.4

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -++++|.+..++.+...+..  .....+.|+|.+|+|||++|+.+++..
T Consensus        64 f~~iiGqs~~i~~l~~al~~--~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCG--PNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhC--CCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            35699999999999987763  334567899999999999999998743

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.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.49  E-value=0.014  Score=49.44  Aligned_cols=115  Identities=17%  Similarity=0.102  Sum_probs=62.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHH--HH--HhC-----CCCCC-----
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLL--SN--LLK-----DKNVM-----  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll--~~--l~~-----~~~~~-----  117 (385)
                      ...|.|+|-.|-||||.|...+-+...+--.+..+....... . .+-...+..+-  ..  .+.     ..+..     
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlKg~~-~-~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~   99 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIKGAW-S-TGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAA   99 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCC-c-cCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHH
Confidence            357899999999999999999887654433344443332211 1 22233333210  00  000     00000     


Q ss_pred             --chHHHHHHHhCC-ceEEEEEeCCC-----ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          118 --PYIDLNFRRLGH-MKVLIVFDDVT-----CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       118 --~~~~~l~~~l~~-k~~LlVlDdv~-----~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                        +.....++.+.. +-=|+|||.+.     ..-..+++...+.....+..||+|-|+.
T Consensus       100 ~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        100 AREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence              233444455544 45699999993     2222333443343344677899999975

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

Probab=96.49  E-value=0.0063  Score=63.26  Aligned_cols=52  Identities=23%  Similarity=0.333  Sum_probs=41.0

Q ss_pred             CCccccchhHHHHHHhhcC----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLGV----ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ...+|.++..+++.++|..    +......+.++|++|+||||+|+.++..+...|
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~  377 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKY  377 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            3589999999999887762    122345799999999999999999998765443

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=96.48  E-value=0.022  Score=48.44  Aligned_cols=28  Identities=32%  Similarity=0.433  Sum_probs=24.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...++.|.|.+|+||||+|+.+...+..
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~~   44 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLES   44 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4569999999999999999999987653

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.47  E-value=0.002  Score=54.67  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=20.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|.|+|++|+||||+|+.++++.
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            57899999999999999999865

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.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.47  E-value=0.014  Score=52.38  Aligned_cols=87  Identities=13%  Similarity=0.112  Sum_probs=52.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh----CCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCC--------CCC--
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS----GDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDK--------NVM--  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~----~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~--------~~~--  117 (385)
                      -+.++|.|-.|+|||+|+..++++..    .+-+..++.. +++..   ....+++.++...-....        ++.  
T Consensus        69 GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~-IGeR~---rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~  144 (276)
T cd01135          69 GQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAA-MGITM---EDARFFKDDFEETGALERVVLFLNLANDPTI  144 (276)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEE-ecccc---HHHHHHHHHhhhcCCcceEEEEEecCCCCHH
Confidence            45789999999999999999887653    2234555554 33321   556666666655311110        111  


Q ss_pred             ------chHHHHHHHh---CCceEEEEEeCCCCh
Q 044214          118 ------PYIDLNFRRL---GHMKVLIVFDDVTCF  142 (385)
Q Consensus       118 ------~~~~~l~~~l---~~k~~LlVlDdv~~~  142 (385)
                            -..-.+.+++   .++++|+++||+-..
T Consensus       145 ~r~~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         145 ERIITPRMALTTAEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCeEEEEEcChhHH
Confidence                  1122233333   368999999999543

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>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=96.47  E-value=0.013  Score=49.29  Aligned_cols=112  Identities=21%  Similarity=0.194  Sum_probs=57.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH--------------HHHHHhCCCCCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK--------------LLSNLLKDKNVMP  118 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~--------------ll~~l~~~~~~~~  118 (385)
                      .+++|.|..|+|||||.+.++.... ...+.+++.. .....  .........              +...+  -.....
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~~-~~~G~i~~~g-~~~~~--~~~~~~~~~i~~~~q~~~~~~~tv~~~l--LS~G~~  102 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILGLLR-PTSGRVRLDG-ADISQ--WDPNELGDHVGYLPQDDELFSGSIAENI--LSGGQR  102 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccC-CCCCeEEECC-EEccc--CCHHHHHhheEEECCCCccccCcHHHHC--cCHHHH
Confidence            4899999999999999999987543 2344444431 11110  111111100              00000  000002


Q ss_pred             hHHHHHHHhCCceEEEEEeCCC---Chhh---hhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          119 YIDLNFRRLGHMKVLIVFDDVT---CFSQ---LESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       119 ~~~~l~~~l~~k~~LlVlDdv~---~~~~---~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      ..-.+.+.+-.++=++++|+..   +...   +..++..+.  ..|..||++|.+.+...
T Consensus       103 qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~--~~~~tii~~sh~~~~~~  160 (173)
T cd03246         103 QRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALK--AAGATRIVIAHRPETLA  160 (173)
T ss_pred             HHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHH--hCCCEEEEEeCCHHHHH
Confidence            2334455556677789999984   2222   323333332  23667888888776553

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

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.46  E-value=0.019  Score=49.62  Aligned_cols=109  Identities=17%  Similarity=0.157  Sum_probs=56.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC---CC-ceE-EEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD---FD-GSC-FLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLG  128 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~---f~-~~~-w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~  128 (385)
                      -..|.|++|+|||||.+.+++-+...   |. ..+ .+..-++.........+.....--++....+  ...-++...-.
T Consensus       139 ntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cp--k~~gmmmaIrs  216 (308)
T COG3854         139 NTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCP--KAEGMMMAIRS  216 (308)
T ss_pred             eeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccch--HHHHHHHHHHh
Confidence            36789999999999999999865443   32 222 2221111100000111111111111111111  22222222223


Q ss_pred             CceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEecc
Q 044214          129 HMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       129 ~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      -.+=++|+|.+-..++...+...+.   .|-+++.|..-
T Consensus       217 m~PEViIvDEIGt~~d~~A~~ta~~---~GVkli~TaHG  252 (308)
T COG3854         217 MSPEVIIVDEIGTEEDALAILTALH---AGVKLITTAHG  252 (308)
T ss_pred             cCCcEEEEeccccHHHHHHHHHHHh---cCcEEEEeecc
Confidence            4677999999988877777766653   67777777653

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

Probab=96.46  E-value=0.064  Score=52.06  Aligned_cols=53  Identities=21%  Similarity=0.168  Sum_probs=36.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      -.++.|.|.+|+|||++|..++.... ..-..++|++ .     . .+..++...++....
T Consensus       194 g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fS-l-----E-m~~~~l~~Rl~~~~~  247 (421)
T TIGR03600       194 GDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFS-L-----E-MSAEQLGERLLASKS  247 (421)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEE-C-----C-CCHHHHHHHHHHHHc
Confidence            45889999999999999999997653 3333455654 2     1 456677777766543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

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

Probab=96.46  E-value=0.0081  Score=50.44  Aligned_cols=112  Identities=18%  Similarity=0.237  Sum_probs=58.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHH--------------HHHHHHhCCCCCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQ--------------KLLSNLLKDKNVMP  118 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~--------------~ll~~l~~~~~~~~  118 (385)
                      .+++|.|..|.|||||.+.++.... ...+.+++... ....  ........              .+...+.  .....
T Consensus        29 ~~~~l~G~nGsGKstLl~~i~G~~~-~~~G~i~~~g~-~~~~--~~~~~~~~~i~~~~~~~~~~~~t~~e~lL--S~G~~  102 (171)
T cd03228          29 EKVAIVGPSGSGKSTLLKLLLRLYD-PTSGEILIDGV-DLRD--LDLESLRKNIAYVPQDPFLFSGTIRENIL--SGGQR  102 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCCC-CCCCEEEECCE-Ehhh--cCHHHHHhhEEEEcCCchhccchHHHHhh--CHHHH
Confidence            4899999999999999999987543 23455554311 1100  00000000              0000000  00002


Q ss_pred             hHHHHHHHhCCceEEEEEeCCC---Chhh---hhHhhccCCCCCCCcEEEEEeccHHHHhh
Q 044214          119 YIDLNFRRLGHMKVLIVFDDVT---CFSQ---LESLMGSLDWLTPVSRIILTTRNKQVLRN  173 (385)
Q Consensus       119 ~~~~l~~~l~~k~~LlVlDdv~---~~~~---~~~l~~~~~~~~~gs~ilvTtR~~~~~~~  173 (385)
                      ..-.+.+.+-.++-++++|+-.   +...   +..++..+.   .+..||++|.+.+....
T Consensus       103 ~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~---~~~tii~~sh~~~~~~~  160 (171)
T cd03228         103 QRIAIARALLRDPPILILDEATSALDPETEALILEALRALA---KGKTVIVIAHRLSTIRD  160 (171)
T ss_pred             HHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhc---CCCEEEEEecCHHHHHh
Confidence            2233555566778899999984   2222   333333332   34668888887765543

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.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=96.45  E-value=0.0045  Score=51.15  Aligned_cols=113  Identities=19%  Similarity=0.132  Sum_probs=59.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC---CCCCCchHHHHHHHhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK---DKNVMPYIDLNFRRLGH  129 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~---~~~~~~~~~~l~~~l~~  129 (385)
                      .+++|+|..|.|||||++.++..+. ...+.+++... ....  ......    ...+..   -.......-.+...+..
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~-~~~G~i~~~~~-~~~~--~~~~~~----~~~i~~~~qlS~G~~~r~~l~~~l~~   97 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLK-PTSGEILIDGK-DIAK--LPLEEL----RRRIGYVPQLSGGQRQRVALARALLL   97 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC-CCccEEEECCE-Eccc--CCHHHH----HhceEEEeeCCHHHHHHHHHHHHHhc
Confidence            5899999999999999999987543 34555655421 1110  111111    111110   00111223335555556


Q ss_pred             ceEEEEEeCCC---ChhhhhHhhccCCCC-CCCcEEEEEeccHHHHhh
Q 044214          130 MKVLIVFDDVT---CFSQLESLMGSLDWL-TPVSRIILTTRNKQVLRN  173 (385)
Q Consensus       130 k~~LlVlDdv~---~~~~~~~l~~~~~~~-~~gs~ilvTtR~~~~~~~  173 (385)
                      .+=++++|+..   +......+...+... ..+..++++|.+......
T Consensus        98 ~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~  145 (157)
T cd00267          98 NPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAEL  145 (157)
T ss_pred             CCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            67899999984   333333332222111 124568888877665544

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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.45  E-value=0.0028  Score=53.87  Aligned_cols=36  Identities=19%  Similarity=0.323  Sum_probs=30.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+++.|+|+.|+|||||+..+.+...+.|...+..+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcccccccceeec
Confidence            368999999999999999999999888886555554

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.44  E-value=0.0025  Score=51.71  Aligned_cols=24  Identities=38%  Similarity=0.654  Sum_probs=21.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|.|.|++|+||||+|+.+++.+.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~g   25 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLG   25 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhC
Confidence            689999999999999999998753

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.43  E-value=0.039  Score=50.02  Aligned_cols=36  Identities=17%  Similarity=-0.022  Sum_probs=28.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      -.++.|.|.+|+||||++.+++...... -..++|++
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            3588899999999999999998875433 45677776

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK12678 transcription termination factor Rho; Provisional

Probab=96.43  E-value=0.0081  Score=58.96  Aligned_cols=89  Identities=17%  Similarity=0.118  Sum_probs=51.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCC-CceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC---------chH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDF-DGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM---------PYI  120 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~---------~~~  120 (385)
                      +-+..+|+|.+|+|||||++.+++.+.... +..+++..+.+-.   ..+.++.+.+-..+.....+.         ...
T Consensus       415 kGQR~LIvgpp~aGKTtLL~~IAn~i~~n~~~~~~ivvLIgERp---eEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~a  491 (672)
T PRK12678        415 KGQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERP---EEVTDMQRSVKGEVIASTFDRPPSDHTTVAELA  491 (672)
T ss_pred             cCCEeEEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCch---hhHHHHHHhccceEEEECCCCCHHHHHHHHHHH
Confidence            345788999999999999999999775433 4444555444332   333333333211111111111         222


Q ss_pred             HHHHHHh--CCceEEEEEeCCCCh
Q 044214          121 DLNFRRL--GHMKVLIVFDDVTCF  142 (385)
Q Consensus       121 ~~l~~~l--~~k~~LlVlDdv~~~  142 (385)
                      -.+.+++  .++.+||++|++...
T Consensus       492 i~~Ae~fre~G~dVlillDSlTR~  515 (672)
T PRK12678        492 IERAKRLVELGKDVVVLLDSITRL  515 (672)
T ss_pred             HHHHHHHHHcCCCEEEEEeCchHH
Confidence            2233333  579999999999543

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

Probab=96.43  E-value=0.0041  Score=59.04  Aligned_cols=52  Identities=21%  Similarity=0.305  Sum_probs=40.0

Q ss_pred             CCccccchhHHHHHHhhcCC--------C----CCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLGVE--------S----KGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~--------~----~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..++|.++..+.+..++...        .    ...+.+.++|++|+|||+||+.++..+...|
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~f   78 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPF   78 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChh
Confidence            45899999998888776420        0    1146789999999999999999999775543

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

Probab=96.41  E-value=0.0081  Score=56.85  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -|-..++|++|.|||++..++++.+
T Consensus       235 KRGYLLYGPPGTGKSS~IaAmAn~L  259 (457)
T KOG0743|consen  235 KRGYLLYGPPGTGKSSFIAAMANYL  259 (457)
T ss_pred             hccceeeCCCCCCHHHHHHHHHhhc
Confidence            4678899999999999999999865

>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=96.40  E-value=0.0026  Score=53.16  Aligned_cols=24  Identities=29%  Similarity=0.538  Sum_probs=20.8

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhC
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      |.|+|.+|+|||||++.+++.+++
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            789999999999999999998754

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.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=96.40  E-value=0.012  Score=56.91  Aligned_cols=87  Identities=18%  Similarity=0.216  Sum_probs=52.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~------  117 (385)
                      -+.++|.|.+|+|||||+..++.......+.++-+..+++.   ...+.+++.++...-...        .++.      
T Consensus       144 GQR~gIfa~~GvGKt~Ll~~i~~~~~~~~~~v~V~~liGER---~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~  220 (463)
T PRK09280        144 GGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGER---TREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLR  220 (463)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccC---cHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            46799999999999999999987665443333333333332   245666666665432111        1110      


Q ss_pred             --chHHHHHHHh---CCceEEEEEeCCCC
Q 044214          118 --PYIDLNFRRL---GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 --~~~~~l~~~l---~~k~~LlVlDdv~~  141 (385)
                        ...-.+.+++   +++++||++|++..
T Consensus       221 a~~~a~tiAEyfrd~~G~~VLll~DslTR  249 (463)
T PRK09280        221 VALTGLTMAEYFRDVEGQDVLLFIDNIFR  249 (463)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecchHH
Confidence              1122344444   67999999999953

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

Probab=96.39  E-value=0.0056  Score=61.30  Aligned_cols=52  Identities=23%  Similarity=0.319  Sum_probs=41.2

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++.-+.|.+..+.|.+.......+..+|.|+|++|+||||+|+.++.++..
T Consensus       367 ~pP~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L~~  418 (568)
T PRK05537        367 EIPEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKLME  418 (568)
T ss_pred             CCChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHhhh
Confidence            3455677877777777776655555668999999999999999999998754

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.37  E-value=0.052  Score=52.06  Aligned_cols=26  Identities=23%  Similarity=0.281  Sum_probs=22.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +..+++++|..|+||||++..++.+.
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~  215 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARA  215 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999988753

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.36  E-value=0.052  Score=55.71  Aligned_cols=25  Identities=28%  Similarity=0.344  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+++++|+.|+||||.+.+++..+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            4799999999999999999999765

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.36  E-value=0.0029  Score=51.45  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=21.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|.|.|.+|+||||+|+.++.+.
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999875

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=96.36  E-value=0.003  Score=57.37  Aligned_cols=126  Identities=20%  Similarity=0.173  Sum_probs=68.1

Q ss_pred             CccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           30 QLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      .+.-.....+.+.+.|...-.....|.|.|..|+||||++..+...+...-..++-+.+..+.........        .
T Consensus       105 ~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~~l~~~~~~--------~  176 (270)
T PF00437_consen  105 DLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPELRLPGPNQI--------Q  176 (270)
T ss_dssp             CCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S--SCSSEE--------E
T ss_pred             hccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccccccceEEeccccceeecccceE--------E
Confidence            33333334455555555321234689999999999999999999877665122222322111100000000        0


Q ss_pred             HhCCCCCCchHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEE-EEEecc
Q 044214          110 LLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRI-ILTTRN  167 (385)
Q Consensus       110 l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~i-lvTtR~  167 (385)
                      +..........+.+...|+..+=.++++.+.+.+.+..+. ..   ..|..+ +-|...
T Consensus       177 ~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~~e~~~~~~-a~---~tGh~~~~tT~Ha  231 (270)
T PF00437_consen  177 IQTRRDEISYEDLLKSALRQDPDVIIIGEIRDPEAAEAIQ-AA---NTGHLGSLTTLHA  231 (270)
T ss_dssp             EEEETTTBSHHHHHHHHTTS--SEEEESCE-SCHHHHHHH-HH---HTT-EEEEEEEE-
T ss_pred             EEeecCcccHHHHHHHHhcCCCCcccccccCCHhHHHHHH-hh---ccCCceeeeeeec
Confidence            0000122366778888899888899999998888777743 32   246667 555543

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 ....

>PRK14738 gmk guanylate kinase; Provisional

Probab=96.35  E-value=0.0037  Score=54.25  Aligned_cols=29  Identities=17%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             CCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           47 VESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        47 ~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+....+.|+|+|++|+|||||+..+.+.
T Consensus         8 ~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          8 NKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            34456789999999999999999998754

>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=96.35  E-value=0.013  Score=49.30  Aligned_cols=112  Identities=20%  Similarity=0.174  Sum_probs=59.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccc--------------cCC--CChHHHHHHHHHHHhCCCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREES--------------QIP--GGLSCLRQKLLSNLLKDKN  115 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~--------------~~~--~~~~~l~~~ll~~l~~~~~  115 (385)
                      -.+++|+|..|.|||||++.++.... ...+.+++.. ....              +.+  +.-..+...+.     -..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~-~~~G~i~~~g-~~~~~~~~~~~~~i~~~~q~~~~~~~~tv~~~~~-----LS~   98 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLLK-PDSGEIKVLG-KDIKKEPEEVKRRIGYLPEEPSLYENLTVRENLK-----LSG   98 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC-CCCeEEEECC-EEcccchHhhhccEEEEecCCccccCCcHHHHhh-----cCH
Confidence            35899999999999999999987432 2344444431 1110              000  00001111110     000


Q ss_pred             CCchHHHHHHHhCCceEEEEEeCCCC---hhh---hhHhhccCCCCCCCcEEEEEeccHHHHh
Q 044214          116 VMPYIDLNFRRLGHMKVLIVFDDVTC---FSQ---LESLMGSLDWLTPVSRIILTTRNKQVLR  172 (385)
Q Consensus       116 ~~~~~~~l~~~l~~k~~LlVlDdv~~---~~~---~~~l~~~~~~~~~gs~ilvTtR~~~~~~  172 (385)
                      .....-.+.+.+..++-++++|+...   ...   +..++..+.  ..|..||++|.+.....
T Consensus        99 G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~--~~g~tiii~th~~~~~~  159 (173)
T cd03230          99 GMKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELK--KEGKTILLSSHILEEAE  159 (173)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHH--HCCCEEEEECCCHHHHH
Confidence            00223345566677888999999842   222   333333332  13567888888876554

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.35  E-value=0.0032  Score=53.25  Aligned_cols=25  Identities=20%  Similarity=0.271  Sum_probs=22.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+++|+|++|+|||||++.++..+.
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3789999999999999999988754

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.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=96.34  E-value=0.0076  Score=50.40  Aligned_cols=29  Identities=24%  Similarity=0.344  Sum_probs=25.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...+++|+|..|+|||||+..+...+..+
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~~   33 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCAR   33 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhhc
Confidence            46799999999999999999999877653

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=96.34  E-value=0.0055  Score=56.53  Aligned_cols=35  Identities=29%  Similarity=0.317  Sum_probs=26.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +++.+.|-|||||||+|...+-....+-..+.-++
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G~rtLlvS   36 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRGKRTLLVS   36 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCCCCeeEee
Confidence            58899999999999999998876655544454554

...

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.34  E-value=0.0067  Score=57.14  Aligned_cols=105  Identities=14%  Similarity=0.040  Sum_probs=60.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCc---eEEEeeccccccCCCChHHHHH--HHHHHHhCCCCCCchHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDG---SCFLENVREESQIPGGLSCLRQ--KLLSNLLKDKNVMPYIDLNFRR  126 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~---~~w~~~~~~~~~~~~~~~~l~~--~ll~~l~~~~~~~~~~~~l~~~  126 (385)
                      -..|.|+|+.|+||||+++.+.+.+....+.   ++.+.+.-+     .....+..  ....+.............++..
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i~~~~~~~~~Ivt~EdpiE-----~~~~~~~~~~~~v~Q~~v~~~~~~~~~~l~~a  208 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIE-----FVYDEIETISASVCQSEIPRHLNNFAAGVRNA  208 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHhhcCCCCcEEEEeCCCce-----EeccccccccceeeeeeccccccCHHHHHHHH
Confidence            3589999999999999999999877544331   222221111     11111000  0001100000112556777888


Q ss_pred             hCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEe
Q 044214          127 LGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTT  165 (385)
Q Consensus       127 l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTt  165 (385)
                      |+..+-.+++..+.+.+.....+....   .|.. ++||
T Consensus       209 LR~~Pd~i~vGEiRd~et~~~al~aa~---tGh~-v~tT  243 (358)
T TIGR02524       209 LRRKPHAILVGEARDAETISAALEAAL---TGHP-VYTT  243 (358)
T ss_pred             hccCCCEEeeeeeCCHHHHHHHHHHHH---cCCc-EEEe
Confidence            999999999999988887765544322   3444 4555

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.

>PRK04132 replication factor C small subunit; Provisional

Probab=96.34  E-value=0.12  Score=54.03  Aligned_cols=95  Identities=17%  Similarity=0.240  Sum_probs=51.9

Q ss_pred             Ec--CCCchHHHHHHHHHHHh-hCCCCc-eEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceEE
Q 044214           58 WG--IGGIGKTTIARAIFDKI-SGDFDG-SCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVL  133 (385)
Q Consensus        58 ~G--~gGiGKTtLA~~~~~~~-~~~f~~-~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~L  133 (385)
                      .|  +.++||||+|..+++++ .+.+.. .+-+. .+..    .+.. ..++++.......+          .-..+.-+
T Consensus       570 ~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElN-ASd~----rgid-~IR~iIk~~a~~~~----------~~~~~~KV  633 (846)
T PRK04132        570 GGNLPTVLHNTTAALALARELFGENWRHNFLELN-ASDE----RGIN-VIREKVKEFARTKP----------IGGASFKI  633 (846)
T ss_pred             cCCCCCcccHHHHHHHHHHhhhcccccCeEEEEe-CCCc----ccHH-HHHHHHHHHHhcCC----------cCCCCCEE
Confidence            46  78899999999999976 333322 23332 2221    2333 23333332221110          00124579


Q ss_pred             EEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          134 IVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       134 lVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      +|+|+++..  .+...|+..+......+++|+++.+.
T Consensus       634 vIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~  670 (846)
T PRK04132        634 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYS  670 (846)
T ss_pred             EEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCCh
Confidence            999999754  45666666665444566666665543

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.34  E-value=0.01  Score=52.30  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=20.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|.|++|+||||+|+.+++++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            38899999999999999999865

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.33  E-value=0.035  Score=51.87  Aligned_cols=47  Identities=17%  Similarity=0.217  Sum_probs=31.4

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh--C----CCCceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS--G----DFDGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~--~----~f~~~~w~~   87 (385)
                      |-++|..+=..-.++-|+|.+|+|||+|+.+++-..+  .    .-..++|++
T Consensus       115 LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyId  167 (344)
T PLN03187        115 LDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYID  167 (344)
T ss_pred             HHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEE
Confidence            3334443334467889999999999999999874321  1    124677887

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

Probab=96.33  E-value=0.0077  Score=59.45  Aligned_cols=51  Identities=22%  Similarity=0.301  Sum_probs=36.8

Q ss_pred             ccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           31 LVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      +=|-++...+|.....-           +-+.++-|.++|++|+|||++|+.+++..+-.|-
T Consensus       436 IGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFl  497 (693)
T KOG0730|consen  436 IGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFL  497 (693)
T ss_pred             ccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCee
Confidence            34466666666654321           2255788999999999999999999998766653

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=96.32  E-value=0.0033  Score=53.53  Aligned_cols=26  Identities=31%  Similarity=0.507  Sum_probs=23.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|+|-||=|+||||||+.+++++.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC
Confidence            45899999999999999999999876

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=96.32  E-value=0.0056  Score=49.54  Aligned_cols=35  Identities=17%  Similarity=0.306  Sum_probs=26.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~   87 (385)
                      ++|.|+|..|+|||||++.+.+.+. ..+...++.+
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~   36 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRGYRVAVIKH   36 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcCCceEEEEE
Confidence            4799999999999999999999876 4455554554

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.32  E-value=0.0028  Score=53.89  Aligned_cols=23  Identities=35%  Similarity=0.546  Sum_probs=21.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|.|.+|+||||+|+.++..+
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999875

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.31  E-value=0.0029  Score=51.81  Aligned_cols=23  Identities=26%  Similarity=0.680  Sum_probs=20.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++.|+|++|+||||+|+.+.+..
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998863

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK15453 phosphoribulokinase; Provisional

Probab=96.31  E-value=0.0068  Score=54.47  Aligned_cols=29  Identities=24%  Similarity=0.270  Sum_probs=25.1

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .+..+|+|.|.+|+||||+|+.+.+.+..
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if~~   31 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIFRR   31 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            45679999999999999999999986654

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.31  E-value=0.049  Score=45.58  Aligned_cols=76  Identities=9%  Similarity=0.016  Sum_probs=42.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC---CchHHHHHHHhCC--
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV---MPYIDLNFRRLGH--  129 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~---~~~~~~l~~~l~~--  129 (385)
                      +.|.|.+|+|||++|.+++..   .....+++... ..    .+. ++...+.+........   .+....+.+.+..  
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~---~~~~~~y~at~-~~----~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~   72 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE---LGGPVTYIATA-EA----FDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKELD   72 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh---cCCCeEEEEcc-Cc----CCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcC
Confidence            679999999999999999865   22355566422 11    322 3444443322222211   1444445554422  


Q ss_pred             ceEEEEEeCC
Q 044214          130 MKVLIVFDDV  139 (385)
Q Consensus       130 k~~LlVlDdv  139 (385)
                      +.-.+++|.+
T Consensus        73 ~~~~VLIDcl   82 (169)
T cd00544          73 PGDVVLIDCL   82 (169)
T ss_pred             CCCEEEEEcH
Confidence            2337999998

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.

>PRK13949 shikimate kinase; Provisional

Probab=96.31  E-value=0.0035  Score=52.57  Aligned_cols=24  Identities=29%  Similarity=0.462  Sum_probs=21.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.|+|++|+||||+++.+++.+.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELG   26 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            588999999999999999998764

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.31  E-value=0.011  Score=53.79  Aligned_cols=28  Identities=36%  Similarity=0.417  Sum_probs=24.1

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+.+|+|.|..|+||||+|+.+...+.
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4578999999999999999988877654

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

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.30  E-value=0.11  Score=48.24  Aligned_cols=122  Identities=11%  Similarity=0.069  Sum_probs=62.9

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeecccc--------ccCCCChHHHHHHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREE--------SQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~--------~~~~~~~~~l~~~ll~~  109 (385)
                      .+.+.+.+..+ .-...+.++|+.|+||+++|..+++.+-..-....  ...+..        ... +++..+..     
T Consensus        11 ~~~l~~~~~~~-rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~--~~Cg~C~sC~~~~~g~H-PD~~~i~p-----   81 (325)
T PRK06871         11 YQQITQAFQQG-LGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGD--QPCGQCHSCHLFQAGNH-PDFHILEP-----   81 (325)
T ss_pred             HHHHHHHHHcC-CcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCC--CCCCCCHHHHHHhcCCC-CCEEEEcc-----
Confidence            34555555522 23467889999999999999999986532110000  000000        000 11110000     


Q ss_pred             HhCCCCCCchHHHHHHHhC-----CceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          110 LLKDKNVMPYIDLNFRRLG-----HMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       110 l~~~~~~~~~~~~l~~~l~-----~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..+..-.++.+..+.+.+.     +++=++|+|+++.  ......++..+.+-.++..+|++|.+.
T Consensus        82 ~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~  147 (325)
T PRK06871         82 IDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLS  147 (325)
T ss_pred             ccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            0000011233344444432     4566888999974  445666666665545666677776654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.29  E-value=0.0081  Score=54.12  Aligned_cols=38  Identities=13%  Similarity=0.177  Sum_probs=30.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..-.++.|.|.+|+|||++|.+++......-..+++++
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            34578999999999999999998875444455677776

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK13948 shikimate kinase; Provisional

Probab=96.29  E-value=0.0036  Score=53.04  Aligned_cols=27  Identities=22%  Similarity=0.281  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ....|.++|+.|+||||+++.+++++.
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456899999999999999999998764

>PRK08506 replicative DNA helicase; Provisional

Probab=96.29  E-value=0.058  Score=53.00  Aligned_cols=53  Identities=21%  Similarity=0.095  Sum_probs=37.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      -.++.|.|.+|+|||++|..++......-..+++++ .     . .+..++...++....
T Consensus       192 G~LivIaarpg~GKT~fal~ia~~~~~~g~~V~~fS-l-----E-Ms~~ql~~Rlla~~s  244 (472)
T PRK08506        192 GDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFS-L-----E-MPAEQLMLRMLSAKT  244 (472)
T ss_pred             CceEEEEcCCCCChHHHHHHHHHHHHhcCCcEEEEe-C-----c-CCHHHHHHHHHHHhc
Confidence            458999999999999999999987643333455554 1     2 556677777766543

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=96.29  E-value=0.0029  Score=51.07  Aligned_cols=27  Identities=22%  Similarity=0.583  Sum_probs=22.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      .|+|+|+.|+|||||++.+.+.....|
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~~~~~   27 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFDPNF   27 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcCCccc
Confidence            378999999999999999998654443

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

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

Probab=96.28  E-value=0.056  Score=47.28  Aligned_cols=47  Identities=23%  Similarity=0.474  Sum_probs=35.6

Q ss_pred             CCccc-cchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           29 NQLVG-VESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        29 ~~~vG-R~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -+.|| -+..++++.+.+..           +-.+++-+.++|++|.|||-||+++++.
T Consensus       146 YeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahh  204 (404)
T KOG0728|consen  146 YEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHH  204 (404)
T ss_pred             HHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhh
Confidence            34565 56777777776642           1245678999999999999999999975

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.27  E-value=0.003  Score=54.47  Aligned_cols=23  Identities=43%  Similarity=0.710  Sum_probs=21.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|.|.+|+||||||+.+...+
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998866

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

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

Probab=96.27  E-value=0.013  Score=50.17  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.+++|+|..|+|||||++.++..
T Consensus        33 Ge~~~l~G~nGsGKSTLl~~l~G~   56 (192)
T cd03232          33 GTLTALMGESGAGKTTLLDVLAGR   56 (192)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999863

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=96.27  E-value=0.0054  Score=62.50  Aligned_cols=47  Identities=21%  Similarity=0.393  Sum_probs=37.6

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..+||++|++++...|.....+-  -.++|.+|||||+++.-++.++.
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~KNN--PvLiGEpGVGKTAIvEGLA~rIv  216 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTKNN--PVLVGEPGVGKTAIVEGLAQRIV  216 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCCCC--CeEecCCCCCHHHHHHHHHHHHh
Confidence            469999999999999998422221  23679999999999999999763

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=96.27  E-value=0.017  Score=55.60  Aligned_cols=88  Identities=18%  Similarity=0.214  Sum_probs=52.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-----
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-----  117 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-----  117 (385)
                      +-+.++|.|.+|+|||+|+..++.........++-+..+++..   ..+.+++..+...-...        .++.     
T Consensus       142 ~GQr~~If~~~G~GKt~L~~~~~~~~~~~~~~v~V~alIGER~---rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~  218 (461)
T TIGR01039       142 KGGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERT---REGNDLYHEMKESGVIDKTALVYGQMNEPPGARM  218 (461)
T ss_pred             cCCEEEeecCCCCChHHHHHHHHHHHHhcCCCeEEEEEecCCc---hHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            3467999999999999999999886644333333333343321   45666666664431111        1111     


Q ss_pred             ---chHHHHHHHh---CCceEEEEEeCCCC
Q 044214          118 ---PYIDLNFRRL---GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 ---~~~~~l~~~l---~~k~~LlVlDdv~~  141 (385)
                         ...-.+.+++   +++++||++||+..
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       219 RVALTGLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCeeEEEecchhH
Confidence               1222334444   56899999999954

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.26  E-value=0.0042  Score=53.37  Aligned_cols=25  Identities=36%  Similarity=0.311  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|.|.|.+|+||||+|+.++++.
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4589999999999999999999874

>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=96.26  E-value=0.0057  Score=52.01  Aligned_cols=33  Identities=21%  Similarity=0.114  Sum_probs=26.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.|.|.+|+|||+||.+++......-..++|++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            679999999999999999886544445677776

A related protein is found in archaea.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=96.26  E-value=0.0038  Score=51.22  Aligned_cols=22  Identities=32%  Similarity=0.564  Sum_probs=20.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|+|++|+||||+|+.++..+
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            6899999999999999999876

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.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.25  E-value=0.0033  Score=51.75  Aligned_cols=20  Identities=35%  Similarity=0.604  Sum_probs=18.7

Q ss_pred             EEEEEcCCCchHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~   73 (385)
                      .|+|+|.||+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999887

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.25  E-value=0.042  Score=49.54  Aligned_cols=154  Identities=14%  Similarity=0.199  Sum_probs=84.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH--HhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC------------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD--KISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM------------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~--~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~------------  117 (385)
                      +-+.+|+|+.|+||++|.+.+..  .+..-=+.++|+.--...... ......-.++.+.-....++.            
T Consensus        87 P~I~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIpp-~E~~aW~~Ql~EgNY~~~~~gTi~P~t~t~~P~  165 (369)
T PF02456_consen   87 PFIGVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIPP-QEITAWETQLCEGNYDCGPDGTIVPQTGTFRPK  165 (369)
T ss_pred             ceEEEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCCH-HHHHHHHHHHHhcCCCCCCCCeecccccccccc
Confidence            55678899999999999998875  344445667777522221111 223333334444322222110            


Q ss_pred             ------------------chHHHHHHHhCCceEEEEEeCCC----ChhhhhHhhccCCC-------CCCCcEEEEEeccH
Q 044214          118 ------------------PYIDLNFRRLGHMKVLIVFDDVT----CFSQLESLMGSLDW-------LTPVSRIILTTRNK  168 (385)
Q Consensus       118 ------------------~~~~~l~~~l~~k~~LlVlDdv~----~~~~~~~l~~~~~~-------~~~gs~ilvTtR~~  168 (385)
                                        .-.....+.-+..++-||+|.+-    .......++.+++.       .+.|.-|+|.-.+.
T Consensus       166 Fv~msy~e~t~~~NldI~~p~NiF~~Aa~~GPiaIImDECMe~Lg~~~~is~fFHAlPSKL~~rfp~CTgy~VfVVLHNm  245 (369)
T PF02456_consen  166 FVEMSYDEATSPENLDITNPNNIFAQAAKKGPIAIIMDECMEKLGSHKSISKFFHALPSKLHDRFPKCTGYYVFVVLHNM  245 (369)
T ss_pred             ceeecHhhhCCccccCCCCchHHHHHHHhcCCEEEEhHHHHHHhcCCCChhHHHhcCcHHHhhhccCCceeEEEEEeccC
Confidence                              12234555667789999999983    23345555555542       12455565544432


Q ss_pred             HHHhhcc--c---------eecccCCCCCCchHHHHHHHHHhCCCccchhHH
Q 044214          169 QVLRNWR--V---------NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL  209 (385)
Q Consensus       169 ~~~~~~~--~---------~~~~~~~~~~~~~~~~~~i~~~~~GlPLal~~~  209 (385)
                      .--...+  +         +...   +.-.-.++.+-|-.+.+|+|.+|.++
T Consensus       246 nPR~d~gGNI~~LKiqAK~HIiS---p~~~p~QlsRFin~yt~glp~~i~~L  294 (369)
T PF02456_consen  246 NPRRDIGGNIANLKIQAKCHIIS---PKMHPSQLSRFINNYTKGLPTAISLL  294 (369)
T ss_pred             CcccccCCCccchhhhceeeeec---CCCCHHHHHHHHHHhccCCChhHHHH
Confidence            1111110  0         1121   11122467788889999999999754

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.25  E-value=0.011  Score=52.59  Aligned_cols=48  Identities=10%  Similarity=0.051  Sum_probs=35.1

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|-++|..+=..-.++.|.|.+|+|||+||.++.......-..++|++
T Consensus         9 ~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877         9 GMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             hHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            344445433345679999999999999999998875434556777886

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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.25  E-value=0.0077  Score=52.54  Aligned_cols=23  Identities=17%  Similarity=0.107  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            47899999999999999999884

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

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=96.24  E-value=0.0033  Score=55.10  Aligned_cols=24  Identities=38%  Similarity=0.519  Sum_probs=21.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|+|.|.+|+||||+|+.+...+.
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999998775

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.24  E-value=0.11  Score=48.56  Aligned_cols=158  Identities=13%  Similarity=0.086  Sum_probs=79.4

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC--C---CceEEEeecc-ccccCCCChHHHHHHHHHHH
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD--F---DGSCFLENVR-EESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~--f---~~~~w~~~~~-~~~~~~~~~~~l~~~ll~~l  110 (385)
                      ..+++.+.+.. +.-...+.++|+.|+||+++|..++..+-..  -   .+..--++.. ..... +++..+        
T Consensus        10 ~~~~l~~~~~~-~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~H-PD~~~i--------   79 (334)
T PRK07993         10 DYEQLVGSYQA-GRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTH-PDYYTL--------   79 (334)
T ss_pred             HHHHHHHHHHc-CCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCC-CCEEEE--------
Confidence            34556666653 2235678899999999999999999865221  1   1100000000 00000 111100        


Q ss_pred             hCCC----CCCchHHHHHHHhC-----CceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH-HHHhhccc--
Q 044214          111 LKDK----NVMPYIDLNFRRLG-----HMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK-QVLRNWRV--  176 (385)
Q Consensus       111 ~~~~----~~~~~~~~l~~~l~-----~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~-~~~~~~~~--  176 (385)
                      .+..    -.++.+..+.+.+.     +++=++|+|+++.  .+....++..+.+-..++.+|++|.+. .+......  
T Consensus        80 ~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRC  159 (334)
T PRK07993         80 TPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRC  159 (334)
T ss_pred             ecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcc
Confidence            0010    11133444444442     4666899999974  445666666665444566666666553 34433222  


Q ss_pred             --eecccC----------CCCCCchHHHHHHHHHhCCCcc
Q 044214          177 --NAFKRN----------HPDVGNEKLSSNVMKYAQGVPL  204 (385)
Q Consensus       177 --~~~~~~----------~~~~~~~~~~~~i~~~~~GlPL  204 (385)
                        ..|...          .......+.+..+++.++|.|.
T Consensus       160 q~~~~~~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~  199 (334)
T PRK07993        160 RLHYLAPPPEQYALTWLSREVTMSQDALLAALRLSAGAPG  199 (334)
T ss_pred             ccccCCCCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHH
Confidence              111110          0001223346678889999985

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=96.23  E-value=0.016  Score=56.21  Aligned_cols=86  Identities=22%  Similarity=0.157  Sum_probs=52.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-----
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-----  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-----  117 (385)
                      -+.++|.|.+|+|||+|+..+++.... +-+.+++.. +++.   ...+.++...+...-...        .++.     
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~~~~~dv~V~~l-iGER---~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~  218 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNISKQHSGSSVFAG-VGER---SREGHELYHEMKESGVLDKTVMVYGQMNEPPGARM  218 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhhCCCEEEEEc-CCcc---hHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHH
Confidence            467999999999999999999986653 345555553 3332   145666666665432111        1111     


Q ss_pred             ---chHHHHHHHh---CCceEEEEEeCCCC
Q 044214          118 ---PYIDLNFRRL---GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 ---~~~~~l~~~l---~~k~~LlVlDdv~~  141 (385)
                         ...-.+.+++   .++++|+++||+..
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLl~~DslTR  248 (461)
T PRK12597        219 RVVLTGLTIAEYLRDEEKEDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEeccchH
Confidence               2223344444   37899999999943

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=96.22  E-value=0.018  Score=51.44  Aligned_cols=25  Identities=36%  Similarity=0.571  Sum_probs=22.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.+++|+|..|+|||||++.++..+
T Consensus        25 Ge~~~i~G~NGsGKSTLlk~L~G~~   49 (246)
T cd03237          25 SEVIGILGPNGIGKTTFIKMLAGVL   49 (246)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3589999999999999999998754

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=96.22  E-value=0.0055  Score=60.46  Aligned_cols=60  Identities=25%  Similarity=0.320  Sum_probs=45.5

Q ss_pred             CCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           26 DNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...++++--.+-++++..||..   +....+++.++|++|+||||.++.+++.+  .|+..-|..
T Consensus        16 ~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el--g~~v~Ew~n   78 (519)
T PF03215_consen   16 KTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL--GFEVQEWIN   78 (519)
T ss_pred             CCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh--CCeeEEecC
Confidence            3345566667788999999874   33446799999999999999999999875  355566654

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=96.22  E-value=0.011  Score=51.22  Aligned_cols=26  Identities=38%  Similarity=0.682  Sum_probs=21.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .|+|+|-||+||||+|..++.++.++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~   27 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSK   27 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhc
Confidence            58999999999999999977665443

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.21  E-value=0.0058  Score=53.92  Aligned_cols=34  Identities=18%  Similarity=0.257  Sum_probs=28.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCce
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGS   83 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~   83 (385)
                      +++..|.++||+|+||||+.+++...+..++...
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~pp   50 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHLHAKKTPP   50 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHHhhccCCC
Confidence            4567889999999999999999999887776543

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=96.21  E-value=0.13  Score=48.78  Aligned_cols=41  Identities=34%  Similarity=0.400  Sum_probs=31.4

Q ss_pred             HHHHHhhcCC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           39 EEIESLLGVE-------SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        39 ~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++|.+.|...       ...+.+|..+|.-|.||||-|.++++.++.+
T Consensus        80 eELv~llG~~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~lkk~  127 (451)
T COG0541          80 EELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYLKKK  127 (451)
T ss_pred             HHHHHHhCCCCcccccCCCCCeEEEEEeccCCChHhHHHHHHHHHHHc
Confidence            4566666521       2347899999999999999999999987663

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=96.20  E-value=0.014  Score=52.42  Aligned_cols=90  Identities=16%  Similarity=0.145  Sum_probs=50.4

Q ss_pred             eEEEEEEcCCCchHHHHH-HHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-----
Q 044214           52 VYALGIWGIGGIGKTTIA-RAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-----  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA-~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-----  117 (385)
                      -+.++|.|.+|+|||+|| ..+.++.  +-+..+.+..+++.   ...+.++..++...-...        .++.     
T Consensus        69 GQr~~Ifg~~g~GKt~L~l~~i~~~~--~~~v~~V~~~iGer---~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  143 (274)
T cd01132          69 GQRELIIGDRQTGKTAIAIDTIINQK--GKKVYCIYVAIGQK---ASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQY  143 (274)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHHhc--CCCeEEEEEecccc---hHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHH
Confidence            457899999999999996 4455443  23444344334332   145566666665432111        1110     


Q ss_pred             -------chHHHHHHHhCCceEEEEEeCCCCh-hhhhHh
Q 044214          118 -------PYIDLNFRRLGHMKVLIVFDDVTCF-SQLESL  148 (385)
Q Consensus       118 -------~~~~~l~~~l~~k~~LlVlDdv~~~-~~~~~l  148 (385)
                             ..++.++.  +++.+|+++||+... ..+.++
T Consensus       144 ~a~~~a~aiAE~fr~--~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         144 LAPYTGCAMGEYFMD--NGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             HHHHHHHHHHHHHHH--CCCCEEEEEcChHHHHHHHHHH
Confidence                   22233333  479999999999544 334443

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

>PLN02924 thymidylate kinase

Probab=96.18  E-value=0.025  Score=49.58  Aligned_cols=28  Identities=18%  Similarity=0.181  Sum_probs=25.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...|+|-|..|+||||+|..+++.+...
T Consensus        16 g~~IviEGiDGsGKsTq~~~L~~~l~~~   43 (220)
T PLN02924         16 GALIVLEGLDRSGKSTQCAKLVSFLKGL   43 (220)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            4689999999999999999999987655

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=96.18  E-value=0.013  Score=54.34  Aligned_cols=42  Identities=24%  Similarity=0.351  Sum_probs=32.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...+.+.+....++..+|+|.|.+|+|||||+..+...++..
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            345555554334567899999999999999999998877654

>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=96.18  E-value=0.018  Score=53.45  Aligned_cols=56  Identities=30%  Similarity=0.283  Sum_probs=38.9

Q ss_pred             CCCCccccchhHHH---HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc
Q 044214           27 NKNQLVGVESTVEE---IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG   82 (385)
Q Consensus        27 ~~~~~vGR~~~l~~---l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~   82 (385)
                      ....+||..+..+.   +.+++..+.=.-+.|.+.|++|.|||+||..+++.+....+.
T Consensus        22 ~~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF   80 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPF   80 (398)
T ss_dssp             EETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-E
T ss_pred             ccccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCe
Confidence            35789998866654   455666433234789999999999999999999999876653

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.

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

Probab=96.17  E-value=0.0074  Score=56.48  Aligned_cols=49  Identities=29%  Similarity=0.279  Sum_probs=39.4

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ..++|+++.+..+...+..+.    .+.+.|.+|+|||+||+.++..+...|-
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~~----~vll~G~PG~gKT~la~~lA~~l~~~~~   72 (329)
T COG0714          24 KVVVGDEEVIELALLALLAGG----HVLLEGPPGVGKTLLARALARALGLPFV   72 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcCC----CEEEECCCCccHHHHHHHHHHHhCCCeE
Confidence            449999888888777666332    5889999999999999999998775544

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.16  E-value=0.0044  Score=52.31  Aligned_cols=23  Identities=35%  Similarity=0.546  Sum_probs=20.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|.|.+|+||||+|+.+++++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999973

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.16  E-value=0.042  Score=47.35  Aligned_cols=23  Identities=30%  Similarity=0.198  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ++++|+|+.|.|||||.+.+...
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~~   48 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGVN   48 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHHH
Confidence            79999999999999999999864

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

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.16  E-value=0.0033  Score=53.54  Aligned_cols=21  Identities=29%  Similarity=0.075  Sum_probs=18.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++.|+|..|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999999884

>PRK13975 thymidylate kinase; Provisional

Probab=96.16  E-value=0.0052  Score=52.78  Aligned_cols=26  Identities=35%  Similarity=0.446  Sum_probs=23.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..|+|.|+.|+||||+|+.+++.+..
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999998754

>PHA02244 ATPase-like protein

Probab=96.16  E-value=0.0076  Score=56.31  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=33.2

Q ss_pred             CCCCccccchhHH----HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVE----EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~----~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ....++|......    .+..++..+    .-|.|+|++|+|||+||+++++....
T Consensus        94 ~d~~~ig~sp~~~~~~~ri~r~l~~~----~PVLL~GppGtGKTtLA~aLA~~lg~  145 (383)
T PHA02244         94 IDTTKIASNPTFHYETADIAKIVNAN----IPVFLKGGAGSGKNHIAEQIAEALDL  145 (383)
T ss_pred             CCCcccCCCHHHHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3455777665554    444444422    24778999999999999999987543

>PRK13946 shikimate kinase; Provisional

Probab=96.15  E-value=0.0044  Score=52.73  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=22.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.|.++|++|+||||+++.+++++.
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~Lg   35 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATMLG   35 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            4799999999999999999999873

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

Probab=96.14  E-value=0.025  Score=56.49  Aligned_cols=92  Identities=22%  Similarity=0.326  Sum_probs=54.9

Q ss_pred             CccccchhHHHHHHhhcCCC-----------CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCC
Q 044214           30 QLVGVESTVEEIESLLGVES-----------KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGG   98 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~-----------~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~   98 (385)
                      ++=|..+..+.+++.+..+.           ....-|.++|++|+|||-||-+++....     .-|++ +...      
T Consensus       668 digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~-----~~fis-vKGP------  735 (952)
T KOG0735|consen  668 DIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSN-----LRFIS-VKGP------  735 (952)
T ss_pred             ecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCC-----eeEEE-ecCH------
Confidence            34555566666666654322           1234588999999999999999987532     23444 2221      


Q ss_pred             hHHHHHHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCCC
Q 044214           99 LSCLRQKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVTC  141 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~  141 (385)
                            +++....+...  +....+..+. ..++|+|++|.+++
T Consensus       736 ------ElL~KyIGaSE--q~vR~lF~rA~~a~PCiLFFDEfdS  771 (952)
T KOG0735|consen  736 ------ELLSKYIGASE--QNVRDLFERAQSAKPCILFFDEFDS  771 (952)
T ss_pred             ------HHHHHHhcccH--HHHHHHHHHhhccCCeEEEeccccc
Confidence                  23333222221  4444444443 45999999999964

>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=96.14  E-value=0.015  Score=52.71  Aligned_cols=24  Identities=21%  Similarity=0.416  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +-+.++|+.|+|||++++.+.+..
T Consensus        34 ~pvLl~G~~GtGKT~li~~~l~~l   57 (272)
T PF12775_consen   34 RPVLLVGPSGTGKTSLIQNFLSSL   57 (272)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHCS
T ss_pred             CcEEEECCCCCchhHHHHhhhccC
Confidence            467899999999999999988754

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

Probab=96.13  E-value=0.023  Score=52.17  Aligned_cols=56  Identities=27%  Similarity=0.267  Sum_probs=42.6

Q ss_pred             CCCCCccccchhHHH---HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           26 DNKNQLVGVESTVEE---IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~---l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ...+.|||-.+..+.   +.++..++.-.-+.|.++|++|.|||+||..+++.+...-+
T Consensus        36 ~~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvP   94 (450)
T COG1224          36 FIGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVP   94 (450)
T ss_pred             EcCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCC
Confidence            445679997765553   56677654444678999999999999999999998876533

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=96.12  E-value=0.0059  Score=49.89  Aligned_cols=25  Identities=28%  Similarity=0.496  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++++|+|.+|+||||+.+.+.+.+
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l   28 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL   28 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH
Confidence            5799999999999999999888765

>PRK14530 adenylate kinase; Provisional

Probab=96.11  E-value=0.005  Score=53.85  Aligned_cols=23  Identities=22%  Similarity=0.367  Sum_probs=21.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|+|++|+||||+|+.+++.+
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999875

>PTZ00494 tuzin-like protein; Provisional

Probab=96.10  E-value=0.04  Score=52.44  Aligned_cols=81  Identities=14%  Similarity=0.022  Sum_probs=58.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      +..+..+|.|+.+-..+...|.+ +...++++++.|.-|+||++|.+....+-   --..+++. ++       ..++-+
T Consensus       367 ~a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE---~~paV~VD-VR-------g~EDtL  435 (664)
T PTZ00494        367 AAAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVE---GVALVHVD-VG-------GTEDTL  435 (664)
T ss_pred             ccccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHc---CCCeEEEE-ec-------CCcchH
Confidence            44567899999999999998886 34568899999999999999999887642   23456665 33       233445


Q ss_pred             HHHHHHHhCCCCC
Q 044214          104 QKLLSNLLKDKNV  116 (385)
Q Consensus       104 ~~ll~~l~~~~~~  116 (385)
                      +.+.+.++.+.-+
T Consensus       436 rsVVKALgV~nve  448 (664)
T PTZ00494        436 RSVVRALGVSNVE  448 (664)
T ss_pred             HHHHHHhCCCChh
Confidence            6666666665543

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=96.10  E-value=0.0053  Score=51.36  Aligned_cols=45  Identities=24%  Similarity=0.350  Sum_probs=32.5

Q ss_pred             ccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           31 LVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +||.+..+.++.+.+..-......|.|+|..|+||+.+|+.+.+.
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            478888888887776642223356779999999999999999883

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 ....

>PTZ00035 Rad51 protein; Provisional

Probab=96.10  E-value=0.052  Score=50.80  Aligned_cols=38  Identities=18%  Similarity=0.233  Sum_probs=27.9

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..|-++|..+=..-.++.|+|.+|+|||||+..++-..
T Consensus       105 ~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~  142 (337)
T PTZ00035        105 TQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTC  142 (337)
T ss_pred             HHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHh
Confidence            34444555333456789999999999999999987543

>TIGR00750 lao LAO/AO transport system ATPase

Probab=96.10  E-value=0.015  Score=53.57  Aligned_cols=41  Identities=20%  Similarity=0.233  Sum_probs=30.9

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+.+.+....+...+|+|+|.+|+|||||+..+.......
T Consensus        21 ~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~   61 (300)
T TIGR00750        21 KQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRR   61 (300)
T ss_pred             HHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            34444454444567899999999999999999999866443

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

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=96.10  E-value=0.012  Score=54.13  Aligned_cols=50  Identities=16%  Similarity=0.123  Sum_probs=36.7

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..+.++=..+....+...+..+    +.|.|.|.+|+||||+|+.++..+.-.|
T Consensus        43 ~d~~y~f~~~~~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~lA~~l~~~~   92 (327)
T TIGR01650        43 IDPAYLFDKATTKAICAGFAYD----RRVMVQGYHGTGKSTHIEQIAARLNWPC   92 (327)
T ss_pred             CCCCccCCHHHHHHHHHHHhcC----CcEEEEeCCCChHHHHHHHHHHHHCCCe
Confidence            3344555555666677777632    3599999999999999999999876444

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.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.10  E-value=0.0096  Score=57.03  Aligned_cols=85  Identities=14%  Similarity=0.192  Sum_probs=48.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~------  117 (385)
                      -..++|.|..|+|||||++.++.....  +.+++.. +++..   ..+.++...++..-...        .++.      
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~~~~--dv~Vi~l-IGER~---rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRGTTA--DVIVVGL-VGERG---REVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccCCCC--CEEEEEE-EcCCh---HHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            357999999999999999888864322  3444432 33321   34455555543331111        0110      


Q ss_pred             --chHHHHHHHh--CCceEEEEEeCCCCh
Q 044214          118 --PYIDLNFRRL--GHMKVLIVFDDVTCF  142 (385)
Q Consensus       118 --~~~~~l~~~l--~~k~~LlVlDdv~~~  142 (385)
                        ...-.+.+++  +++++|+++||+...
T Consensus       236 a~~~A~tiAEyfrd~G~~VLl~~DslTR~  264 (444)
T PRK08972        236 GCETATTIAEYFRDQGLNVLLLMDSLTRY  264 (444)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcChHHH
Confidence              1112233333  579999999999543

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=96.09  E-value=0.0053  Score=50.89  Aligned_cols=27  Identities=33%  Similarity=0.516  Sum_probs=23.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      -|.++|+.|+||||+.+.+++.+.-.|
T Consensus         4 ~IvLiG~mGaGKSTIGr~LAk~L~~~F   30 (172)
T COG0703           4 NIVLIGFMGAGKSTIGRALAKALNLPF   30 (172)
T ss_pred             cEEEEcCCCCCHhHHHHHHHHHcCCCc
Confidence            578999999999999999999876555

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.09  E-value=0.015  Score=51.28  Aligned_cols=47  Identities=21%  Similarity=0.172  Sum_probs=33.3

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |-+.|..+=..-..+.|.|.+|+|||+||.+++......-..++|++
T Consensus         9 LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881         9 LDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             HHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            33444322234568999999999999999998765434456677886

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.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.08  E-value=0.041  Score=48.01  Aligned_cols=24  Identities=38%  Similarity=0.350  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.+++|.|..|.|||||++.++..
T Consensus        37 Ge~~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         37 GEALLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            348999999999999999999864

>PRK14529 adenylate kinase; Provisional

Probab=96.07  E-value=0.032  Score=48.82  Aligned_cols=91  Identities=16%  Similarity=0.065  Sum_probs=47.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCC-CceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc-eE
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDF-DGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM-KV  132 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k-~~  132 (385)
                      |.|.|++|+||||+|+.++.++.-.+ +..-.+..  +.... ..+....+.++.. +...++......+.+.+... .-
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~~is~gdllr~--~i~~~-t~lg~~i~~~i~~-G~lvpdei~~~lv~~~l~~~~~~   78 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLAHIESGAIFRE--HIGGG-TELGKKAKEYIDR-GDLVPDDITIPMILETLKQDGKN   78 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCcccchhhhh--hccCC-ChHHHHHHHHHhc-cCcchHHHHHHHHHHHHhccCCC
Confidence            78899999999999999998764221 11111110  01111 2233333333322 11112224445556665431 34


Q ss_pred             EEEEeCC-CChhhhhHhh
Q 044214          133 LIVFDDV-TCFSQLESLM  149 (385)
Q Consensus       133 LlVlDdv-~~~~~~~~l~  149 (385)
                      -+|||+. .+..+.+.|.
T Consensus        79 g~iLDGfPRt~~Qa~~l~   96 (223)
T PRK14529         79 GWLLDGFPRNKVQAEKLW   96 (223)
T ss_pred             cEEEeCCCCCHHHHHHHH
Confidence            5899999 4555555443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.07  E-value=0.069  Score=52.14  Aligned_cols=26  Identities=23%  Similarity=0.313  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+++++|+.|+||||.+.+++..+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~  281 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCV  281 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHH
Confidence            47999999999999999999998653

>PRK13768 GTPase; Provisional

Probab=96.07  E-value=0.0098  Score=53.36  Aligned_cols=35  Identities=26%  Similarity=0.364  Sum_probs=27.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++.|.|.||+||||++..+...+...-..++.+.
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i~   37 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVN   37 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHHHHhcCCceEEEE
Confidence            57899999999999999999987655444444443

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=96.07  E-value=0.014  Score=50.42  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.+++|+|..|.|||||.+.++..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          26 GEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999998875

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=96.07  E-value=0.013  Score=59.16  Aligned_cols=57  Identities=21%  Similarity=0.336  Sum_probs=44.1

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      ..++++|.++.++.+...+...    +.+.++|++|+|||++|+.+++.+... |...+++.
T Consensus        16 ~~~~viG~~~a~~~l~~a~~~~----~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~   73 (608)
T TIGR00764        16 LIDQVIGQEEAVEIIKKAAKQK----RNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYP   73 (608)
T ss_pred             hHhhccCHHHHHHHHHHHHHcC----CCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEe
Confidence            3467899999998888888743    256699999999999999999987554 44455555

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

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=96.06  E-value=0.0017  Score=34.22  Aligned_cols=19  Identities=21%  Similarity=0.387  Sum_probs=16.1

Q ss_pred             CeeEEEcCCCCCCCCC-CCC
Q 044214          365 KISYLQDPGFAGVKLN-NFG  383 (385)
Q Consensus       365 ~LryL~l~~~~~~~lP-~~~  383 (385)
                      +|+||++++|+++.+| +|+
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~   20 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFS   20 (22)
T ss_dssp             TESEEEETSSEESEEGTTTT
T ss_pred             CccEEECCCCcCEeCChhhc
Confidence            5899999999999888 665

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.06  E-value=0.0072  Score=52.94  Aligned_cols=24  Identities=29%  Similarity=0.210  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..+++.|.|..|.||||+.+.+..
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            346889999999999999999886

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

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=96.05  E-value=0.0042  Score=51.65  Aligned_cols=22  Identities=36%  Similarity=0.671  Sum_probs=19.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|+|++|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999875

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.

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=96.05  E-value=0.0088  Score=54.13  Aligned_cols=34  Identities=29%  Similarity=0.386  Sum_probs=28.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|+|.+|+|||||+.++...++++. .+.-+.
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~IK   35 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLSGRG-RVGTVK   35 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhCC-CEEEEE
Confidence            5899999999999999999999988776 455444

>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=96.05  E-value=0.017  Score=49.83  Aligned_cols=103  Identities=17%  Similarity=0.154  Sum_probs=50.9

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC-------chHH
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM-------PYID  121 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~-------~~~~  121 (385)
                      .+.+.++.+.|.+|+||||++..+.....  ....+.+. ....-...+....+..    . .......       ....
T Consensus        12 ~~~P~~~i~aG~~GsGKSt~~~~~~~~~~--~~~~v~i~-~D~~r~~~p~~~~~~~----~-~~~~~~~~~~~~a~~~~~   83 (199)
T PF06414_consen   12 QEKPTLIIIAGQPGSGKSTLARQLLEEFG--GGGIVVID-ADEFRQFHPDYDELLK----A-DPDEASELTQKEASRLAE   83 (199)
T ss_dssp             -SS-EEEEEES-TTSTTHHHHHHHHHHT---TT-SEEE--GGGGGGGSTTHHHHHH----H-HCCCTHHHHHHHHHHHHH
T ss_pred             ccCCEEEEEeCCCCCCHHHHHHHhhhhcc--CCCeEEEe-hHHHHHhccchhhhhh----h-hhhhhHHHHHHHHHHHHH
Confidence            35678999999999999999999988654  34455554 3332111122332222    1 1111100       3445


Q ss_pred             HHHHHhCCceEEEEEeCCC-ChhhhhHhhccCCCCCCCcEE
Q 044214          122 LNFRRLGHMKVLIVFDDVT-CFSQLESLMGSLDWLTPVSRI  161 (385)
Q Consensus       122 ~l~~~l~~k~~LlVlDdv~-~~~~~~~l~~~~~~~~~gs~i  161 (385)
                      .+.+..-.+++=+|+|..- +.+....+...+..  .|.+|
T Consensus        84 ~~~~~a~~~~~nii~E~tl~~~~~~~~~~~~~k~--~GY~v  122 (199)
T PF06414_consen   84 KLIEYAIENRYNIIFEGTLSNPSKLRKLIREAKA--AGYKV  122 (199)
T ss_dssp             HHHHHHHHCT--EEEE--TTSSHHHHHHHHHHHC--TT-EE
T ss_pred             HHHHHHHHcCCCEEEecCCCChhHHHHHHHHHHc--CCceE
Confidence            5555555667778889874 44445545555443  35444

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.04  E-value=0.013  Score=51.67  Aligned_cols=36  Identities=14%  Similarity=0.008  Sum_probs=28.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -.++.|.|.+|+|||++|.+++.....+-..+++++
T Consensus        64 Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            458999999999999999999876544445566665

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=96.03  E-value=0.014  Score=51.59  Aligned_cols=35  Identities=20%  Similarity=0.254  Sum_probs=28.8

Q ss_pred             EEEEEEcC-CCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGI-GGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~-gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|+|+ ||+||||++..++.-+...-..++-+.
T Consensus         2 ~~iai~s~kGGvG~TTltAnLA~aL~~~G~~VlaID   37 (243)
T PF06564_consen    2 KVIAIVSPKGGVGKTTLTANLAWALARLGESVLAID   37 (243)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            58899998 899999999999987766656666665

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>PLN02674 adenylate kinase

Probab=96.03  E-value=0.028  Score=49.84  Aligned_cols=25  Identities=32%  Similarity=0.224  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...|.|.|++|+||||+|+.++++.
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~   55 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEY   55 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHc
Confidence            3568899999999999999998854

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.03  E-value=0.0095  Score=53.81  Aligned_cols=36  Identities=28%  Similarity=0.348  Sum_probs=26.0

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++++..++..+    ..|.|.|.+|+|||+||+.+++...
T Consensus        11 ~~~~l~~l~~g----~~vLL~G~~GtGKT~lA~~la~~lg   46 (262)
T TIGR02640        11 TSRALRYLKSG----YPVHLRGPAGTGKTTLAMHVARKRD   46 (262)
T ss_pred             HHHHHHHHhcC----CeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            34445555422    2567999999999999999998553

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).

>TIGR03263 guanyl_kin guanylate kinase

Probab=96.01  E-value=0.005  Score=52.09  Aligned_cols=24  Identities=29%  Similarity=0.553  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++++|+|+.|+||||||+.+++..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            478999999999999999999853

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=96.01  E-value=0.0059  Score=51.36  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..|.|+|+.|+||||+|+.+++..
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHc
Confidence            468999999999999999999875

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

Probab=96.00  E-value=0.017  Score=53.67  Aligned_cols=72  Identities=17%  Similarity=0.256  Sum_probs=50.5

Q ss_pred             cHhHHHHHHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHH
Q 044214            2 RESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARA   71 (385)
Q Consensus         2 ~e~~~i~~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~   71 (385)
                      +++.+++.+-.+|.++-++     ..=+++.|-++..+-|.+....          -...-+-|.++|++|.|||-||++
T Consensus       190 ~d~~Lve~lerdIl~~np~-----ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKA  264 (491)
T KOG0738|consen  190 YDADLVEALERDILQRNPN-----IKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKA  264 (491)
T ss_pred             chHHHHHHHHHHHhccCCC-----cChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHH
Confidence            4555666666666555333     3447788888888877775431          113356789999999999999999


Q ss_pred             HHHHhhC
Q 044214           72 IFDKISG   78 (385)
Q Consensus        72 ~~~~~~~   78 (385)
                      |+.....
T Consensus       265 vATEc~t  271 (491)
T KOG0738|consen  265 VATECGT  271 (491)
T ss_pred             HHHhhcC
Confidence            9987653

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=96.00  E-value=0.016  Score=50.86  Aligned_cols=36  Identities=33%  Similarity=0.319  Sum_probs=24.8

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+.+...+...    .+..|+|++|.|||+++..+...+
T Consensus         6 Q~~Ai~~~~~~~----~~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen    6 QREAIQSALSSN----GITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             HHHHHHHHCTSS----E-EEEE-STTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCC----CCEEEECCCCCChHHHHHHHHHHh
Confidence            445565555522    178999999999998888887766

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.00  E-value=0.012  Score=48.62  Aligned_cols=37  Identities=27%  Similarity=0.269  Sum_probs=30.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ++..+|=++|++|.||||+|.++.+.+......+...
T Consensus        21 ~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~L   57 (197)
T COG0529          21 QKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLL   57 (197)
T ss_pred             CCCeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            4567899999999999999999999887765544444

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.98  E-value=0.083  Score=49.18  Aligned_cols=25  Identities=36%  Similarity=0.327  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+.++|+.|+|||++|..+++.+
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~l   45 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQAL   45 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHH
Confidence            5578899999999999999999865

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

Probab=95.97  E-value=0.015  Score=45.55  Aligned_cols=47  Identities=26%  Similarity=0.414  Sum_probs=33.9

Q ss_pred             Cccccchh----HHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           30 QLVGVEST----VEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        30 ~~vGR~~~----l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++|-.-.    ++.|...+.. .++++-|++.+|.+|+|||.+++.+++.+
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            46665544    4445555543 34567789999999999999999998863

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

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.96  E-value=0.062  Score=50.29  Aligned_cols=49  Identities=14%  Similarity=0.163  Sum_probs=32.8

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      ..|-++|..+=..-.++-|+|.+|+|||+||..++-...-      .-..++|++
T Consensus       110 ~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyId  164 (342)
T PLN03186        110 RELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYID  164 (342)
T ss_pred             HHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEE
Confidence            3444445433345678999999999999999988853221      112577887

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=95.96  E-value=0.012  Score=51.07  Aligned_cols=30  Identities=27%  Similarity=0.483  Sum_probs=26.5

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +.++++|+++|..|+|||||..++.+....
T Consensus        19 ~~~~~~i~~~G~~gsGKTTli~~l~~~~~~   48 (207)
T TIGR00073        19 KHGLVVLNFMSSPGSGKTTLIEKLIDNLKD   48 (207)
T ss_pred             hcCcEEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            457999999999999999999999987543

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=95.96  E-value=0.01  Score=44.11  Aligned_cols=25  Identities=32%  Similarity=0.557  Sum_probs=22.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++.+.|.+|+||||++..++..+++
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4788999999999999999998765

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK14527 adenylate kinase; Provisional

Probab=95.95  E-value=0.007  Score=51.82  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|.|.|++|+||||+|+.++++.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998765

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

Probab=95.95  E-value=0.011  Score=56.88  Aligned_cols=52  Identities=17%  Similarity=0.192  Sum_probs=37.2

Q ss_pred             CCccccchhHHHHHHhhc-------CCC-------CCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLG-------VES-------KGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~-------~~~-------~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..++|.+...+.+...+.       ...       -.-..+.++|++|+|||++|+.++..+...|
T Consensus        71 ~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf  136 (412)
T PRK05342         71 QYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPF  136 (412)
T ss_pred             hHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCc
Confidence            358999988887755441       100       0125689999999999999999998764433

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

Probab=95.95  E-value=0.01  Score=48.87  Aligned_cols=36  Identities=25%  Similarity=0.457  Sum_probs=29.8

Q ss_pred             chhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           35 ESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        35 ~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+.+++|.++|..     ++++++|.+|||||||...+...
T Consensus        23 ~~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   23 GEGIEELKELLKG-----KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHHHHhh
Confidence            3567888888872     58999999999999999998863

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

>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=95.95  E-value=0.031  Score=52.12  Aligned_cols=77  Identities=10%  Similarity=0.211  Sum_probs=49.0

Q ss_pred             cchhHHHHHHhhcCCC-CCeEEEEEEcCCCchHHHHHHHHHHHhhCC---CCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           34 VESTVEEIESLLGVES-KGVYALGIWGIGGIGKTTIARAIFDKISGD---FDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        34 R~~~l~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~---f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      |+...+.|.+.+...+ +...+|+|.|.=|+|||++.+.+.+.+.+.   -...+++..-...... .....++..+...
T Consensus         1 ~~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~fn~w~~~~~~-~~~~~~~~~l~~~   79 (325)
T PF07693_consen    1 RKPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYFNAWEYDGED-DLWASFLEELFDQ   79 (325)
T ss_pred             ChHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEEccccCCCcc-hHHHHHHHHHHHH
Confidence            3445667777777543 678899999999999999999999988766   1223333322212112 3345555556555


Q ss_pred             Hh
Q 044214          110 LL  111 (385)
Q Consensus       110 l~  111 (385)
                      +.
T Consensus        80 l~   81 (325)
T PF07693_consen   80 LE   81 (325)
T ss_pred             HH
Confidence            54

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 [].

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=95.95  E-value=0.0067  Score=47.27  Aligned_cols=21  Identities=29%  Similarity=0.567  Sum_probs=19.3

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~   75 (385)
                      |.|+|..|+|||||.+.+...
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~   22 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGG   22 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            789999999999999999973

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.94  E-value=0.12  Score=48.43  Aligned_cols=27  Identities=30%  Similarity=0.310  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+.+.++|+.|+|||++|+.+++.+-
T Consensus        20 l~ha~Lf~Gp~G~GK~~lA~~~A~~Ll   46 (342)
T PRK06964         20 LPHALLLHGQAGIGKLDFAQHLAQGLL   46 (342)
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHHc
Confidence            456888999999999999999998653

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=95.94  E-value=0.022  Score=48.75  Aligned_cols=26  Identities=27%  Similarity=0.456  Sum_probs=23.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +|+|.|+.|+||||+++.+++.+...
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~~   27 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEAR   27 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            68999999999999999999987543

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=95.93  E-value=0.027  Score=48.30  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.+++|.|..|.|||||.+.++...
T Consensus        35 Ge~~~l~G~nGsGKStLl~~i~Gl~   59 (194)
T cd03213          35 GELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3589999999999999999998754

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK14737 gmk guanylate kinase; Provisional

Probab=95.93  E-value=0.0062  Score=51.89  Aligned_cols=26  Identities=27%  Similarity=0.347  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.++|.|+|++|+|||||++.+.++.
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45789999999999999999998764

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.90  E-value=0.051  Score=50.42  Aligned_cols=49  Identities=20%  Similarity=0.240  Sum_probs=33.1

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC--C----CCceEEEe
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG--D----FDGSCFLE   87 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~--~----f~~~~w~~   87 (385)
                      ..|-.+|..+=..-.++.|+|.+|+|||+|+..++..+.-  .    -..++|++
T Consensus        83 ~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyId  137 (316)
T TIGR02239        83 KELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYID  137 (316)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEE
Confidence            3444555543345679999999999999999998763211  1    12457876

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).

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=95.90  E-value=0.011  Score=48.85  Aligned_cols=33  Identities=21%  Similarity=0.302  Sum_probs=26.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEE
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFL   86 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~   86 (385)
                      +++|+|..|+|||||+.++...++.+ +...+.-
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~G~~V~viK   34 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKARGYRVATIK   34 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEe
Confidence            57899999999999999999987655 4444333

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.90  E-value=0.0058  Score=52.84  Aligned_cols=22  Identities=36%  Similarity=0.093  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|+|..|.|||||.+.++.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6899999999999999999984

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

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.88  E-value=0.0046  Score=52.71  Aligned_cols=88  Identities=22%  Similarity=0.158  Sum_probs=51.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC-----CCCCchHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD-----KNVMPYIDLNFRRL  127 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~-----~~~~~~~~~l~~~l  127 (385)
                      ..++|+|..|+||||+++.+...+... ...+.+....+.... .      .....-....     .......+.+...+
T Consensus        26 ~~i~I~G~tGSGKTTll~aL~~~i~~~-~~~i~ied~~E~~~~-~------~~~~~~~~~~~~~~~~~~~~~~~~l~~~l   97 (186)
T cd01130          26 KNILISGGTGSGKTTLLNALLAFIPPD-ERIITIEDTAELQLP-H------PNWVRLVTRPGNVEGSGEVTMADLLRSAL   97 (186)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhcCCC-CCEEEECCccccCCC-C------CCEEEEEEecCCCCCCCccCHHHHHHHHh
Confidence            479999999999999999998866433 223333211111000 0      0000000000     01125566677778


Q ss_pred             CCceEEEEEeCCCChhhhhHh
Q 044214          128 GHMKVLIVFDDVTCFSQLESL  148 (385)
Q Consensus       128 ~~k~~LlVlDdv~~~~~~~~l  148 (385)
                      +..+=.++++.+.+.+.+..+
T Consensus        98 R~~pd~i~igEir~~ea~~~~  118 (186)
T cd01130          98 RMRPDRIIVGEVRGGEALDLL  118 (186)
T ss_pred             ccCCCEEEEEccCcHHHHHHH
Confidence            888888999999887766544

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.

>TIGR01287 nifH nitrogenase iron protein

Probab=95.88  E-value=0.01  Score=53.95  Aligned_cols=27  Identities=33%  Similarity=0.583  Sum_probs=22.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.|+|+|-|||||||+|..++.-+...
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~La~~   27 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAALAEM   27 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHHHHC
Confidence            368999999999999999999866543

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PRK04182 cytidylate kinase; Provisional

Probab=95.88  E-value=0.0073  Score=50.94  Aligned_cols=23  Identities=43%  Similarity=0.606  Sum_probs=21.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|.|.|+.|+||||+|+.+++++
T Consensus         2 ~I~i~G~~GsGKstia~~la~~l   24 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999999875

>PLN02200 adenylate kinase family protein

Probab=95.88  E-value=0.0083  Score=53.10  Aligned_cols=26  Identities=23%  Similarity=0.262  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.+|.|.|++|+||||+|+.+++..
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            35689999999999999999998764

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.87  E-value=0.054  Score=46.78  Aligned_cols=26  Identities=19%  Similarity=0.258  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+++|+|..|+|||||++.++....
T Consensus        33 Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          33 GEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             CcEEEEECCCCCCHHHHHHHhcccCC
Confidence            35899999999999999999987543

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]

Probab=95.87  E-value=0.03  Score=46.13  Aligned_cols=35  Identities=17%  Similarity=0.349  Sum_probs=29.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH-hhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK-ISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~-~~~~f~~~~w~~   87 (385)
                      --++|+|-|||||+++.+.+|.- ..+.|...+|+.
T Consensus        21 iK~vivGng~VGKssmiqryCkgifTkdykktIgvd   56 (246)
T KOG4252|consen   21 IKFVIVGNGSVGKSSMIQRYCKGIFTKDYKKTIGVD   56 (246)
T ss_pred             EEEEEECCCccchHHHHHHHhccccccccccccchh
Confidence            34679999999999999999984 466788889987

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=95.87  E-value=0.0073  Score=50.66  Aligned_cols=23  Identities=35%  Similarity=0.472  Sum_probs=21.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|+|++|+||||+|+.+++++
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~l   26 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQAL   26 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58889999999999999999876

>PF13245 AAA_19: Part of AAA domain

Probab=95.86  E-value=0.044  Score=39.12  Aligned_cols=22  Identities=32%  Similarity=0.249  Sum_probs=16.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +++.|.|.+|.|||+++.....
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~   32 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIA   32 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4778899999999955555444

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

Probab=95.86  E-value=0.029  Score=55.57  Aligned_cols=116  Identities=16%  Similarity=0.109  Sum_probs=0.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEee--ccccccCCCChHHHHHHHHHHHhCCCCCC--------------
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLEN--VREESQIPGGLSCLRQKLLSNLLKDKNVM--------------  117 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~--~~~~~~~~~~~~~l~~~ll~~l~~~~~~~--------------  117 (385)
                      .|+|+|+.|+|||||.+.+.......-..+.|-..  +....+. .+....-..++..+....++.              
T Consensus       350 riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~-~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~F  428 (530)
T COG0488         350 RIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQH-RDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFGF  428 (530)
T ss_pred             EEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEeh-hhhcCccCcHHHHHHhhCccccHHHHHHHHHHcCC


Q ss_pred             ----------------chHHHHHHHhCCceEEEEEeCC------CChhhhhHhhccCCCCCCCcEEEEEeccHHHHhhcc
Q 044214          118 ----------------PYIDLNFRRLGHMKVLIVFDDV------TCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWR  175 (385)
Q Consensus       118 ----------------~~~~~l~~~l~~k~~LlVlDdv------~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~  175 (385)
                                      ...-.+...+-.++-+||||.-      ++.+.++..+..++    |+ ||+.|.++.......
T Consensus       429 ~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f~----Gt-vl~VSHDr~Fl~~va  503 (530)
T COG0488         429 TGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDFE----GT-VLLVSHDRYFLDRVA  503 (530)
T ss_pred             ChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhCC----Ce-EEEEeCCHHHHHhhc

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.86  E-value=0.007  Score=48.45  Aligned_cols=23  Identities=30%  Similarity=0.439  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-|.|+|.+|+||||+|.+++..
T Consensus         8 PNILvtGTPG~GKstl~~~lae~   30 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEK   30 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHH
Confidence            35889999999999999999964

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.86  E-value=0.02  Score=55.14  Aligned_cols=86  Identities=17%  Similarity=0.150  Sum_probs=52.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-----
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-----  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-----  117 (385)
                      -+.++|.|.+|+|||+|+..+..... .+-+.++|.. +++.   ...+.+++..+...-...        .++.     
T Consensus       138 GQr~~Ifg~~G~GKt~l~~~~~~~~~~~~~~v~V~~~-iGeR---~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~  213 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCG-IGER---CREGEELYREMKEAGVLDNTVMVFGQMNEPPGARF  213 (449)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEE-eccC---cHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHH
Confidence            45799999999999999999987654 3335566654 3322   145566666655431111        1111     


Q ss_pred             ---chHHHHHHHh---CCceEEEEEeCCCC
Q 044214          118 ---PYIDLNFRRL---GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 ---~~~~~l~~~l---~~k~~LlVlDdv~~  141 (385)
                         ...-.+.+++   +++++|+++||+-.
T Consensus       214 ~~~~~a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       214 RVGHTALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEecChHH
Confidence               2222344444   46899999999954

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.86  E-value=0.052  Score=54.12  Aligned_cols=51  Identities=22%  Similarity=0.119  Sum_probs=37.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ...-+.++|....++++.+.+..-...-..|.|+|..|+||+.+|+.+...
T Consensus       200 ~~~f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        200 DSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             cccccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHh
Confidence            344467999999888887766531222335889999999999999997653

>PRK06761 hypothetical protein; Provisional

Probab=95.86  E-value=0.011  Score=53.54  Aligned_cols=27  Identities=33%  Similarity=0.448  Sum_probs=24.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++|.|.|++|+||||+++.+++.+...
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~~~   30 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILSQN   30 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCcC
Confidence            579999999999999999999987654

>PRK00300 gmk guanylate kinase; Provisional

Probab=95.86  E-value=0.0073  Score=52.27  Aligned_cols=25  Identities=24%  Similarity=0.440  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|+|++|+||||||+.++...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3589999999999999999999864

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=95.85  E-value=0.015  Score=48.18  Aligned_cols=27  Identities=30%  Similarity=0.510  Sum_probs=24.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++++|+|..|+|||||+..+...+...
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l~~~   28 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPALSAR   28 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999987655

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.85  E-value=0.029  Score=56.23  Aligned_cols=25  Identities=24%  Similarity=0.238  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-..++|+|..|+|||||++.+..-
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3458999999999999999998753

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK08149 ATP synthase SpaL; Validated

Probab=95.84  E-value=0.025  Score=54.23  Aligned_cols=84  Identities=14%  Similarity=0.175  Sum_probs=47.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~------  117 (385)
                      -..++|.|.+|+|||||+..++.....  +..++.. +..   ....+.++..+........        .++.      
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~~--dv~v~g~-Ig~---rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSEA--DVFVIGL-IGE---RGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCCC--CeEEEEE-Eee---CCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHh
Confidence            357999999999999999988864322  2222221 211   1155666666665532211        1111      


Q ss_pred             --chHHHHHHHh--CCceEEEEEeCCCC
Q 044214          118 --PYIDLNFRRL--GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 --~~~~~l~~~l--~~k~~LlVlDdv~~  141 (385)
                        .....+.+++  +++++||++||+..
T Consensus       225 a~~~a~tiAE~fr~~G~~Vll~~DslTr  252 (428)
T PRK08149        225 AALVATTVAEYFRDQGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEccchHH
Confidence              1112222332  58999999999953

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.84  E-value=0.094  Score=46.57  Aligned_cols=52  Identities=23%  Similarity=0.163  Sum_probs=35.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      .-.++.|.|.+|+|||+++.+++...... -..++|++ ..      .....+...++..
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s-~E------~~~~~~~~r~~~~   64 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS-LE------MSKEQLLQRLLAS   64 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe-CC------CCHHHHHHHHHHH
Confidence            34689999999999999999998765433 44566665 21      3445555555443

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.

>CHL00206 ycf2 Ycf2; Provisional

Probab=95.84  E-value=0.048  Score=60.60  Aligned_cols=27  Identities=11%  Similarity=0.175  Sum_probs=23.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++-|.++|++|+|||.||++++...
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~es 1654 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATNS 1654 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHhc
Confidence            345679999999999999999999864

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=95.84  E-value=0.028  Score=48.17  Aligned_cols=26  Identities=35%  Similarity=0.357  Sum_probs=23.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..|+|.|..|+||||+++.+++.+..
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~   29 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQE   29 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57999999999999999999998765

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

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

Probab=95.83  E-value=0.0089  Score=52.06  Aligned_cols=22  Identities=45%  Similarity=0.638  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..++|+|.+|+|||||++.++.
T Consensus        34 e~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          34 ETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhc
Confidence            4899999999999999999985

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=95.83  E-value=0.055  Score=49.92  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.+++|.|+.|.|||||.+.++..
T Consensus        28 Gei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        28 GRIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999864

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=95.82  E-value=0.0096  Score=55.45  Aligned_cols=50  Identities=22%  Similarity=0.220  Sum_probs=37.9

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.+-..++|.+..++.+.-.+..  .+..-+.+.|.+|+||||+|+.+..-+
T Consensus         4 ~~~f~~i~Gq~~~~~~l~~~~~~--~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          4 PFPFSAIVGQEEMKQAMVLTAID--PGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CCCHHHhCCHHHHHHHHHHHHhc--cCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            33456789999998887754431  223458999999999999999998854

>PLN02348 phosphoribulokinase

Probab=95.81  E-value=0.011  Score=55.76  Aligned_cols=31  Identities=26%  Similarity=0.464  Sum_probs=26.8

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+++.+|+|.|.+|+||||+|+.+.+.+...
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~~Lg~~   76 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTSVFGGA   76 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            4567899999999999999999999987543

>PRK04328 hypothetical protein; Provisional

Probab=95.80  E-value=0.021  Score=51.18  Aligned_cols=47  Identities=11%  Similarity=0.047  Sum_probs=33.9

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |-++|..+=..-.++.|.|.+|+|||+||.+++......-..++|++
T Consensus        12 LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         12 MDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             HHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            33444432234568999999999999999998876444456677876

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.80  E-value=0.02  Score=55.15  Aligned_cols=82  Identities=20%  Similarity=0.157  Sum_probs=45.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC-------CCCCC-------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK-------DKNVM-------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~-------~~~~~-------  117 (385)
                      -..++|+|..|+|||||++.++.... ...++++....+.     ..+..+....+.....       +.++.       
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~~-pd~gvv~liGerg-----rev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~  238 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARADA-FDTVVIALVGERG-----REVREFLEDTLADNLKKAVAVVATSDESPMMRRLA  238 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC-CCeeeeeecccCC-----ccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHH
Confidence            35799999999999999987775432 2223334321111     3444444433333211       11111       


Q ss_pred             -----chHHHHHHHhCCceEEEEEeCCCC
Q 044214          118 -----PYIDLNFRRLGHMKVLIVFDDVTC  141 (385)
Q Consensus       118 -----~~~~~l~~~l~~k~~LlVlDdv~~  141 (385)
                           ..++.++.  +++.+|+++||+..
T Consensus       239 ~~~a~~iAEyfrd--~G~~Vll~~DslTr  265 (450)
T PRK06002        239 PLTATAIAEYFRD--RGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHHHHH--cCCCEEEeccchHH
Confidence                 22233332  47999999999954

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=95.80  E-value=0.015  Score=61.31  Aligned_cols=114  Identities=20%  Similarity=0.198  Sum_probs=63.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-C---CceEEEeeccccccCCCChH-HHHHHHHHHHhCCCCCCchHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-F---DGSCFLENVREESQIPGGLS-CLRQKLLSNLLKDKNVMPYIDLNFRR  126 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f---~~~~w~~~~~~~~~~~~~~~-~l~~~ll~~l~~~~~~~~~~~~l~~~  126 (385)
                      ..-+.|+|.+|.||||+...++-....+ +   +..+++.............. .+..-+...+.......+......++
T Consensus       222 ~~~~~Ilg~pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~~~~q~~~~~~l~~~~~~~~~~~~~~~~~~e~  301 (824)
T COG5635         222 YAKLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQGIAKQLIEAHQEL  301 (824)
T ss_pred             hhheeeecCCCCCceehHHHHHHHhccCcCCcccCceeeechhHHHhhhhHhhccHHHHHHHHHhccCCcchhhHHHHHH
Confidence            3478999999999999999998754222 1   33334331100000001111 22222222222222222344444688


Q ss_pred             hCCceEEEEEeCCCChhh---------hhHhhccCCCCCCCcEEEEEeccHH
Q 044214          127 LGHMKVLIVFDDVTCFSQ---------LESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus       127 l~~k~~LlVlDdv~~~~~---------~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      ++..++++++|.++....         +..+.+..    +.+++|+|+|...
T Consensus       302 l~~g~~llLlDGlDe~~~~~~~~~~~~i~~f~~~~----~~~~~iltcR~~~  349 (824)
T COG5635         302 LKTGKLLLLLDGLDELEPKNQRALIREINKFLQEY----PDAQVLLTCRPDT  349 (824)
T ss_pred             HhccchhhHhhccchhhhhhHHHHHHHHHHHhhhc----cCCeEEEEeccch
Confidence            999999999999975322         33333333    4789999998653

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=95.79  E-value=0.013  Score=53.40  Aligned_cols=34  Identities=24%  Similarity=0.331  Sum_probs=26.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ++|+|+|-|||||||+|..++..+...-..+.-+
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~La~~G~rVLli   35 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAALAESGKKVLVV   35 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHhCCCEEEEE
Confidence            5788999999999999999998765543334444

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.78  E-value=0.026  Score=57.88  Aligned_cols=48  Identities=17%  Similarity=0.292  Sum_probs=37.5

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -+.++|.+..+.++.+.+..-......|.|+|..|+||+++|+.+.+.
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            466999999888887776542223335889999999999999999875

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=95.77  E-value=0.0087  Score=49.77  Aligned_cols=21  Identities=33%  Similarity=0.363  Sum_probs=17.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~   75 (385)
                      |+|+|..|+|||||+..+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999987

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=95.77  E-value=0.0088  Score=50.00  Aligned_cols=23  Identities=39%  Similarity=0.583  Sum_probs=21.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|.|..|+||||+|+.+.+++
T Consensus         2 iI~i~G~~GSGKstia~~la~~l   24 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKL   24 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999999864

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=95.77  E-value=0.0077  Score=51.33  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++|+|+.|+|||||++.++...
T Consensus         4 ~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHhccC
Confidence            78999999999999999998754

>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]

Probab=95.76  E-value=0.018  Score=50.31  Aligned_cols=27  Identities=33%  Similarity=0.480  Sum_probs=24.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+.+|.|-|.+||||||+|.++++++
T Consensus        87 ~~p~IILIGGasGVGkStIA~ElA~rL  113 (299)
T COG2074          87 KRPLIILIGGASGVGKSTIAGELARRL  113 (299)
T ss_pred             CCCeEEEecCCCCCChhHHHHHHHHHc
Confidence            346799999999999999999999975

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=95.76  E-value=0.0049  Score=30.15  Aligned_cols=17  Identities=12%  Similarity=-0.091  Sum_probs=10.9

Q ss_pred             CCeeEEEcCCCCCCCCC
Q 044214          364 CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       364 ~~LryL~l~~~~~~~lP  380 (385)
                      .+||.|++++|+++.||
T Consensus         1 ~~L~~L~l~~n~L~~lP   17 (17)
T PF13504_consen    1 PNLRTLDLSNNRLTSLP   17 (17)
T ss_dssp             TT-SEEEETSS--SSE-
T ss_pred             CccCEEECCCCCCCCCc
Confidence            36889999999988887

...

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=95.76  E-value=0.014  Score=50.92  Aligned_cols=27  Identities=30%  Similarity=0.569  Sum_probs=22.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++|+|.|-||+||||++..++.-+...
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~la~~   27 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAALAEM   27 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHHHHHC
Confidence            468999999999999999998866543

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.76  E-value=0.016  Score=58.11  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+|+++|++|.||||+|.-+.+
T Consensus       495 e~vALVGPSGsGKSTiasLL~r  516 (716)
T KOG0058|consen  495 EVVALVGPSGSGKSTIASLLLR  516 (716)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999987755

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.75  E-value=0.16  Score=44.02  Aligned_cols=78  Identities=12%  Similarity=0.149  Sum_probs=43.3

Q ss_pred             HHHHHHhCCceEEEEEeCCCChhhhhHhh------ccCCCCCCCcEEEEEeccHHHHhhccc---eecccC-CCCCCchH
Q 044214          121 DLNFRRLGHMKVLIVFDDVTCFSQLESLM------GSLDWLTPVSRIILTTRNKQVLRNWRV---NAFKRN-HPDVGNEK  190 (385)
Q Consensus       121 ~~l~~~l~~k~~LlVlDdv~~~~~~~~l~------~~~~~~~~gs~ilvTtR~~~~~~~~~~---~~~~~~-~~~~~~~~  190 (385)
                      .++.+.+-=++-+.|||..++--+.+.+.      ..+.  .+|+-+++.|....++.....   +.+... -..+...+
T Consensus       153 ~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr--~~~~~~liITHy~rll~~i~pD~vhvl~~GrIv~sG~~e  230 (251)
T COG0396         153 NEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALR--EEGRGVLIITHYQRLLDYIKPDKVHVLYDGRIVKSGDPE  230 (251)
T ss_pred             HHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHh--cCCCeEEEEecHHHHHhhcCCCEEEEEECCEEEecCCHH
Confidence            34444555567899999998644433322      2232  346667777777777766543   333222 22234457


Q ss_pred             HHHHHHHHhC
Q 044214          191 LSSNVMKYAQ  200 (385)
Q Consensus       191 ~~~~i~~~~~  200 (385)
                      +++++-+.|-
T Consensus       231 l~~~le~~gy  240 (251)
T COG0396         231 LAEELEEKGY  240 (251)
T ss_pred             HHHHHHHhch
Confidence            7777766543

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.092  Score=44.08  Aligned_cols=34  Identities=32%  Similarity=0.349  Sum_probs=25.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ..+.|.|..|+|||||.+.++--.+..--.+.|-
T Consensus        29 e~~~i~G~NG~GKTtLLRilaGLl~p~~G~v~~~   62 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAGLLRPDAGEVYWQ   62 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHcccCCCCCeEEec
Confidence            3788999999999999999987554443334443

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=95.73  E-value=0.014  Score=48.06  Aligned_cols=36  Identities=25%  Similarity=0.290  Sum_probs=29.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++++|+|..|+|||||..++..+++.+--.+.-+-
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G~rVa~iK   37 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARGYRVATVK   37 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCCcEEEEEE
Confidence            468999999999999999999998877754444443

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=95.73  E-value=0.019  Score=44.82  Aligned_cols=33  Identities=30%  Similarity=0.406  Sum_probs=25.8

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |.+.|.||+||||++..+++.+...-..+..+.
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~g~~V~~id   34 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAID   34 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            789999999999999999987765544444444

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.72  E-value=0.016  Score=51.25  Aligned_cols=37  Identities=11%  Similarity=0.046  Sum_probs=27.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .-.++.|.|.+|+||||||.+++......-..+++++
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            3458999999999999999888775533334556665

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.72  E-value=0.049  Score=56.06  Aligned_cols=93  Identities=16%  Similarity=0.168  Sum_probs=55.8

Q ss_pred             HHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC
Q 044214           38 VEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV  116 (385)
Q Consensus        38 l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~  116 (385)
                      ...|-.+|. .+=..-+++-|+|.+|+||||||.+++......-..++|+. ..+.    .+     ...+..++-...+
T Consensus        45 i~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId-~E~t----~~-----~~~A~~lGvDl~~  114 (790)
T PRK09519         45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFID-AEHA----LD-----PDYAKKLGVDTDS  114 (790)
T ss_pred             cHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC-Cccc----hh-----HHHHHHcCCChhH
Confidence            345555565 33345678999999999999999998776555556678886 2221    22     1233444332221


Q ss_pred             C---------chHHHHHHHhC-CceEEEEEeCCC
Q 044214          117 M---------PYIDLNFRRLG-HMKVLIVFDDVT  140 (385)
Q Consensus       117 ~---------~~~~~l~~~l~-~k~~LlVlDdv~  140 (385)
                      .         +....+...++ ++.-|+|+|.+.
T Consensus       115 llv~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        115 LLVSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCeEEEEcchh
Confidence            1         33333444443 467799999984

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=95.71  E-value=0.029  Score=51.13  Aligned_cols=26  Identities=27%  Similarity=0.393  Sum_probs=23.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+-+|.|.|.+|+||||+|..+++++
T Consensus        91 ~p~iIlI~G~sgsGKStlA~~La~~l  116 (301)
T PRK04220         91 EPIIILIGGASGVGTSTIAFELASRL  116 (301)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999999876

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=95.70  E-value=0.025  Score=55.67  Aligned_cols=113  Identities=16%  Similarity=0.102  Sum_probs=64.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC-CCCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK-DKNV  116 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~-~~~~  116 (385)
                      ++.+..++..   ...++.|+|+.|+||||+...+.+.+...-..++-+.+--+. .. ..+        .+... ....
T Consensus       231 ~~~l~~~~~~---~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE~-~~-~~~--------~q~~v~~~~g  297 (486)
T TIGR02533       231 LSRFERLIRR---PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY-QI-EGI--------GQIQVNPKIG  297 (486)
T ss_pred             HHHHHHHHhc---CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCeee-ec-CCC--------ceEEEccccC
Confidence            3444544442   234899999999999999998887664332223333211110 00 111        01000 1112


Q ss_pred             CchHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEec
Q 044214          117 MPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus       117 ~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      ......++..|+..+=.|++.++.+.+..........   .|..|+-|-.
T Consensus       298 ~~f~~~lr~~LR~dPDvI~vGEiRd~eta~~a~~aa~---tGHlvlsTlH  344 (486)
T TIGR02533       298 LTFAAGLRAILRQDPDIIMVGEIRDLETAQIAIQASL---TGHLVLSTLH  344 (486)
T ss_pred             ccHHHHHHHHHhcCCCEEEEeCCCCHHHHHHHHHHHH---hCCcEEEEEC
Confidence            2567788899999999999999988876655443322   3444444443

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.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.70  E-value=0.014  Score=57.82  Aligned_cols=29  Identities=24%  Similarity=0.563  Sum_probs=25.3

Q ss_pred             CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           48 ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        48 ~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+++.+|+|.|.+|+||||||+.+...+
T Consensus        61 ~~~~riIIGIaGpSGSGKTTLAk~LaglL   89 (656)
T PLN02318         61 KNDGIILVGVAGPSGAGKTVFTEKVLNFM   89 (656)
T ss_pred             cCCCeEEEEEECCCCCcHHHHHHHHHhhC
Confidence            34567899999999999999999998764

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.69  E-value=0.041  Score=52.95  Aligned_cols=84  Identities=18%  Similarity=0.101  Sum_probs=47.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC--------CCCCC------
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK--------DKNVM------  117 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~--------~~~~~------  117 (385)
                      -+.++|.|..|+|||||++.+++....  +.+++.. +++..   ..+.++....+..-+.        ..++.      
T Consensus       158 Gqri~I~G~sG~GKTtLL~~I~~~~~~--d~~v~~~-iGER~---rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~  231 (442)
T PRK08927        158 GQRMGIFAGSGVGKSVLLSMLARNADA--DVSVIGL-IGERG---REVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQ  231 (442)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccCC--CEEEEEE-EecCc---HHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHH
Confidence            468899999999999999988875432  3344332 32221   3344555444332110        01110      


Q ss_pred             --chHHHHHHHh--CCceEEEEEeCCCC
Q 044214          118 --PYIDLNFRRL--GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 --~~~~~l~~~l--~~k~~LlVlDdv~~  141 (385)
                        ...-.+.+++  +++++|+++||+..
T Consensus       232 a~~~a~tiAEyfrd~G~~Vll~~DslTr  259 (442)
T PRK08927        232 AAYLTLAIAEYFRDQGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCcHH
Confidence              1111223333  57999999999943

>PRK14532 adenylate kinase; Provisional

Probab=95.69  E-value=0.0088  Score=51.03  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=20.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.++++.
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7789999999999999999754

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=95.69  E-value=0.013  Score=52.02  Aligned_cols=34  Identities=21%  Similarity=0.351  Sum_probs=22.8

Q ss_pred             EEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccc
Q 044214           57 IWGIGGIGKTTIARAIFDKISGDFDGSCFLENVRE   91 (385)
Q Consensus        57 I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~   91 (385)
                      |+|++|+||||+++.+.+.+...-..++.+ |...
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~v-NLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNGRDVYIV-NLDP   34 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT-S-EEEE-E--T
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCceEE-Ecch
Confidence            689999999999999999776654444444 3443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.68  E-value=0.012  Score=54.58  Aligned_cols=109  Identities=19%  Similarity=0.078  Sum_probs=60.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      ...+.|+|..|+|||||++.+...+.... .++.+....+......+...+.   ...-..........+.+...|+..+
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~~~~~~~-~iv~ied~~El~~~~~~~~~l~---~~~~~~~~~~~~~~~~l~~~Lr~~p  219 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVDEIPKDE-RIITIEDTREIFLPHPNYVHLF---YSKGGQGLAKVTPKDLLQSCLRMRP  219 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHccCCccc-cEEEEcCccccCCCCCCEEEEE---ecCCCCCcCccCHHHHHHHHhcCCC
Confidence            35899999999999999999987654332 2333332222111000000000   0000001112356677777888888


Q ss_pred             EEEEEeCCCChhhhhHhhccCCCCCCCcE-EEEEeccH
Q 044214          132 VLIVFDDVTCFSQLESLMGSLDWLTPVSR-IILTTRNK  168 (385)
Q Consensus       132 ~LlVlDdv~~~~~~~~l~~~~~~~~~gs~-ilvTtR~~  168 (385)
                      =.+++|.+...+.+.. +....   .|.. ++.|+...
T Consensus       220 d~ii~gE~r~~e~~~~-l~a~~---~g~~~~i~T~Ha~  253 (308)
T TIGR02788       220 DRIILGELRGDEAFDF-IRAVN---TGHPGSITTLHAG  253 (308)
T ss_pred             CeEEEeccCCHHHHHH-HHHHh---cCCCeEEEEEeCC
Confidence            8999999988766553 43333   2332 46666544

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK10436 hypothetical protein; Provisional

Probab=95.68  E-value=0.028  Score=54.81  Aligned_cols=102  Identities=14%  Similarity=0.080  Sum_probs=59.4

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC-CCC
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK-DKN  115 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~-~~~  115 (385)
                      .++.+.+++..   ...+|.|+|+.|+||||....+.+.+...-..++-+.+--+     +.+..     ..+..- ...
T Consensus       206 ~~~~l~~~~~~---~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPvE-----~~l~g-----i~Q~~v~~~~  272 (462)
T PRK10436        206 QLAQFRQALQQ---PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPVE-----IPLAG-----INQTQIHPKA  272 (462)
T ss_pred             HHHHHHHHHHh---cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCcc-----ccCCC-----cceEeeCCcc
Confidence            34445555542   23489999999999999887777765433222222211100     11100     001100 111


Q ss_pred             CCchHHHHHHHhCCceEEEEEeCCCChhhhhHhhcc
Q 044214          116 VMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGS  151 (385)
Q Consensus       116 ~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~  151 (385)
                      .......++..|+..+=.|++.++.+.+........
T Consensus       273 g~~f~~~lr~~LR~dPDvI~vGEIRD~eta~~al~A  308 (462)
T PRK10436        273 GLTFQRVLRALLRQDPDVIMVGEIRDGETAEIAIKA  308 (462)
T ss_pred             CcCHHHHHHHHhcCCCCEEEECCCCCHHHHHHHHHH
Confidence            236778889999999999999999888876654433

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.67  E-value=0.014  Score=48.71  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.+++|.|++|+|||||++.+..+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3588999999999999999999865

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.66  E-value=0.082  Score=53.46  Aligned_cols=26  Identities=27%  Similarity=0.215  Sum_probs=22.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++..|.|.+|.||||+++.+...+..
T Consensus       168 ~~~vItGgpGTGKTt~v~~ll~~l~~  193 (615)
T PRK10875        168 RISVISGGPGTGKTTTVAKLLAALIQ  193 (615)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            58899999999999999999876533

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.66  E-value=0.05  Score=50.43  Aligned_cols=48  Identities=21%  Similarity=0.286  Sum_probs=33.5

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEe
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLE   87 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~   87 (385)
                      .+..+|..+=..-.++-|+|.+|+|||+|+.+++......      -..++|++
T Consensus        83 ~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~  136 (310)
T TIGR02236        83 ELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID  136 (310)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE
Confidence            3444454333446789999999999999999998764321      12677887

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.

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=95.66  E-value=0.0093  Score=51.02  Aligned_cols=22  Identities=32%  Similarity=0.345  Sum_probs=20.2

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.++++.
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999864

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=95.65  E-value=0.015  Score=51.84  Aligned_cols=34  Identities=24%  Similarity=0.303  Sum_probs=26.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +|+|.|.+|+||||+|+++.+.++..-..+..++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~~g~~v~vI~   34 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAREGIHPAVVE   34 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhcCCceEEEe
Confidence            5899999999999999999987765433344443

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

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

Probab=95.64  E-value=0.017  Score=55.23  Aligned_cols=52  Identities=17%  Similarity=0.250  Sum_probs=37.6

Q ss_pred             CCccccchhHHHHHHhhc-------C---CC--C----CeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLG-------V---ES--K----GVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~-------~---~~--~----~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ...+|.++..+.+...+.       .   ..  +    ....+.++|++|+|||++|+.++..+...|
T Consensus        77 ~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf  144 (413)
T TIGR00382        77 EYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPF  144 (413)
T ss_pred             ceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCe
Confidence            457999998888865541       1   01  1    125799999999999999999998764333

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.

>PRK14531 adenylate kinase; Provisional

Probab=95.64  E-value=0.011  Score=50.17  Aligned_cols=23  Identities=30%  Similarity=0.250  Sum_probs=21.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|+|++|+||||+++.+++..
T Consensus         4 ~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          4 RLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999875

>PRK12338 hypothetical protein; Provisional

Probab=95.63  E-value=0.011  Score=54.32  Aligned_cols=25  Identities=36%  Similarity=0.510  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.+|.|.|.+|+||||+|..++.++
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l   28 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTL   28 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHC
Confidence            4689999999999999999999864

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=95.63  E-value=0.016  Score=48.78  Aligned_cols=35  Identities=17%  Similarity=0.381  Sum_probs=30.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ...|.|.|++|+|||+|..+.++.++++|...+-.
T Consensus        13 ~~~i~v~Gp~GSGKTaLie~~~~~L~~~~~~aVI~   47 (202)
T COG0378          13 MLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVIT   47 (202)
T ss_pred             eEEEEecCCCCcCHHHHHHHHHHHHHhhCCeEEEe
Confidence            47999999999999999999999998888755443

>cd03114 ArgK-like The function of this protein family is unkown

Probab=95.63  E-value=0.017  Score=47.24  Aligned_cols=26  Identities=31%  Similarity=0.616  Sum_probs=22.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ++++.|.+|+||||++..+.......
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~~~~~   26 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITALRAR   26 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            37899999999999999999876544

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

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

Probab=95.62  E-value=0.011  Score=45.01  Aligned_cols=22  Identities=36%  Similarity=0.432  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~   73 (385)
                      -..++|.|++|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            3579999999999999999986

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

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

Probab=95.61  E-value=0.034  Score=50.17  Aligned_cols=30  Identities=33%  Similarity=0.474  Sum_probs=26.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      .+..++|||++|.|||-+|+.++.++.-.|
T Consensus       165 ~Pkg~ll~GppGtGKTlla~~Vaa~mg~nf  194 (388)
T KOG0651|consen  165 PPKGLLLYGPPGTGKTLLARAVAATMGVNF  194 (388)
T ss_pred             CCceeEEeCCCCCchhHHHHHHHHhcCCce
Confidence            367899999999999999999999876554

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

Probab=95.61  E-value=0.23  Score=46.87  Aligned_cols=36  Identities=17%  Similarity=0.230  Sum_probs=23.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh--CCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS--GDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~--~~f~~~~w~~   87 (385)
                      .++|+++|+.||||||-..+++.+..  ..=..+..++
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiIT  240 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIIT  240 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEE
Confidence            68999999999999954444444332  3334455665

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

Probab=95.60  E-value=0.02  Score=56.83  Aligned_cols=31  Identities=26%  Similarity=0.375  Sum_probs=25.7

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ...+.+.++|++|.|||.||+++++.....|
T Consensus       274 ~~~~giLl~GpPGtGKT~lAkava~~~~~~f  304 (494)
T COG0464         274 RPPKGVLLYGPPGTGKTLLAKAVALESRSRF  304 (494)
T ss_pred             CCCCeeEEECCCCCCHHHHHHHHHhhCCCeE
Confidence            3456899999999999999999999655444

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=95.60  E-value=0.06  Score=49.67  Aligned_cols=50  Identities=20%  Similarity=0.199  Sum_probs=35.7

Q ss_pred             HHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           38 VEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        38 l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...|-..|. .+-+.-+++-|+|..|+||||||..+....+..-...+|+.
T Consensus        38 ~~~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~~q~~g~~~a~ID   88 (322)
T PF00154_consen   38 SPALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKQGGICAFID   88 (322)
T ss_dssp             -HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEE
T ss_pred             CcccchhhccCccccCceEEEeCCCCCchhhhHHHHHHhhhcccceeEEec
Confidence            344555554 22233568999999999999999999987766666777886

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.60  E-value=0.038  Score=50.80  Aligned_cols=88  Identities=22%  Similarity=0.204  Sum_probs=52.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC-ceE-EEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD-GSC-FLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~-~~~-w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      ..+.|+|..|+||||+++.+.+.+....+ ..+ -+.+..+......+...        +..........+.++..|+..
T Consensus       133 ~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~--------~~~~~~~~~~~~~l~~aLR~~  204 (299)
T TIGR02782       133 KNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQ--------LRTSDDAISMTRLLKATLRLR  204 (299)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEE--------EEecCCCCCHHHHHHHHhcCC
Confidence            46789999999999999999988755321 222 22221111000000000        000000115567788888888


Q ss_pred             eEEEEEeCCCChhhhhHh
Q 044214          131 KVLIVFDDVTCFSQLESL  148 (385)
Q Consensus       131 ~~LlVlDdv~~~~~~~~l  148 (385)
                      +=.||+..+...+.+..+
T Consensus       205 pD~iivGEiR~~ea~~~l  222 (299)
T TIGR02782       205 PDRIIVGEVRGGEALDLL  222 (299)
T ss_pred             CCEEEEeccCCHHHHHHH
Confidence            889999999888776543

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.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=95.60  E-value=0.011  Score=54.59  Aligned_cols=24  Identities=33%  Similarity=0.322  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+|.+.|.+|+||||+|+.+.++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHC
Confidence            578899999999999999998865

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.59  E-value=0.047  Score=51.63  Aligned_cols=105  Identities=17%  Similarity=0.106  Sum_probs=60.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC-ceEE-EeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD-GSCF-LENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~-~~~w-~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      ..+.|+|..|+||||++..+.+.+....+ ..+. +.+.-+...  .....+....-.+++.  ........++..|+..
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~--~~~~~~~~~~q~evg~--~~~~~~~~l~~aLR~~  225 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYIL--GSPDDLLPPAQSQIGR--DVDSFANGIRLALRRA  225 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhcc--CCCceeecccccccCC--CccCHHHHHHHhhccC
Confidence            37889999999999999999887754432 2332 221111100  0000000000011111  1115567788899999


Q ss_pred             eEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEe
Q 044214          131 KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTT  165 (385)
Q Consensus       131 ~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTt  165 (385)
                      +=.|+++.+.+.+.++..+....   .|.. ++||
T Consensus       226 PD~I~vGEiRd~et~~~al~aa~---TGH~-v~tT  256 (372)
T TIGR02525       226 PKIIGVGEIRDLETFQAAVLAGQ---SGHF-CLGT  256 (372)
T ss_pred             CCEEeeCCCCCHHHHHHHHHHHh---cCCc-EEEe
Confidence            99999999998888776544422   3544 4444

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=95.56  E-value=0.018  Score=52.18  Aligned_cols=35  Identities=23%  Similarity=0.380  Sum_probs=26.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|.|-||+||||++..++..+...-..+.-+.
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~La~~G~kVlliD   36 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAALAEMGKKVMIVG   36 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            46888899999999999999987654433344443

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.56  E-value=0.056  Score=45.25  Aligned_cols=23  Identities=17%  Similarity=0.159  Sum_probs=20.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++.|.|.+|+|||++|..++.+.
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~   25 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS   25 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc
Confidence            68999999999999999998764

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=95.56  E-value=0.1  Score=54.04  Aligned_cols=35  Identities=31%  Similarity=0.130  Sum_probs=26.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC-CceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF-DGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~~   87 (385)
                      +++.|.|.+|.||||+++.+.+.+...- ...+++.
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~  374 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLA  374 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEE
Confidence            4889999999999999999988665432 1344544

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.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.55  E-value=0.22  Score=44.38  Aligned_cols=46  Identities=22%  Similarity=0.323  Sum_probs=37.3

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.+.++++.-..+.+...  .++.+...++|++|.||-|.+..+.+++
T Consensus        13 ~~l~~~~e~~~~Lksl~~--~~d~PHll~yGPSGaGKKTrimclL~el   58 (351)
T KOG2035|consen   13 DELIYHEELANLLKSLSS--TGDFPHLLVYGPSGAGKKTRIMCLLREL   58 (351)
T ss_pred             hhcccHHHHHHHHHHhcc--cCCCCeEEEECCCCCCchhhHHHHHHHH
Confidence            447788887788887666  4567889999999999999998888865

>smart00072 GuKc Guanylate kinase homologues

Probab=95.55  E-value=0.011  Score=50.30  Aligned_cols=29  Identities=24%  Similarity=0.502  Sum_probs=23.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      +.|.|+|++|+|||||+..+.+.....|.
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~~~~~~~   31 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQEIPDAFE   31 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhcCCcceE
Confidence            57999999999999999999886543443

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.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=95.55  E-value=0.056  Score=50.18  Aligned_cols=49  Identities=18%  Similarity=0.149  Sum_probs=32.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      -+.++|.|..|+|||+|++++++..  +-+.++++- +++.   ...+.+++.++
T Consensus       157 Gqr~~I~G~~G~GKT~L~~~Iak~~--~~dvvVyv~-iGER---g~Ev~e~l~ef  205 (369)
T cd01134         157 GGTAAIPGPFGCGKTVIQQSLSKYS--NSDIVIYVG-CGER---GNEMTEVLEEF  205 (369)
T ss_pred             CCEEEEECCCCCChHHHHHHHHhCC--CCCEEEEEE-eCCC---hHHHHHHHHHH
Confidence            3579999999999999999998853  234555554 2221   14455555554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.55  E-value=0.016  Score=53.70  Aligned_cols=52  Identities=19%  Similarity=0.288  Sum_probs=43.2

Q ss_pred             CCCccccchhHHHHHHhhcCC----CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           28 KNQLVGVESTVEEIESLLGVE----SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~----~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...|+|.++.++++.+.+...    ...-+++.+.|+.|.||||||..+-+-+.+.
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y  115 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEEY  115 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhheE
Confidence            347999999999999988742    2346899999999999999999998866544

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

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.54  E-value=0.023  Score=53.93  Aligned_cols=36  Identities=19%  Similarity=0.183  Sum_probs=28.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ....+.|.|.||.|||+|.+++.+.++..-..++..
T Consensus        21 ~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~   56 (364)
T PF05970_consen   21 EGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVT   56 (364)
T ss_pred             CCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEe
Confidence            445789999999999999999999887654444433

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	385
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-24
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-09
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	1e-21
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-18
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	9e-13

>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 =  104 bits (259), Expect = 3e-24
 Identities = 70/426 (16%), Positives = 138/426 (32%), Gaps = 99/426 (23%)

Query: 2   RESELINEVVNHILKRL---DEVFRPRDNKNQLVGVESTVEEI-ESLLGVES-KGVYALG 56
           R+  ++  +      RL   ++VF   +     V       ++ ++LL +   K V    
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKYN-----VSRLQPYLKLRQALLELRPAKNV---L 154

Query: 57  IWGIGGIGKTTIARAI--FDKISGDFDGSCF---LENVREESQIPGGLSCLRQKLLSNLL 111
           I G+ G GKT +A  +    K+    D   F   L+N      +   L  L  ++  N  
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214

Query: 112 KDKNVMPYIDLNF-------RRL----GHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSR 160
              +    I L         RRL     +   L+V  +V   ++        +      +
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-QNAKA------WNAFNLSCK 267

Query: 161 IILTTRNKQVLRNWRVNAFKRNHPDVGN----------EKLSSNV--MKYA-------QG 201
           I+LTTR KQV     ++A    H  + +          + L       +           
Sbjct: 268 ILLTTRFKQVTD--FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325

Query: 202 VPLALKVLVWES---AISKLQRILHPS---ILEVLKISYDSLEDKE-KNIFLDVACFFQG 254
            P  L  ++ ES    ++      H +   +  +++ S + LE  E + +F  ++ F   
Sbjct: 326 NPRRLS-IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS 384

Query: 255 EHVDP--VMKFF--NASGFYPEIRISVLVDKPLIAICSYKK--IRMRDLLQELGGEIVRK 308
            H+ P  ++     +       + ++ L    L+     K+  I +  +  EL  ++  +
Sbjct: 385 AHI-PTILLSLIWFDVIKSDVMVVVNKLHKYSLVE-KQPKESTISIPSIYLELKVKLENE 442

Query: 309 --------ESINPGNRKQGQKIEDICLD----------MSKVIEICLNTSTFTKMPK--- 347
                   +  N         +    LD          +        +    T       
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN----IEHPERMTLFRMVFL 498

Query: 348 -LRFLK 352
             RFL+
Sbjct: 499 DFRFLE 504

>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 = 57.2 bits (137), Expect = 6e-09
 Identities = 57/404 (14%), Positives = 122/404 (30%), Gaps = 127/404 (31%)

Query: 6   LINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGK 65
           L  E ++HI+   D V                                 L  W +    +
Sbjct: 46  LSKEEIDHIIMSKDAVSG----------------------------TLRL-FWTLLSKQE 76

Query: 66  TTIARAIFDKISGDFDGSCFL-ENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNF 124
             + + + + +  ++    FL   ++ E + P  ++ +  +    L  D     +   N 
Sbjct: 77  EMVQKFVEEVLRINYK---FLMSPIKTEQRQPSMMTRMYIEQRDRLYND--NQVFAKYNV 131

Query: 125 RRLGHMKVLIVFDDVTCFSQLESL-------MG----SLDWLTPVSRIILTTRNKQVLRN 173
            RL     L          +L          +     +  W+      +    + +V   
Sbjct: 132 SRLQPYLKLR-----QALLELRPAKNVLIDGVLGSGKT--WVA-----LDVCLSYKVQCK 179

Query: 174 ------WRVNAFKRNHPDV---GNEKLSSNVMK-------YAQGVPLALKVLVWESAISK 217
                 W +N    N P+      +KL   +         ++  + L +      S  ++
Sbjct: 180 MDFKIFW-LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI-----HSIQAE 233

Query: 218 LQRIL----HPSILEVLKISYDSLEDKEK-NIFLDVAC-------------FFQGEHVDP 259
           L+R+L    + + L VL     ++++ +  N F +++C             F        
Sbjct: 234 LRRLLKSKPYENCLLVL----LNVQNAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTH 288

Query: 260 VMKFFNASGFYPEIRISVLVDKPLIAICSYKKIRMRDLLQE----------LGGEIVRKE 309
           +    ++    P+   S+L+         Y   R +DL +E          +  E +R  
Sbjct: 289 ISLDHHSMTLTPDEVKSLLL--------KYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340

Query: 310 SINPGNRKQGQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKF 353
                N K        C  ++ +IE  LN     +  +  F + 
Sbjct: 341 LATWDNWKHVN-----CDKLTTIIESSLNVLEPAEY-RKMFDRL 378

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 95.4 bits (237), Expect = 1e-21
 Identities = 54/399 (13%), Positives = 126/399 (31%), Gaps = 81/399 (20%)

Query: 30  QLVGVESTVEEI-ESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK----ISGDFDGSC 84
                E  V+ + + L  +     + L + G  G GK+ IA     K    I  ++D   
Sbjct: 129 TCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIV 188

Query: 85  FLENVRE-ESQIPGGLSCLRQKL--------LSNLLKDKNVMPYIDLNFRRLGHMKVLIV 135
           +L++            + +   L          ++    +V+    +    +     L V
Sbjct: 189 WLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFV 248

Query: 136 FDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN------------------WRV- 176
           FDDV    Q E++           R ++TTR+ ++                     +   
Sbjct: 249 FDDV---VQEETI---RWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFL 302

Query: 177 --NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL----------VWESAISKLQRIL-- 222
                     +   E + +  ++ + G P  L +                 +KL+     
Sbjct: 303 EAYGMPMPVGEK-EEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLV 361

Query: 223 ---------HPSILEVLKISYDSLEDKEKNIFLDVACFFQGEHVDPVMKFFNASGFYPEI 273
                    + S+   L+   + L D++++          G                 +I
Sbjct: 362 GVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGV----------------DI 405

Query: 274 RISVLVDKPLIAICSYKKIRMRDLLQELGGEIVRKESINPGNRKQGQ--KIEDICLDMSK 331
            + +      + ICS ++ ++ D + +    + ++ ++  G R      KI+ I     K
Sbjct: 406 PVKLWSCVIPVDICSNEEEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLK 465

Query: 332 VIEICLNTSTFTKMPKLRFLKFYSSSFNGENKCKISYLQ 370
            +      +    + + R L+  +++ +   +   S+ Q
Sbjct: 466 HVVDAQTIANGISILEQRLLEIGNNNVSVPERHIPSHFQ 504

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 85.7 bits (212), Expect = 2e-18
 Identities = 50/273 (18%), Positives = 97/273 (35%), Gaps = 61/273 (22%)

Query: 31  LVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIF---DKISGDFDGSCFLE 87
            V  +  V  I+  L         + I G+ G GK+ +A         + G F G     
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 88  NVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLG----------HMKVLIVFD 137
           +V ++ +  G L  L+  L + L +D++    + LN               H + L++ D
Sbjct: 186 SVGKQDKS-GLLMKLQ-NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILD 243

Query: 138 DVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN-------------------WRVNA 178
           DV            L       +I+LTTR+K V  +                     + +
Sbjct: 244 DV-------WDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILS 296

Query: 179 FKRNHPDVGNEKLSSNVMKYAQGVPLALKVL---------VWESAISKLQRIL------- 222
              N       + + +++K  +G PL + ++          WE  + +LQ          
Sbjct: 297 LFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKS 356

Query: 223 ----HPSILEVLKISYDSLEDKEKNIFLDVACF 251
               + ++ E + IS + L +  K+ + D++  
Sbjct: 357 SSYDYEALDEAMSISVEMLREDIKDYYTDLSIL 389

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 69.1 bits (169), Expect = 9e-13
 Identities = 48/270 (17%), Positives = 93/270 (34%), Gaps = 61/270 (22%)

Query: 32  VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAI---FDKISGDFDGSCFLEN 88
           V  +  V  I+  L   +     + I+G+ G GK+ +A         + G F G     +
Sbjct: 127 VTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS 186

Query: 89  VREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLG----------HMKVLIVFDD 138
           + +  Q   GL    Q L   L ++++    + LN               H + L++ DD
Sbjct: 187 IGK--QDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD 244

Query: 139 VTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN-------------------AF 179
           V     +      L       +I+LTTR+K V  +                       + 
Sbjct: 245 V-WDPWV------LKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSL 297

Query: 180 KRNHPDVGNEKLSSNVMKYAQGVPLALKV---LVWE-----------------SAISKLQ 219
             N         + +++K  +G PL + +   L+ +                   I K  
Sbjct: 298 FVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSS 357

Query: 220 RILHPSILEVLKISYDSLEDKEKNIFLDVA 249
              + ++ E + IS + L +  K+ + D++
Sbjct: 358 SYDYEALDEAMSISVEMLREDIKDYYTDLS 387

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	385
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.71
2fna_A	357	Conserved hypothetical protein; structural genomic	99.68
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.66
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.49
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.48
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.42
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.42
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.16
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.1
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.97
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.78
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.77
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.73
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.69
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.67
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.65
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.63
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.55
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.5
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.46
3bos_A	242	Putative DNA replication factor; P-loop containing	98.45
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.42
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.42
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.38
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.35
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.31
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.3
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.28
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.27
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.27
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.24
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.23
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.22
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.21
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.19
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.19
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.17
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.16
3pvs_A	447	Replication-associated recombination protein A; ma	98.14
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.14
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.11
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.07
3co5_A	143	Putative two-component system transcriptional RES	98.02
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.01
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.99
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.98
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.96
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.96
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.94
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.93
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.91
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.9
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.86
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.85
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.83
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.82
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.81
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.77
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.73
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.61
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.6
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.59
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.56
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.49
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.48
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.44
2qgz_A	308	Helicase loader, putative primosome component; str	97.4
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.39
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.3
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.25
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.21
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.19
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.16
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.12
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.1
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.07
2r44_A	331	Uncharacterized protein; putative ATPase, structur	97.06
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.06
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.05
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.04
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.03
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.03
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.01
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.01
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	97.0
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.95
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.94
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.94
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.93
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.86
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.85
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.82
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.8
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.79
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.79
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.75
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.72
3io5_A	333	Recombination and repair protein; storage dimer, i	96.7
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	96.7
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.69
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.65
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.64
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.64
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.63
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.63
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.62
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.62
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.61
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.61
2xxa_A	433	Signal recognition particle protein; protein trans	96.6
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.6
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.6
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.59
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.58
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.57
3ice_A	422	Transcription termination factor RHO; transcriptio	96.57
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.56
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.56
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.52
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.5
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.48
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.48
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.47
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.47
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.47
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.44
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.43
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.43
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.42
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.42
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.42
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.41
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.41
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.4
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.39
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.38
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.38
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.37
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.36
2og2_A	359	Putative signal recognition particle receptor; nuc	96.35
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	96.35
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.34
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.33
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.33
2hf9_A	226	Probable hydrogenase nickel incorporation protein	96.33
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.32
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.31
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.31
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.29
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.29
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	96.28
3fwy_A	314	Light-independent protochlorophyllide reductase I	96.28
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.28
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.27
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.27
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.26
1tue_A	212	Replication protein E1; helicase, replication, E1E	96.24
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.24
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.24
1via_A	175	Shikimate kinase; structural genomics, transferase	96.24
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.22
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.21
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.2
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.2
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.19
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	96.19
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.19
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	96.18
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.16
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.15
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.14
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.14
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	96.13
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.12
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.11
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.11
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.11
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.09
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.08
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.07
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.06
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.06
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.06
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.0
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.0
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.0
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.99
3e6j_A	229	Variable lymphocyte receptor diversity region; var	95.99
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.99
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.99
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.98
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.98
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.98
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.97
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.97
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.96
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.96
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.93
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.92
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.91
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.9
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.88
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.87
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.87
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	95.84
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.83
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	95.83
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	95.83
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.83
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.82
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.81
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.8
3end_A	307	Light-independent protochlorophyllide reductase ir	95.77
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	95.76
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.75
3e6j_A	229	Variable lymphocyte receptor diversity region; var	95.75
3l0o_A	427	Transcription termination factor RHO; helicase, RH	95.74
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.74
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.72
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.69
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.69
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	95.68
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.67
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.66
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	95.65
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.64
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	95.64
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.63
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.63
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.61
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	95.61
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	95.61
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.6
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.59
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	95.59
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.58
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.58
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	95.58
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.58
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.57
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.57
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.56
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	95.54
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.54
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	95.53
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	95.53
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.53
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	95.5
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.49
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.49
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	95.48
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	95.47
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.47
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	95.46
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.44
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.43
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.43
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.42
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.42
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.39
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.39
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	95.38
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	95.38
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.37
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.36
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.36
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.33
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	95.32
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.31
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.31
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.3
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.29
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	95.28
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.28
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.27
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	95.24
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	95.24
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.23
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.22
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	95.19
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	95.17
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	95.17
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	95.16
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.14
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	95.12
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.11
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	95.11
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	95.1
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	95.1
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	95.09
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.07
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	95.07
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	95.05
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	95.04
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.03
3m19_A	251	Variable lymphocyte receptor A diversity region; a	95.03
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	95.03
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	95.01
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.01
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	95.0
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.0
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	95.0
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	94.99
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.98
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	94.94
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	94.92
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	94.92
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	94.91
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.89
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.88
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.87
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	94.86
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	94.85
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	94.82
2wji_A	165	Ferrous iron transport protein B homolog; membrane	94.81
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	94.8
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	94.8
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	94.77
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.76
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	94.75
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	94.74
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	94.74
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.73
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	94.73
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	94.72
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.72
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	94.71
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	94.7
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	94.69
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.69
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	94.68
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	94.66
3m19_A	251	Variable lymphocyte receptor A diversity region; a	94.66
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.66
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	94.65
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.65
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	94.64
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	94.64
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	94.63
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.62
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	94.61
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	94.59
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.57
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	94.54
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.54
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	94.54
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	94.53
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	94.49
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	94.48
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	94.47
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	94.46
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	94.46
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.43
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.43
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.41
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.4
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	94.4
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	94.4
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.39
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	94.37
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	94.36
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	94.35
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.35
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	94.34
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	94.34
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	94.32
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	94.32
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	94.32
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.31
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.31
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.29
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.28
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.28
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	94.27
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	94.26
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	94.25
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	94.24
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	94.24
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.23
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.22
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	94.2
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	94.2
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.19
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	94.18
1nrj_B	218	SR-beta, signal recognition particle receptor beta	94.18
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	94.17
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.17
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	94.17
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.17
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.16
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	94.15
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	94.15
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.14
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.14
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	94.13
1g6h_A	257	High-affinity branched-chain amino acid transport	94.13
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.13
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	94.13
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	94.12
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	94.12
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.11
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	94.11
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	94.11
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.1
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	94.1
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	94.1
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	94.1
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.09
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	94.07
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	94.07
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.06
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.06
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.05
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	94.04
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	94.02
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	94.01
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	93.99
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.99
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	93.99
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	93.99
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.98
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	93.98
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.97
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	93.97
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	93.95
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.94
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	93.94
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	93.93
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.93
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.92
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	93.92
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.92
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	93.91
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	93.9
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	93.89
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	93.87
3cwq_A	209	Para family chromosome partitioning protein; alpha	93.87
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.87
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.86
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.85
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	93.84
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.83
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.83
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.83
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	93.82
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.82
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.82
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	93.81
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	93.8
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	93.79
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.79
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	93.78
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.77
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	93.76
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.76
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.74
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	93.74
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	93.74
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	93.73
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	93.73
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	93.71
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.7
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	93.69
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	93.69
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	93.69
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	93.69
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.69
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	93.68
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	93.68
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	93.68
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	93.64
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	93.64
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	93.64
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	93.63
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	93.63
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.61
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	93.61
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	93.59
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	93.57
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.57
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	93.56
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.55
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	93.54
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.53
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	93.53
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	93.52
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.52
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	93.52
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	93.51
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.51
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	93.5
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.5
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	93.5
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	93.48

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=1.4e-42  Score=344.94  Aligned_cols=266  Identities=16%  Similarity=0.154  Sum_probs=209.6

Q ss_pred             cccchhHHHHHHhhcCC-CCCeEEEEEEcCCCchHHHHHHHHHH----HhhCCCCceEEEeeccccccCCCChHHHHHHH
Q 044214           32 VGVESTVEEIESLLGVE-SKGVYALGIWGIGGIGKTTIARAIFD----KISGDFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~-~~~~~vv~I~G~gGiGKTtLA~~~~~----~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      |||+.++++|.++|..+ .+..++|+|+|||||||||||+++|+    +++.+|++++|++ +++...  ++...++..+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~-vs~~~~--~~~~~~~~~i  207 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK-DSGTAP--KSTFDLFTDI  207 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE-CCCCST--THHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEE-ECCCCC--CCHHHHHHHH
Confidence            59999999999999753 34689999999999999999999996    6889999999996 433211  3688999999


Q ss_pred             HHHHhCCCC-----CC------chHHHHHHHhCCc-eEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHHHhhc
Q 044214          107 LSNLLKDKN-----VM------PYIDLNFRRLGHM-KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNW  174 (385)
Q Consensus       107 l~~l~~~~~-----~~------~~~~~l~~~l~~k-~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~  174 (385)
                      +.+++....     ..      .....+++.|+++ |+||||||||+.+++ .+..     .+||+||||||++.++..+
T Consensus       208 l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~  281 (549)
T 2a5y_B          208 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAA  281 (549)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGC
T ss_pred             HHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHc
Confidence            999986532     11      2478899999996 999999999998876 2222     2799999999999888766


Q ss_pred             c-c--------------------eecccCCCCCCchHHHHHHHHHhCCCccchhHH-------hHHHHHHHhh----hcc
Q 044214          175 R-V--------------------NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL-------VWESAISKLQ----RIL  222 (385)
Q Consensus       175 ~-~--------------------~~~~~~~~~~~~~~~~~~i~~~~~GlPLal~~~-------~w~~~l~~l~----~~~  222 (385)
                      + .                    .+|.... .+...+++++|+++|+|+||||+++       .|... +.+.    ...
T Consensus       282 ~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~-~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~w~~~-~~l~~~l~~~~  359 (549)
T 2a5y_B          282 SQTCEFIEVTSLEIDECYDFLEAYGMPMPV-GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKM-AQLNNKLESRG  359 (549)
T ss_dssp             CSCEEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHH-HHHHHHHHHHC
T ss_pred             CCCCeEEECCCCCHHHHHHHHHHHhcCCCC-chhHHHHHHHHHHHhCCChHHHHHHHHHhccchHHHH-HHhHHHhhccc
Confidence            3 1                    2232221 2456778999999999999999999       56543 3332    224


Q ss_pred             CcccchhhhhccccCchhhhhhhh-----------hccccCCCccHHHHHHHHHHc--CCch-----------hhhHHHh
Q 044214          223 HPSILEVLKISYDSLEDKEKNIFL-----------DVACFFQGEHVDPVMKFFNAS--GFYP-----------EIRISVL  278 (385)
Q Consensus       223 ~~~~~~~l~~sy~~L~~~~k~~~~-----------~la~fp~~~~~~~l~~~~~~~--g~~~-----------~~~l~~L  278 (385)
                      ...+..++.+||+.||++.|.||+           |||+||++++..  +.+|+++  |++.           .+++++|
T Consensus       360 ~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~--i~~w~a~~~G~i~~~~~~~~~~~~~~~l~~L  437 (549)
T 2a5y_B          360 LVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP--VKLWSCVIPVDICSNEEEQLDDEVADRLKRL  437 (549)
T ss_dssp             SSTTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE--HHHHHHHSCC-------CCCTHHHHHHHHHT
T ss_pred             HHHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee--eeeeeeeccceeccCCCCCCHHHHHHHHHHH
Confidence            577999999999999999999999           999999986666  7899999  6663           2379999


Q ss_pred             hcCCceeEecC---CcEEeCHHHHHHHHHHHhhcc
Q 044214          279 VDKPLIAICSY---KKIRMRDLLQELGGEIVRKES  310 (385)
Q Consensus       279 ~~~sLi~~~~~---~~~~mH~lv~~~a~~~~~~e~  310 (385)
                      +++|||+....   ++|+|||+||+||++++.+++
T Consensus       438 ~~rsLl~~~~~~~~~~~~mHdlv~~~a~~~~~~~~  472 (549)
T 2a5y_B          438 SKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQT  472 (549)
T ss_dssp             TTBSSCSEEECSSSCEEECCHHHHHHHHTTSCTHH
T ss_pred             HHcCCeeEecCCCceEEEeChHHHHHHHHHHHHHH
Confidence            99999997643   369999999999998876654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=9.3e-39  Score=346.18  Aligned_cols=277  Identities=19%  Similarity=0.238  Sum_probs=218.6

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH---hhCCCCceE-EEeeccccccCCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK---ISGDFDGSC-FLENVREESQIPGG   98 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~---~~~~f~~~~-w~~~~~~~~~~~~~   98 (385)
                      .+|..++.||||++++++|.++|...++.+++|+|+||||+||||||++++++   ...+|...+ |+. ++....  ..
T Consensus       118 ~~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~-~~~~~~--~~  194 (1249)
T 3sfz_A          118 GVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS-IGKQDK--SG  194 (1249)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEE-CCSCCH--HH
T ss_pred             CCCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEE-ECCcCc--hH
Confidence            34667788999999999999999766677899999999999999999999985   456676666 554 443211  33


Q ss_pred             hHHHHHHHHHHHhCCCCC---C-----chHHHHHHHhCCc--eEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214           99 LSCLRQKLLSNLLKDKNV---M-----PYIDLNFRRLGHM--KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~---~-----~~~~~l~~~l~~k--~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ....+..++..+......   .     .....++..+.++  |+||||||+|+..+|..+       ++||+||||||++
T Consensus       195 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~  267 (1249)
T 3sfz_A          195 LLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDK  267 (1249)
T ss_dssp             HHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESST
T ss_pred             HHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCH
Confidence            445566677776654321   1     5666777778776  999999999998877664       5789999999999


Q ss_pred             HHHhhcc-c----------------eeccc--CCCCCCchHHHHHHHHHhCCCccchhHH---------hHHHHHHHhhh
Q 044214          169 QVLRNWR-V----------------NAFKR--NHPDVGNEKLSSNVMKYAQGVPLALKVL---------VWESAISKLQR  220 (385)
Q Consensus       169 ~~~~~~~-~----------------~~~~~--~~~~~~~~~~~~~i~~~~~GlPLal~~~---------~w~~~l~~l~~  220 (385)
                      .++..+. .                ..|..  ....+...+.+++|+++|+|+||||+++         .|...++.+..
T Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~~~~~~~l~~l~~  347 (1249)
T 3sfz_A          268 SVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQN  347 (1249)
T ss_dssp             TTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSSSCHHHHHHHHHS
T ss_pred             HHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcChhHHHHHHHHHhh
Confidence            8874321 1                11111  1223456678999999999999999999         78888888765


Q ss_pred             ccC-----------cccchhhhhccccCchhhhhhhhhccccCCC--ccHHHHHHHHHHcCCchhhhHHHhhcCCceeEe
Q 044214          221 ILH-----------PSILEVLKISYDSLEDKEKNIFLDVACFFQG--EHVDPVMKFFNASGFYPEIRISVLVDKPLIAIC  287 (385)
Q Consensus       221 ~~~-----------~~~~~~l~~sy~~L~~~~k~~~~~la~fp~~--~~~~~l~~~~~~~g~~~~~~l~~L~~~sLi~~~  287 (385)
                      ...           ..+..++.+||+.|++++|.||++||+||++  ++.+.++.+|.+++..++.++++|+++|||+..
T Consensus       348 ~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~~~~~~~~l~~L~~~sl~~~~  427 (1249)
T 3sfz_A          348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLLFCN  427 (1249)
T ss_dssp             CCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEE
T ss_pred             hhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCCHHHHHHHHHHHHhccceEEe
Confidence            332           3488999999999999999999999999987  788999999988877888999999999999987


Q ss_pred             cCCc---EEeCHHHHHHHHHHHhhc
Q 044214          288 SYKK---IRMRDLLQELGGEIVRKE  309 (385)
Q Consensus       288 ~~~~---~~mH~lv~~~a~~~~~~e  309 (385)
                      .++.   |+||++||+||++.+.++
T Consensus       428 ~~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          428 RNGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             ESSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             cCCCceEEEecHHHHHHHHhhhhHH
Confidence            6664   999999999999987766

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=3.8e-36  Score=301.99  Aligned_cols=274  Identities=20%  Similarity=0.221  Sum_probs=204.3

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh---hCCCC-ceEEEeeccccccCCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI---SGDFD-GSCFLENVREESQIPGG   98 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~---~~~f~-~~~w~~~~~~~~~~~~~   98 (385)
                      ..|..++.||||+.++++|.++|...+++.++|+|+||||+||||||.+++++.   +.+|+ .++|++ ++....  ..
T Consensus       118 ~~P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~-~~~~~~--~~  194 (591)
T 1z6t_A          118 GVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVS-VGKQDK--SG  194 (591)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEE-EESCCH--HH
T ss_pred             CCCCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEE-CCCCch--HH
Confidence            345677889999999999999998655678999999999999999999999743   67895 577776 332211  11


Q ss_pred             hHHHHHHHHHHHhCCC------CCC--chHHHHHHHhCC--ceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214           99 LSCLRQKLLSNLLKDK------NVM--PYIDLNFRRLGH--MKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~------~~~--~~~~~l~~~l~~--k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      +...+..+...+....      ...  .....+...+.+  +++||||||+|+...++.+       ++|++||||||+.
T Consensus       195 ~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~  267 (591)
T 1z6t_A          195 LLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDK  267 (591)
T ss_dssp             HHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCG
T ss_pred             HHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCc
Confidence            2222233344444211      111  455666776665  7899999999997766543       4689999999999


Q ss_pred             HHHhhccc-----------------eecccC--CCCCCchHHHHHHHHHhCCCccchhHH---------hHHHHHHHhhh
Q 044214          169 QVLRNWRV-----------------NAFKRN--HPDVGNEKLSSNVMKYAQGVPLALKVL---------VWESAISKLQR  220 (385)
Q Consensus       169 ~~~~~~~~-----------------~~~~~~--~~~~~~~~~~~~i~~~~~GlPLal~~~---------~w~~~l~~l~~  220 (385)
                      .++..+..                 ..|...  .+.....+.+.+|+++|+|+||||+++         .|...++.+..
T Consensus       268 ~~~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~~~w~~~l~~l~~  347 (591)
T 1z6t_A          268 SVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQN  347 (591)
T ss_dssp             GGGTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHSTTCHHHHHHHHHS
T ss_pred             HHHHhcCCCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHHHHHHhcCchhHHHHHHHHHH
Confidence            87654321                 111110  111233567899999999999999998         59888888764


Q ss_pred             ccC-----------cccchhhhhccccCchhhhhhhhhccccCCC--ccHHHHHHHHHHcCCchhhhHHHhhcCCceeEe
Q 044214          221 ILH-----------PSILEVLKISYDSLEDKEKNIFLDVACFFQG--EHVDPVMKFFNASGFYPEIRISVLVDKPLIAIC  287 (385)
Q Consensus       221 ~~~-----------~~~~~~l~~sy~~L~~~~k~~~~~la~fp~~--~~~~~l~~~~~~~g~~~~~~l~~L~~~sLi~~~  287 (385)
                      ...           .++..++..||+.||++.|.||.++|+||.+  ++.+.+..+|..++.....++++|+++|||+..
T Consensus       348 ~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~~~~~~~~l~~L~~~~Ll~~~  427 (591)
T 1z6t_A          348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCD  427 (591)
T ss_dssp             CCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEE
T ss_pred             hHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccCHHHHHHHHHHHHhCcCeEEe
Confidence            321           3578899999999999999999999999876  788899999987655677889999999999976


Q ss_pred             cCC---cEEeCHHHHHHHHHHH
Q 044214          288 SYK---KIRMRDLLQELGGEIV  306 (385)
Q Consensus       288 ~~~---~~~mH~lv~~~a~~~~  306 (385)
                      .++   +|+||+++|+++++..
T Consensus       428 ~~~~~~~~~~H~lv~~~~~~~~  449 (591)
T 1z6t_A          428 RNGKSFRYYLHDLQVDFLTEKN  449 (591)
T ss_dssp             EETTEEEEECCHHHHHHHHHHT
T ss_pred             cCCCccEEEEcHHHHHHHHhhh
Confidence            433   6999999999999873

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=2.4e-34  Score=292.30  Aligned_cols=258  Identities=16%  Similarity=0.120  Sum_probs=187.1

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH--HhhCCCCc-eEEEeeccccccCCCChHHHHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD--KISGDFDG-SCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~--~~~~~f~~-~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      +..|||+.++++|.++|... +..++|+|+||||+||||||+++++  +++.+|+. ++|++ ++.   . .+...++..
T Consensus       128 k~~VGRe~eLeeL~elL~~~-d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVs-Vs~---~-~d~~~IL~~  201 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN-LKN---C-NSPETVLEM  201 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHHC-CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEE-CCC---S-SSHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhcc-CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEE-eCC---C-CCHHHHHHH
Confidence            34599999999999999742 3478999999999999999999997  57888997 67776 433   3 666677777


Q ss_pred             HHHHHhCCC------CC----C-----chHHHHHHHh---CCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEecc
Q 044214          106 LLSNLLKDK------NV----M-----PYIDLNFRRL---GHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       106 ll~~l~~~~------~~----~-----~~~~~l~~~l---~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      ++..+....      .+    .     .....+++.|   .++|+||||||+|+.+.|+.+.       +||+||||||+
T Consensus       202 Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd  274 (1221)
T 1vt4_I          202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRF  274 (1221)
T ss_dssp             HHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSC
T ss_pred             HHHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccC
Confidence            666432211      01    0     3345666655   6899999999999998888762       68999999999


Q ss_pred             HHHHhhccc------e------ecccCC--------CCCCchHHHHHHHHHhCCCccchhHH--hHHHH---HHHhhhcc
Q 044214          168 KQVLRNWRV------N------AFKRNH--------PDVGNEKLSSNVMKYAQGVPLALKVL--VWESA---ISKLQRIL  222 (385)
Q Consensus       168 ~~~~~~~~~------~------~~~~~~--------~~~~~~~~~~~i~~~~~GlPLal~~~--~w~~~---l~~l~~~~  222 (385)
                      +.++..+..      .      .+....        ......++..   +.|+|+||||+++  .....   .+......
T Consensus       275 ~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~---eICgGLPLALkLaGs~Lr~k~~s~eeW~~~~  351 (1221)
T 1vt4_I          275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLTTNPRRLSIIAESIRDGLATWDNWKHVN  351 (1221)
T ss_dssp             SHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHH---HHCCCCHHHHHHHHHHHHHSCSSHHHHHHCS
T ss_pred             hHHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHH---HHhCCCHHHHHHHHHHHhCCCCCHHHHhcCC
Confidence            988753221      1      111000        0001122333   3499999999998  11000   01111123


Q ss_pred             CcccchhhhhccccCchhh-hhhhhhccccCCC--ccHHHHHHHHHHcCC-chhhhHHHhhcCCceeEec-CCcEEeCHH
Q 044214          223 HPSILEVLKISYDSLEDKE-KNIFLDVACFFQG--EHVDPVMKFFNASGF-YPEIRISVLVDKPLIAICS-YKKIRMRDL  297 (385)
Q Consensus       223 ~~~~~~~l~~sy~~L~~~~-k~~~~~la~fp~~--~~~~~l~~~~~~~g~-~~~~~l~~L~~~sLi~~~~-~~~~~mH~l  297 (385)
                      ...+..++.+||+.||+++ |.||++||+||++  ++.+.+..+|.++|. .++.++++|+++|||+... .++|+|||+
T Consensus       352 ~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeGeedAe~~L~eLvdRSLLq~d~~~~rYrMHDL  431 (1221)
T 1vt4_I          352 CDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI  431 (1221)
T ss_dssp             CHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSCSHHHHHHHHHHHTSSSSSBCSSSSEEBCCCH
T ss_pred             hhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHhhCCEEEeCCCCEEEehHH
Confidence            4679999999999999999 9999999999986  677889999998863 3677899999999999863 567999999


Q ss_pred             HHHHH
Q 044214          298 LQELG  302 (385)
Q Consensus       298 v~~~a  302 (385)
                      +++++
T Consensus       432 llELr  436 (1221)
T 1vt4_I          432 YLELK  436 (1221)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99855

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.71  E-value=1.5e-17  Score=155.41  Aligned_cols=264  Identities=15%  Similarity=0.127  Sum_probs=156.0

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccc--cCCCChH
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREES--QIPGGLS  100 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~--~~~~~~~  100 (385)
                      .++..++.|+||+.++++|.+++..+    +++.|+|++|+|||+|+++++++..     .+|+. .....  ....+..
T Consensus         6 ~~~~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~~-----~~~~~-~~~~~~~~~~~~~~   75 (350)
T 2qen_A            6 RPKTRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNERP-----GILID-CRELYAERGHITRE   75 (350)
T ss_dssp             SCCCSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHSS-----EEEEE-HHHHHHTTTCBCHH
T ss_pred             CCCCChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHcC-----cEEEE-eecccccccCCCHH
Confidence            45667788999999999999998742    5899999999999999999998751     56665 22211  0002445


Q ss_pred             HHHHHHHHHHhC-----------------CCC----CC-chHHHHHHHhCC-ceEEEEEeCCCChh--------hhhHhh
Q 044214          101 CLRQKLLSNLLK-----------------DKN----VM-PYIDLNFRRLGH-MKVLIVFDDVTCFS--------QLESLM  149 (385)
Q Consensus       101 ~l~~~ll~~l~~-----------------~~~----~~-~~~~~l~~~l~~-k~~LlVlDdv~~~~--------~~~~l~  149 (385)
                      .++..+...+..                 ..+    .. +....+.+.... ++++||+||++...        .+..++
T Consensus        76 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L  155 (350)
T 2qen_A           76 ELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALF  155 (350)
T ss_dssp             HHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHH
Confidence            555555544321                 000    01 233344444432 38999999996532        222222


Q ss_pred             ccCCCCCCCcEEEEEeccHHHHhhc----c-----------c------------eeccc---CCCCCCchHHHHHHHHHh
Q 044214          150 GSLDWLTPVSRIILTTRNKQVLRNW----R-----------V------------NAFKR---NHPDVGNEKLSSNVMKYA  199 (385)
Q Consensus       150 ~~~~~~~~gs~ilvTtR~~~~~~~~----~-----------~------------~~~~~---~~~~~~~~~~~~~i~~~~  199 (385)
                      ..+....++.++|+|++........    .           .            ..+..   ........+.+.++++.|
T Consensus       156 ~~~~~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~t  235 (350)
T 2qen_A          156 AYAYDSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELL  235 (350)
T ss_dssp             HHHHHHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence            2221112477899998876432211    0           0            00000   011112356788999999


Q ss_pred             CCCccchhHH---hHH-----HHHHHhhhccCcccchhhhhccccC---chhhhhhhhhccccCCCccHHHHHHHHHHc-
Q 044214          200 QGVPLALKVL---VWE-----SAISKLQRILHPSILEVLKISYDSL---EDKEKNIFLDVACFFQGEHVDPVMKFFNAS-  267 (385)
Q Consensus       200 ~GlPLal~~~---~w~-----~~l~~l~~~~~~~~~~~l~~sy~~L---~~~~k~~~~~la~fp~~~~~~~l~~~~~~~-  267 (385)
                      +|+|+++..+   .|.     .....+.    +.+...+...+..+   ++..+.++..+|+ . ..+...+...+... 
T Consensus       236 gG~P~~l~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~l~~l~~~~~~~~~~l~~la~-g-~~~~~~l~~~~~~~~  309 (350)
T 2qen_A          236 DGIPGWLVVFGVEYLRNGDFGRAMKRTL----EVAKGLIMGELEELRRRSPRYVDILRAIAL-G-YNRWSLIRDYLAVKG  309 (350)
T ss_dssp             TTCHHHHHHHHHHHHHHCCHHHHHHHHH----HHHHHHHHHHHHHHHHHCHHHHHHHHHHHT-T-CCSHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHhccccHhHHHHHHH----HHHHHHHHHHHHHHHhCChhHHHHHHHHHh-C-CCCHHHHHHHHHHHh
Confidence            9999999876   122     1111110    11222222233344   7888999999988 3 35666666655322 


Q ss_pred             -CCc---hhhhHHHhhcCCceeEecCCcEE-eCHHHHHHHH
Q 044214          268 -GFY---PEIRISVLVDKPLIAICSYKKIR-MRDLLQELGG  303 (385)
Q Consensus       268 -g~~---~~~~l~~L~~~sLi~~~~~~~~~-mH~lv~~~a~  303 (385)
                       +..   ...+++.|.+.+||... ++.|. .|++++++.+
T Consensus       310 ~~~~~~~~~~~l~~L~~~gli~~~-~~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          310 TKIPEPRLYALLENLKKMNWIVEE-DNTYKIADPVVATVLR  349 (350)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEEE-TTEEEESSHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHhCCCEEec-CCEEEEecHHHHHHHc
Confidence             232   35679999999999987 45554 5788888754

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.68  E-value=5e-16  Score=145.35  Aligned_cols=262  Identities=15%  Similarity=0.158  Sum_probs=147.9

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccc--cCCCChH
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREES--QIPGGLS  100 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~--~~~~~~~  100 (385)
                      .++..++.|+||+++++.|.+ +..     +++.|+|++|+|||+|+++++++...   ..+|+. .....  .. .+..
T Consensus         7 ~~~~~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~~~~---~~~~~~-~~~~~~~~~-~~~~   75 (357)
T 2fna_A            7 SPKDNRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINELNL---PYIYLD-LRKFEERNY-ISYK   75 (357)
T ss_dssp             SCCCSGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHHHTC---CEEEEE-GGGGTTCSC-CCHH
T ss_pred             CCCCCHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHhcCC---CEEEEE-chhhccccC-CCHH
Confidence            455667889999999999999 763     58999999999999999999988753   256665 32210  00 2233


Q ss_pred             HHHHHHHHHHh-------------CC-------CC---------CCchHHHHHHHhCC---ceEEEEEeCCCCh-----h
Q 044214          101 CLRQKLLSNLL-------------KD-------KN---------VMPYIDLNFRRLGH---MKVLIVFDDVTCF-----S  143 (385)
Q Consensus       101 ~l~~~ll~~l~-------------~~-------~~---------~~~~~~~l~~~l~~---k~~LlVlDdv~~~-----~  143 (385)
                      .+...+...+.             ..       ..         .......+.+.+..   ++++|||||++..     .
T Consensus        76 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~  155 (357)
T 2fna_A           76 DFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGV  155 (357)
T ss_dssp             HHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTC
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCch
Confidence            44444333221             00       00         01122333333321   4999999999542     2


Q ss_pred             hhhHhhccCCCCCCCcEEEEEeccHHHHhhc----c-----------c----------------eecccCCCCCCchHHH
Q 044214          144 QLESLMGSLDWLTPVSRIILTTRNKQVLRNW----R-----------V----------------NAFKRNHPDVGNEKLS  192 (385)
Q Consensus       144 ~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~----~-----------~----------------~~~~~~~~~~~~~~~~  192 (385)
                      ++..++..+....++.++|+|++........    .           .                ..+......  ... .
T Consensus       156 ~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~--~~~-~  232 (357)
T 2fna_A          156 NLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADID--FKD-Y  232 (357)
T ss_dssp             CCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCC--CCC-H
T ss_pred             hHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCC--CCc-H
Confidence            2323332222112467899999976532211    0           0                001000000  011 2


Q ss_pred             HHHHHHhCCCccchhHH---hHH-----HHHHHhhhccCcccchhhh-hcc--ccCchhhhhhhhhccccCCCccHHHHH
Q 044214          193 SNVMKYAQGVPLALKVL---VWE-----SAISKLQRILHPSILEVLK-ISY--DSLEDKEKNIFLDVACFFQGEHVDPVM  261 (385)
Q Consensus       193 ~~i~~~~~GlPLal~~~---~w~-----~~l~~l~~~~~~~~~~~l~-~sy--~~L~~~~k~~~~~la~fp~~~~~~~l~  261 (385)
                      ..+++.|+|+|+++..+   .|.     .....+.......+..-+. ..+  ..|++..+.++..+|+ ..  +...+.
T Consensus       233 ~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~la~-g~--~~~~l~  309 (357)
T 2fna_A          233 EVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSK-CG--KWSDVK  309 (357)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHTT-CB--CHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHc-CC--CHHHHH
Confidence            78999999999999876   121     1111110000000111111 111  1688999999999998 32  566665


Q ss_pred             HHHH-HcC--Cc---hhhhHHHhhcCCceeEecCCcEE-eCHHHHHHH
Q 044214          262 KFFN-ASG--FY---PEIRISVLVDKPLIAICSYKKIR-MRDLLQELG  302 (385)
Q Consensus       262 ~~~~-~~g--~~---~~~~l~~L~~~sLi~~~~~~~~~-mH~lv~~~a  302 (385)
                      .... ..|  ..   ...+++.|.+.+||...+ +.|+ .|++++++.
T Consensus       310 ~~~~~~~g~~~~~~~~~~~L~~L~~~gli~~~~-~~y~f~~~~~~~~l  356 (357)
T 2fna_A          310 RALELEEGIEISDSEIYNYLTQLTKHSWIIKEG-EKYCPSEPLISLAF  356 (357)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHHHTTSEEESS-SCEEESSHHHHHHT
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhCCCEEecC-CEEEecCHHHHHhh
Confidence            4432 223  22   356799999999999874 5555 688988874

>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=99.66  E-value=1e-15  Score=146.29  Aligned_cols=271  Identities=13%  Similarity=0.087  Sum_probs=156.2

Q ss_pred             CCCCCCCCccccchhHHHHHHhh-cC--CC--CCeEEEEE--EcCCCchHHHHHHHHHHHhhCC-----CC-ceEEEeec
Q 044214           23 RPRDNKNQLVGVESTVEEIESLL-GV--ES--KGVYALGI--WGIGGIGKTTIARAIFDKISGD-----FD-GSCFLENV   89 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L-~~--~~--~~~~vv~I--~G~gGiGKTtLA~~~~~~~~~~-----f~-~~~w~~~~   89 (385)
                      .+...++.|+||+.++++|.+++ ..  ..  .....+.|  +|++|+|||+||+++++.....     +. ..+|+. .
T Consensus        16 ~~~~~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~-~   94 (412)
T 1w5s_A           16 DENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN-A   94 (412)
T ss_dssp             STTCCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE-G
T ss_pred             CCccCCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE-C
Confidence            44455688999999999999988 42  11  23456667  9999999999999999876542     23 234554 2


Q ss_pred             cccccCCCChHHHHHHHHHHHhCCCCC--C---chHHHHHHHhC--CceEEEEEeCCCCh--------hhhhHhhccCCC
Q 044214           90 REESQIPGGLSCLRQKLLSNLLKDKNV--M---PYIDLNFRRLG--HMKVLIVFDDVTCF--------SQLESLMGSLDW  154 (385)
Q Consensus        90 ~~~~~~~~~~~~l~~~ll~~l~~~~~~--~---~~~~~l~~~l~--~k~~LlVlDdv~~~--------~~~~~l~~~~~~  154 (385)
                      .   .. .+...++..++..++...+.  .   +....+.+.+.  +++++|||||++..        +.+..+...+..
T Consensus        95 ~---~~-~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~  170 (412)
T 1w5s_A           95 F---NA-PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEE  170 (412)
T ss_dssp             G---GC-CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHH
T ss_pred             C---CC-CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHh
Confidence            2   22 66778888888888654321  1   33455555554  67999999999653        334333332211


Q ss_pred             C---C--CCcEEEEEeccHHHHhhcc-------------c-----------eec----cc-CCCCCCchHHHHHHHHHhC
Q 044214          155 L---T--PVSRIILTTRNKQVLRNWR-------------V-----------NAF----KR-NHPDVGNEKLSSNVMKYAQ  200 (385)
Q Consensus       155 ~---~--~gs~ilvTtR~~~~~~~~~-------------~-----------~~~----~~-~~~~~~~~~~~~~i~~~~~  200 (385)
                      .   +  .+..+|+||+...+.....             .           ..+    .. ........+.+..+++.|+
T Consensus       171 ~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~  250 (412)
T 1w5s_A          171 IPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYG  250 (412)
T ss_dssp             SCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHC
T ss_pred             cccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHH
Confidence            1   2  3455787887654322111             0           011    00 0111233567888999999


Q ss_pred             ------CCccchhHH---hHHHHHHH---------hhhccCccc-chhhhhccccCchhhhhhhhhccccC----CCccH
Q 044214          201 ------GVPLALKVL---VWESAISK---------LQRILHPSI-LEVLKISYDSLEDKEKNIFLDVACFF----QGEHV  257 (385)
Q Consensus       201 ------GlPLal~~~---~w~~~l~~---------l~~~~~~~~-~~~l~~sy~~L~~~~k~~~~~la~fp----~~~~~  257 (385)
                            |+|..+..+   .+......         +........ ...+..++..||+..+.++..++.+.    ..++.
T Consensus       251 ~~~~~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~~~~~~~~l~~l~~~~~~~l~aia~l~~~~~~~~~~  330 (412)
T 1w5s_A          251 EDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINA  330 (412)
T ss_dssp             GGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------CCSSSSSCHHHHHHHHHHHHHHHTTCSSBCH
T ss_pred             HhccCCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccchHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccH
Confidence                  999755544   11111000         000000111 34456677899999999999888753    22555


Q ss_pred             HHHHHHH-----HHcCCc------hhhhHHHhhcCCceeEec-----CCcEEeCHHH
Q 044214          258 DPVMKFF-----NASGFY------PEIRISVLVDKPLIAICS-----YKKIRMRDLL  298 (385)
Q Consensus       258 ~~l~~~~-----~~~g~~------~~~~l~~L~~~sLi~~~~-----~~~~~mH~lv  298 (385)
                      ..+...+     ...|..      ...+++.|.+.+||....     .|+|++|.+.
T Consensus       331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~~~~~~~~g~~~~~~l~  387 (412)
T 1w5s_A          331 GLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLA  387 (412)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEECC-------CCEEEEC
T ss_pred             HHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhCCCEEeecccCCCCCceeEEEeC
Confidence            5443322     222321      246799999999998653     3445555443

>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=99.49  E-value=7.9e-13  Score=125.14  Aligned_cols=280  Identities=13%  Similarity=0.102  Sum_probs=162.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcC----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC-CceEEEeeccccccCCCCh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV----ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF-DGSCFLENVREESQIPGGL   99 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~   99 (385)
                      ...++.++||+.+++++.+++..    ..+..+.+.|+|++|+||||||+.+++...... ...+++. .   ... .+.
T Consensus        13 ~~~p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~-~---~~~-~~~   87 (389)
T 1fnn_A           13 SYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN-G---FIY-RNF   87 (389)
T ss_dssp             TCCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE-T---TTC-CSH
T ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe-C---ccC-CCH
Confidence            34457899999999999998874    222334899999999999999999999876553 3344554 2   222 556


Q ss_pred             HHHHHHHHHHHhCCCCCC-----chHHHHHHHh--CCceEEEEEeCCCC--hhhhhHhhccCCCCC----CCcEEEEEec
Q 044214          100 SCLRQKLLSNLLKDKNVM-----PYIDLNFRRL--GHMKVLIVFDDVTC--FSQLESLMGSLDWLT----PVSRIILTTR  166 (385)
Q Consensus       100 ~~l~~~ll~~l~~~~~~~-----~~~~~l~~~l--~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~----~gs~ilvTtR  166 (385)
                      ..++..++..++......     .....+...+  .+++.+||||+++.  ...+..+...+....    .+..||++|+
T Consensus        88 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~  167 (389)
T 1fnn_A           88 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGH  167 (389)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEES
T ss_pred             HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEEC
Confidence            778888887775533211     3334444444  35689999999964  344555554443211    3667788877


Q ss_pred             cHHHHhhccc--------------------------eeccc-CCCCCCchHHHHHHHHHh---------CCCccchhHH-
Q 044214          167 NKQVLRNWRV--------------------------NAFKR-NHPDVGNEKLSSNVMKYA---------QGVPLALKVL-  209 (385)
Q Consensus       167 ~~~~~~~~~~--------------------------~~~~~-~~~~~~~~~~~~~i~~~~---------~GlPLal~~~-  209 (385)
                      ..........                          ..+.. .......++..+.+++.+         +|.|..+..+ 
T Consensus       168 ~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l  247 (389)
T 1fnn_A          168 NDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDIL  247 (389)
T ss_dssp             STHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHH
T ss_pred             CchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHH
Confidence            6533222110                          11110 011123456778899999         7887655433 


Q ss_pred             --hHHHHHHHh-hhccCcc--------cchhhhhccccCchhhhhhhhhccccC---C--CccHHHHHHHHHH----cCC
Q 044214          210 --VWESAISKL-QRILHPS--------ILEVLKISYDSLEDKEKNIFLDVACFF---Q--GEHVDPVMKFFNA----SGF  269 (385)
Q Consensus       210 --~w~~~l~~l-~~~~~~~--------~~~~l~~sy~~L~~~~k~~~~~la~fp---~--~~~~~~l~~~~~~----~g~  269 (385)
                        .|......- .....+.        ....+...+..|+++.+.++..++.+.   .  .+....+...+..    .|.
T Consensus       248 ~~a~~~a~~~~~~~i~~~~v~~~~~~~~~~~~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  327 (389)
T 1fnn_A          248 YRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGE  327 (389)
T ss_dssp             HHHHHHHHHTTCSSCCHHHHHHHHHHHSCCCCHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHHHHhhhhHHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHHHcCC
Confidence              221111000 0000011        123344456789999998888887654   2  3555555544433    222


Q ss_pred             c------hhhhHHHhhcCCceeEecC-------CcE-------EeCHHHHHHHHHHHhhc
Q 044214          270 Y------PEIRISVLVDKPLIAICSY-------KKI-------RMRDLLQELGGEIVRKE  309 (385)
Q Consensus       270 ~------~~~~l~~L~~~sLi~~~~~-------~~~-------~mH~lv~~~a~~~~~~e  309 (385)
                      .      ...+++.|.++++|.....       |++       ..|+++..+...+..+|
T Consensus       328 ~~~~~~~~~~~l~~L~~~gli~~~~~~~~~g~~g~~~~~~l~~~~~~v~~~~~~~~~~~~  387 (389)
T 1fnn_A          328 RPRVHSQLWSYLNDLREKGIVETRQNKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKEE  387 (389)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSSEEEEC---------CEEEECCSSCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhCCCeEEeeeccCCCCCCceeEEEeCCCHHHHHHHHHHHHHHHh
Confidence            1      2357999999999997533       322       24566666665555443

>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=99.48  E-value=6.3e-13  Score=125.72  Aligned_cols=250  Identities=16%  Similarity=0.088  Sum_probs=145.1

Q ss_pred             CCCccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC--------CCceEEEeeccccccCCC
Q 044214           28 KNQLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGD--------FDGSCFLENVREESQIPG   97 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~--------f~~~~w~~~~~~~~~~~~   97 (385)
                      ++.|+||+.+++++.+++..  .....+.+.|+|++|+|||+||+.+++.+...        ....+|+. ....    .
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~-~~~~----~   93 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN-CREV----G   93 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE-HHHH----C
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE-CccC----C
Confidence            37899999999999987763  23445689999999999999999999876332        23344554 2222    4


Q ss_pred             -ChHHHHHHHHHHHhCCCCC------CchHHHHHHHhCCceEEEEEeCCCChhh-------hhHhhccCCCCCCCcEEEE
Q 044214           98 -GLSCLRQKLLSNLLKDKNV------MPYIDLNFRRLGHMKVLIVFDDVTCFSQ-------LESLMGSLDWLTPVSRIIL  163 (385)
Q Consensus        98 -~~~~l~~~ll~~l~~~~~~------~~~~~~l~~~l~~k~~LlVlDdv~~~~~-------~~~l~~~~~~~~~gs~ilv  163 (385)
                       +...++..++..+.+....      ......+.+.+..++.+|||||++....       +..+....    .+..+|+
T Consensus        94 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~iI~  169 (384)
T 2qby_B           94 GTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD----ANISVIM  169 (384)
T ss_dssp             SCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS----SCEEEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC----cceEEEE
Confidence             6677888888877433221      1456677777877666999999965432       33333322    5778888


Q ss_pred             EeccHHH--------Hhhccc-----------------eecccC-CCCCCchHHHHHHHHHhC---CCcc-chhHH--hH
Q 044214          164 TTRNKQV--------LRNWRV-----------------NAFKRN-HPDVGNEKLSSNVMKYAQ---GVPL-ALKVL--VW  211 (385)
Q Consensus       164 TtR~~~~--------~~~~~~-----------------~~~~~~-~~~~~~~~~~~~i~~~~~---GlPL-al~~~--~w  211 (385)
                      ||+....        ....+.                 ..+... ......++..+.+++.++   |.|. ++..+  .+
T Consensus       170 ~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~  249 (384)
T 2qby_B          170 ISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAA  249 (384)
T ss_dssp             ECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHH
T ss_pred             EECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence            8886521        122111                 111100 111233566778888888   8776 33333  11


Q ss_pred             HHHHHHhhhccCcc--------cchhhhhccccCchhhhhhhhhccccCCCccH-HHHHHHHHHcCCc------hhhhHH
Q 044214          212 ESAISKLQRILHPS--------ILEVLKISYDSLEDKEKNIFLDVACFFQGEHV-DPVMKFFNASGFY------PEIRIS  276 (385)
Q Consensus       212 ~~~l~~l~~~~~~~--------~~~~l~~sy~~L~~~~k~~~~~la~fp~~~~~-~~l~~~~~~~g~~------~~~~l~  276 (385)
                      .... .-.....+.        ....+..+++.|++.++..+..++....+-+. +....+....|..      ...+++
T Consensus       250 ~~a~-~~~~i~~~~v~~~~~~~~~~~~~~~~~~l~~~~~~~l~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~l~  328 (384)
T 2qby_B          250 QLAS-GGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSAHKMYTDLCNKFKQKPLSYRRFSDIIS  328 (384)
T ss_dssp             HHTT-SSSCCCHHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHTCCBHHHHHHHHHHHHHHTTCCCCCHHHHHHHHH
T ss_pred             HHhc-CCCccCHHHHHHHHHHHhcchHHHHHHcCCHHHHHHHHHHHHhcccChHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            1000 000000011        11335556788999988888877761110111 2222333333321      245689


Q ss_pred             HhhcCCceeEe
Q 044214          277 VLVDKPLIAIC  287 (385)
Q Consensus       277 ~L~~~sLi~~~  287 (385)
                      .|.++|+|+..
T Consensus       329 ~L~~~gli~~~  339 (384)
T 2qby_B          329 ELDMFGIVKIR  339 (384)
T ss_dssp             HHHHTTSEEEE
T ss_pred             HHHhCCCEEEE
Confidence            99999999964

>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=99.42  E-value=1.6e-12  Score=122.76  Aligned_cols=258  Identities=16%  Similarity=0.098  Sum_probs=145.6

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCC--CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC---CceEEEeeccccccCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVE--SKGVYALGIWGIGGIGKTTIARAIFDKISGDF---DGSCFLENVREESQIPG   97 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f---~~~~w~~~~~~~~~~~~   97 (385)
                      .+...++.|+||+.+++.+.+++...  ......+.|+|++|+||||||+.+++.....+   ...+|+. ....    .
T Consensus        14 ~~~~~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~-~~~~----~   88 (386)
T 2qby_A           14 LPDYIPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN-TRQI----D   88 (386)
T ss_dssp             SSSCCCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE-HHHH----C
T ss_pred             CCccCCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE-CCCC----C
Confidence            34455688999999999999988742  34456899999999999999999999775543   2344554 2222    4


Q ss_pred             ChHHHHHHHHHHHhCCCCCC-----chHHHHHHHhC--CceEEEEEeCCCC------hhhhhHhhccCCC-CCCCcEEEE
Q 044214           98 GLSCLRQKLLSNLLKDKNVM-----PYIDLNFRRLG--HMKVLIVFDDVTC------FSQLESLMGSLDW-LTPVSRIIL  163 (385)
Q Consensus        98 ~~~~l~~~ll~~l~~~~~~~-----~~~~~l~~~l~--~k~~LlVlDdv~~------~~~~~~l~~~~~~-~~~gs~ilv  163 (385)
                      ....+...++..++......     +....+.+.+.  +++.+||||+++.      ...+..+...+.. ...+..+|+
T Consensus        89 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~  168 (386)
T 2qby_A           89 TPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIG  168 (386)
T ss_dssp             SHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEE
Confidence            55566666666654332211     33444555543  4589999999964      2334444433311 134556777


Q ss_pred             EeccHHHHhh--------cc--c----------------eecccC-CCCCCchHHHHHHHHHhC---CCccchhHH---h
Q 044214          164 TTRNKQVLRN--------WR--V----------------NAFKRN-HPDVGNEKLSSNVMKYAQ---GVPLALKVL---V  210 (385)
Q Consensus       164 TtR~~~~~~~--------~~--~----------------~~~~~~-~~~~~~~~~~~~i~~~~~---GlPLal~~~---~  210 (385)
                      ||+.......        ..  .                ..+... .......+..+.+++.++   |.|..+..+   .
T Consensus       169 ~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a  248 (386)
T 2qby_A          169 ITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVS  248 (386)
T ss_dssp             EESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             EECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            8876532211        11  1                000000 112233566677888887   888744433   1


Q ss_pred             HHHHHHHhhhccC---cc--------cchhhhhccccCchhhhhhhhhccccCC-C---ccHHHH----HHHHHHcCCc-
Q 044214          211 WESAISKLQRILH---PS--------ILEVLKISYDSLEDKEKNIFLDVACFFQ-G---EHVDPV----MKFFNASGFY-  270 (385)
Q Consensus       211 w~~~l~~l~~~~~---~~--------~~~~l~~sy~~L~~~~k~~~~~la~fp~-~---~~~~~l----~~~~~~~g~~-  270 (385)
                      +....  ......   +.        ....+..++..+++..+..+..++.+.+ +   +....+    ..+...-|.. 
T Consensus       249 ~~~a~--~~~~~~i~~~~v~~a~~~~~~~~~~~~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g~~~  326 (386)
T 2qby_A          249 GEIAE--RMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGVEA  326 (386)
T ss_dssp             HHHHH--HTTCSSCCHHHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHH--hcCCCccCHHHHHHHHHHHhhchHHHHHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhcCCCC
Confidence            11110  000000   11        1234556678899988888887775321 1   444333    2222222222 


Q ss_pred             -----hhhhHHHhhcCCceeEe
Q 044214          271 -----PEIRISVLVDKPLIAIC  287 (385)
Q Consensus       271 -----~~~~l~~L~~~sLi~~~  287 (385)
                           ...+++.|.+.|+|+..
T Consensus       327 ~~~~~~~~~l~~L~~~gli~~~  348 (386)
T 2qby_A          327 VTQRRVSDIINELDMVGILTAK  348 (386)
T ss_dssp             CCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCHHHHHHHHHHHHhCCCEEEE
Confidence                 34579999999999864

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.42  E-value=3e-12  Score=120.97  Aligned_cols=258  Identities=14%  Similarity=0.112  Sum_probs=146.0

Q ss_pred             CCCCCCccccchhHHHHHHhhcCC--CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEeeccccccCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVE--SKGVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLENVREESQIP   96 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~~~~~~~~~~   96 (385)
                      ...++.|+||+.+++++..++...  ....+.+.|+|++|+|||++|+.+++.....      -...+|+. .   ... 
T Consensus        15 ~~~p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~-~---~~~-   89 (387)
T 2v1u_A           15 DYVPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN-A---RHR-   89 (387)
T ss_dssp             TCCCSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE-T---TTS-
T ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE-C---CcC-
Confidence            344588999999999999988532  3456689999999999999999999876432      12234444 2   222 


Q ss_pred             CChHHHHHHHHHHHhCCCCCC-----chHHHHHHHh--CCceEEEEEeCCCChh-------hhhHhhccCCCC--CCCcE
Q 044214           97 GGLSCLRQKLLSNLLKDKNVM-----PYIDLNFRRL--GHMKVLIVFDDVTCFS-------QLESLMGSLDWL--TPVSR  160 (385)
Q Consensus        97 ~~~~~l~~~ll~~l~~~~~~~-----~~~~~l~~~l--~~k~~LlVlDdv~~~~-------~~~~l~~~~~~~--~~gs~  160 (385)
                      .+...++..++..++......     +....+.+.+  .+++.+||||+++...       .+..+.......  ..+..
T Consensus        90 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~  169 (387)
T 2v1u_A           90 ETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVS  169 (387)
T ss_dssp             CSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CE
T ss_pred             CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEE
Confidence            567788888888886543311     3345566666  3468999999997543       223333322211  34556


Q ss_pred             EEEEeccHH--------HHhhccc------------------eeccc-CCCCCCchHHHHHHHHHhC---CCccch-hHH
Q 044214          161 IILTTRNKQ--------VLRNWRV------------------NAFKR-NHPDVGNEKLSSNVMKYAQ---GVPLAL-KVL  209 (385)
Q Consensus       161 ilvTtR~~~--------~~~~~~~------------------~~~~~-~~~~~~~~~~~~~i~~~~~---GlPLal-~~~  209 (385)
                      +|+||+...        +......                  ..+.. .......++..+.+++.++   |.|-.+ .++
T Consensus       170 ~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l  249 (387)
T 2v1u_A          170 LVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLL  249 (387)
T ss_dssp             EEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHH
T ss_pred             EEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHH
Confidence            777776552        2222211                  11110 0111223456677888888   888433 333


Q ss_pred             --hHHHHHHHh-hhccCcc--------cchhhhhccccCchhhhhhhhhccccCCC---ccHHHHHHHH----HHcCCc-
Q 044214          210 --VWESAISKL-QRILHPS--------ILEVLKISYDSLEDKEKNIFLDVACFFQG---EHVDPVMKFF----NASGFY-  270 (385)
Q Consensus       210 --~w~~~l~~l-~~~~~~~--------~~~~l~~sy~~L~~~~k~~~~~la~fp~~---~~~~~l~~~~----~~~g~~-  270 (385)
                        .|......- .....+.        ....+.-++..|+++.+..+..++....+   +....+.+..    ...|.. 
T Consensus       250 ~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (387)
T 2v1u_A          250 RVAGEIAERRREERVRREHVYSARAEIERDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLGLEH  329 (387)
T ss_dssp             HHHHHHHHHTTCSCBCHHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHHhhchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhcCCCC
Confidence              111110000 0000011        12234456788999988888777643222   4444333332    222321 


Q ss_pred             -----hhhhHHHhhcCCceeEe
Q 044214          271 -----PEIRISVLVDKPLIAIC  287 (385)
Q Consensus       271 -----~~~~l~~L~~~sLi~~~  287 (385)
                           ...+++.|...|+++..
T Consensus       330 ~~~~~~~~~l~~L~~~gli~~~  351 (387)
T 2v1u_A          330 VTLRRVSGIISELDMLGIVKSR  351 (387)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHhCCCeEEE
Confidence                 34579999999999974

>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=99.16  E-value=1.7e-10  Score=101.32  Aligned_cols=132  Identities=16%  Similarity=0.140  Sum_probs=76.2

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      .....++||+..++.+..++..+. ..+.+.|+|++|+||||||+.+++.....+....+-+         ...... ..
T Consensus        20 ~~~~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~---------~~~~~~-~~   88 (250)
T 1njg_A           20 QTFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPC---------GVCDNC-RE   88 (250)
T ss_dssp             CSGGGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCC---------SCSHHH-HH
T ss_pred             ccHHHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCC---------cccHHH-HH
Confidence            344679999999999999987432 2347899999999999999999987755432110000         000000 00


Q ss_pred             HHHHHhC-----CCCCC---chHHHHHHHh-----CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          106 LLSNLLK-----DKNVM---PYIDLNFRRL-----GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       106 ll~~l~~-----~~~~~---~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      +......     .....   .....+.+.+     .+++.+||+||++.  ...+..+...+.....+..+|+||+..
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~  166 (250)
T 1njg_A           89 IEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDP  166 (250)
T ss_dssp             HHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCG
T ss_pred             HhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCCh
Confidence            0000000     00000   1111222221     34679999999954  455666665554445677888888764

>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=99.10  E-value=5.8e-10  Score=96.46  Aligned_cols=127  Identities=19%  Similarity=0.301  Sum_probs=76.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe-eccccccCCCChHHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE-NVREESQIPGGLSCLR  103 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~-~~~~~~~~~~~~~~l~  103 (385)
                      |.....++||+..++.+.+++...  ..+.+.|+|++|+|||++|+.+++.+........++. +..   .. .....+.
T Consensus        13 p~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~---~~-~~~~~~~   86 (226)
T 2chg_A           13 PRTLDEVVGQDEVIQRLKGYVERK--NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNAS---DE-RGIDVVR   86 (226)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTT--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETT---CT-TCHHHHH
T ss_pred             CCCHHHHcCcHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccc---cc-cChHHHH
Confidence            344567999999999999999853  3334899999999999999999987644322222222 111   11 2222222


Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          104 QKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..+ ........          ...+++.+||+||++..  ...+.+...+.....+..+|+||+..
T Consensus        87 ~~~-~~~~~~~~----------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~  142 (226)
T 2chg_A           87 HKI-KEFARTAP----------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV  142 (226)
T ss_dssp             HHH-HHHHTSCC----------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             HHH-HHHhcccC----------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCCh
Confidence            222 11111100          11257899999999643  34444544443334577888888765

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.97  E-value=2.2e-09  Score=98.68  Aligned_cols=164  Identities=14%  Similarity=0.209  Sum_probs=92.4

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC-C-ceEEEeeccccccCCCChHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF-D-GSCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~-~~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      .....++|++..++.+.+++..+  ..+.+.|+|++|+|||++|+.+++.+.... . ..+++. .   +.. .... ..
T Consensus        18 ~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~-~---~~~-~~~~-~i   89 (323)
T 1sxj_B           18 QVLSDIVGNKETIDRLQQIAKDG--NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN-A---SDD-RGID-VV   89 (323)
T ss_dssp             SSGGGCCSCTHHHHHHHHHHHSC--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC-T---TSC-CSHH-HH
T ss_pred             CCHHHHHCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEec-C---ccc-cChH-HH
Confidence            34467999999999999999843  333489999999999999999999764322 1 122222 1   111 2222 22


Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccHH-----HHhhcc
Q 044214          104 QKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNKQ-----VLRNWR  175 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~~-----~~~~~~  175 (385)
                      ..++..+....          ..+ .+++.++|+||++.  ....+.+...+.....++.+|+||+...     +...+.
T Consensus        90 ~~~~~~~~~~~----------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~  159 (323)
T 1sxj_B           90 RNQIKHFAQKK----------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCA  159 (323)
T ss_dssp             HTHHHHHHHBC----------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             HHHHHHHHhcc----------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhce
Confidence            22222221000          011 34689999999974  3344444444333345677888876542     122221


Q ss_pred             ceeccc---------------CCCCCCchHHHHHHHHHhCCCccchh
Q 044214          176 VNAFKR---------------NHPDVGNEKLSSNVMKYAQGVPLALK  207 (385)
Q Consensus       176 ~~~~~~---------------~~~~~~~~~~~~~i~~~~~GlPLal~  207 (385)
                      ...|..               .......++.+..+++.++|.|..+.
T Consensus       160 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~a~  206 (323)
T 1sxj_B          160 ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAI  206 (323)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCHHHHH
T ss_pred             EEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            111110               01111234567788999999995433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.79  E-value=1.2e-08  Score=93.75  Aligned_cols=125  Identities=20%  Similarity=0.283  Sum_probs=73.5

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCc--eEEEeeccccccCCCChHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDG--SCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~--~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      ..-..++|++..++.+.+++..+  ..+.+.|+|++|+|||++|+.+++.+......  .+.+. ....    .+.. ..
T Consensus        22 ~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~-~~~~----~~~~-~~   93 (327)
T 1iqp_A           22 QRLDDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELN-ASDE----RGIN-VI   93 (327)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE-TTCH----HHHH-TT
T ss_pred             CCHHHhhCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEee-cccc----CchH-HH
Confidence            34467999999999999998843  33348999999999999999999976433211  22222 1110    0000 00


Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          104 QKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ...+.......          ....+++.++|+||++..  .....+...+.....++++|+||...
T Consensus        94 ~~~~~~~~~~~----------~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  150 (327)
T 1iqp_A           94 REKVKEFARTK----------PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYS  150 (327)
T ss_dssp             HHHHHHHHHSC----------CGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHHHHHHhhC----------CcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCc
Confidence            11111110000          011256789999999743  44555554444334577888888654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.78  E-value=2.1e-08  Score=84.30  Aligned_cols=50  Identities=18%  Similarity=0.314  Sum_probs=42.1

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-..++||+++++++.+.+..  ...+.+.|+|++|+|||++|+.+++.+..
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~--~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           20 KLDPVIGRDEEIRRTIQVLQR--RTKNNPVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS--SSSCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             cccccccchHHHHHHHHHHhc--CCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            346799999999999999884  33456889999999999999999987643

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.77  E-value=3e-09  Score=97.93  Aligned_cols=52  Identities=23%  Similarity=0.406  Sum_probs=41.6

Q ss_pred             CCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..-+.|+|++..++.+..++..   .......+.|+|++|+|||++|+.+++...
T Consensus         9 ~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~   63 (324)
T 1hqc_A            9 KTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG   63 (324)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHT
T ss_pred             ccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhC
Confidence            3457899999999998887752   112345788999999999999999998774

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.73  E-value=4.5e-08  Score=89.61  Aligned_cols=124  Identities=16%  Similarity=0.252  Sum_probs=74.4

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCc-eEEEeeccccccCCCChHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD-FDG-SCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~-~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      ..-.+++|++..++.+.+++..+  ..+.+.++|++|+|||++|+.+++.+... +.. .+.+. ....... ..+....
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~-~~~~~~~-~~~~~~~   89 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGYVERK--NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN-ASDERGI-DVVRHKI   89 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTTTTTT--CCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEE-TTSTTCT-TTSSHHH
T ss_pred             CCHHHHhCCHHHHHHHHHHHhCC--CCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEe-CccccCh-HHHHHHH
Confidence            33467999999999999998853  33348999999999999999999976332 211 12222 1111010 1111111


Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          104 QKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ......               ..+ .+++.++|+|+++.  ......+...+.....+..+|+||...
T Consensus        90 ~~~~~~---------------~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  142 (319)
T 2chq_A           90 KEFART---------------APIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYV  142 (319)
T ss_dssp             HHHHHS---------------CCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCG
T ss_pred             HHHHhc---------------CCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCh
Confidence            111100               001 25678999999964  344555666555445677788877654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.69  E-value=1.1e-07  Score=79.66  Aligned_cols=50  Identities=20%  Similarity=0.297  Sum_probs=42.0

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-..++||+.+++.+.+.+..  ...+.+.|+|++|+|||++|+.+++....
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~--~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSR--RTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS--SSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             ccchhhcchHHHHHHHHHHhC--CCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            346799999999999999874  33456789999999999999999997744

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.67  E-value=1.5e-07  Score=88.24  Aligned_cols=51  Identities=25%  Similarity=0.294  Sum_probs=42.0

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-..++|++..++.+.+.+..+. ..+.+.|+|++|+|||++|+.+++.+..
T Consensus        14 ~~~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~l~~   64 (373)
T 1jr3_A           14 TFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNC   64 (373)
T ss_dssp             STTTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHHHSC
T ss_pred             chhhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34669999999999999987432 2357889999999999999999987643

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.65  E-value=1.7e-07  Score=85.27  Aligned_cols=108  Identities=12%  Similarity=0.088  Sum_probs=72.1

Q ss_pred             CccccchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC-----Cc--eEEEeeccccccCCCChH
Q 044214           30 QLVGVESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF-----DG--SCFLENVREESQIPGGLS  100 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-----~~--~~w~~~~~~~~~~~~~~~  100 (385)
                      .+.||+++++++...|..  ..+....+.|+|++|+|||++++.+++++....     +.  .+.+. ..   .. .+..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~IN-c~---~~-~t~~   95 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHID-AL---EL-AGMD   95 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEE-TT---CC-C--H
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEe-cc---cc-CCHH
Confidence            388999999999887763  234567889999999999999999999875322     11  23333 21   22 5566


Q ss_pred             HHHHHHHHHHhCCCCCC----chHHHHHHHh---CCceEEEEEeCCCCh
Q 044214          101 CLRQKLLSNLLKDKNVM----PYIDLNFRRL---GHMKVLIVFDDVTCF  142 (385)
Q Consensus       101 ~l~~~ll~~l~~~~~~~----~~~~~l~~~l---~~k~~LlVlDdv~~~  142 (385)
                      .+...|++++.+.....    .....+...+   .+++++++||+++..
T Consensus        96 ~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l  144 (318)
T 3te6_A           96 ALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENL  144 (318)
T ss_dssp             HHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSS
T ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHh
Confidence            78888888886543211    2233333333   457899999999754

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.63  E-value=1.2e-07  Score=87.67  Aligned_cols=53  Identities=25%  Similarity=0.369  Sum_probs=42.7

Q ss_pred             CCCCccccchhHHHHHHhhcCC---CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           27 NKNQLVGVESTVEEIESLLGVE---SKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .-+.++|++..++.+..++...   ......|.|+|++|+|||++|+.+++.....
T Consensus        27 ~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~   82 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSAN   82 (338)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCC
Confidence            4567999999999999888631   3344568999999999999999999876443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=98.55  E-value=4e-07  Score=84.90  Aligned_cols=70  Identities=24%  Similarity=0.351  Sum_probs=50.0

Q ss_pred             HhHHHHHHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHH
Q 044214            3 ESELINEVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAI   72 (385)
Q Consensus         3 e~~~i~~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~   72 (385)
                      +..+++.|..++..+     .++..-..++|.+..++.|.+.+..          .....+.|.|+|++|+|||+||+.+
T Consensus        63 ~~~~~~~i~~~i~~~-----~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~ai  137 (357)
T 3d8b_A           63 EPKMIELIMNEIMDH-----GPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCI  137 (357)
T ss_dssp             CHHHHHHHHHHTBCC-----SCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHH
T ss_pred             ChHHHHHHHhhcccC-----CCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHH
Confidence            344555555554332     3344557799999999999887642          1133567899999999999999999


Q ss_pred             HHHhh
Q 044214           73 FDKIS   77 (385)
Q Consensus        73 ~~~~~   77 (385)
                      ++...
T Consensus       138 a~~~~  142 (357)
T 3d8b_A          138 ASQSG  142 (357)
T ss_dssp             HHHTT
T ss_pred             HHHcC
Confidence            98763

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.50  E-value=5e-07  Score=83.89  Aligned_cols=51  Identities=18%  Similarity=0.274  Sum_probs=41.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |..-..++|++..++.+..++..+.  ...+.|+|++|+||||+|+.+++.+.
T Consensus        33 p~~~~~i~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~la~~l~   83 (353)
T 1sxj_D           33 PKNLDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTKELY   83 (353)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHhcCC--CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3345679999999999999998532  23389999999999999999998753

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.46  E-value=2.9e-06  Score=76.85  Aligned_cols=68  Identities=22%  Similarity=0.302  Sum_probs=49.2

Q ss_pred             HHHHHHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214            9 EVVNHILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus         9 ~i~~~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++++.+.+.+... .++..-..++|.+..++.+.+.+..          -....+.+.|+|++|+|||++|+.+++...
T Consensus         2 ~~~~~~~~~~~~~-~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~   79 (297)
T 3b9p_A            2 KLVQLILDEIVEG-GAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS   79 (297)
T ss_dssp             CHHHHHHTTTBCC-SSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHhccC-CCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC
Confidence            3455555555442 3445557899999999999887632          012346789999999999999999998764

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.45  E-value=1.6e-07  Score=82.10  Aligned_cols=60  Identities=17%  Similarity=0.230  Sum_probs=42.3

Q ss_pred             CCCCCccccc---hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           26 DNKNQLVGVE---STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        26 ~~~~~~vGR~---~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..-+.|+|++   ..++.+..+...  +..+.+.|+|++|+|||+||+.+++........+.|+.
T Consensus        25 ~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~   87 (242)
T 3bos_A           25 ETFTSYYPAAGNDELIGALKSAASG--DGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIP   87 (242)
T ss_dssp             CSTTTSCC--CCHHHHHHHHHHHHT--CSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CChhhccCCCCCHHHHHHHHHHHhC--CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            3446788743   556667666653  24567899999999999999999997765544556665

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.42  E-value=7.2e-07  Score=80.33  Aligned_cols=56  Identities=23%  Similarity=0.412  Sum_probs=43.8

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCC-----------CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVE-----------SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .|...-..++|.+..+++|.+.+...           ....+.+.|+|++|+|||+||+.+++....
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~   77 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNA   77 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCC
Confidence            44455678999999999998877421           133456899999999999999999987643

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.42  E-value=5.5e-07  Score=72.50  Aligned_cols=47  Identities=23%  Similarity=0.253  Sum_probs=36.0

Q ss_pred             CccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           30 QLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++|++..++++.+.+..-.....-|.|+|.+|+|||++|+.+++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC
Confidence            58999999999988775322223357899999999999999998854

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=98.38  E-value=2.4e-06  Score=78.45  Aligned_cols=56  Identities=20%  Similarity=0.343  Sum_probs=43.3

Q ss_pred             CCCCCCCCccccchhHHHHHHhhc----------CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLG----------VESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~----------~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .|...-..++|.+..++.|.+.+.          ......+-+.|+|++|+|||+||+.+++....
T Consensus        12 ~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~   77 (322)
T 3eie_A           12 KPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANS   77 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCC
Confidence            344455789999999999998772          12223467899999999999999999997643

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.35  E-value=7.5e-07  Score=85.38  Aligned_cols=124  Identities=13%  Similarity=0.155  Sum_probs=69.1

Q ss_pred             CCcc-ccchhH--HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           29 NQLV-GVESTV--EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        29 ~~~v-GR~~~l--~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      +.|+ |.....  ..+......... ...+.|+|++|+||||||+.+++.+...++..-++.         .+...+...
T Consensus       105 d~fv~g~~n~~a~~~~~~~a~~~~~-~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~---------v~~~~~~~~  174 (440)
T 2z4s_A          105 ENFVVGPGNSFAYHAALEVAKHPGR-YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMY---------ITSEKFLND  174 (440)
T ss_dssp             GGCCCCTTTHHHHHHHHHHHHSTTS-SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEE---------EEHHHHHHH
T ss_pred             hhcCCCCchHHHHHHHHHHHhCCCC-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEE---------eeHHHHHHH
Confidence            4566 654433  344444443222 567899999999999999999998765543322222         111223334


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh----hhhhHhhccCCC-CCCCcEEEEEecc
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF----SQLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~----~~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      +...+...     ....+...+..++-+|++||++..    ...+.++..+.. ...|..||+||.+
T Consensus       175 ~~~~~~~~-----~~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          175 LVDSMKEG-----KLNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             HHHHHHTT-----CHHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             HHHHHHcc-----cHHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            44433321     223444555546779999999532    223333322210 1346778888875

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.31  E-value=1.4e-06  Score=79.36  Aligned_cols=49  Identities=20%  Similarity=0.337  Sum_probs=38.2

Q ss_pred             CccccchhHHHHHHhhcC-------------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLGV-------------ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~-------------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++|.+...+.+.+.+..             .......+.|+|++|+|||++|+.+++.+..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   93 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR   93 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            489999999888876541             1234457899999999999999999987643

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.30  E-value=1.4e-06  Score=72.76  Aligned_cols=120  Identities=18%  Similarity=0.166  Sum_probs=63.6

Q ss_pred             CCccc----cchhHHHHHHhhcCCC-CCeEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHH
Q 044214           29 NQLVG----VESTVEEIESLLGVES-KGVYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        29 ~~~vG----R~~~l~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      +.|++    .+..++.+.+++..-. .....+.|+|++|+||||||+.+++.+. ..-..++++.           ..++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~-----------~~~~   78 (180)
T 3ec2_A           10 DTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFD-----------TKDL   78 (180)
T ss_dssp             SSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEE-----------HHHH
T ss_pred             ccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEE-----------HHHH
Confidence            44554    4445555555554311 2346899999999999999999999764 2222233433           2233


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCC--hhh-----hhHhhccCCCCCCCcEEEEEecc
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTC--FSQ-----LESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~-----~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      ...+..........     .+.+.+. ++-+|||||++.  .+.     +..++....  ..|..+|+||..
T Consensus        79 ~~~~~~~~~~~~~~-----~~~~~~~-~~~llilDE~~~~~~~~~~~~~l~~ll~~~~--~~~~~ii~tsn~  142 (180)
T 3ec2_A           79 IFRLKHLMDEGKDT-----KFLKTVL-NSPVLVLDDLGSERLSDWQRELISYIITYRY--NNLKSTIITTNY  142 (180)
T ss_dssp             HHHHHHHHHHTCCS-----HHHHHHH-TCSEEEEETCSSSCCCHHHHHHHHHHHHHHH--HTTCEEEEECCC
T ss_pred             HHHHHHHhcCchHH-----HHHHHhc-CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHH--HcCCCEEEEcCC
Confidence            33333332222111     1222222 456899999962  222     222222211  246678888864

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=98.28  E-value=6.9e-06  Score=78.81  Aligned_cols=54  Identities=20%  Similarity=0.356  Sum_probs=41.9

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|+..-..++|.+...+.|.+.+..          .....+.|.|+|++|+|||+||+.+++..
T Consensus       128 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          128 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            3444557799999999999887621          11234678999999999999999999976

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=98.27  E-value=3.7e-06  Score=78.23  Aligned_cols=54  Identities=20%  Similarity=0.368  Sum_probs=41.3

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++..-..++|.+..++.|.+.+..          .....+-|.|+|++|+|||+||+.+++...
T Consensus        46 ~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~  109 (355)
T 2qp9_X           46 PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN  109 (355)
T ss_dssp             -CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC
Confidence            344457799999999999887621          112235688999999999999999999874

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.27  E-value=1.8e-06  Score=79.35  Aligned_cols=121  Identities=17%  Similarity=0.171  Sum_probs=73.9

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      ..-++++|.+..++.+.+++..+. ...++.++|++|+|||++|+.+++.+..   ..+.+. .   +.  .... ....
T Consensus        23 ~~~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~l~~---~~~~i~-~---~~--~~~~-~i~~   91 (324)
T 3u61_B           23 STIDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHDVNA---DMMFVN-G---SD--CKID-FVRG   91 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHHTTE---EEEEEE-T---TT--CCHH-HHHT
T ss_pred             CCHHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHHhCC---CEEEEc-c---cc--cCHH-HHHH
Confidence            345779999999999999998432 3457888999999999999999987632   122332 1   11  2222 2222


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCChh---hhhHhhccCCCCCCCcEEEEEeccH
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFS---QLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~---~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      .+.......           ...+++.++++|+++...   ....+...+.....+.++|+||...
T Consensus        92 ~~~~~~~~~-----------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~  146 (324)
T 3u61_B           92 PLTNFASAA-----------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNI  146 (324)
T ss_dssp             HHHHHHHBC-----------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSG
T ss_pred             HHHHHHhhc-----------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCc
Confidence            222211110           012477899999998654   3444444333223456788887654

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.24  E-value=5.4e-06  Score=73.45  Aligned_cols=52  Identities=19%  Similarity=0.240  Sum_probs=39.4

Q ss_pred             CCCCccccchhHHHHHHhhc---CC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLG---VE-------SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-.+++|.+...+.+.+++.   ..       ....+.+.|+|++|+|||++|+.+++....
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~   65 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQV   65 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTC
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34679999988888876543   11       123456889999999999999999997653

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=98.23  E-value=1.8e-05  Score=70.60  Aligned_cols=50  Identities=16%  Similarity=0.145  Sum_probs=38.4

Q ss_pred             CCCccccchhHHHHHH-------hhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           28 KNQLVGVESTVEEIES-------LLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~-------~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+.++|.+..++.+..       .+.. .....+.+.|+|++|+|||+||+.+++...
T Consensus        32 ~~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~   89 (272)
T 1d2n_A           32 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESN   89 (272)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             hcCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            3568999888776666       2321 244577899999999999999999999754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.22  E-value=3e-05  Score=71.02  Aligned_cols=53  Identities=19%  Similarity=0.333  Sum_probs=40.9

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |...-.+++|.++..+.|.+.+..          .....+.|.|+|++|+|||+||+.+++..
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc
Confidence            344557799999988888876521          11234679999999999999999999976

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.21  E-value=3e-06  Score=72.12  Aligned_cols=61  Identities=16%  Similarity=0.139  Sum_probs=41.5

Q ss_pred             CCCCccccch----hHHHHHHhhcCCCC--CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           27 NKNQLVGVES----TVEEIESLLGVESK--GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        27 ~~~~~vGR~~----~l~~l~~~L~~~~~--~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .-+.|++.+.    .++.+.+++.....  ..+.+.|+|.+|+|||+||+.+++........++++.
T Consensus        23 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           23 SLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             CTTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CHhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            3456776553    34455555553221  1267899999999999999999998766555566664

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.19  E-value=6.1e-06  Score=77.07  Aligned_cols=52  Identities=23%  Similarity=0.224  Sum_probs=39.9

Q ss_pred             CCCccccchhHHHH---HHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           28 KNQLVGVESTVEEI---ESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        28 ~~~~vGR~~~l~~l---~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+.|+|++...+.+   ...+..+....+.+.|+|++|+|||++|+.+++.+...
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~   97 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPD   97 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSS
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            45799999887764   44455433334689999999999999999999988644

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.19  E-value=8e-06  Score=77.00  Aligned_cols=53  Identities=17%  Similarity=0.264  Sum_probs=41.1

Q ss_pred             CCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..-..++|.+..++.|.+++..          .....+.+.|+|.+|+|||+||+.+++...
T Consensus       111 ~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~  173 (389)
T 3vfd_A          111 AVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESN  173 (389)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTT
T ss_pred             CCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhc
Confidence            33446799999999999987721          012246789999999999999999998754

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=98.17  E-value=7.2e-06  Score=74.48  Aligned_cols=54  Identities=24%  Similarity=0.355  Sum_probs=41.7

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |...-..++|.+..+++|.+++..           +-...+.+.|+|++|+|||+||+.+++...
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~   74 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ   74 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhC
Confidence            334446799999998888877642           123456789999999999999999998764

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.16  E-value=1.2e-05  Score=74.61  Aligned_cols=48  Identities=27%  Similarity=0.271  Sum_probs=39.5

Q ss_pred             CCCCccccchhHHHHHHhh-cCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           27 NKNQLVGVESTVEEIESLL-GVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L-~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-..++|.+..++.+.+++ ..+. ... +.|+|++|+||||+|+.+++.+
T Consensus        12 ~~~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E           12 SLNALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHHHH
Confidence            3467999999999999998 5322 233 8999999999999999999865

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.14  E-value=2.8e-06  Score=81.41  Aligned_cols=53  Identities=25%  Similarity=0.421  Sum_probs=42.5

Q ss_pred             CCCCCCccccchhH---HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           25 RDNKNQLVGVESTV---EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        25 ~~~~~~~vGR~~~l---~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      |..-..++|.+..+   ..|...+..  +..+.+.|+|++|+||||||+.+++.....
T Consensus        22 P~~l~~ivGq~~~~~~~~~L~~~i~~--~~~~~vLL~GppGtGKTtlAr~ia~~~~~~   77 (447)
T 3pvs_A           22 PENLAQYIGQQHLLAAGKPLPRAIEA--GHLHSMILWGPPGTGKTTLAEVIARYANAD   77 (447)
T ss_dssp             CCSTTTCCSCHHHHSTTSHHHHHHHH--TCCCEEEEECSTTSSHHHHHHHHHHHTTCE
T ss_pred             CCCHHHhCCcHHHHhchHHHHHHHHc--CCCcEEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            34457799999888   678887773  344678999999999999999999976543

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.14  E-value=7e-06  Score=75.33  Aligned_cols=126  Identities=17%  Similarity=0.151  Sum_probs=66.0

Q ss_pred             CCCCCCcc-ccch--hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHH
Q 044214           25 RDNKNQLV-GVES--TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        25 ~~~~~~~v-GR~~--~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      ...-+.|+ |...  ....+......+......+.|+|++|+|||+||+.+++.....-...+++.           ...
T Consensus         7 ~~~f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~-----------~~~   75 (324)
T 1l8q_A            7 KYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS-----------ADD   75 (324)
T ss_dssp             TCCSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE-----------HHH
T ss_pred             CCCcccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE-----------HHH
Confidence            33445676 5443  334555555543324567899999999999999999997744322233443           112


Q ss_pred             HHHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCChh----hhhHhhccCCC-CCCCcEEEEEecc
Q 044214          102 LRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCFS----QLESLMGSLDW-LTPVSRIILTTRN  167 (385)
Q Consensus       102 l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~----~~~~l~~~~~~-~~~gs~ilvTtR~  167 (385)
                      +...+...+...     ....+...+. ++.+|++||++...    ..+.+...+.. ...+..||+||..
T Consensus        76 ~~~~~~~~~~~~-----~~~~~~~~~~-~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~  140 (324)
T 1l8q_A           76 FAQAMVEHLKKG-----TINEFRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  140 (324)
T ss_dssp             HHHHHHHHHHHT-----CHHHHHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             HHHHHHHHHHcC-----cHHHHHHHhc-CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            223333332211     1122222232 36799999995432    22223222110 1235578887753

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.11  E-value=4.8e-06  Score=81.55  Aligned_cols=50  Identities=30%  Similarity=0.364  Sum_probs=41.8

Q ss_pred             CCCCccccchhHHHHHHhhcCC---------------CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           27 NKNQLVGVESTVEEIESLLGVE---------------SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~---------------~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-.+++|++..++++.+++...               .+..+.+.|+|++|+|||++|+.+++..
T Consensus        37 ~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           37 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4467999999999999998741               0134689999999999999999999987

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.07  E-value=1.6e-05  Score=76.83  Aligned_cols=49  Identities=20%  Similarity=0.332  Sum_probs=40.9

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++||+.+++.+...|...  ...-+.|+|.+|+|||++|+.+++.+..
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~--~~~~~LL~G~pG~GKT~la~~la~~l~~  227 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQIIN  227 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             CCCccCcHHHHHHHHHHHhcc--CCCCeEEECCCCCCHHHHHHHHHHHHHh
Confidence            356999999999999999742  2335679999999999999999998754

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.02  E-value=1e-06  Score=70.68  Aligned_cols=48  Identities=17%  Similarity=0.167  Sum_probs=34.1

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.++|++..++++.+.+..-.....-|.|+|.+|+|||++|+.+++..
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG   51 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            458999999998888775311222347899999999999999998753

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.01  E-value=1.5e-05  Score=82.93  Aligned_cols=48  Identities=19%  Similarity=0.317  Sum_probs=40.2

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -+.++||+++++++...|...  ....+.|+|.+|+|||++|+.+++.+.
T Consensus       169 ld~viGr~~~i~~l~~~l~~~--~~~~vlL~G~pG~GKT~la~~la~~l~  216 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRR--TKNNPVLIGEPGVGKTAIVEGLAQRIV  216 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCS--SCCCCEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcC--CCCceEEEcCCCCCHHHHHHHHHHHHh
Confidence            356899999999999998742  334578999999999999999999763

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.99  E-value=6.9e-05  Score=76.89  Aligned_cols=47  Identities=28%  Similarity=0.330  Sum_probs=40.0

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++||+.+++.+.+.|...  ...-+.|+|.+|+|||++|+.+++.+.
T Consensus       186 d~~iGr~~~i~~l~~~l~~~--~~~~vlL~G~~GtGKT~la~~la~~l~  232 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhcc--CCCCeEEEcCCCCCHHHHHHHHHHHHH
Confidence            56899999999999998843  334578999999999999999998763

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.98  E-value=4.2e-05  Score=71.41  Aligned_cols=52  Identities=21%  Similarity=0.345  Sum_probs=40.8

Q ss_pred             CCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           28 KNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      -+++.|-++..++|.+.+..           +-..++-|.++|++|+|||.||+++++.....
T Consensus       147 ~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~  209 (405)
T 4b4t_J          147 YDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK  209 (405)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC
Confidence            35688999998888876531           22345679999999999999999999987644

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.96  E-value=7.6e-06  Score=72.85  Aligned_cols=57  Identities=25%  Similarity=0.318  Sum_probs=41.8

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ++..-..++|.+...+.+.+.+..          +....+-+.|+|++|+|||+||+.+++.....|
T Consensus         6 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~   72 (268)
T 2r62_A            6 PNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPF   72 (268)
T ss_dssp             CCCCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCC
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCE
Confidence            344457899999988888876541          111233478999999999999999999875443

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=97.96  E-value=3.2e-05  Score=71.28  Aligned_cols=52  Identities=21%  Similarity=0.329  Sum_probs=40.4

Q ss_pred             CCCCccccchhHHHHHHhhcCC---CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           27 NKNQLVGVESTVEEIESLLGVE---SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~---~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-..++|.+..++.+...+..+   ......+.|+|++|+||||||+.+++.+..
T Consensus        23 ~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~   77 (334)
T 1in4_A           23 SLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQT   77 (334)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTC
T ss_pred             cHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCC
Confidence            3367899988888887776532   223457899999999999999999998754

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.94  E-value=1.1e-05  Score=73.39  Aligned_cols=58  Identities=14%  Similarity=0.300  Sum_probs=42.3

Q ss_pred             CCccccchhHHHHHHhhcCC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           29 NQLVGVESTVEEIESLLGVE-------SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ..++|.+..++.+...+...       ......+.++|++|+|||++|+.+++.....-...+.+
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~   81 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI   81 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEE
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEe
Confidence            35889999988888877531       11235799999999999999999999775443333344

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.93  E-value=2.6e-05  Score=68.89  Aligned_cols=55  Identities=24%  Similarity=0.262  Sum_probs=39.6

Q ss_pred             CCCCCCCccccchhHHHHHHhhc---CC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           24 PRDNKNQLVGVESTVEEIESLLG---VE-------SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++..-.+++|.+...+++.+.+.   ..       ....+-+.|+|++|+||||||+.+++....
T Consensus         7 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~   71 (257)
T 1lv7_A            7 IKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKV   71 (257)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCC
Confidence            34445779999988887766432   11       112345889999999999999999987643

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=97.91  E-value=1.7e-05  Score=76.74  Aligned_cols=48  Identities=25%  Similarity=0.439  Sum_probs=39.6

Q ss_pred             CCccccchhHHHHHHhhcCC-----------CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVE-----------SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~-----------~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|.+..+++|.+++...           ....+-|.|+|.+|+|||++|+.+++..
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~  262 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET  262 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh
Confidence            56899999999998877531           2345578999999999999999999875

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.90  E-value=7.7e-05  Score=70.71  Aligned_cols=54  Identities=20%  Similarity=0.347  Sum_probs=41.6

Q ss_pred             CCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           26 DNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..-.++.|-++..++|.+.+..           +-..++-|.++|++|+|||.||+++++.....
T Consensus       178 v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~  242 (437)
T 4b4t_L          178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN  242 (437)
T ss_dssp             SCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE
T ss_pred             CChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            3345688999888888776531           22446789999999999999999999987543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.86  E-value=1.5e-05  Score=73.74  Aligned_cols=49  Identities=20%  Similarity=0.336  Sum_probs=40.3

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -..++|.+..++.|...+..+  +.+.+.++|++|+||||+|+.+++.+..
T Consensus        24 ~~~~~g~~~~~~~L~~~i~~g--~~~~~ll~Gp~G~GKTtla~~la~~l~~   72 (340)
T 1sxj_C           24 LDEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVALAREIYG   72 (340)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHHHHHHHT
T ss_pred             HHHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHcC
Confidence            356889999999999988843  3334899999999999999999997643

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.85  E-value=1.8e-05  Score=70.35  Aligned_cols=49  Identities=22%  Similarity=0.173  Sum_probs=34.8

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++|.+..+.++.+.+..-......|.|+|.+|+|||++|+.+++...
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~   54 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSS   54 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTST
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcC
Confidence            4589999999888776653112224678999999999999999998653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.83  E-value=6.1e-05  Score=77.28  Aligned_cols=49  Identities=20%  Similarity=0.332  Sum_probs=40.8

Q ss_pred             CCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++||+.+++++...|...  ...-+.++|.+|+|||++|+.+++.+..
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~--~~~~vLL~G~pGtGKT~la~~la~~l~~  227 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQIIN  227 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHHHS
T ss_pred             CCCccCchHHHHHHHHHHhCC--CCCCeEEECCCCCCHHHHHHHHHHHHhc
Confidence            356999999999999999742  2334789999999999999999998743

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.82  E-value=0.00014  Score=65.92  Aligned_cols=117  Identities=10%  Similarity=0.076  Sum_probs=67.9

Q ss_pred             ccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh---CCCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           33 GVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS---GDFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~---~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      |-++.++.|.+.+..+.  .+...++|++|+|||++|+.+++...   ........+...+   .. ..+..+ +++...
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~---~~-~~id~i-r~li~~   73 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG---EN-IGIDDI-RTIKDF   73 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS---SC-BCHHHH-HHHHHH
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCc---CC-CCHHHH-HHHHHH
Confidence            44566778888887543  67899999999999999999998532   2233444443111   01 222222 233333


Q ss_pred             HhCCCCCCchHHHHHHHhCCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          110 LLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       110 l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      .....            ..+++-++|+|+++.  ....+.++..+....+.+.+|++|.++
T Consensus        74 ~~~~p------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~  122 (305)
T 2gno_A           74 LNYSP------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  122 (305)
T ss_dssp             HTSCC------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             Hhhcc------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            32211            124567899999964  345566665554444567777766543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.81  E-value=1.7e-05  Score=63.94  Aligned_cols=36  Identities=17%  Similarity=0.350  Sum_probs=27.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -..++|+|..|+|||||++.++......-...+++.
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            357999999999999999999997754312255654

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.77  E-value=0.00024  Score=65.38  Aligned_cols=43  Identities=19%  Similarity=0.232  Sum_probs=32.5

Q ss_pred             chhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           35 ESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        35 ~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++..+.+.+.+..+ .-.+.+.++|++|+|||++|+.+++.+..
T Consensus         8 ~~~~~~l~~~i~~~-~~~~a~L~~G~~G~GKt~~a~~la~~l~~   50 (334)
T 1a5t_A            8 RPDFEKLVASYQAG-RGHHALLIQALPGMGDDALIYALSRYLLC   50 (334)
T ss_dssp             HHHHHHHHHHHHTT-CCCSEEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcC-CcceeEEEECCCCchHHHHHHHHHHHHhC
Confidence            44566777777632 23457899999999999999999997643

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.73  E-value=6.4e-05  Score=68.22  Aligned_cols=48  Identities=19%  Similarity=0.311  Sum_probs=37.8

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.++|++..+.++.+.+..-......|.|+|.+|+|||++|+.+++..
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            458999999999888776422233457899999999999999999864

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=97.61  E-value=0.00019  Score=68.96  Aligned_cols=51  Identities=24%  Similarity=0.333  Sum_probs=37.7

Q ss_pred             CCCccccchhHHHHHHhhcC----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLGV----------ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -.+++|.++.++++.+....          +..-.+-|.|+|++|+|||+||+.+++....
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~   75 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANV   75 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            35689999888777765431          1112345889999999999999999997643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.60  E-value=0.00019  Score=67.95  Aligned_cols=54  Identities=19%  Similarity=0.323  Sum_probs=42.0

Q ss_pred             CCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           26 DNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..-.++.|-++..++|.+.+..           +-..++-|.++|++|+|||.||+++++.....
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~  270 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDAT  270 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCE
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCC
Confidence            3345789999999888875421           22456789999999999999999999987644

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.59  E-value=0.00016  Score=68.45  Aligned_cols=53  Identities=17%  Similarity=0.287  Sum_probs=41.2

Q ss_pred             CCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           27 NKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .-.++.|-++..++|.+.+..           +-..++-|.++|++|+|||.||+++++.....
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~  233 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAA  233 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCE
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            335688999888888776531           22446779999999999999999999987543

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.56  E-value=0.00019  Score=68.96  Aligned_cols=51  Identities=27%  Similarity=0.313  Sum_probs=39.2

Q ss_pred             CCccccchhHHHHHHhh---cCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLL---GVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L---~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..++|.+...+.+..++   ..+....+-+.++|++|+|||++|+.+++.+...
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~   90 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSK   90 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTT
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCC
Confidence            67999998877655543   3333334578899999999999999999987644

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.49  E-value=0.00026  Score=67.00  Aligned_cols=55  Identities=20%  Similarity=0.296  Sum_probs=42.2

Q ss_pred             CCCCCCccccchhHHHHHHhhc----C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLG----V-------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~----~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...-..+.|-++..++|.+.+.    .       +-..++-|.++|++|+|||.||+++++.....
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~  242 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT  242 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCC
Confidence            3344678999999998887542    1       22346789999999999999999999987543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.48  E-value=0.00021  Score=73.30  Aligned_cols=59  Identities=22%  Similarity=0.393  Sum_probs=42.6

Q ss_pred             CCccccchhHHHHHHhhcCC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           29 NQLVGVESTVEEIESLLGVE-------SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..++|.+..++.+...+...       ......+.++|++|+|||++|+.+++.....-...+.+.
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~  556 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRID  556 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEE
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEe
Confidence            45899999888887776521       112337999999999999999999998744433344443

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.44  E-value=0.00033  Score=65.72  Aligned_cols=54  Identities=26%  Similarity=0.430  Sum_probs=41.3

Q ss_pred             CCCCCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           26 DNKNQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..-.++.|-++..++|.+.+..           +-..++-|.++|++|+|||.||+++++.....
T Consensus       179 v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~  243 (437)
T 4b4t_I          179 ESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT  243 (437)
T ss_dssp             CCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE
T ss_pred             CcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC
Confidence            3345688899888888775531           22346789999999999999999999987644

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.40  E-value=0.00036  Score=63.37  Aligned_cols=59  Identities=17%  Similarity=0.173  Sum_probs=38.5

Q ss_pred             CCccccc----hhHHHHHHhhcCCC-CCeEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEe
Q 044214           29 NQLVGVE----STVEEIESLLGVES-KGVYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLE   87 (385)
Q Consensus        29 ~~~vGR~----~~l~~l~~~L~~~~-~~~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~   87 (385)
                      +.|++.+    ..++.+.+++.... .....+.|+|.+|+|||+||..+++... .....+.++.
T Consensus       124 d~f~~~~~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          124 SDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             GGSCCCSHHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             hhCcCCChHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            4566433    34445556665321 1246788999999999999999999766 4434455554

>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=97.39  E-value=0.00047  Score=58.95  Aligned_cols=33  Identities=18%  Similarity=0.127  Sum_probs=26.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -.++.|+|.+|+||||||..++. .  .-..++|+.
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~-~--~~~~v~~i~   52 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL-L--SGKKVAYVD   52 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH-H--HCSEEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-H--cCCcEEEEE
Confidence            35899999999999999999988 2  224566665

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.30  E-value=0.00028  Score=71.85  Aligned_cols=49  Identities=24%  Similarity=0.405  Sum_probs=38.3

Q ss_pred             CCccccchhHHHHHHhhc----C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLG----V-------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~----~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +++.|-++.+++|.+.+.    .       +-..++-|.++|++|+|||+||+++++...
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg  263 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG  263 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTT
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            457888988888887653    1       123467899999999999999999998654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.25  E-value=0.00092  Score=64.62  Aligned_cols=54  Identities=24%  Similarity=0.378  Sum_probs=38.8

Q ss_pred             CCCCCCCccccchhHHHHHHhhc---CC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLG---VE-------SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~---~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +...-.+++|.++...++.+...   ..       -.-.+-+.|+|++|+|||+||+.++....
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~   89 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   89 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            34445779999988777766532   11       01123489999999999999999998764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.21  E-value=0.0009  Score=69.48  Aligned_cols=49  Identities=16%  Similarity=0.374  Sum_probs=38.1

Q ss_pred             CccccchhHHHHHHhhcCC-------CCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLGVE-------SKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++|.+..++.+...+...       ......+.|+|++|+|||++|+.+++....
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~  614 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFD  614 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHS
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            4789999888887766421       112357899999999999999999997644

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=97.19  E-value=0.00016  Score=65.37  Aligned_cols=49  Identities=20%  Similarity=0.278  Sum_probs=38.8

Q ss_pred             CCccccchhHHHHHHhhcC------------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGV------------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~------------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++|.+..++.+...+..            .......+.|+|.+|+|||++|+.+++...
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4589999999998877653            012345688999999999999999999774

>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=97.16  E-value=0.0032  Score=58.07  Aligned_cols=81  Identities=15%  Similarity=0.129  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHhhccCCCCCCC-----CCC-ccccchhHHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214            5 ELINEVVNHILKRLDEVFRPRDN-----KNQ-LVGVESTVEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus         5 ~~i~~i~~~v~~~l~~~~~~~~~-----~~~-~vGR~~~l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++....++.+.+..  ..+..     ... .-....-...|-..|. .+=..-.++.|+|.+|+||||||.+++....
T Consensus         9 ~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~i~TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~   86 (356)
T 3hr8_A            9 SVLEKALKRIEENFGK--GSIMILGDETQVQPVEVIPTGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQ   86 (356)
T ss_dssp             HHHHHHHHHHHHHHCT--TSSCCTTCCSCCCCCCEECCSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC--CCceechhccccCCCceecCCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3466666677666654  21111     011 1122223345555554 2223346999999999999999999998765


Q ss_pred             CCCCceEEEe
Q 044214           78 GDFDGSCFLE   87 (385)
Q Consensus        78 ~~f~~~~w~~   87 (385)
                      ..-..++|+.
T Consensus        87 ~~gg~VlyId   96 (356)
T 3hr8_A           87 KMGGVAAFID   96 (356)
T ss_dssp             HTTCCEEEEE
T ss_pred             hcCCeEEEEe
Confidence            4434567775

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.12  E-value=0.0008  Score=66.06  Aligned_cols=48  Identities=29%  Similarity=0.349  Sum_probs=35.0

Q ss_pred             ccccchhHHHHHHhhc----CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           31 LVGVESTVEEIESLLG----VESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~----~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .+|-++....+.+.+.    ........+.++|++|+||||||+.++.....
T Consensus        83 i~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~  134 (543)
T 3m6a_A           83 HHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGR  134 (543)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTC
T ss_pred             hccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            6787777666655332    11224558999999999999999999987743

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.10  E-value=0.0011  Score=55.49  Aligned_cols=114  Identities=18%  Similarity=0.168  Sum_probs=60.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHH---hC----CCCC----C----
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNL---LK----DKNV----M----  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l---~~----~~~~----~----  117 (385)
                      ..|.|++-.|.||||.|...+-+...+--.+.++...... .. .+-..++..+.-.+   +.    ...+    .    
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~-~~-~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~  106 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGT-WP-NGERNLLEPHGVEFQVMATGFTWETQNREADTAACM  106 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCS-SC-CHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCC-CC-ccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHH
Confidence            3566666677999999999998765554455555423221 11 33333333331000   00    0000    0    


Q ss_pred             chHHHHHHHhCC-ceEEEEEeCCC-----ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          118 PYIDLNFRRLGH-MKVLIVFDDVT-----CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       118 ~~~~~l~~~l~~-k~~LlVlDdv~-----~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ......++.+.+ +-=|||||++.     ..-..+.++..+........||+|+|..
T Consensus       107 ~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          107 AVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            333445555554 44599999993     2222333333333334567899999985

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.07  E-value=0.00037  Score=63.01  Aligned_cols=33  Identities=18%  Similarity=0.126  Sum_probs=25.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+++.|+|++|+|||+||.+++.. .  -..+.|+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-~--G~~VlyIs  155 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-L--GGKDKYAT  155 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-H--HTTSCCEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-C--CCCEEEEE
Confidence            356789999999999999999886 1  12345665

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=97.06  E-value=0.0003  Score=64.46  Aligned_cols=47  Identities=15%  Similarity=0.176  Sum_probs=39.3

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.++|++..++.+...+..+    ..+.++|.+|+|||+||+.+++.....
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~----~~vll~G~pGtGKT~la~~la~~~~~~   73 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTG----GHILLEGVPGLAKTLSVNTLAKTMDLD   73 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT----CCEEEESCCCHHHHHHHHHHHHHTTCC
T ss_pred             cceeCcHHHHHHHHHHHHcC----CeEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            56999999999988887742    258899999999999999999876543

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.06  E-value=0.00046  Score=61.59  Aligned_cols=54  Identities=24%  Similarity=0.401  Sum_probs=37.7

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC--C--------CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV--E--------SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~--~--------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +...-++++|.+....++.+....  .        -.-.+-+.|+|++|+||||||+.++....
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~   98 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   98 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC
Confidence            344446789998877776654321  0        01112389999999999999999998765

>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=97.04  E-value=0.00019  Score=66.38  Aligned_cols=109  Identities=12%  Similarity=0.078  Sum_probs=64.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE-eeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL-ENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~-~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      .+++|+|+.|+|||||.+.+...+.......++. ....+...  ....    ....+.............+...|...+
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~--~~~~----~~v~q~~~~~~~~~~~~~La~aL~~~P  197 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVH--ESKK----CLVNQREVHRDTLGFSEALRSALREDP  197 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCC--CCSS----SEEEEEEBTTTBSCHHHHHHHHTTSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhh--hccc----cceeeeeeccccCCHHHHHHHHhhhCc
Confidence            4899999999999999999988664432233322 21110000  0000    000000000011245568888899999


Q ss_pred             EEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHHH
Q 044214          132 VLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQV  170 (385)
Q Consensus       132 ~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~~  170 (385)
                      =+|++|.+.+.+.++.+....   ..|..|++|+...+.
T Consensus       198 dvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~  233 (356)
T 3jvv_A          198 DIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSA  233 (356)
T ss_dssp             SEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSH
T ss_pred             CEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChH
Confidence            999999998877766655442   246668888876543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.03  E-value=0.0011  Score=56.07  Aligned_cols=44  Identities=23%  Similarity=0.370  Sum_probs=33.7

Q ss_pred             cchhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           34 VESTVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        34 R~~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |++.++.+.+.+.. ......+|+|.|.+|+||||+++.+...+.
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            45566777666653 234567999999999999999999998664

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.03  E-value=0.0021  Score=57.25  Aligned_cols=50  Identities=20%  Similarity=0.157  Sum_probs=33.4

Q ss_pred             CCCccccchhHHHHHHhhc----C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           28 KNQLVGVESTVEEIESLLG----V-------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~----~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.++.|-++..++|.+.+.    .       +-.-.+-+.|+|++|+||||||+.++....
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~   69 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESG   69 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            3567787777777766432    0       001122399999999999999999998754

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.01  E-value=0.0016  Score=66.73  Aligned_cols=48  Identities=21%  Similarity=0.335  Sum_probs=37.5

Q ss_pred             CCccccchhHHHHHHhhcC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           29 NQLVGVESTVEEIESLLGV-------ESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|.+..++.+...+..       .......+.++|++|+|||++|+.+++..
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            3588999888888776642       11223478999999999999999999977

>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=97.01  E-value=0.018  Score=54.55  Aligned_cols=36  Identities=22%  Similarity=0.088  Sum_probs=28.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ++.+|.++|.+|+||||++..++..++..-..+..+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv  134 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVV  134 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            468999999999999999999998776553334444

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=97.00  E-value=0.001  Score=54.72  Aligned_cols=21  Identities=29%  Similarity=0.406  Sum_probs=18.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAI   72 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~   72 (385)
                      -.+++|+|+.|+|||||++.+
T Consensus         9 gei~~l~G~nGsGKSTl~~~~   29 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKH   29 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            358999999999999999963

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.95  E-value=0.00083  Score=57.13  Aligned_cols=41  Identities=20%  Similarity=0.293  Sum_probs=30.9

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+++|.+.+....+...+|+|.|..|+|||||++.+...+.
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            44555555543234567999999999999999999998765

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=96.94  E-value=0.00039  Score=57.41  Aligned_cols=25  Identities=20%  Similarity=0.252  Sum_probs=22.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|.|+|++|+||||+|+.+++++.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4789999999999999999998764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.94  E-value=0.00014  Score=60.85  Aligned_cols=107  Identities=12%  Similarity=-0.053  Sum_probs=51.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCC--CCchHHHHHHHhCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKN--VMPYIDLNFRRLGHM  130 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~--~~~~~~~l~~~l~~k  130 (385)
                      .++.|+|..|+||||++..++.+....-..+.++.....  .. .+...+.    ..++....  .......+.+.+.++
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d--~r-~~~~~i~----s~~g~~~~~~~~~~~~~~~~~~~~~   76 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKID--SR-YHSTMIV----SHSGNGVEAHVIERPEEMRKYIEED   76 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC--------CCCEEC----C----CEECEEESSGGGGGGGCCTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccc--cc-cCcccEE----ecCCCceeeEEECCHHHHHHHhcCC
Confidence            478899999999999998888765333222333321100  00 0000000    00000000  001112233333445


Q ss_pred             eEEEEEeCCCCh-hhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          131 KVLIVFDDVTCF-SQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       131 ~~LlVlDdv~~~-~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      .-+|++|.+... ..|...+..+.+  .|..|++|.++.
T Consensus        77 ~dvviIDE~Q~~~~~~~~~l~~l~~--~~~~Vi~~Gl~~  113 (184)
T 2orw_A           77 TRGVFIDEVQFFNPSLFEVVKDLLD--RGIDVFCAGLDL  113 (184)
T ss_dssp             EEEEEECCGGGSCTTHHHHHHHHHH--TTCEEEEEEESB
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHH--CCCCEEEEeecc
Confidence            679999999543 223333332221  277899988754

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=96.93  E-value=0.00071  Score=62.88  Aligned_cols=48  Identities=19%  Similarity=0.210  Sum_probs=37.4

Q ss_pred             CccccchhHHHHHHhhc-------------CCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           30 QLVGVESTVEEIESLLG-------------VESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~-------------~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++|.+..++.+...+.             ........+.++|++|+|||++|+.+++...
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~   76 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD   76 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            37899988888887772             1111345789999999999999999998763

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=96.86  E-value=0.00055  Score=56.02  Aligned_cols=25  Identities=16%  Similarity=0.080  Sum_probs=22.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|.|++|+||||+|+.+++++.
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999998764

>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=96.85  E-value=0.00069  Score=58.23  Aligned_cols=107  Identities=13%  Similarity=-0.048  Sum_probs=57.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCC--C----chHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNV--M----PYIDLNFR  125 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~--~----~~~~~l~~  125 (385)
                      -.++.|+|..|+||||++..++.+...+-..++.+.........        ..+.+.++.....  .    +....+.+
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~--------~~i~srlG~~~~~~~~~~~~~i~~~i~~   83 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSI--------RNIQSRTGTSLPSVEVESAPEILNYIMS   83 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGC--------SSCCCCCCCSSCCEEESSTHHHHHHHHS
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHH--------HHHHHhcCCCccccccCCHHHHHHHHHH
Confidence            46899999999999999999998876554444444311110000        0112222211111  1    22333333


Q ss_pred             HhCC-ceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccHH
Q 044214          126 RLGH-MKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus       126 ~l~~-k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      .+.+ +.-+||+|.+..  .++++.+.. +.+  .|-.||+|.+..+
T Consensus        84 ~~~~~~~dvViIDEaQ~l~~~~ve~l~~-L~~--~gi~Vil~Gl~~d  127 (223)
T 2b8t_A           84 NSFNDETKVIGIDEVQFFDDRICEVANI-LAE--NGFVVIISGLDKN  127 (223)
T ss_dssp             TTSCTTCCEEEECSGGGSCTHHHHHHHH-HHH--TTCEEEEECCSBC
T ss_pred             HhhCCCCCEEEEecCccCcHHHHHHHHH-HHh--CCCeEEEEecccc
Confidence            3333 345999999953  334333322 221  2678999998543

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.82  E-value=0.0014  Score=54.50  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=24.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..|.|.|++|+||||+|+.+++++...
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   28 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            478999999999999999999987643

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.80  E-value=0.0016  Score=58.44  Aligned_cols=29  Identities=21%  Similarity=0.248  Sum_probs=25.2

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++..+|+|+|..|+||||||+.+...+.
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            45678999999999999999999988654

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.79  E-value=0.0078  Score=54.90  Aligned_cols=29  Identities=24%  Similarity=0.355  Sum_probs=25.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...+++|+|+.|+||||+++.++..++..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~  156 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNH  156 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            46799999999999999999999866443

>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=96.79  E-value=0.034  Score=49.85  Aligned_cols=37  Identities=19%  Similarity=0.177  Sum_probs=27.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~   87 (385)
                      ...+++|+|.+|+||||++..++..+.. .-..+.++.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            4569999999999999999999987653 323344443

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.75  E-value=0.0008  Score=56.77  Aligned_cols=26  Identities=31%  Similarity=0.431  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|+|+|++|+||||+|+.+++.+.
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            45899999999999999999998763

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.72  E-value=0.011  Score=54.68  Aligned_cols=50  Identities=24%  Similarity=0.211  Sum_probs=34.8

Q ss_pred             HHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           38 VEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        38 l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...|-..|. .+=..-.++.|+|.+|+||||||.+++......-..++|++
T Consensus        59 ~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~  109 (366)
T 1xp8_A           59 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFID  109 (366)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEE
Confidence            444555554 11123358899999999999999999887654444677886

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.70  E-value=0.0075  Score=54.30  Aligned_cols=34  Identities=12%  Similarity=0.003  Sum_probs=27.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC--CCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD--FDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~--f~~~~w~~   87 (385)
                      ++.|+|.+|+||||||.+++......  -..++|++
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId   65 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYD   65 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            78999999999999999998866543  24567776

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=96.70  E-value=0.0034  Score=57.08  Aligned_cols=37  Identities=16%  Similarity=0.077  Sum_probs=28.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+++|+|.+|+||||++..++..+...-..+.++.
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid  140 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAA  140 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            4679999999999999999999987654433344443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.69  E-value=0.00087  Score=55.65  Aligned_cols=25  Identities=20%  Similarity=0.353  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.|.|+|++|+||||+|+.+++++
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3578999999999999999999876

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=96.65  E-value=0.012  Score=54.12  Aligned_cols=80  Identities=15%  Similarity=0.165  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHhhccCCCCCCC-----CCCccccchhHHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214            6 LINEVVNHILKRLDEVFRPRDN-----KNQLVGVESTVEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus         6 ~i~~i~~~v~~~l~~~~~~~~~-----~~~~vGR~~~l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+++....+.++...  ..+..     ....-+...-...|-..|. .+=..-.++.|+|.+|+||||||.+++......
T Consensus        11 ~~~~~~~~i~~~~~~--~~~~~l~~~~~~~~~~i~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~   88 (349)
T 2zr9_A           11 ALELAMAQIDKNFGK--GSVMRLGEEVRQPISVIPTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA   88 (349)
T ss_dssp             HHHHHHHHHHHHHCT--TSSCCTTCCCCCCCCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhCC--CCceeccccccccCCccccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            456666666655544  21111     1112222223344444454 222234589999999999999999999766544


Q ss_pred             CCceEEEe
Q 044214           80 FDGSCFLE   87 (385)
Q Consensus        80 f~~~~w~~   87 (385)
                      -..++|++
T Consensus        89 g~~vlyi~   96 (349)
T 2zr9_A           89 GGIAAFID   96 (349)
T ss_dssp             TCCEEEEE
T ss_pred             CCeEEEEE
Confidence            44577776

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.64  E-value=0.0047  Score=53.46  Aligned_cols=36  Identities=14%  Similarity=0.109  Sum_probs=27.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      -.++.|+|.+|+|||||++.++.....      .-..++|+.
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~   65 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYID   65 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEE
Confidence            358999999999999999999985322      134667776

>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=96.64  E-value=0.0021  Score=54.16  Aligned_cols=27  Identities=26%  Similarity=0.341  Sum_probs=24.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+|+|+|++|+||||+|+.++..+.
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            457999999999999999999998775

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.63  E-value=0.0013  Score=59.12  Aligned_cols=30  Identities=37%  Similarity=0.582  Sum_probs=25.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..++.+.++|++|+|||+||+.+++.....
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~l~~~   63 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRKMGIN   63 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHHHTCC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            345688999999999999999999987433

>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=96.63  E-value=0.0083  Score=56.73  Aligned_cols=37  Identities=19%  Similarity=0.096  Sum_probs=28.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+|.++|.+|+||||++..++..++..-..+..+.
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3689999999999999999999987655433344443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.62  E-value=0.0024  Score=53.09  Aligned_cols=28  Identities=32%  Similarity=0.360  Sum_probs=24.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...+|.|.|++|+||||+++.++..+..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            3568999999999999999999987754

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.62  E-value=0.0012  Score=54.37  Aligned_cols=22  Identities=32%  Similarity=0.344  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999987

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=96.61  E-value=0.0016  Score=56.92  Aligned_cols=42  Identities=19%  Similarity=0.074  Sum_probs=29.9

Q ss_pred             chhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           35 ESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        35 ~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+.++.+.+.........|+|.|++|+||||+|+.+.+++
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           12 IDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             HHHHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            344444544433223356789999999999999999999865

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.61  E-value=0.0032  Score=57.21  Aligned_cols=47  Identities=26%  Similarity=0.309  Sum_probs=34.3

Q ss_pred             ccccchhHHHHHHhhcCC--CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           31 LVGVESTVEEIESLLGVE--SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        31 ~vGR~~~l~~l~~~L~~~--~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++|-...+..+...+...  ...+.+|+|.|..|+||||||+.+...+.
T Consensus        69 ~~~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           69 YVTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hhcchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            455555566555544432  34577999999999999999999987665

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.60  E-value=0.011  Score=55.96  Aligned_cols=81  Identities=15%  Similarity=0.166  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHHHhhccCCCC--CCCC-CCccccchhHHHHHHhhcCC-------CCCeEEEEEEcCCCchHHHHHHHHH
Q 044214            4 SELINEVVNHILKRLDEVFRP--RDNK-NQLVGVESTVEEIESLLGVE-------SKGVYALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus         4 ~~~i~~i~~~v~~~l~~~~~~--~~~~-~~~vGR~~~l~~l~~~L~~~-------~~~~~vv~I~G~gGiGKTtLA~~~~   73 (385)
                      .+.++++++.+..+.... ..  ...+ ..++  +...+++.+.|...       ...+++|.++|.+|+||||++..++
T Consensus        45 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA  121 (433)
T 2xxa_A           45 LPVVREFINRVKEKAVGH-EVNKSLTPGQEFV--KIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLG  121 (433)
T ss_dssp             HHHHHHHHHHHHHHHSSS-CCCSSSCTTTTTH--HHHHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc-cccccCChHHHHH--HHHHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            345666676665544331 10  0111 1121  23345566666531       1346899999999999999999999


Q ss_pred             HHhhCC-CCceEEEe
Q 044214           74 DKISGD-FDGSCFLE   87 (385)
Q Consensus        74 ~~~~~~-f~~~~w~~   87 (385)
                      ..+... -..+..+.
T Consensus       122 ~~l~~~~G~kVllvd  136 (433)
T 2xxa_A          122 KFLREKHKKKVLVVS  136 (433)
T ss_dssp             HHHHHTSCCCEEEEE
T ss_pred             HHHHHhcCCeEEEEe
Confidence            877654 33444443

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.60  E-value=0.0092  Score=54.17  Aligned_cols=51  Identities=18%  Similarity=0.062  Sum_probs=36.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      -.++.|.|.+|+||||||..++......-..++|++ ..      .+..++...+...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s-lE------~s~~~l~~R~~~~  118 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS-LE------MGKKENIKRLIVT  118 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE-SS------SCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE-CC------CCHHHHHHHHHHH
Confidence            358999999999999999999976544335666765 21      4455666665544

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=96.60  E-value=0.0015  Score=54.44  Aligned_cols=26  Identities=23%  Similarity=0.247  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|.|.|++|+||||+|+.+++.+
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999999876

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=96.59  E-value=0.00092  Score=58.70  Aligned_cols=54  Identities=24%  Similarity=0.401  Sum_probs=37.3

Q ss_pred             CCCCCCCccccchhHHHHHHhhcC--C--------CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           24 PRDNKNQLVGVESTVEEIESLLGV--E--------SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~~--~--------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      |...-++++|.+....++.+....  .        -.-.+-+.|+|++|+||||||+.++....
T Consensus        11 ~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~   74 (254)
T 1ixz_A           11 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   74 (254)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            344446789988777666554321  0        01122389999999999999999998764

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.58  E-value=0.0054  Score=55.96  Aligned_cols=36  Identities=14%  Similarity=0.200  Sum_probs=28.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~   87 (385)
                      -.++.|+|.+|+||||||.+++......      -..++|++
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~  148 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYID  148 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            3589999999999999999999865332      24567776

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.57  E-value=0.0013  Score=53.75  Aligned_cols=27  Identities=22%  Similarity=0.297  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+.|+|.|+.|+||||+|+.+++++.
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            457899999999999999999998764

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=96.57  E-value=0.00073  Score=62.46  Aligned_cols=27  Identities=22%  Similarity=-0.001  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -+.++|+|.+|+|||||++.+++.+..
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i~~  200 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSIAY  200 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHHhh
Confidence            358999999999999999999886643

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.56  E-value=0.01  Score=54.53  Aligned_cols=38  Identities=13%  Similarity=0.110  Sum_probs=29.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      ..-.++.|+|.+|+||||||..++.....      .-..++|++
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~  163 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID  163 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            34579999999999999999999986432      234567776

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.56  E-value=0.0023  Score=61.92  Aligned_cols=45  Identities=18%  Similarity=0.053  Sum_probs=37.7

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++|++..++.+...+..+    ..|.|+|++|+|||+||+.+++...
T Consensus        22 ~~ivGq~~~i~~l~~al~~~----~~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHT----CEEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             hhhHHHHHHHHHHHHHHhcC----CeeEeecCchHHHHHHHHHHHHHHh
Confidence            45999999999888877633    2688999999999999999998663

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=96.52  E-value=0.0012  Score=53.88  Aligned_cols=22  Identities=27%  Similarity=0.453  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+|+|.|++|+||||+|+.+ ++
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~   23 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KE   23 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HH
Confidence            37899999999999999999 54

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=96.50  E-value=0.0018  Score=60.48  Aligned_cols=48  Identities=17%  Similarity=0.195  Sum_probs=36.5

Q ss_pred             CccccchhHHHHHHhhc----C------------------------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           30 QLVGVESTVEEIESLLG----V------------------------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~----~------------------------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++|.+...+.|...+.    .                        .......+.++|++|+|||++|+.+++...
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~   97 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLD   97 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhC
Confidence            47898888888877661    0                        011234688999999999999999999774

>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=96.48  E-value=0.00086  Score=55.92  Aligned_cols=29  Identities=28%  Similarity=0.517  Sum_probs=23.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      +.|+|+|++|+|||||++++..+..+.|.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~~~   30 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDSFG   30 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCCeE
Confidence            45889999999999999999887554443

>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=96.48  E-value=0.0026  Score=51.99  Aligned_cols=33  Identities=15%  Similarity=0.164  Sum_probs=26.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCce
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD-FDGS   83 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~   83 (385)
                      ..++++|.|..|+|||||+..+...++.+ +...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~   36 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVREGWRVG   36 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHhcCCeee
Confidence            45689999999999999999999877554 4433

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=96.47  E-value=0.003  Score=52.43  Aligned_cols=27  Identities=22%  Similarity=0.442  Sum_probs=23.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..|.|.|++|+||||+|+.+++++...
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   30 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKE   30 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            479999999999999999999977643

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=96.47  E-value=0.0024  Score=52.46  Aligned_cols=26  Identities=19%  Similarity=0.401  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|+|+|++|+||||+++.++...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            34689999999999999999998865

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.47  E-value=0.0034  Score=53.10  Aligned_cols=28  Identities=29%  Similarity=0.274  Sum_probs=24.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..|+|.|++|+||||+|+.+++.+...+
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g   32 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKR   32 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTS
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcC
Confidence            5899999999999999999999876544

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.44  E-value=0.009  Score=53.84  Aligned_cols=28  Identities=25%  Similarity=0.302  Sum_probs=24.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...+++|+|+.|+||||+++.++..++.
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  126 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  126 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3579999999999999999999986653

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=96.43  E-value=0.0035  Score=53.12  Aligned_cols=23  Identities=30%  Similarity=0.325  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|.|.|++|+||||.|+.+++++
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999999999999865

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=96.43  E-value=0.0011  Score=61.15  Aligned_cols=51  Identities=20%  Similarity=0.148  Sum_probs=36.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..-+.++|.+...+.+...+....  ..-+.|+|.+|+|||++|+.+++...
T Consensus        20 ~~~f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           20 VFPFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CCCchhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHHhCc
Confidence            3444679999987666554443211  22388999999999999999998764

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.42  E-value=0.0014  Score=53.75  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=22.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|+|++|+||||+++.++..+.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4699999999999999999998753

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.42  E-value=0.0013  Score=55.49  Aligned_cols=25  Identities=24%  Similarity=0.453  Sum_probs=22.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|++|+||||+|+.++..+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999999876

>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=96.42  E-value=0.0028  Score=53.79  Aligned_cols=29  Identities=17%  Similarity=0.228  Sum_probs=24.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..+|+|.|+.|+||||+|+.+++.+...+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~   37 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCAAG   37 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence            35899999999999999999999875443

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.41  E-value=0.0023  Score=53.99  Aligned_cols=27  Identities=22%  Similarity=0.254  Sum_probs=23.8

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+|+|.|++|+||||+|+.+++..
T Consensus        13 ~~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           13 DQVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            356789999999999999999999864

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.41  E-value=0.0019  Score=56.79  Aligned_cols=25  Identities=28%  Similarity=0.240  Sum_probs=22.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|+|++|+||||||+.++.+..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999998753

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=96.40  E-value=0.0016  Score=53.78  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.|.|+|++|+||||+|+.+++.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            3578899999999999999999875

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=96.39  E-value=0.0018  Score=54.02  Aligned_cols=24  Identities=38%  Similarity=0.346  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ..+++|+|++|+|||||++.++..
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            368999999999999999999874

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.38  E-value=0.0029  Score=53.34  Aligned_cols=26  Identities=35%  Similarity=0.510  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|+|+|+.|+|||||++.++..+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            34689999999999999999999876

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.38  E-value=0.0018  Score=59.30  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=31.8

Q ss_pred             cchhHHHHHHhhcC--CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           34 VESTVEEIESLLGV--ESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        34 R~~~l~~l~~~L~~--~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      -+...+.+.+.+..  ..+....|.|+|++|+||||+++.++..+.-.|
T Consensus         4 ~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~~~f   52 (359)
T 2ga8_A            4 THKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINEKY   52 (359)
T ss_dssp             HHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhCCCe
Confidence            34444445444431  234566799999999999999999998654333

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.37  E-value=0.0074  Score=57.39  Aligned_cols=33  Identities=27%  Similarity=0.594  Sum_probs=25.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCC-CceEEE
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDF-DGSCFL   86 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~   86 (385)
                      .++|+|.+|+|||||+..+.......+ ...++.
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~  186 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFA  186 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEE
T ss_pred             EEEEECCCCCCccHHHHHHHhhhhhccCcEEEEe
Confidence            588999999999999999998654433 333444

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.36  E-value=0.0023  Score=53.28  Aligned_cols=25  Identities=28%  Similarity=0.288  Sum_probs=22.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|++|+||||+|+.+++.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998865

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.35  E-value=0.0078  Score=55.54  Aligned_cols=28  Identities=25%  Similarity=0.302  Sum_probs=24.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...+++|+|..|+||||+++.++..++.
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  183 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  183 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccc
Confidence            3579999999999999999999987654

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=96.35  E-value=0.0051  Score=50.56  Aligned_cols=59  Identities=14%  Similarity=0.135  Sum_probs=35.0

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+....  ...+.+..|.++++|++|+|+++   .+|..+ .  .+|++|+|+++.++.+|
T Consensus        33 ~~L~~L~Ls~N~--l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~~l~   97 (174)
T 2r9u_A           33 TDKQRLWLNNNQ--ITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIP   97 (174)
T ss_dssp             TTCSEEECCSSC--CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             CCCcEEEeCCCC--ccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccceeC
Confidence            344555554443  23344566667777777777766   555443 3  67777777777776666

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=96.34  E-value=0.0086  Score=53.84  Aligned_cols=36  Identities=22%  Similarity=0.168  Sum_probs=28.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+++++|.+|+||||++..++..+...-..+.++.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            678999999999999999999987654433444544

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.33  E-value=0.0071  Score=55.90  Aligned_cols=42  Identities=24%  Similarity=0.282  Sum_probs=31.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..++.+.+....++..+|+|+|.+|+|||||+..++..+...
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~~~  106 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIER  106 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            334444454444567899999999999999999998876443

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.33  E-value=0.0023  Score=53.52  Aligned_cols=25  Identities=28%  Similarity=0.248  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|++|+||||+|+.+++.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999999865

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=96.33  E-value=0.0043  Score=53.08  Aligned_cols=41  Identities=27%  Similarity=0.447  Sum_probs=30.1

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+.+...+.  ......|+|+|.+|+|||||+..+.......
T Consensus        25 ~a~~~r~~~~--~~~~~~i~ivG~~gvGKTtl~~~l~~~~~~~   65 (226)
T 2hf9_A           25 LADKNRKLLN--KHGVVAFDFMGAIGSGKTLLIEKLIDNLKDK   65 (226)
T ss_dssp             HHHHHHHHHH--HTTCEEEEEEESTTSSHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHH--hCCCeEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            3445555544  3356789999999999999999999865433

>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=96.32  E-value=0.0025  Score=55.92  Aligned_cols=28  Identities=18%  Similarity=0.366  Sum_probs=24.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+.+|+|.|++|+||||+|+.+.+.+.
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4567899999999999999999998654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.31  E-value=0.0013  Score=54.35  Aligned_cols=26  Identities=27%  Similarity=0.374  Sum_probs=18.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|.|.|++|+||||+|+.+++.+.
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            45899999999999999999988654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.31  E-value=0.0024  Score=53.71  Aligned_cols=24  Identities=38%  Similarity=0.631  Sum_probs=22.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|+|.|+.|+||||+|+.+++.+.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999998765

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=96.29  E-value=0.0026  Score=52.78  Aligned_cols=25  Identities=32%  Similarity=0.333  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....|+|+|++|+||||+++.+++.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3457999999999999999999986

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.29  E-value=0.0024  Score=52.91  Aligned_cols=25  Identities=24%  Similarity=0.453  Sum_probs=22.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++++|+|++|+|||||++.+.....
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5899999999999999999998654

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=96.28  E-value=0.0041  Score=53.03  Aligned_cols=45  Identities=24%  Similarity=0.348  Sum_probs=33.1

Q ss_pred             ccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           33 GVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.++..+.+.+.+.  ....+.|+|+|.+|+|||||+..+.......
T Consensus        13 ~~~~~~~~~~~~~~--~~~~~~i~i~G~~g~GKTTl~~~l~~~~~~~   57 (221)
T 2wsm_A           13 ENKRLAEKNREALR--ESGTVAVNIMGAIGSGKTLLIERTIERIGNE   57 (221)
T ss_dssp             HHHHHHHHHHHHHH--HHTCEEEEEEECTTSCHHHHHHHHHHHHTTT
T ss_pred             hcHHHHHHHHHhhc--ccCceEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            33445555555554  2356799999999999999999999876544

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=96.28  E-value=0.0041  Score=56.40  Aligned_cols=38  Identities=24%  Similarity=0.310  Sum_probs=29.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++.++|+|+|-|||||||.|..++.-+...-..+.-+.
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~GkkVllID   83 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSILGKRVLQIG   83 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            46799999999999999999998886655434455554

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=96.28  E-value=0.0018  Score=53.72  Aligned_cols=24  Identities=29%  Similarity=0.475  Sum_probs=21.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|.|+|++|+||||+|+.+++++.
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC
Confidence            589999999999999999998764

>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=96.27  E-value=0.0027  Score=55.98  Aligned_cols=26  Identities=23%  Similarity=0.501  Sum_probs=23.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|.|.|++|+||||+|+.++..+.
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999998754

>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=96.27  E-value=0.0028  Score=53.29  Aligned_cols=26  Identities=35%  Similarity=0.343  Sum_probs=23.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ++..+|+|+|+.|+||||+|+.+++.
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            45679999999999999999999874

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.26  E-value=0.0033  Score=52.09  Aligned_cols=25  Identities=28%  Similarity=0.262  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...|+|.|++|+||||+|+.+++.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999999865

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=96.24  E-value=0.0036  Score=52.61  Aligned_cols=43  Identities=19%  Similarity=0.217  Sum_probs=32.2

Q ss_pred             chhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           35 ESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        35 ~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..-+..+..++.. -++...+.|+|++|+|||++|..+++.+..
T Consensus        42 ~~f~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~~l~g   84 (212)
T 1tue_A           42 ITFLGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIHFIQG   84 (212)
T ss_dssp             HHHHHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3446667777663 223346899999999999999999998753

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=96.24  E-value=0.0031  Score=53.11  Aligned_cols=26  Identities=27%  Similarity=0.307  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|+|.|++|+||||+|+.+++.+.
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999998763

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=96.24  E-value=0.0037  Score=51.93  Aligned_cols=25  Identities=24%  Similarity=0.207  Sum_probs=22.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|++|+||||+|+.+++.+
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999865

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.24  E-value=0.0021  Score=52.87  Aligned_cols=24  Identities=33%  Similarity=0.531  Sum_probs=21.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.|.|++|+||||+|+.+++++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcC
Confidence            589999999999999999998764

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.22  E-value=0.0041  Score=55.70  Aligned_cols=26  Identities=35%  Similarity=0.461  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|.|.|++|+||||+|+.+..+.
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998865

>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=96.21  E-value=0.0028  Score=54.21  Aligned_cols=26  Identities=23%  Similarity=0.300  Sum_probs=22.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|+|.|++|+||||+|+.+++.+.
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999998763

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=96.20  E-value=0.0023  Score=52.35  Aligned_cols=25  Identities=24%  Similarity=0.360  Sum_probs=22.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..|.|.|++|+||||+|+.+++.+.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999998763

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.20  E-value=0.0028  Score=53.11  Aligned_cols=25  Identities=28%  Similarity=0.275  Sum_probs=22.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|.|++|+||||+|+.+++++.
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4899999999999999999998764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.19  E-value=0.0022  Score=54.18  Aligned_cols=26  Identities=23%  Similarity=0.525  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++|+|+|++|+|||||++.+.....
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            45899999999999999999998763

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=96.19  E-value=0.007  Score=49.45  Aligned_cols=58  Identities=10%  Similarity=0.085  Sum_probs=33.5

Q ss_pred             CeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          321 KIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       321 ~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      .++.+.+....  ...+.+..|.++.+|++|+|+++   .+|... .  .+|++|+|+++.++.+|
T Consensus        31 ~l~~L~L~~N~--i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~   94 (170)
T 3g39_A           31 TTQVLYLYDNQ--ITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLKSIP   94 (170)
T ss_dssp             TCSEEECCSSC--CCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             CCcEEEcCCCc--CCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccCEeC
Confidence            44444444443  23344556666777777777666   444433 3  66777777777666666

>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=96.19  E-value=0.0027  Score=53.96  Aligned_cols=28  Identities=25%  Similarity=0.379  Sum_probs=23.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ...+++|+|+.|+|||||++.+......
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            3458999999999999999999986543

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=96.18  E-value=0.0079  Score=51.41  Aligned_cols=59  Identities=17%  Similarity=0.167  Sum_probs=31.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      .+++.+.+.....  ..+.+..|.++++|++|+|+++   .+|..+ .  .+|++|+|+++.++.+|
T Consensus        56 ~~L~~L~Ls~N~i--~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~  120 (220)
T 2v9t_B           56 KKLRRIDLSNNQI--SELAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLR  120 (220)
T ss_dssp             TTCCEEECCSSCC--CEECTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             CCCCEEECCCCcC--CCcCHHHhhCCcCCCEEECCCCcCCccCHhHccCCCCCCEEECCCCCCCEeC
Confidence            3444444444332  2344555666666666666665   444443 2  56666666666666554

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.16  E-value=0.0032  Score=51.19  Aligned_cols=24  Identities=17%  Similarity=0.266  Sum_probs=21.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|+|.|++|+||||+|+.+.+.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999998764

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.15  E-value=0.0038  Score=53.33  Aligned_cols=27  Identities=22%  Similarity=0.245  Sum_probs=24.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.++|.|.|++|+||||.|+.+++++
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            467899999999999999999999865

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.14  E-value=0.011  Score=53.70  Aligned_cols=26  Identities=23%  Similarity=0.204  Sum_probs=22.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-.++.|+|.+|+|||+||.+++...
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999998753

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.14  E-value=0.0052  Score=52.01  Aligned_cols=28  Identities=14%  Similarity=0.225  Sum_probs=24.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..+|+|.|+.|+||||+|+.+.+.+...
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            4589999999999999999999876543

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=96.13  E-value=0.003  Score=64.33  Aligned_cols=62  Identities=16%  Similarity=0.195  Sum_probs=44.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC-CCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN-NFG  383 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP-~~~  383 (385)
                      ...++.|.+..+...   ..+..|.++++|++|+|+++   .+|.+|+  .+|++|+|++|.++.+| .|+
T Consensus       246 l~~L~~L~Ls~N~l~---~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~~lp~~~~  313 (727)
T 4b8c_D          246 YDFLTRLYLNGNSLT---ELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFG  313 (727)
T ss_dssp             CCSCSCCBCTTSCCS---CCCGGGGGGTTCCEEECTTSCCSSCCSSGGGGTTCSEEECCSSCCCCCCSSTT
T ss_pred             CCCCCEEEeeCCcCc---ccChhhhCCCCCCEEeCcCCcCCccChhhcCCCCCCEEECCCCCCCccChhhh
Confidence            345666666655432   23455678888888888887   7788777  78888888888888888 454

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=96.12  E-value=0.0037  Score=52.86  Aligned_cols=26  Identities=31%  Similarity=0.569  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....+|+|+|.+|+||||+|+.+...
T Consensus        19 ~~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           19 SKTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            34578999999999999999998864

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.11  E-value=0.0042  Score=52.66  Aligned_cols=27  Identities=33%  Similarity=0.485  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+|+|+|..|+|||||++.+...+.
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999998654

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.11  E-value=0.01  Score=53.51  Aligned_cols=53  Identities=21%  Similarity=0.281  Sum_probs=35.9

Q ss_pred             chhHHHHHHhhcCC------CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           35 ESTVEEIESLLGVE------SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        35 ~~~l~~l~~~L~~~------~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +...++|.+.|...      .....+++|+|.+|+||||++..++..++..-..+.++.
T Consensus        81 ~~~~~~l~~~l~~~~~~~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~  139 (306)
T 1vma_A           81 ESLKEIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA  139 (306)
T ss_dssp             HHHHHHHHHHTCSCCCCCCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHhCCCCCCcccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEc
Confidence            34455566666432      134679999999999999999999987754433344443

>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=96.11  E-value=0.0035  Score=52.14  Aligned_cols=22  Identities=27%  Similarity=0.348  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||++.++.
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999986

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.08  E-value=0.0037  Score=52.05  Aligned_cols=25  Identities=32%  Similarity=0.565  Sum_probs=22.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +|+|.|+.|+||||+|+.+.+.+..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~   26 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQ   26 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999997743

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=96.07  E-value=0.0037  Score=53.61  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+|+|+|++|+||||+|+.++..+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999998865

>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=96.06  E-value=0.0056  Score=58.00  Aligned_cols=51  Identities=20%  Similarity=0.266  Sum_probs=37.5

Q ss_pred             CCccccchhHHHHHHhhcC------------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLLGV------------ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~------------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..++|-++..+.+...+..            .....+-|.++|++|+|||++|+.++..+...
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~   77 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAP   77 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            3578888888877665521            01124568899999999999999999987543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=96.06  E-value=0.021  Score=47.86  Aligned_cols=34  Identities=18%  Similarity=0.162  Sum_probs=27.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|+|-|.-|+||||.++.+++.+......+++..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~tr   35 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKR   35 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            4789999999999999999998876654454443

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=96.06  E-value=0.016  Score=53.83  Aligned_cols=110  Identities=11%  Similarity=0.048  Sum_probs=60.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      -.+++|+|+.|+||||+++.+...+.....+.+.+... ..........    .+..+.............+...+...+
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e~-~~e~~~~~~~----~~v~Q~~~g~~~~~~~~~l~~~L~~~p  210 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIED-PIEYVFKHKK----SIVNQREVGEDTKSFADALRAALREDP  210 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEES-SCCSCCCCSS----SEEEEEEBTTTBSCSHHHHHHHTTSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEecc-cHhhhhccCc----eEEEeeecCCCHHHHHHHHHHHhhhCc
Confidence            45899999999999999999998664432344433211 0000000000    000000000011144566777777778


Q ss_pred             EEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHH
Q 044214          132 VLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus       132 ~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      =+|++|.+.+.+.+...+...   ..|..|+.|+...+
T Consensus       211 d~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~  245 (372)
T 2ewv_A          211 DVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNT  245 (372)
T ss_dssp             SEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCS
T ss_pred             CEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcch
Confidence            899999998766655544332   24556777776543

>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=96.00  E-value=0.0037  Score=52.65  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+|+|+|+.|+||||+++.++.
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999987

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.00  E-value=0.0034  Score=53.99  Aligned_cols=25  Identities=28%  Similarity=0.357  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...|+|.|++|+||||+|+.+++.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4579999999999999999999865

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.00  E-value=0.0039  Score=52.51  Aligned_cols=24  Identities=29%  Similarity=0.546  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+|+|+|++|+||||+++.+....
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            489999999999999999998765

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.99  E-value=0.0034  Score=53.76  Aligned_cols=26  Identities=27%  Similarity=0.157  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|.|.|++|+||||+|+.+++.+.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998764

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=95.99  E-value=0.0081  Score=51.68  Aligned_cols=60  Identities=10%  Similarity=0.097  Sum_probs=45.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|..+.+|++|+|+++   .+|..+.  .+|++|+++++.++.+|
T Consensus        87 l~~L~~L~Ls~N~l--~~l~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~~~~  151 (229)
T 3e6j_A           87 LTQLTVLDLGTNQL--TVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQNQLKSIP  151 (229)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCSCCTTGGGCTTCSEEECCSSCCCCCC
T ss_pred             CCCcCEEECCCCcC--CccChhHhCcchhhCeEeccCCcccccCcccccCCCCCEEECCCCcCCccC
Confidence            45667777666543  3456677888888888888887   7777777  88888888888888877

>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=95.99  E-value=0.0035  Score=52.63  Aligned_cols=28  Identities=25%  Similarity=0.490  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..++++|+|+.|+|||||++.+......
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~~   45 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNPE   45 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCTT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCCc
Confidence            3468999999999999999999986543

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.99  E-value=0.0038  Score=52.54  Aligned_cols=24  Identities=29%  Similarity=0.408  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|+|+.|+|||||++.++...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhC
Confidence            489999999999999999998764

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=95.98  E-value=0.014  Score=53.79  Aligned_cols=50  Identities=18%  Similarity=0.214  Sum_probs=34.7

Q ss_pred             HHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           38 VEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        38 l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...|-..|. .+=..-+++.|+|.+|+||||||.+++......-..++|++
T Consensus        48 ~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid   98 (356)
T 1u94_A           48 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   98 (356)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            344444453 22223458999999999999999999987654444677876

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=95.98  E-value=0.0073  Score=54.47  Aligned_cols=36  Identities=17%  Similarity=0.139  Sum_probs=27.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +..+++|+|++|+||||+++.++..++.. .+.+++.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~~-~g~V~l~  136 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQNL-GKKVMFC  136 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEE
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc-CCEEEEE
Confidence            35699999999999999999999876544 3344443

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=95.98  E-value=0.0042  Score=54.19  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|++|+|||||++.+++.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999765

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.97  E-value=0.023  Score=53.91  Aligned_cols=53  Identities=21%  Similarity=0.341  Sum_probs=36.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      +.++|.|.+|+|||+|+..+++.+.. +-+..++.- +++.   +....++.+++...
T Consensus       154 Qr~~Ifgg~G~GKT~L~~~i~~~~~~~~~~v~V~~~-iGER---~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          154 GKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG-VGER---TREGNDLYHEMIES  207 (482)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTTTCSSEEEEEE-ESCC---HHHHHHHHHHHHHH
T ss_pred             CeeeeecCCCCChHHHHHHHHHhhHhhCCCEEEEEE-CCCc---chHHHHHHHHhhhc
Confidence            47899999999999999999987643 334455543 3322   14466666666554

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=95.97  E-value=0.0053  Score=50.56  Aligned_cols=26  Identities=27%  Similarity=0.392  Sum_probs=23.1

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|+|+|+.|+||||+++.+...+.
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~   30 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLV   30 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46889999999999999999998764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.96  E-value=0.039  Score=50.39  Aligned_cols=51  Identities=20%  Similarity=0.135  Sum_probs=36.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l  110 (385)
                      .++.|.|.+|+||||||..++......-..++|++ .     . .+..++...++...
T Consensus        47 ~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS-l-----E-ms~~ql~~Rlls~~   97 (338)
T 4a1f_A           47 SLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS-L-----E-MSAEQLALRALSDL   97 (338)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE-S-----S-SCHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe-C-----C-CCHHHHHHHHHHHh
Confidence            48999999999999999999986644334555654 2     2 45667777766554

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.96  E-value=0.0056  Score=53.66  Aligned_cols=27  Identities=33%  Similarity=0.336  Sum_probs=23.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+|.|+|++|+||||+|+.+...+.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            457899999999999999999998754

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.92  E-value=0.0048  Score=52.49  Aligned_cols=23  Identities=35%  Similarity=0.533  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|+|.|++|+||||+|+.++++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998865

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=95.91  E-value=0.0056  Score=51.26  Aligned_cols=26  Identities=27%  Similarity=0.420  Sum_probs=23.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|+|+|+.|+||||+|+.+.+.+
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999998863

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.90  E-value=0.0039  Score=53.28  Aligned_cols=24  Identities=29%  Similarity=0.232  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..|.|.|++|+||||+|+.+++.+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=95.88  E-value=0.0053  Score=50.73  Aligned_cols=24  Identities=33%  Similarity=0.599  Sum_probs=21.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .++|+|..|+|||||++.++..+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999998654

>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=95.87  E-value=0.0045  Score=52.26  Aligned_cols=22  Identities=50%  Similarity=0.620  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+|+|+|+.|+||||+++.++.
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=95.87  E-value=0.019  Score=54.93  Aligned_cols=36  Identities=22%  Similarity=0.405  Sum_probs=28.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+++|+|..|+|||||++.++..++.. .+.+++.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~-~G~V~l~  327 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQ-GKSVMLA  327 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhc-CCeEEEe
Confidence            45799999999999999999999876543 3444553

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=95.84  E-value=0.0069  Score=55.24  Aligned_cols=59  Identities=10%  Similarity=0.126  Sum_probs=37.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCC-CCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGF-AGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~-~~~~lP  380 (385)
                      ...++.+.+......   ..+..|.++++|++|+|+++   .+|..++  .+|++|++++| .+..+|
T Consensus       103 l~~L~~L~L~~n~l~---~lp~~~~~l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L~L~~n~~~~~~p  167 (328)
T 4fcg_A          103 LSHLQHMTIDAAGLM---ELPDTMQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELP  167 (328)
T ss_dssp             GTTCSEEEEESSCCC---CCCSCGGGGTTCSEEEEESCCCCCCCGGGGGCTTCCEEEEEEETTCCCCC
T ss_pred             CCCCCEEECCCCCcc---chhHHHhccCCCCEEECCCCccccCcHHHhcCcCCCEEECCCCCCccccC
Confidence            455666666655432   23345667777777777776   5666666  67777777775 345566

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=95.83  E-value=0.0064  Score=51.59  Aligned_cols=27  Identities=19%  Similarity=0.279  Sum_probs=23.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+|.|.|+.|+||||+|+.+...+.
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            346899999999999999999998764

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=95.83  E-value=0.0079  Score=49.30  Aligned_cols=40  Identities=15%  Similarity=0.116  Sum_probs=17.7

Q ss_pred             ccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          341 TFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       341 ~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      .|.++++|++|+|+++   .+|..+ .  .+|++|++++|.++.+|
T Consensus        59 ~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~  104 (176)
T 1a9n_A           59 GFPLLRRLKTLLVNNNRICRIGEGLDQALPDLTELILTNNSLVELG  104 (176)
T ss_dssp             CCCCCSSCCEEECCSSCCCEECSCHHHHCTTCCEEECCSCCCCCGG
T ss_pred             ccccCCCCCEEECCCCcccccCcchhhcCCCCCEEECCCCcCCcch
Confidence            3444444444444444   333332 2  44444444444444444

>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=95.83  E-value=0.031  Score=47.16  Aligned_cols=30  Identities=27%  Similarity=0.473  Sum_probs=25.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCc
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDG   82 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~   82 (385)
                      +-|+|-|..|+||||+++.+++.+...++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~~~~~v   32 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLVKDYDV   32 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCE
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHCCCCE
Confidence            468999999999999999999988665553

>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=95.83  E-value=0.0029  Score=53.68  Aligned_cols=25  Identities=24%  Similarity=0.447  Sum_probs=22.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +|+|.|..|+||||+|+.+...+..
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            6899999999999999999987653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.82  E-value=0.0082  Score=51.97  Aligned_cols=35  Identities=14%  Similarity=0.071  Sum_probs=27.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++.|.|.+|+||||||.+++......-..++|+.
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            48999999999999999998876543434566665

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=95.81  E-value=0.013  Score=50.16  Aligned_cols=36  Identities=17%  Similarity=0.167  Sum_probs=27.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      -.+++|+|.+|+|||||++.++.....      .-...+|+.
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~   66 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   66 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEE
Confidence            469999999999999999999875432      133466665

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=95.80  E-value=0.0052  Score=52.32  Aligned_cols=23  Identities=35%  Similarity=0.504  Sum_probs=20.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|+|.|++|+||||+|+.+++++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998764

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=95.76  E-value=0.013  Score=48.90  Aligned_cols=60  Identities=15%  Similarity=0.111  Sum_probs=42.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ...++.+.+.....  ..+.+..|.++.+|+.|+|+++   .+| ..+.  .+|++|+|+++.+..+|
T Consensus        53 l~~L~~L~Ls~N~i--~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~L~~N~l~~~~  118 (193)
T 2wfh_A           53 YKHLTLIDLSNNRI--STLSNQSFSNMTQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLHGNDISVVP  118 (193)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCCCBCC
T ss_pred             ccCCCEEECCCCcC--CEeCHhHccCCCCCCEEECCCCccCEeCHHHhCCCCCCCEEECCCCCCCeeC
Confidence            45566666665543  3456677888888888888877   444 3455  78888888888888877

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=95.75  E-value=0.0061  Score=54.37  Aligned_cols=25  Identities=40%  Similarity=0.840  Sum_probs=22.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +.+.+|+|+|+.|+||||+|+.+..
T Consensus        73 ~~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           73 SGLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TTCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999999984

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=95.75  E-value=0.015  Score=49.98  Aligned_cols=60  Identities=12%  Similarity=0.106  Sum_probs=42.5

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++.+|++|+|+++   .+|.. +.  .+|++|+++++.++.+|
T Consensus        63 l~~L~~L~L~~N~l--~~i~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~Ls~N~l~~lp  128 (229)
T 3e6j_A           63 LINLKELYLGSNQL--GALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELP  128 (229)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCSCC
T ss_pred             ccCCcEEECCCCCC--CCcChhhcccCCCcCEEECCCCcCCccChhHhCcchhhCeEeccCCcccccC
Confidence            45666666666543  3456677788888888888877   45544 34  78888888888888887

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=95.74  E-value=0.0013  Score=60.62  Aligned_cols=38  Identities=24%  Similarity=0.102  Sum_probs=27.4

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +..+.|.+ -.+-+.++|.|.+|+|||+|+..+++.+..
T Consensus       164 raID~l~P-igrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~  201 (427)
T 3l0o_A          164 RLIDLFAP-IGKGQRGMIVAPPKAGKTTILKEIANGIAE  201 (427)
T ss_dssp             HHHHHHSC-CBTTCEEEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             hhhhhccc-ccCCceEEEecCCCCChhHHHHHHHHHHhh
Confidence            34445543 123347899999999999999999987643

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=95.74  E-value=0.0059  Score=51.30  Aligned_cols=24  Identities=29%  Similarity=0.324  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..|+|.|+.|+||||+++.+.+.+
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999865

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.72  E-value=0.0044  Score=52.13  Aligned_cols=25  Identities=28%  Similarity=0.485  Sum_probs=22.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.++|+|+.|+|||||++.+.....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCc
Confidence            4789999999999999999988654

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.69  E-value=0.0062  Score=53.37  Aligned_cols=25  Identities=24%  Similarity=0.436  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..+|+|.|+.|+||||+++.+++++
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhc
Confidence            3589999999999999999999765

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.69  E-value=0.008  Score=51.47  Aligned_cols=35  Identities=23%  Similarity=0.289  Sum_probs=26.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+++|.|.+|+|||||++.++......-..+.|+.
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            58999999999999999999975533223455554

>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=95.68  E-value=0.01  Score=57.34  Aligned_cols=49  Identities=6%  Similarity=0.053  Sum_probs=35.7

Q ss_pred             CccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .-+.|.+..+.+.+..........+|.+.|++|+||||+|+.+++++..
T Consensus       373 ~~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          373 EWFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TTTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ccccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            3455555556666655322334578999999999999999999998864

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=95.67  E-value=0.019  Score=52.46  Aligned_cols=103  Identities=16%  Similarity=0.056  Sum_probs=59.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      ..++|+|..|+|||||++.+...+.. -.+.+.+....+...  .....    .. .+.. .........+...|..++=
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~-~~g~i~i~~~~e~~~--~~~~~----~i-~~~~-ggg~~~r~~la~aL~~~p~  242 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPK-EERIISIEDTEEIVF--KHHKN----YT-QLFF-GGNITSADCLKSCLRMRPD  242 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCT-TSCEEEEESSCCCCC--SSCSS----EE-EEEC-BTTBCHHHHHHHHTTSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcC-CCcEEEECCeecccc--ccchh----EE-EEEe-CCChhHHHHHHHHhhhCCC
Confidence            37999999999999999999876543 345666653322110  00000    00 0000 0122445667777888888


Q ss_pred             EEEEeCCCChhhhhHhhccCCCCCCCc-EEEEEeccH
Q 044214          133 LIVFDDVTCFSQLESLMGSLDWLTPVS-RIILTTRNK  168 (385)
Q Consensus       133 LlVlDdv~~~~~~~~l~~~~~~~~~gs-~ilvTtR~~  168 (385)
                      +|++|.+...+.++.+ ..+.   .|. -+|+||...
T Consensus       243 ilildE~~~~e~~~~l-~~~~---~g~~tvi~t~H~~  275 (330)
T 2pt7_A          243 RIILGELRSSEAYDFY-NVLC---SGHKGTLTTLHAG  275 (330)
T ss_dssp             EEEECCCCSTHHHHHH-HHHH---TTCCCEEEEEECS
T ss_pred             EEEEcCCChHHHHHHH-HHHh---cCCCEEEEEEccc
Confidence            9999999875555433 3332   222 267777543

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=95.66  E-value=0.0075  Score=51.38  Aligned_cols=23  Identities=39%  Similarity=0.499  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999976

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=95.65  E-value=0.018  Score=47.04  Aligned_cols=60  Identities=15%  Similarity=0.163  Sum_probs=39.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ...++.+.+.....  ..+++..|..+.+|++|+|+++   .+|.. +.  .+|++|+++++.++.+|
T Consensus        51 l~~L~~L~l~~n~l--~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~  116 (177)
T 2o6r_A           51 LTQLTKLSLSQNQI--QSLPDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELALDTNQLKSVP  116 (177)
T ss_dssp             CTTCSEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCC
T ss_pred             cccccEEECCCCcc--eEeChhHccCCCccCEEECCCCCccccCHHHhhCCcccCEEECcCCcceEeC
Confidence            34566666655432  2455566777777788887776   44443 34  77888888877777777

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=95.64  E-value=0.034  Score=52.46  Aligned_cols=27  Identities=19%  Similarity=0.175  Sum_probs=23.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+|.|+|++|+||||+|+.++++.
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            346799999999999999999998754

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=95.64  E-value=0.018  Score=49.18  Aligned_cols=60  Identities=13%  Similarity=0.105  Sum_probs=46.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++.+|++|+|+++   .+ |..+.  .+|++|+|+++.++.+|
T Consensus        79 l~~L~~L~Ls~N~l--~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~  144 (220)
T 2v9t_B           79 LRSLNSLVLYGNKI--TELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQTIA  144 (220)
T ss_dssp             CSSCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCC
T ss_pred             CcCCCEEECCCCcC--CccCHhHccCCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCCCcCCEEC
Confidence            46677777776653  3567778889999999999988   33 45566  88999999999888887

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.63  E-value=0.0062  Score=60.57  Aligned_cols=48  Identities=23%  Similarity=0.375  Sum_probs=39.6

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..++|.+..++.+...+..+    ..+.|+|++|+||||||+.++.......
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~l~~~~   88 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAELLPTET   88 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHTSCCSS
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhccCCccc
Confidence            45899999998888888743    3789999999999999999998664443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.63  E-value=0.0085  Score=52.18  Aligned_cols=26  Identities=23%  Similarity=0.468  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ...+|+|.|..|+|||||++.++..+
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            44689999999999999999998865

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.61  E-value=0.0074  Score=55.08  Aligned_cols=25  Identities=24%  Similarity=0.355  Sum_probs=22.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|.|+.|+||||||..++..+.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            5899999999999999999998753

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=95.61  E-value=0.0076  Score=48.89  Aligned_cols=17  Identities=18%  Similarity=-0.052  Sum_probs=8.2

Q ss_pred             CCeeEEEcCCCCCCCCC
Q 044214          364 CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       364 ~~LryL~l~~~~~~~lP  380 (385)
                      .+|++|++++|++..+|
T Consensus       120 ~~L~~L~l~~N~l~~~~  136 (168)
T 2ell_A          120 ECLKSLDLFNCEVTNLN  136 (168)
T ss_dssp             SCCCEEECCSSGGGTST
T ss_pred             CCCCEEEeeCCcCcchH
Confidence            44555555555444444

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=95.61  E-value=0.0087  Score=54.19  Aligned_cols=29  Identities=24%  Similarity=0.389  Sum_probs=25.1

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ....+|+|.|..|+|||||++.+...+..
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhccc
Confidence            45679999999999999999999986653

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=95.60  E-value=0.034  Score=53.00  Aligned_cols=53  Identities=23%  Similarity=0.296  Sum_probs=37.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      +.++|.|.+|+|||+|+..+++.+. .+-+..+++- +++.   .....++.+++...
T Consensus       166 qr~gIfgg~GvGKT~L~~~l~~~~a~~~~~v~V~~~-iGER---~rEv~e~~~~~~~~  219 (498)
T 1fx0_B          166 GKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGG-VGER---TREGNDLYMEMKES  219 (498)
T ss_dssp             CCEEEEECSSSSHHHHHHHHHHHTTTTCSSCEEEEE-ESCC---SHHHHHHHHHHHHT
T ss_pred             CeEEeecCCCCCchHHHHHHHHHHHhhCCCEEEEEE-cccC---cHHHHHHHHhhhcc
Confidence            4689999999999999999998764 3445566664 3332   14566677766553

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=95.59  E-value=0.0079  Score=50.64  Aligned_cols=24  Identities=25%  Similarity=0.383  Sum_probs=22.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|+|.|..|+||||+|+.++..+.
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            799999999999999999998764

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=95.59  E-value=0.014  Score=47.78  Aligned_cols=60  Identities=12%  Similarity=0.074  Sum_probs=49.8

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++.+|++|+|+++   .+|.. +.  .+|++|+++++++...|
T Consensus        56 l~~L~~L~Ls~N~l--~~i~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~~~c~~  121 (174)
T 2r9u_A           56 LVNLQQLYFNSNKL--TAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCEC  121 (174)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCBCTTB
T ss_pred             CcCCCEEECCCCCC--CccChhHhCCcchhhEEECCCCccceeCHHHhccccCCCEEEeCCCCccccc
Confidence            56788888877753  4567788999999999999998   67765 66  89999999999998776

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.58  E-value=0.0047  Score=54.04  Aligned_cols=25  Identities=24%  Similarity=0.430  Sum_probs=22.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..|+|+|+.|+||||+++.++..+.
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcC
Confidence            3799999999999999999998764

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=95.58  E-value=0.057  Score=51.63  Aligned_cols=27  Identities=26%  Similarity=0.363  Sum_probs=23.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      .+.|.|.+|+|||+++..+...+....
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~   73 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTG   73 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcC
Confidence            889999999999999999998764443

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=95.58  E-value=0.012  Score=50.39  Aligned_cols=34  Identities=12%  Similarity=-0.169  Sum_probs=25.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .|.+.|.||+||||+|..++......-..+.++.
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d   41 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGV   41 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEE
Confidence            4788999999999999999987654433344443

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=95.58  E-value=0.008  Score=51.89  Aligned_cols=26  Identities=23%  Similarity=0.183  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|.|.|++|+||||+|+.+++++.
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35799999999999999999998764

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=95.57  E-value=0.008  Score=51.11  Aligned_cols=23  Identities=30%  Similarity=0.315  Sum_probs=21.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|+|.|++|+||||+|+.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999876

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=95.57  E-value=0.0092  Score=60.80  Aligned_cols=49  Identities=24%  Similarity=0.369  Sum_probs=37.0

Q ss_pred             CCccccchhHHHHHHhhcC-----------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLGV-----------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~-----------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ....|.++..++|.+.+..           +-...+-|.++|++|+|||.+|+++++...
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~  536 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ  536 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTT
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhC
Confidence            4567888888888776542           112345688999999999999999998654

>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=95.56  E-value=0.012  Score=48.30  Aligned_cols=27  Identities=22%  Similarity=0.379  Sum_probs=23.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++++|+|..|+|||||+..+...+..
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            568999999999999999999987643

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=95.54  E-value=0.016  Score=51.06  Aligned_cols=35  Identities=23%  Similarity=0.361  Sum_probs=27.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|.|-||+||||+|..++..+...-..+..+.
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~G~~VlliD   36 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVG   36 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHCCCcEEEEc
Confidence            57888999999999999999987765544455554

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.54  E-value=0.019  Score=54.74  Aligned_cols=36  Identities=19%  Similarity=0.037  Sum_probs=28.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -.++.|.|.+|+||||||..++......-..++|++
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            358999999999999999999987644333556664

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=95.53  E-value=0.01  Score=58.84  Aligned_cols=61  Identities=11%  Similarity=0.078  Sum_probs=38.9

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+.  -..+++.+|.++++|++|+|+++   .+|. .|.  .+|++|++++|.++.+|.
T Consensus        75 l~~L~~L~Ls~N~--i~~i~~~~f~~L~~L~~L~Ls~N~l~~l~~~~f~~L~~L~~L~Ls~N~l~~l~~  141 (635)
T 4g8a_A           75 FPELQVLDLSRCE--IQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLEN  141 (635)
T ss_dssp             CTTCCEEECTTCC--CCEECTTTTTTCTTCCEEECTTCCCCEECGGGGTTCTTCCEEECTTSCCCCSTT
T ss_pred             CCCCCEEECCCCc--CCCcChhHhcCCCCCCEEEccCCcCCCCCHHHhcCCCCCCEEECCCCcCCCCCh
Confidence            3445555555443  23456667777777777777776   5554 344  777777777777777773

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=95.53  E-value=0.021  Score=46.67  Aligned_cols=56  Identities=16%  Similarity=0.125  Sum_probs=27.1

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGV  377 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~  377 (385)
                      .+++.+.+.....  ..+++..|.++++|++|+|+++   .+|..+ .  .+|++|+++++++.
T Consensus        76 ~~L~~L~l~~N~l--~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~  137 (177)
T 2o6r_A           76 TKLTILYLHENKL--QSLPNGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWD  137 (177)
T ss_dssp             TTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCBC
T ss_pred             CccCEEECCCCCc--cccCHHHhhCCcccCEEECcCCcceEeCHHHhcCCcccCEEEecCCCee
Confidence            3444444444332  2334444555555555555554   444332 2  45555555555543

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.53  E-value=0.0082  Score=51.47  Aligned_cols=23  Identities=35%  Similarity=0.447  Sum_probs=21.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|+|.|++|+||||+|+.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999876

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=95.50  E-value=0.0074  Score=61.45  Aligned_cols=62  Identities=18%  Similarity=0.165  Sum_probs=49.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC-CCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN-NFG  383 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP-~~~  383 (385)
                      ...++.|.+.....  ..++...| ++.+|++|+|+++   .+|.+|+  .+|++|+|++|.++.+| .|+
T Consensus       223 l~~L~~L~Ls~n~l--~~l~~~~~-~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~  290 (727)
T 4b8c_D          223 DQLWHALDLSNLQI--FNISANIF-KYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELG  290 (727)
T ss_dssp             CCCCCEEECTTSCC--SCCCGGGG-GCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCSSCCSSGG
T ss_pred             CCCCcEEECCCCCC--CCCChhhc-CCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCCccChhhc
Confidence            45677777766653  24555655 8999999999998   7888888  99999999999999999 553

>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=95.49  E-value=0.017  Score=50.61  Aligned_cols=27  Identities=22%  Similarity=0.252  Sum_probs=24.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...++.+.|.||+||||++..++..+.
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            467889999999999999999998766

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.49  E-value=0.0081  Score=54.41  Aligned_cols=24  Identities=33%  Similarity=0.378  Sum_probs=22.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++|.|+|+.|+||||||..+++++
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            589999999999999999999865

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=95.48  E-value=0.0065  Score=49.82  Aligned_cols=26  Identities=27%  Similarity=0.371  Sum_probs=22.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++++|+|..|+|||||++.+...+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            57999999999999999999986644

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=95.47  E-value=0.022  Score=47.91  Aligned_cols=60  Identities=17%  Similarity=0.188  Sum_probs=40.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++++|++|+|+++   .+|.. +.  .+|++|+++++.++.+|
T Consensus        51 l~~L~~L~l~~n~l--~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~  116 (208)
T 2o6s_A           51 LTSLTQLYLGGNKL--QSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTNQLQSLP  116 (208)
T ss_dssp             CTTCSEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             cccCcEEECCCCcc--CccChhhcCCCCCcCEEECCCCcCCccCHhHhcCccCCCEEEcCCCcCcccC
Confidence            45566666665543  2455666778888888888877   44543 34  78888888888887777

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=95.47  E-value=0.0092  Score=51.51  Aligned_cols=26  Identities=19%  Similarity=0.450  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+|+|.|++|+||||+|+.+++.+.
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35899999999999999999998763

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=95.46  E-value=0.017  Score=52.94  Aligned_cols=60  Identities=15%  Similarity=0.105  Sum_probs=45.8

Q ss_pred             cCCeeEEEeec-CCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDM-SKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~-~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.|.+.. ..  ...+++..|.++.+|+.|+|+++   .+| ..|.  .+|++|+|+++.+..+|
T Consensus        30 ~~~L~~L~l~~~n~--l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~   96 (347)
T 2ifg_A           30 AENLTELYIENQQH--LQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLS   96 (347)
T ss_dssp             CSCCSEEECCSCSS--CCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCC
T ss_pred             CCCeeEEEccCCCC--CCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCccceeC
Confidence            34577777764 43  34567788999999999999988   444 4556  89999999999999988

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.44  E-value=0.061  Score=51.21  Aligned_cols=52  Identities=15%  Similarity=-0.014  Sum_probs=36.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l  110 (385)
                      -.++.|.|.+|+||||||..++..+... -..++|++ .     . .+...+...++...
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~s-l-----E-~~~~~l~~R~~~~~  252 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYS-L-----E-MPAAQLTLRMMCSE  252 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE-S-----S-SCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE-C-----C-CCHHHHHHHHHHHH
Confidence            3589999999999999999999876432 23566665 2     1 44556666665543

>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=95.43  E-value=0.0086  Score=50.64  Aligned_cols=25  Identities=24%  Similarity=0.480  Sum_probs=22.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+++|+|+.|+|||||++.+...+.
T Consensus        21 ei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4899999999999999999988653

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.42  E-value=0.0074  Score=54.91  Aligned_cols=26  Identities=19%  Similarity=0.271  Sum_probs=22.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|+|+|+.|+||||||..+++++
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHC
Confidence            34689999999999999999999854

>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=95.42  E-value=0.011  Score=53.17  Aligned_cols=26  Identities=23%  Similarity=0.151  Sum_probs=23.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|+|.|+.|+||||||..++++.
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhC
Confidence            45789999999999999999999864

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.39  E-value=0.0068  Score=51.83  Aligned_cols=24  Identities=33%  Similarity=0.703  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|+|+.|+|||||++.+....
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            579999999999999999998865

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.39  E-value=0.0048  Score=55.35  Aligned_cols=27  Identities=15%  Similarity=0.218  Sum_probs=20.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..+|+|.|..|+||||+|+.+.+.+.
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999988654

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=95.38  E-value=0.024  Score=47.61  Aligned_cols=61  Identities=13%  Similarity=0.129  Sum_probs=47.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ...++.+.+.....  ..+++..|.++++|++|+|+++   .+|.. +.  .+|++|+++++.++.+|.
T Consensus        75 l~~L~~L~Ls~n~l--~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~  141 (208)
T 2o6s_A           75 LTSLTYLNLSTNQL--QSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPD  141 (208)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCT
T ss_pred             CCCcCEEECCCCcC--CccCHhHhcCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCCCccceeCH
Confidence            56778887776653  3566777899999999999988   55554 45  899999999999988883

>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=95.38  E-value=0.017  Score=50.80  Aligned_cols=36  Identities=22%  Similarity=0.211  Sum_probs=27.2

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +..++....++...+.++|++|.|||.+|..+++.+
T Consensus        93 l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           93 FLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            455555332444579999999999999999999853

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=95.37  E-value=0.022  Score=51.46  Aligned_cols=28  Identities=32%  Similarity=0.421  Sum_probs=24.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ....+|+|.|..|+|||||++.+...+.
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4457999999999999999999998765

>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=95.36  E-value=0.011  Score=47.73  Aligned_cols=26  Identities=31%  Similarity=0.392  Sum_probs=23.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-.+++|.|+.|+|||||++.++..+
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            34589999999999999999999866

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.36  E-value=0.013  Score=51.53  Aligned_cols=110  Identities=11%  Similarity=0.051  Sum_probs=60.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCce
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMK  131 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~  131 (385)
                      -.+++|+|+.|+|||||++.+...+...+.+.+++.... ....+.....+..+  ..++.  ........+.+.+..++
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g~~-i~~~~~~~~~~v~q--~~~gl--~~~~l~~~la~aL~~~p   99 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDP-IEYVFKHKKSIVNQ--REVGE--DTKSFADALRAALREDP   99 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEESS-CCSCCCCSSSEEEE--EEBTT--TBSCHHHHHHHHHHHCC
T ss_pred             CCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcCCc-ceeecCCcceeeeH--HHhCC--CHHHHHHHHHHHHhhCC
Confidence            358999999999999999999886644334555543211 10000000000000  00000  01133455666666677


Q ss_pred             EEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEeccHH
Q 044214          132 VLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus       132 ~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      =+|++|...+.+....+....   ..|.-|++||.+.+
T Consensus       100 ~illlDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~  134 (261)
T 2eyu_A          100 DVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNT  134 (261)
T ss_dssp             SEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSS
T ss_pred             CEEEeCCCCCHHHHHHHHHHH---ccCCEEEEEeCcch
Confidence            789999997665554444332   24666888887654

>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=95.33  E-value=0.0092  Score=53.66  Aligned_cols=24  Identities=21%  Similarity=0.329  Sum_probs=21.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++|+|.|+.|+||||||..+++++
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhC
Confidence            589999999999999999999754

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=95.32  E-value=0.017  Score=51.47  Aligned_cols=36  Identities=22%  Similarity=0.372  Sum_probs=27.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++|+|.|-||+||||+|..++..+...-..+..+.
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~~G~rVlliD   37 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVG   37 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            468888999999999999999987654433444444

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.31  E-value=0.026  Score=54.47  Aligned_cols=38  Identities=18%  Similarity=0.159  Sum_probs=27.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.++|+|+|.+|+||||++..++..+...-..+..+.
T Consensus        99 ~~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd  136 (504)
T 2j37_W           99 GKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLIC  136 (504)
T ss_dssp             S--EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEe
Confidence            34679999999999999999999987654422344443

>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=95.31  E-value=0.016  Score=52.00  Aligned_cols=35  Identities=14%  Similarity=0.079  Sum_probs=26.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC-ceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD-GSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~-~~~w~~   87 (385)
                      .+++|.|.+|+|||||++.++..+..... .++|+.
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            48999999999999999999987654322 455554

>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=95.30  E-value=0.0092  Score=51.07  Aligned_cols=26  Identities=15%  Similarity=0.202  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+++|+|+.|+|||||.+.+.....
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            35899999999999999999998654

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.29  E-value=0.043  Score=52.44  Aligned_cols=35  Identities=14%  Similarity=0.162  Sum_probs=27.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~   87 (385)
                      .++.|.|.+|+||||||..++..+.. .-..++|++
T Consensus       204 ~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          204 DLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            58999999999999999999986643 223566665

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=95.28  E-value=0.027  Score=48.04  Aligned_cols=60  Identities=13%  Similarity=0.146  Sum_probs=39.8

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|..+++|++|+|+++   .+ |..+.  .+|++|+|+++.++.+|
T Consensus        80 l~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~  145 (220)
T 2v70_A           80 ASGVNEILLTSNRL--ENVQHKMFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQITTVA  145 (220)
T ss_dssp             CTTCCEEECCSSCC--CCCCGGGGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSCCCCBC
T ss_pred             CCCCCEEECCCCcc--CccCHhHhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCcCCEEC
Confidence            44566666655542  3455666777888888888777   23 45565  77888888888777763

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=95.28  E-value=0.01  Score=53.24  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+|.|.|++|+||||+|+.+.++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57999999999999999999874

>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=95.27  E-value=0.043  Score=46.61  Aligned_cols=27  Identities=19%  Similarity=0.263  Sum_probs=24.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..|+|.|+.|+||||+++.+.+.+...
T Consensus         7 ~~i~~eG~~gsGKsT~~~~l~~~l~~~   33 (213)
T 4edh_A            7 LFVTLEGPEGAGKSTNRDYLAERLRER   33 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999988654

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=95.24  E-value=0.0058  Score=48.48  Aligned_cols=17  Identities=18%  Similarity=0.018  Sum_probs=8.3

Q ss_pred             CCeeEEEcCCCCCCCCC
Q 044214          364 CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       364 ~~LryL~l~~~~~~~lP  380 (385)
                      .+|++|++++|++..+|
T Consensus       113 ~~L~~L~l~~N~l~~~~  129 (149)
T 2je0_A          113 ENLKSLDLFNCEVTNLN  129 (149)
T ss_dssp             TTCCEEECTTCGGGGST
T ss_pred             CCCCEEeCcCCcccchH
Confidence            44555555555444444

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=95.24  E-value=0.025  Score=48.21  Aligned_cols=60  Identities=10%  Similarity=0.024  Sum_probs=45.9

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++++|++|+|+++   .+|. .+.  .+|++|+++++.++.+|
T Consensus        56 l~~L~~L~L~~N~i--~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~  121 (220)
T 2v70_A           56 LPQLRKINFSNNKI--TDIEEGAFEGASGVNEILLTSNRLENVQHKMFKGLESLKTLMLRSNRITCVG  121 (220)
T ss_dssp             CTTCCEEECCSSCC--CEECTTTTTTCTTCCEEECCSSCCCCCCGGGGTTCSSCCEEECTTSCCCCBC
T ss_pred             CCCCCEEECCCCcC--CEECHHHhCCCCCCCEEECCCCccCccCHhHhcCCcCCCEEECCCCcCCeEC
Confidence            45677777766653  3466778999999999999988   4444 355  89999999999998874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.23  E-value=0.034  Score=61.88  Aligned_cols=80  Identities=16%  Similarity=0.134  Sum_probs=49.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC---------chHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM---------PYID  121 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~---------~~~~  121 (385)
                      ..+.|.|+|++|+|||+||.+++.....+-..++|+. ..+.    .+...     ++.++.+..+.         +...
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~-~e~~----~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~ 1495 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID-AEHA----LDPIY-----ARKLGVDIDNLLCSQPDTGEQALE 1495 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC-TTSC----CCHHH-----HHHTTCCTTTCEEECCSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEE-cccc----cCHHH-----HHHcCCCchhceeecCChHHHHHH
Confidence            3568999999999999999999987766655677776 2221    22222     33333111111         3333


Q ss_pred             HHHHHh-CCceEEEEEeCCC
Q 044214          122 LNFRRL-GHMKVLIVFDDVT  140 (385)
Q Consensus       122 ~l~~~l-~~k~~LlVlDdv~  140 (385)
                      .+.+.. ..+.-+||+|.+.
T Consensus      1496 ~~~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1496 ICDALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHHHHTCCSEEEESCGG
T ss_pred             HHHHHHhcCCCCEEEEcChh
Confidence            333333 2567899999994

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.22  E-value=0.01  Score=49.47  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +++|+|..|+|||||++.++..++
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            689999999999999999998654

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=95.19  E-value=0.023  Score=51.53  Aligned_cols=59  Identities=15%  Similarity=0.106  Sum_probs=38.1

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+....  -..+++..|.++++|++|+|+++   .+ |..++  .+|++|+++++.++.+|
T Consensus        52 ~~l~~L~L~~n~--i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~l~  116 (330)
T 1xku_A           52 PDTALLDLQNNK--ITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELP  116 (330)
T ss_dssp             TTCCEEECCSSC--CCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCC
T ss_pred             CCCeEEECCCCc--CCEeChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEECCCCcCCccC
Confidence            345555555443  23345556777777777777776   33 55666  77777777777777777

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=95.17  E-value=0.022  Score=55.67  Aligned_cols=47  Identities=19%  Similarity=0.322  Sum_probs=31.7

Q ss_pred             cccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           32 VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +.+.+..+.+.......-.+-.+++|+|+.|+|||||++.++..+..
T Consensus       349 f~~peV~~vLR~~~~~~~~~G~iI~LiG~sGSGKSTLar~La~~L~~  395 (552)
T 3cr8_A          349 YSFPEVLAELHRQTPPRERQGFTVFFTGLSGAGKSTLARALAARLME  395 (552)
T ss_dssp             TSCHHHHHHHHHHSCCGGGSCEEEEEEESSCHHHHHHHHHHHHHHHT
T ss_pred             ccccchhhhhhhhcccccccceEEEEECCCCChHHHHHHHHHHhhcc
Confidence            34444444444433211123468999999999999999999998764

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=95.17  E-value=0.029  Score=51.56  Aligned_cols=39  Identities=18%  Similarity=0.270  Sum_probs=30.4

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhh--CCCCceEEEe
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKIS--GDFDGSCFLE   87 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~--~~f~~~~w~~   87 (385)
                      ....+++.+.|-||+||||+|..++..+.  ..-..+.-+.
T Consensus        15 ~~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~g~~vllid   55 (348)
T 3io3_A           15 HDSLKWIFVGGKGGVGKTTTSSSVAVQLALAQPNEQFLLIS   55 (348)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHHHHHHHCTTSCEEEEE
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            34567999999999999999999998776  5544555554

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=95.16  E-value=0.024  Score=56.14  Aligned_cols=59  Identities=14%  Similarity=0.161  Sum_probs=29.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+..+..  ..+.+..|.++++||+|+|+++   .+ |..|+  .+|++|++++|.+..+|
T Consensus        56 ~~L~~L~Ls~n~l--~~i~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~  120 (606)
T 3vq2_A           56 SELQWLDLSRCEI--ETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLE  120 (606)
T ss_dssp             TTCCEEECTTCCC--CEECTTTTTTCTTCCEEECTTCCCCCCCTTSSTTCTTCCEEECTTSCCCCSS
T ss_pred             ccCcEEeCCCCcc--cccCHHHhhchhhcCEeECCCCcccccChhhcCCcccCCEEEccCCcccccc
Confidence            3444444444332  2344455555566666666555   22 44454  55555555555555544

>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=95.14  E-value=0.024  Score=50.30  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=22.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .++.|+|.+|+|||||+..++..+..
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~~~~~   56 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAAQIAG   56 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            48999999999999999999976543

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=95.12  E-value=0.031  Score=51.24  Aligned_cols=29  Identities=28%  Similarity=0.315  Sum_probs=24.8

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+..+|+|+|.+|+|||||+..++....
T Consensus        53 ~~~~~~i~i~G~~g~GKSTl~~~l~~~~~   81 (341)
T 2p67_A           53 CGNTLRLGVTGTPGAGKSTFLEAFGMLLI   81 (341)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            45668999999999999999999987654

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.11  E-value=0.022  Score=51.08  Aligned_cols=36  Identities=22%  Similarity=0.147  Sum_probs=27.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ...+++|+|.+|+||||++..++..+...-..+.++
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~  132 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            357899999999999999999998765443334444

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=95.11  E-value=0.03  Score=50.82  Aligned_cols=60  Identities=12%  Similarity=0.160  Sum_probs=46.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+.+..|..+++|+.|+|+++   .+|..+.  .+|++|++++|+++.+|
T Consensus       215 l~~L~~L~Ls~n~l--~~~~~~~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~L~~L~l~~N~i~~~~  279 (330)
T 1xku_A          215 LNNLAKLGLSFNSI--SAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIG  279 (330)
T ss_dssp             CTTCCEEECCSSCC--CEECTTTGGGSTTCCEEECCSSCCSSCCTTTTTCSSCCEEECCSSCCCCCC
T ss_pred             CCCCCEEECCCCcC--ceeChhhccCCCCCCEEECCCCcCccCChhhccCCCcCEEECCCCcCCccC
Confidence            45667777666543  3345567888899999999988   7788777  88999999999998887

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=95.10  E-value=0.014  Score=50.41  Aligned_cols=27  Identities=26%  Similarity=0.331  Sum_probs=23.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+|+|.|+.|+||||+++.++..+
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            345689999999999999999999865

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=95.10  E-value=0.014  Score=49.11  Aligned_cols=44  Identities=18%  Similarity=0.184  Sum_probs=20.2

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..--|+....+.+.+...  ..+.-.|+|+|.+|+|||||...+.+
T Consensus         9 ~~~~~~~~~~~~m~~~~~--~~~~~ki~vvG~~~~GKSsLi~~l~~   52 (204)
T 4gzl_A            9 HHSSGLVPRGSHMENLYF--QGQAIKCVVVGDGAVGKTCLLISYTT   52 (204)
T ss_dssp             -----------------------CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cccCCcccchhHHHhHhh--cCCeEEEEEECcCCCCHHHHHHHHHh
Confidence            333444444555544443  23345678999999999999998886

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=95.09  E-value=0.038  Score=46.74  Aligned_cols=109  Identities=12%  Similarity=-0.008  Sum_probs=54.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCC--CCchHHHHHHHhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKN--VMPYIDLNFRRLG  128 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~--~~~~~~~l~~~l~  128 (385)
                      .-.+..++|..|.||||.+...+.+....-..++.+.....  .. ++...    +.+.++....  .......+.+...
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d--~R-~ge~~----i~s~~g~~~~a~~~~~~~~~~~~~~   99 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCID--NR-YSEED----VVSHNGLKVKAVPVSASKDIFKHIT   99 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC------------------------CCEEECSSGGGGGGGCC
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccC--Cc-chHHH----HHhhcCCeeEEeecCCHHHHHHHHh
Confidence            34688999999999999999998876554434444431111  11 22222    2233222211  0111122333333


Q ss_pred             CceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEEEeccHH
Q 044214          129 HMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNKQ  169 (385)
Q Consensus       129 ~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilvTtR~~~  169 (385)
                      ++-=+|++|.+.  +.++++.+. .+.  ..|-.||+|.++.+
T Consensus       100 ~~~dvViIDEaQF~~~~~V~~l~-~l~--~~~~~Vi~~Gl~~D  139 (214)
T 2j9r_A          100 EEMDVIAIDEVQFFDGDIVEVVQ-VLA--NRGYRVIVAGLDQD  139 (214)
T ss_dssp             SSCCEEEECCGGGSCTTHHHHHH-HHH--HTTCEEEEEECSBC
T ss_pred             cCCCEEEEECcccCCHHHHHHHH-HHh--hCCCEEEEEecccc
Confidence            333499999984  344453333 222  13678999999654

>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=95.07  E-value=0.027  Score=48.42  Aligned_cols=28  Identities=21%  Similarity=0.321  Sum_probs=24.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ....|+|.|++|+||||+++.+.+.+..
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            4568999999999999999999998765

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=95.07  E-value=0.015  Score=50.44  Aligned_cols=26  Identities=23%  Similarity=0.259  Sum_probs=23.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...|+|.|..|+||||+++.+++.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999998764

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=95.05  E-value=0.02  Score=45.24  Aligned_cols=56  Identities=16%  Similarity=0.154  Sum_probs=31.3

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcc----cCCCCC--CCeeEEEcCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSS----FNGENK--CKISYLQDPGFAGVKL  379 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~----lp~~i~--~~LryL~l~~~~~~~l  379 (385)
                      .+++.+.+..+.....    ..|.++++|++|+|+++.    +|..++  .+|++|++++|.++.+
T Consensus        42 ~~L~~L~l~~n~l~~~----~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~ls~N~i~~~  103 (149)
T 2je0_A           42 EELEFLSTINVGLTSI----ANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDL  103 (149)
T ss_dssp             TTCCEEECTTSCCCCC----TTCCCCTTCCEEECCSSCCCSCTHHHHHHCTTCCEEECTTSCCCSH
T ss_pred             CCCcEEECcCCCCCCc----hhhhcCCCCCEEECCCCcccchHHHHhhhCCCCCEEECCCCcCCCh
Confidence            4455555554432211    556666677777776662    333333  6677777777766654

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=95.04  E-value=0.011  Score=56.15  Aligned_cols=37  Identities=24%  Similarity=0.191  Sum_probs=27.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.+|+|+|.+|+||||++..++......-..+..+.
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3568999999999999999999986643322344443

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.03  E-value=0.0079  Score=51.80  Aligned_cols=24  Identities=29%  Similarity=0.375  Sum_probs=16.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHH-HHh
Q 044214           53 YALGIWGIGGIGKTTIARAIF-DKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~-~~~   76 (385)
                      .+++|+|+.|+|||||++.+. ...
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC---
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            589999999999999999998 654

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=95.03  E-value=0.034  Score=48.26  Aligned_cols=59  Identities=14%  Similarity=0.221  Sum_probs=33.4

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .+++.+.+.....  ..+++..|.++.+|++|+|+++   .+|. .++  .+|++|+++++.++.+|
T Consensus       107 ~~L~~L~L~~N~l--~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~  171 (251)
T 3m19_A          107 TQLDKLYLGGNQL--KSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQLQSVP  171 (251)
T ss_dssp             TTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCC
T ss_pred             CCCCEEEcCCCcC--CCcChhHhccCCcccEEECcCCcCCccCHHHcCcCcCCCEEECCCCcCCccC
Confidence            4455555554432  2344555666666666666665   3443 344  56666666666666665

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=95.03  E-value=0.029  Score=45.69  Aligned_cols=60  Identities=13%  Similarity=0.065  Sum_probs=48.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++++|++|+|+++   .+|.. +.  .+|++|+|+++++...+
T Consensus        53 l~~L~~L~Ls~N~l--~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~~~c~c  118 (170)
T 3g39_A           53 LTQLTRLDLDNNQL--TVLPAGVFDKLTQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWLLNNPWDCAC  118 (170)
T ss_dssp             CTTCSEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCBCTTB
T ss_pred             cccCCEEECCCCCc--CccChhhccCCCCCCEEECCCCccCEeCHHHhcCCCCCCEEEeCCCCCCCCc
Confidence            56788888877653  3677888999999999999998   66654 66  89999999999887654

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=95.01  E-value=0.027  Score=46.83  Aligned_cols=58  Identities=7%  Similarity=0.033  Sum_probs=26.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKL  379 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~l  379 (385)
                      .+++.+.+.....  ..+.+..|.++.+|++|+|+++   .+| ..+.  .+|++|+++++.+..+
T Consensus        54 ~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~  117 (192)
T 1w8a_A           54 PHLVKLELKRNQL--TGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCV  117 (192)
T ss_dssp             TTCCEEECCSSCC--CCBCTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEE
T ss_pred             CCCCEEECCCCCC--CCcCHhHcCCcccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCee
Confidence            3444444444332  2233444555555555555554   222 2233  5555555555555443

>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=95.01  E-value=0.011  Score=49.52  Aligned_cols=24  Identities=25%  Similarity=0.336  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.|.|.|.+|+||||||.+++++.
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            568999999999999999998753

>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=95.00  E-value=0.36  Score=41.46  Aligned_cols=40  Identities=23%  Similarity=0.091  Sum_probs=28.8

Q ss_pred             cccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           32 VGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        32 vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -=|+...+.+..++..   +  -+.|+|..|.|||.+|..++...
T Consensus        93 ~l~~~Q~~ai~~~~~~---~--~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A           93 SLRDYQEKALERWLVD---K--RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             CCCHHHHHHHHHHTTT---S--EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHHHHhC---C--CEEEEeCCCCCHHHHHHHHHHHc
Confidence            3355556666666552   1  27789999999999999888765

>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=95.00  E-value=0.091  Score=51.73  Aligned_cols=27  Identities=26%  Similarity=0.241  Sum_probs=23.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +++.|+|.+|.||||++..+...+...
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~  231 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESL  231 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            488899999999999999999866544

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=95.00  E-value=0.025  Score=56.05  Aligned_cols=59  Identities=12%  Similarity=0.066  Sum_probs=39.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKL  379 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~l  379 (385)
                      ..+++.+.+.....  ..+++..|.++.+|++|+|+++   .+|. .|+  .+|++|+++++.+..+
T Consensus        99 L~~L~~L~Ls~N~l--~~l~~~~f~~L~~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~l~~~  163 (635)
T 4g8a_A           99 LSHLSTLILTGNPI--QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSF  163 (635)
T ss_dssp             CTTCCEEECTTCCC--CEECGGGGTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCC
T ss_pred             CCCCCEEEccCCcC--CCCCHHHhcCCCCCCEEECCCCcCCCCChhhhhcCcccCeeccccCccccC
Confidence            45666666665542  3456677788888888888776   4544 355  7788888887777653

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=94.99  E-value=0.012  Score=57.90  Aligned_cols=57  Identities=7%  Similarity=-0.046  Sum_probs=41.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKL  379 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~l  379 (385)
                      ..+++.+.+..+...   ..+..|.++++|++|+|+++   .+| +++  .+|++|+|++|.++.+
T Consensus       462 l~~L~~L~Ls~N~l~---~lp~~~~~l~~L~~L~Ls~N~l~~lp-~l~~l~~L~~L~Ls~N~l~~~  523 (567)
T 1dce_A          462 LLLVTHLDLSHNRLR---ALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCNNRLQQS  523 (567)
T ss_dssp             GTTCCEEECCSSCCC---CCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCSSCCCSS
T ss_pred             cccCcEeecCccccc---ccchhhhcCCCCCEEECCCCCCCCCc-ccCCCCCCcEEECCCCCCCCC
Confidence            456677777666432   23456778888888888887   666 566  7888888888888877

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.98  E-value=0.016  Score=46.13  Aligned_cols=22  Identities=18%  Similarity=0.330  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +.|+|+|.+|+|||||...+..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~   23 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLK   23 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999999986

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=94.94  E-value=0.035  Score=50.71  Aligned_cols=38  Identities=21%  Similarity=0.264  Sum_probs=29.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+++.+.|-||+||||+|..++..+...-..+..+.
T Consensus        14 ~~~~i~~~sgkGGvGKTt~a~~lA~~la~~g~~vllid   51 (334)
T 3iqw_A           14 RSLRWIFVGGKGGVGKTTTSCSLAIQLAKVRRSVLLLS   51 (334)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHTTSSSCEEEEE
T ss_pred             CCeEEEEEeCCCCccHHHHHHHHHHHHHhCCCcEEEEE
Confidence            34578889999999999999999987766544555554

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=94.92  E-value=0.013  Score=47.37  Aligned_cols=61  Identities=16%  Similarity=0.242  Sum_probs=42.3

Q ss_pred             cCCeeEEEeecCCceeeeeCc-cccCCCCCCcEEEecCc---ccCC----CCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNT-STFTKMPKLRFLKFYSS---SFNG----ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~-~~~~~~~~LrvL~l~~~---~lp~----~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+...  .++. ..|.++++|++|+|+++   .+|.    .+.  .+|++|++++|.+..+|+
T Consensus        94 l~~L~~L~Ls~N~l~--~~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l~~n~~~~~~~  164 (168)
T 2ell_A           94 LPNLTHLNLSGNKLK--DISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDREDQEAPD  164 (168)
T ss_dssp             CTTCCEEECBSSSCC--SSGGGGGGSSCSCCCEEECCSSGGGTSTTHHHHHHTTCSSCCEETTEETTSCBCCS
T ss_pred             CCCCCEEeccCCccC--cchhHHHHhcCCCCCEEEeeCCcCcchHHHHHHHHHhCccCcEecCCCCChhhccc
Confidence            456667766665431  1221 56788888888888887   5555    455  788888888888888884

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=94.92  E-value=0.014  Score=48.69  Aligned_cols=41  Identities=10%  Similarity=0.020  Sum_probs=24.4

Q ss_pred             ccccCCCCCCcEEEecCcc----cCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          339 TSTFTKMPKLRFLKFYSSS----FNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       339 ~~~~~~~~~LrvL~l~~~~----lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      +..|.++++|+.|+|++|.    +| .+.  .+|++|++++|.+..+|
T Consensus       129 ~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~i~~~~  175 (197)
T 4ezg_A          129 LTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDGVHDYR  175 (197)
T ss_dssp             HHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBCCCCCT
T ss_pred             HHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCCCcChH
Confidence            3455666666666666653    32 233  56777777776666655

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=94.91  E-value=0.041  Score=50.02  Aligned_cols=36  Identities=28%  Similarity=0.232  Sum_probs=27.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..++...|-||+||||+|..++..+...-..+.-++
T Consensus        14 ~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   49 (324)
T 3zq6_A           14 TTFVFIGGKGGVGKTTISAATALWMARSGKKTLVIS   49 (324)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEEeCCCCchHHHHHHHHHHHHHHCCCcEEEEe
Confidence            467788899999999999999987765544455554

>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=94.89  E-value=0.033  Score=54.79  Aligned_cols=28  Identities=25%  Similarity=0.292  Sum_probs=24.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +...+|.|.|++|+||||+|+.+.+++.
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHHhc
Confidence            3457899999999999999999998765

>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=94.88  E-value=0.016  Score=48.19  Aligned_cols=24  Identities=17%  Similarity=0.429  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ...|+|+|.+|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            457899999999999999999874

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=94.87  E-value=0.027  Score=54.79  Aligned_cols=30  Identities=17%  Similarity=0.100  Sum_probs=25.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ...+|.++|++|+||||+|+++++.+.-.|
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~~~~   63 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLNWIG   63 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcC
Confidence            456899999999999999999998764444

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=94.86  E-value=0.042  Score=53.76  Aligned_cols=46  Identities=17%  Similarity=0.177  Sum_probs=32.0

Q ss_pred             ccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           33 GVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        33 GR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .|.+..+.+.+..........+|.++|++|+||||+|+.+.+.+..
T Consensus       353 ~r~eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~  398 (546)
T 2gks_A          353 TRPEVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQA  398 (546)
T ss_dssp             SCHHHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhh
Confidence            3444444555555322234578999999999999999999987643

>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=94.85  E-value=0.021  Score=53.00  Aligned_cols=27  Identities=26%  Similarity=0.112  Sum_probs=23.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+++|+|++|+|||||++.++...
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            345689999999999999999999864

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=94.82  E-value=0.046  Score=48.11  Aligned_cols=60  Identities=15%  Similarity=0.174  Sum_probs=39.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+..+..  ..+++..|.++++|++|+|+++   .+|.. ++  .+|++|++++|.++.+|
T Consensus       108 l~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~  173 (272)
T 3rfs_A          108 LTNLKELVLVENQL--QSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLP  173 (272)
T ss_dssp             CTTCCEEECTTSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             CcCCCEEECCCCcC--CccCHHHhccCCCCCEEECCCCccCccCHHHhccCccCCEEECCCCCcCccC
Confidence            45566666655542  2455566777788888888777   44443 34  77888888888777776

>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=94.81  E-value=0.021  Score=46.11  Aligned_cols=22  Identities=32%  Similarity=0.557  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..|+|+|.+|+|||||...+..
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999999975

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=94.80  E-value=0.026  Score=51.83  Aligned_cols=61  Identities=13%  Similarity=0.253  Sum_probs=34.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+..  ..+.+..|.++++|++|+|+++   .+|.. ++  .+|++|++++|.++.+|.
T Consensus        75 l~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~  141 (353)
T 2z80_A           75 CVNLQALVLTSNGI--NTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGE  141 (353)
T ss_dssp             CTTCCEEECTTSCC--CEECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCSEEECTTCCCSSSCS
T ss_pred             CCCCCEEECCCCcc--CccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCCEEECCCCCCcccCc
Confidence            34455555554432  2344555666666666666665   34433 33  566666666666666654

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=94.80  E-value=0.036  Score=54.77  Aligned_cols=63  Identities=16%  Similarity=0.257  Sum_probs=49.9

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCC-C-CCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKL-N-NFG  383 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~l-P-~~~  383 (385)
                      ...++.+.+.....  ..+++..|.++++|++|+|+++   .+ |..++  .+||+|++++|.++.+ | .|+
T Consensus        31 ~~~l~~L~Ls~n~l--~~~~~~~~~~l~~L~~L~Ls~n~l~~i~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~  101 (606)
T 3vq2_A           31 PSSTKNIDLSFNPL--KILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFS  101 (606)
T ss_dssp             CTTCCEEECTTSCC--CEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCCCCTTSST
T ss_pred             CCCcCEEECCCCCc--CEeChhhccCCccCcEEeCCCCcccccCHHHhhchhhcCEeECCCCcccccChhhcC
Confidence            35677777776653  4567778999999999999988   44 56777  9999999999999988 5 453

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=94.77  E-value=0.036  Score=46.16  Aligned_cols=58  Identities=7%  Similarity=0.097  Sum_probs=45.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+......  .+ +..|.++++|++|+|+++   .+| ..+.  .+|++|+|+++.++.+|
T Consensus        31 ~~l~~L~L~~n~i~--~i-p~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~l~~i~   94 (193)
T 2wfh_A           31 RDVTELYLDGNQFT--LV-PKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNRLRCIP   94 (193)
T ss_dssp             TTCCEEECCSSCCC--SC-CGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCC
T ss_pred             CCCCEEECCCCcCc--hh-HHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCccCEeC
Confidence            46777777766542  23 378899999999999998   444 4466  89999999999999988

>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=94.76  E-value=0.019  Score=53.48  Aligned_cols=25  Identities=24%  Similarity=0.422  Sum_probs=22.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++|+|.|+.|+||||||..++..+.
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            5899999999999999999998753

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=94.75  E-value=0.012  Score=48.20  Aligned_cols=61  Identities=8%  Similarity=0.109  Sum_probs=47.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC--CCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG--ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~--~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+..  ..+++..|..+++|++|+|+++   .+|.  .++  .+|++|++++|++..+|.
T Consensus        63 l~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~l~~N~i~~~~~  130 (176)
T 1a9n_A           63 LRRLKTLLVNNNRI--CRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNPVTNKKH  130 (176)
T ss_dssp             CSSCCEEECCSSCC--CEECSCHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGGGSTT
T ss_pred             CCCCCEEECCCCcc--cccCcchhhcCCCCCEEECCCCcCCcchhhHhhhcCCCCCEEEecCCCCCCcHh
Confidence            45677777776654  3456677889999999999998   5665  566  899999999999988875

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=94.74  E-value=0.026  Score=48.57  Aligned_cols=61  Identities=11%  Similarity=0.125  Sum_probs=27.0

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecC-c---ccCC-CCC--CCeeEEEcCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYS-S---SFNG-ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~-~---~lp~-~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      .+++.+.+..... ...+++..|.++++|++|+|++ +   .+|. .+.  .+|++|++++|.++.+|.
T Consensus        55 ~~L~~L~l~~n~~-l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~~L~l~~n~l~~lp~  122 (239)
T 2xwt_C           55 PNISRIYVSIDVT-LQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFLGIFNTGLKMFPD  122 (239)
T ss_dssp             TTCCEEEEECCSS-CCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTCCEEEEEEECCCSCCC
T ss_pred             CCCcEEeCCCCCC-cceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCCEEeCCCCCCccccc
Confidence            3444444444320 1123344455555555555554 2   3332 222  455555555555555554

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=94.74  E-value=0.028  Score=55.22  Aligned_cols=42  Identities=14%  Similarity=0.021  Sum_probs=21.0

Q ss_pred             eCccccCCCCCCcEEEecCc---ccCCCCC-CCeeEEEcCCCCCCCC
Q 044214          337 LNTSTFTKMPKLRFLKFYSS---SFNGENK-CKISYLQDPGFAGVKL  379 (385)
Q Consensus       337 ~~~~~~~~~~~LrvL~l~~~---~lp~~i~-~~LryL~l~~~~~~~l  379 (385)
                      +.+..|.++++|++|+|+++   .+|.. . .+|++|++++|.+..+
T Consensus        91 ~~~~~~~~l~~L~~L~Ls~N~l~~lp~~-~l~~L~~L~Ls~N~l~~l  136 (562)
T 3a79_B           91 LDFHVFLFNQDLEYLDVSHNRLQNISCC-PMASLRHLDLSFNDFDVL  136 (562)
T ss_dssp             ECTTTTTTCTTCCEEECTTSCCCEECSC-CCTTCSEEECCSSCCSBC
T ss_pred             CCHHHhCCCCCCCEEECCCCcCCccCcc-ccccCCEEECCCCCcccc
Confidence            33444555555555555544   44444 4 5555555555555444

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.73  E-value=0.027  Score=48.66  Aligned_cols=36  Identities=25%  Similarity=0.184  Sum_probs=26.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH-hhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK-ISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~-~~~~f~~~~w~~   87 (385)
                      -.++.|.|.+|+|||+||.+++.. ....-..+++++
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            358999999999999999998754 333334455554

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=94.72  E-value=0.042  Score=49.02  Aligned_cols=60  Identities=13%  Similarity=0.117  Sum_probs=39.9

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++.+|+.|+|+++   .+|..+ .  .+|++|+++++.++.+|
T Consensus       123 l~~L~~L~L~~N~l--~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~ip  188 (290)
T 1p9a_G          123 LGELQELYLKGNEL--KTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIP  188 (290)
T ss_dssp             CTTCCEEECTTSCC--CCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             CCCCCEEECCCCCC--CccChhhcccccCCCEEECCCCcCCccCHHHhcCcCCCCEEECCCCcCCccC
Confidence            34566666655543  2456666777777777777776   555544 3  67788888877777777

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.72  E-value=0.016  Score=50.25  Aligned_cols=23  Identities=22%  Similarity=0.161  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            68999999999999999999864

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=94.71  E-value=0.035  Score=50.42  Aligned_cols=43  Identities=14%  Similarity=0.071  Sum_probs=20.6

Q ss_pred             CccccCCCCCCcEEEecCc---ccCCCCCCCeeEEEcCCCCCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS---SFNGENKCKISYLQDPGFAGVKLN  380 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~---~lp~~i~~~LryL~l~~~~~~~lP  380 (385)
                      .+..|.++++|++|+|+++   .+|..+..+|++|+++++.++.+|
T Consensus        94 ~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~L~~L~l~~n~i~~~~  139 (332)
T 2ft3_A           94 HEKAFSPLRKLQKLYISKNHLVEIPPNLPSSLVELRIHDNRIRKVP  139 (332)
T ss_dssp             CGGGSTTCTTCCEEECCSSCCCSCCSSCCTTCCEEECCSSCCCCCC
T ss_pred             CHhHhhCcCCCCEEECCCCcCCccCccccccCCEEECCCCccCccC
Confidence            3444455555555555544   333333345555555555555444

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=94.70  E-value=0.045  Score=49.27  Aligned_cols=63  Identities=10%  Similarity=-0.021  Sum_probs=42.4

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCCCCeeEEEcCCCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENKCKISYLQDPGFAGVKLNNFG  383 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~~~LryL~l~~~~~~~lP~~~  383 (385)
                      .+++.+.+........ .+...+..+++|++|+|+++   .+|..+..+|++|+++++.++.+|.|+
T Consensus       228 ~~L~~L~Ls~N~l~~~-~~~~~~~~l~~L~~L~Ls~N~l~~ip~~~~~~L~~L~Ls~N~l~~~p~~~  293 (312)
T 1wwl_A          228 VQLQGLDLSHNSLRDA-AGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPD  293 (312)
T ss_dssp             CCCSEEECTTSCCCSS-CCCSCCCCCTTCCEEECTTSCCSSCCSSCCSEEEEEECCSSCCCSCCCTT
T ss_pred             CCCCEEECCCCcCCcc-cchhhhhhcCCCCEEECCCCccChhhhhccCCceEEECCCCCCCCChhHh
Confidence            4566666665543111 12355667788888888887   555555578888888888888888654

>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=94.69  E-value=0.024  Score=45.40  Aligned_cols=24  Identities=17%  Similarity=0.336  Sum_probs=20.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-.|+|+|.+|+|||||...+..
T Consensus         4 ~~~~i~v~G~~~~GKssl~~~l~~   27 (168)
T 1z2a_A            4 VAIKMVVVGNGAVGKSSMIQRYCK   27 (168)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEEECcCCCCHHHHHHHHHc
Confidence            345688999999999999999986

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.69  E-value=0.028  Score=53.11  Aligned_cols=84  Identities=14%  Similarity=0.075  Sum_probs=48.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC----ceEEEeeccccccCCCChHHHHHHHHHHHh--------CCCCCC---
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD----GSCFLENVREESQIPGGLSCLRQKLLSNLL--------KDKNVM---  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~----~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~--------~~~~~~---  117 (385)
                      +.++|.|.+|+|||+|+..+++....+.+    ..+++- +++..   ..+.++.+.+...-.        ...++.   
T Consensus       152 Qr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~-iGeR~---~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~  227 (465)
T 3vr4_D          152 QKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAA-IGITF---EEAEFFMEDFRQTGAIDRSVMFMNLANDPAIE  227 (465)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEE-EEECH---HHHHHHHHHHHHHTGGGGEEEEEEETTSCHHH
T ss_pred             CEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEE-ecCCc---HHHHHHHHHHhhcCCccceEEEEECCCCCHHH
Confidence            35789999999999999999987654323    333333 33221   445666666544210        011111   


Q ss_pred             -----chHHHHHHHh---CCceEEEEEeCCC
Q 044214          118 -----PYIDLNFRRL---GHMKVLIVFDDVT  140 (385)
Q Consensus       118 -----~~~~~l~~~l---~~k~~LlVlDdv~  140 (385)
                           ...-.+.+++   .++.+|+++||+.
T Consensus       228 r~~a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          228 RIATPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence                 1112233333   3789999999994

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=94.68  E-value=0.015  Score=52.55  Aligned_cols=60  Identities=10%  Similarity=0.011  Sum_probs=39.0

Q ss_pred             cCCeeEEEeec-CCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCC-CCC
Q 044214          319 GQKIEDICLDM-SKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGV-KLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~-~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~-~lP  380 (385)
                      ...++.+.+.. ...  ....+..|.++++|++|+|+++    .+|..+.  .+|++|++++|.+. .+|
T Consensus        75 l~~L~~L~L~~~n~l--~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p  142 (313)
T 1ogq_A           75 LPYLNFLYIGGINNL--VGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLP  142 (313)
T ss_dssp             CTTCSEEEEEEETTE--ESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCEEECCSSEEESCCC
T ss_pred             CCCCCeeeCCCCCcc--cccCChhHhcCCCCCEEECcCCeeCCcCCHHHhCCCCCCEEeCCCCccCCcCC
Confidence            45566666653 321  2234556777788888888776    5666666  78888888887776 455

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=94.66  E-value=0.05  Score=49.74  Aligned_cols=29  Identities=28%  Similarity=0.457  Sum_probs=24.6

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.+..+++|+|.+|+|||||.+.+...+.
T Consensus        52 ~~~g~~v~i~G~~GaGKSTLl~~l~g~~~   80 (337)
T 2qm8_A           52 TGRAIRVGITGVPGVGKSTTIDALGSLLT   80 (337)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            34567999999999999999999987554

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=94.66  E-value=0.042  Score=47.71  Aligned_cols=61  Identities=18%  Similarity=0.139  Sum_probs=42.2

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+.....  ..+.+..|.++++|++|+|+++   .+|. .+.  .+|++|+++++.++.+|.
T Consensus        58 l~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~  124 (251)
T 3m19_A           58 LTKLTWLNLDYNQL--QTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPS  124 (251)
T ss_dssp             CTTCCEEECTTSCC--CCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCT
T ss_pred             cccCCEEECCCCcC--CccCHhHhccCCcCCEEECCCCcccccChhHhcccCCCCEEEcCCCcCCCcCh
Confidence            45566666665542  3356667788888888888887   4443 334  788888888888888773

>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=94.66  E-value=0.018  Score=48.11  Aligned_cols=24  Identities=17%  Similarity=0.429  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ...|+|+|.+|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            356899999999999999999863

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=94.65  E-value=0.035  Score=48.05  Aligned_cols=33  Identities=33%  Similarity=0.652  Sum_probs=26.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |+|.|-||+||||+|..++..+...-..+.-+.
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~g~~VlliD   35 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASDYDKIYAVD   35 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTTCSCEEEEE
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            666999999999999999998766544455554

>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=94.65  E-value=0.03  Score=45.91  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=21.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .....|+|+|.+|+|||||...+..
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~   38 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLAS   38 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhc
Confidence            3456788999999999999998875

>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=94.64  E-value=0.014  Score=48.05  Aligned_cols=21  Identities=38%  Similarity=0.502  Sum_probs=19.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+..
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999999876

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=94.64  E-value=0.03  Score=46.88  Aligned_cols=35  Identities=23%  Similarity=0.212  Sum_probs=26.7

Q ss_pred             EEEEEE-cCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIW-GIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~-G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|+ +-||+||||+|..++..+...-..+..+.
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~~la~~g~~vlliD   37 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIATALSRSGYNIAVVD   37 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEE
Confidence            578787 67999999999999987765444455554

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=94.63  E-value=0.087  Score=44.78  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=23.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..|++.|+.|+||||++..+.+.+..
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            58999999999999999999998865

>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=94.62  E-value=0.016  Score=50.21  Aligned_cols=23  Identities=30%  Similarity=0.255  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~Gl   54 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGCL   54 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            48999999999999999998763

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=94.61  E-value=0.032  Score=50.77  Aligned_cols=60  Identities=15%  Similarity=0.137  Sum_probs=40.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCC-CCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAG-VKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~-~~lP  380 (385)
                      ..+++.+.+..+..  ....+..|.++++|+.|+|++|    .+|..++  .+|++|++++|++ +.+|
T Consensus       228 l~~L~~L~Ls~n~~--~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~iP  294 (328)
T 4fcg_A          228 LPKLEELDLRGCTA--LRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLP  294 (328)
T ss_dssp             CTTCCEEECTTCTT--CCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTCTTCCCCC
T ss_pred             CCCCCEEECcCCcc--hhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCCCchhhcc
Confidence            44566666655432  2334556778888888888876    6777777  7888888888653 5566

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=94.59  E-value=0.011  Score=58.43  Aligned_cols=49  Identities=16%  Similarity=0.007  Sum_probs=35.3

Q ss_pred             CCCccccchhHHHHHHhhcCCCCC---------eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           28 KNQLVGVESTVEEIESLLGVESKG---------VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~~~~~~---------~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.++|.+.....+.-.+..+...         -.-|.++|.+|+|||+||+.+++..
T Consensus       294 ~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          294 APSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             SSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTC
T ss_pred             cchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhC
Confidence            367899998777776555532100         0158899999999999999998754

>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=94.57  E-value=0.041  Score=51.84  Aligned_cols=36  Identities=22%  Similarity=0.147  Sum_probs=28.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ...+++|+|.+|+||||++..++..+...-..+..+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllv  132 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLV  132 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            457899999999999999999998776553334444

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=94.54  E-value=0.02  Score=45.59  Aligned_cols=22  Identities=27%  Similarity=0.623  Sum_probs=19.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .|+++|.+|+|||||+..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999999863

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.54  E-value=0.016  Score=49.69  Aligned_cols=23  Identities=26%  Similarity=0.215  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998763

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=94.54  E-value=0.017  Score=56.03  Aligned_cols=56  Identities=14%  Similarity=0.146  Sum_probs=31.4

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC-CCeeEEEcCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK-CKISYLQDPGFAGVK  378 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~-~~LryL~l~~~~~~~  378 (385)
                      .+++.+.+..+..  ..+.+..|.++++|++|+|+++   .+|.. . .+|++|++++|.+..
T Consensus        45 ~~L~~L~Ls~n~l--~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~-~l~~L~~L~L~~N~l~~  104 (520)
T 2z7x_B           45 SKLRILIISHNRI--QYLDISVFKFNQELEYLDLSHNKLVKISCH-PTVNLKHLDLSFNAFDA  104 (520)
T ss_dssp             TTCCEEECCSSCC--CEEEGGGGTTCTTCCEEECCSSCCCEEECC-CCCCCSEEECCSSCCSS
T ss_pred             ccccEEecCCCcc--CCcChHHhhcccCCCEEecCCCceeecCcc-ccCCccEEeccCCcccc
Confidence            3445554444432  2334555666666666666665   45554 5 666666666666654

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=94.53  E-value=0.024  Score=46.56  Aligned_cols=23  Identities=30%  Similarity=0.518  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...|+|+|.+|+|||||...+..
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~   29 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTG   29 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45789999999999999999986

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=94.49  E-value=0.025  Score=51.10  Aligned_cols=60  Identities=8%  Similarity=0.022  Sum_probs=33.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCC-CCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGV-KLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~-~lP  380 (385)
                      ..+++.+.+.....  ....+..|.++++|++|+|+++    .+|..+.  .+|++|++++|.+. .+|
T Consensus       100 l~~L~~L~Ls~n~l--~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p  166 (313)
T 1ogq_A          100 LTQLHYLYITHTNV--SGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIP  166 (313)
T ss_dssp             CTTCSEEEEEEECC--EEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECC
T ss_pred             CCCCCEEECcCCee--CCcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCCCCCeEECcCCcccCcCC
Confidence            44566666554432  1234455666666666666665    3555555  66666666666665 444

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=94.48  E-value=0.05  Score=50.59  Aligned_cols=60  Identities=15%  Similarity=0.224  Sum_probs=34.5

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|.++++|++|+|+++   .+|..+ .  .+|++|++++|.+..+|
T Consensus        92 l~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~  157 (390)
T 3o6n_A           92 AHTIQKLYMGFNAI--RYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIE  157 (390)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCC
T ss_pred             CCCcCEEECCCCCC--CcCCHHHhcCCCCCCEEECCCCccCcCCHHHhcCCCCCcEEECCCCccCccC
Confidence            34455555544432  2344555666666666666665   555543 3  66777777766666654

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=94.47  E-value=0.057  Score=49.64  Aligned_cols=39  Identities=23%  Similarity=0.213  Sum_probs=27.9

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+...++.+.|-||+||||+|..++..+...-..+.-++
T Consensus        23 ~~~~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   61 (349)
T 3ug7_A           23 KDGTKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVS   61 (349)
T ss_dssp             SCSCEEEEEECSSSTTHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             cCCCEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEe
Confidence            344567788899999999999999887654433344443

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=94.46  E-value=0.063  Score=45.55  Aligned_cols=34  Identities=24%  Similarity=0.317  Sum_probs=26.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~   86 (385)
                      ..|++.|..|+||||+++.+.+.+... +..+++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~~v~~~   38 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFT   38 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCCcceee
Confidence            478999999999999999999987544 4344433

>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=94.46  E-value=0.034  Score=45.17  Aligned_cols=26  Identities=23%  Similarity=0.411  Sum_probs=22.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....-|+|+|.+|+|||||...+...
T Consensus         7 ~~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            7 SETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             SCEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhC
Confidence            34567899999999999999999864

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.43  E-value=0.024  Score=46.90  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....|+|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3457899999999999999998863

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.43  E-value=0.033  Score=47.63  Aligned_cols=28  Identities=32%  Similarity=0.426  Sum_probs=24.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ....|+|.|+.|+||||+++.+.+.+..
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            4578999999999999999999997754

>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=94.41  E-value=0.039  Score=53.00  Aligned_cols=30  Identities=17%  Similarity=0.046  Sum_probs=24.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ...+|.++|++|+||||+++.+++.....|
T Consensus        38 ~~~~IvlvGlpGsGKSTia~~La~~l~~~~   67 (469)
T 1bif_A           38 CPTLIVMVGLPARGKTYISKKLTRYLNFIG   67 (469)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHHhccC
Confidence            345889999999999999999998765444

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.40  E-value=0.016  Score=49.17  Aligned_cols=22  Identities=32%  Similarity=0.160  Sum_probs=20.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +++|+|+.|+|||||++.++..
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            7999999999999999998864

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=94.40  E-value=0.025  Score=47.64  Aligned_cols=25  Identities=16%  Similarity=0.181  Sum_probs=23.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+|+|.|+.|+||||+|+.+++++.
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg   31 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYN   31 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            4899999999999999999999864

>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=94.40  E-value=0.031  Score=45.18  Aligned_cols=23  Identities=30%  Similarity=0.536  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||||...+..
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEEECCCCccHHHHHHHHhc
Confidence            45689999999999999999875

>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=94.39  E-value=0.019  Score=49.75  Aligned_cols=23  Identities=22%  Similarity=0.416  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||++.++.-
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999999864

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=94.37  E-value=0.047  Score=52.04  Aligned_cols=80  Identities=20%  Similarity=0.181  Sum_probs=45.4

Q ss_pred             EEEEEEcCCCchHHHHHH-HHHHHhhCCCCc-eEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC-----
Q 044214           53 YALGIWGIGGIGKTTIAR-AIFDKISGDFDG-SCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM-----  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~-~~~~~~~~~f~~-~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~-----  117 (385)
                      +.++|.|..|+|||+||. .+.++  .+-+. ++++- +++.   ...+.++.+.+...-...        .++.     
T Consensus       163 QR~~Ifg~~g~GKT~l~l~~I~n~--~~~dv~~V~~~-IGeR---~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~  236 (513)
T 3oaa_A          163 QRELIIGDRQTGKTALAIDAIINQ--RDSGIKCIYVA-IGQK---ASTISNVVRKLEEHGALANTIVVVATASESAALQY  236 (513)
T ss_dssp             CBCEEEESSSSSHHHHHHHHHHTT--SSSSCEEEEEE-ESCC---HHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHH
T ss_pred             CEEEeecCCCCCcchHHHHHHHhh--ccCCceEEEEE-ecCC---hHHHHHHHHHHhhcCcccceEEEEECCCCChHHHH
Confidence            468899999999999974 55554  22333 33443 3322   144556666654321111        1111     


Q ss_pred             -------chHHHHHHHhCCceEEEEEeCCC
Q 044214          118 -------PYIDLNFRRLGHMKVLIVFDDVT  140 (385)
Q Consensus       118 -------~~~~~l~~~l~~k~~LlVlDdv~  140 (385)
                             ..++.++.  +++.+||++||+.
T Consensus       237 ~a~~~a~tiAEyfrd--~G~dVLli~Dslt  264 (513)
T 3oaa_A          237 LAPYAGCAMGEYFRD--RGEDALIIYDDLS  264 (513)
T ss_dssp             HHHHHHHHHHHHHHH--TTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHh--cCCCEEEEecChH
Confidence                   22333333  5899999999994

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=94.36  E-value=0.061  Score=47.21  Aligned_cols=61  Identities=18%  Similarity=0.167  Sum_probs=40.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+.....  ..++...|.++++|+.|+|+++   .+|. .+.  .+|++|++++|.++.+|.
T Consensus        84 l~~L~~L~l~~n~l--~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~  150 (270)
T 2o6q_A           84 LKNLETLWVTDNKL--QALPIGVFDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPK  150 (270)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCT
T ss_pred             CCCCCEEECCCCcC--CcCCHhHcccccCCCEEECCCCccCeeCHHHhCcCcCCCEEECCCCcCCccCH
Confidence            44566666655442  3455667778888888888877   3333 344  788888888888887773

>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=94.35  E-value=0.023  Score=46.78  Aligned_cols=23  Identities=30%  Similarity=0.709  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.|+|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999999863

>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=94.35  E-value=0.069  Score=46.09  Aligned_cols=35  Identities=20%  Similarity=0.295  Sum_probs=27.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEE
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFL   86 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~   86 (385)
                      ...|+|.|+.|+||||+++.+.+.+... +..+...
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~~~~~~~~~   62 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRT   62 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCeeeee
Confidence            3589999999999999999999977543 4434443

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=94.34  E-value=0.05  Score=56.29  Aligned_cols=43  Identities=19%  Similarity=0.167  Sum_probs=26.6

Q ss_pred             eeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCCC
Q 044214          336 CLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGVK  378 (385)
Q Consensus       336 ~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~~  378 (385)
                      .+.+..|.++++|++|+|+++    ..|..++  .+|++|+|++|.+..
T Consensus        63 ~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~Ls~n~l~~  111 (844)
T 3j0a_A           63 TIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRLYFCGLSD  111 (844)
T ss_dssp             EECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSCCCEECTTCCCSS
T ss_pred             ccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCcccCEeeCcCCCCCc
Confidence            344556666666666666665    2355666  667777776666654

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=94.34  E-value=0.057  Score=49.77  Aligned_cols=43  Identities=23%  Similarity=0.205  Sum_probs=20.9

Q ss_pred             CccccCCCCCCcEEEecCc---ccCCCC----C--CCeeEEEcCCCCCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS---SFNGEN----K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~---~lp~~i----~--~~LryL~l~~~~~~~lP  380 (385)
                      .+..|.++.+|+.|+|+++   .+|..+    .  .+|++|+|+++.++.+|
T Consensus       128 ~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~  179 (361)
T 2xot_A          128 DRNAFEDMAQLQKLYLSQNQISRFPVELIKDGNKLPKLMLLDLSSNKLKKLP  179 (361)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCCSCCGGGTC----CTTCCEEECCSSCCCCCC
T ss_pred             CHHHhCCcccCCEEECCCCcCCeeCHHHhcCcccCCcCCEEECCCCCCCccC
Confidence            3444555555555555554   333332    2  45555555555555554

>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=94.32  E-value=0.13  Score=51.04  Aligned_cols=25  Identities=28%  Similarity=0.236  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.+.|.|.+|.||||++..+...+.
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l~  189 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAALI  189 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            5899999999999999998887554

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=94.32  E-value=0.053  Score=51.89  Aligned_cols=43  Identities=16%  Similarity=0.149  Sum_probs=20.3

Q ss_pred             CccccCCCCCCcEEEecCc---c-cCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS---S-FNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~---~-lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .+..|.++++|++|+|+++   . .|..++  .+|++|+|++|.++.+|
T Consensus        48 ~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~   96 (477)
T 2id5_A           48 NQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIP   96 (477)
T ss_dssp             CTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCSCC
T ss_pred             CHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCCcCCccC
Confidence            3444455555555555544   1 133444  45555555555554444

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=94.32  E-value=0.053  Score=47.61  Aligned_cols=60  Identities=15%  Similarity=0.080  Sum_probs=38.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..++...|.++++|++|+|+++   .+|.. +.  .+|++|+++++.++.+|
T Consensus        60 l~~L~~L~l~~n~l--~~i~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~  125 (270)
T 2o6q_A           60 LTKLRLLYLNDNKL--QTLPAGIFKELKNLETLWVTDNKLQALPIGVFDQLVNLAELRLDRNQLKSLP  125 (270)
T ss_dssp             CTTCCEEECCSSCC--SCCCTTTTSSCTTCCEEECCSSCCCCCCTTTTTTCSSCCEEECCSSCCCCCC
T ss_pred             CCCCCEEECCCCcc--CeeChhhhcCCCCCCEEECCCCcCCcCCHhHcccccCCCEEECCCCccCeeC
Confidence            44566666655432  2455666777777788877776   44433 33  67888888877777766

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=94.31  E-value=0.024  Score=49.52  Aligned_cols=23  Identities=22%  Similarity=0.409  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||.+.++.-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999874

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.31  E-value=0.041  Score=52.55  Aligned_cols=83  Identities=20%  Similarity=0.139  Sum_probs=45.3

Q ss_pred             EEEEEEcCCCchHHHHHH-HHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCC--------CCCC------
Q 044214           53 YALGIWGIGGIGKTTIAR-AIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD--------KNVM------  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~-~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~--------~~~~------  117 (385)
                      +.++|.|.+|+|||+||. .++++..  -+..+.+..+++.   ...+.++.+.+...-...        .++.      
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~~~--~dv~~V~~~iGeR---~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~  237 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQKG--QDVICIYVAIGQK---QSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYL  237 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGGGS--CSEEEEEEEESCC---HHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHhhc--CCcEEEEEECCCc---chHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHH
Confidence            468899999999999965 5666542  3433222223322   134555666655421111        1111      


Q ss_pred             --chHHHHHHHh--CCceEEEEEeCCC
Q 044214          118 --PYIDLNFRRL--GHMKVLIVFDDVT  140 (385)
Q Consensus       118 --~~~~~l~~~l--~~k~~LlVlDdv~  140 (385)
                        ...-.+.+++  .++.+|+++||+.
T Consensus       238 a~~~a~tiAEyfrd~G~dVLl~~Dslt  264 (502)
T 2qe7_A          238 APYAGCAMGEYFMYKGKHALVVYDDLS  264 (502)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEEecHH
Confidence              0111222222  5799999999994

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.29  E-value=0.02  Score=50.41  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        33 e~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998864

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=94.28  E-value=0.02  Score=50.75  Aligned_cols=23  Identities=26%  Similarity=0.342  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||++.++.-
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl   57 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGI   57 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            48999999999999999998763

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.28  E-value=0.047  Score=46.85  Aligned_cols=28  Identities=29%  Similarity=0.311  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...|+|.|+.|+||||+++.+++.+...
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~~   52 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQER   52 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhh
Confidence            3589999999999999999999977543

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=94.27  E-value=0.061  Score=52.60  Aligned_cols=40  Identities=13%  Similarity=0.018  Sum_probs=18.2

Q ss_pred             CccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGV  377 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~  377 (385)
                      ++..|.++++|++|+|+++   .+|. .++  .+|++|++++|.++
T Consensus        92 ~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~  137 (570)
T 2z63_A           92 ALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQ  137 (570)
T ss_dssp             CTTTTTTCTTCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSSCCC
T ss_pred             CHhhhcCccccccccccccccccCCCccccccccccEEecCCCccc
Confidence            3344444455555555444   2222 233  45555555555444

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=94.26  E-value=0.073  Score=46.80  Aligned_cols=61  Identities=13%  Similarity=0.081  Sum_probs=47.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+..  ..+++..|.++++|+.|+|+++   .+|.. ++  .+|++|++++|.+..+|.
T Consensus       132 l~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~  198 (272)
T 3rfs_A          132 LTNLTYLNLAHNQL--QSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPD  198 (272)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCT
T ss_pred             CCCCCEEECCCCcc--CccCHHHhccCccCCEEECCCCCcCccCHHHhcCCccCCEEECCCCcCCccCH
Confidence            56778888776653  3566777899999999999998   45544 34  899999999999988873

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=94.25  E-value=0.056  Score=49.78  Aligned_cols=60  Identities=12%  Similarity=0.145  Sum_probs=49.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+++..|..+.+|++|+|+++   .+ |..+.  .+|++|+|+++.++.+|
T Consensus        87 l~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~~l~  152 (361)
T 2xot_A           87 VPNLRYLDLSSNHL--HTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQISRFP  152 (361)
T ss_dssp             CTTCCEEECCSSCC--CEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCSCC
T ss_pred             CCCCCEEECCCCcC--CcCCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCcCCeeC
Confidence            56788888777653  4567788999999999999998   33 56677  89999999999999988

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=94.24  E-value=0.041  Score=51.09  Aligned_cols=39  Identities=18%  Similarity=0.147  Sum_probs=29.1

Q ss_pred             CCCeEEEEEEc-CCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           49 SKGVYALGIWG-IGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        49 ~~~~~vv~I~G-~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+.++|+|+| -||+||||+|..++..+...-..+..+.
T Consensus       140 ~~~~kvIav~s~KGGvGKTT~a~nLA~~La~~g~rVlliD  179 (373)
T 3fkq_A          140 NDKSSVVIFTSPCGGVGTSTVAAACAIAHANMGKKVFYLN  179 (373)
T ss_dssp             TTSCEEEEEECSSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCCceEEEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEE
Confidence            34578898886 8999999999999987654433455554

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=94.24  E-value=0.082  Score=46.69  Aligned_cols=52  Identities=19%  Similarity=0.118  Sum_probs=36.0

Q ss_pred             hhHHHHHHhhc--CCCCCeEEEEEEcC-CCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           36 STVEEIESLLG--VESKGVYALGIWGI-GGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        36 ~~l~~l~~~L~--~~~~~~~vv~I~G~-gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++.|...|.  ......++|+|+|. ||+||||+|..++..+...-..+..+.
T Consensus        64 Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTt~a~nLA~~lA~~G~rVLLID  118 (271)
T 3bfv_A           64 EKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVD  118 (271)
T ss_dssp             HHHHHHHHHHHHSSTTCCCCEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHhhccCCCCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCeEEEEe
Confidence            44555555443  22345689999975 899999999999987765544566665

>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=94.23  E-value=0.023  Score=49.41  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -.+++|+|..|+|||||.+.++.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999876

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=94.22  E-value=0.025  Score=49.89  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||.+.++.-
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999874

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=94.20  E-value=0.029  Score=45.53  Aligned_cols=24  Identities=33%  Similarity=0.232  Sum_probs=21.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +...|+|+|.+|+|||||...+..
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            456789999999999999999876

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=94.20  E-value=0.063  Score=46.25  Aligned_cols=37  Identities=19%  Similarity=0.131  Sum_probs=27.7

Q ss_pred             CeEEEEEEc-CCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           51 GVYALGIWG-IGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G-~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      ..++|+|+| -||+||||+|..++..+... -..+..+.
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA~~la~~~g~~VlliD   41 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFAFALSQEPDIHVLAVD   41 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHHHHHTTSTTCCEEEEE
T ss_pred             CCeEEEEECCCCCcchHHHHHHHHHHHHhCcCCCEEEEE
Confidence            456787775 59999999999999988765 44455554

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=94.19  E-value=0.022  Score=49.43  Aligned_cols=23  Identities=35%  Similarity=0.380  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998763

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=94.18  E-value=0.062  Score=51.88  Aligned_cols=48  Identities=17%  Similarity=0.165  Sum_probs=32.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKL  106 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~l  106 (385)
                      +.++|.|..|+|||+|+.++++..  +-+..+++- +++.   .....++.+.+
T Consensus       228 qr~~I~g~~g~GKT~L~~~ia~~~--~~~~~V~~~-iGER---~~Ev~e~~~~~  275 (588)
T 3mfy_A          228 GTAAIPGPAGSGKTVTQHQLAKWS--DAQVVIYIG-CGER---GNEMTDVLEEF  275 (588)
T ss_dssp             CEEEECSCCSHHHHHHHHHHHHHS--SCSEEEEEE-CCSS---SSHHHHHHHHT
T ss_pred             CeEEeecCCCCCHHHHHHHHHhcc--CCCEEEEEE-eccc---HHHHHHHHHHH
Confidence            478999999999999999988753  224455554 3322   24555666554

>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=94.18  E-value=0.029  Score=47.40  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....|+|+|.+|+|||||...+...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999999864

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=94.17  E-value=0.019  Score=50.12  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+++|+|..|+|||||.+.++.-+.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            4899999999999999999886543

>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=94.17  E-value=0.042  Score=43.85  Aligned_cols=23  Identities=22%  Similarity=0.439  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||||...+..
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~   26 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999999886

>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=94.17  E-value=0.021  Score=49.14  Aligned_cols=26  Identities=27%  Similarity=0.157  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....+|+|.|..|+||||+++.+...
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            34579999999999999999998875

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=94.17  E-value=0.022  Score=50.30  Aligned_cols=23  Identities=30%  Similarity=0.419  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||++.++.-
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            48999999999999999999763

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=94.16  E-value=0.034  Score=51.14  Aligned_cols=26  Identities=23%  Similarity=0.264  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-.++.|+|.+|+|||||++.++..+
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45799999999999999999999876

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=94.15  E-value=0.045  Score=49.65  Aligned_cols=60  Identities=12%  Similarity=0.089  Sum_probs=44.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..+.+..|..+++|+.|+|+++   .+|..+.  .+|++|+++++.++.+|
T Consensus       216 l~~L~~L~L~~N~l--~~~~~~~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~L~~L~l~~N~l~~~~  280 (332)
T 2ft3_A          216 YSKLYRLGLGHNQI--RMIENGSLSFLPTLRELHLDNNKLSRVPAGLPDLKLLQVVYLHTNNITKVG  280 (332)
T ss_dssp             CTTCSCCBCCSSCC--CCCCTTGGGGCTTCCEEECCSSCCCBCCTTGGGCTTCCEEECCSSCCCBCC
T ss_pred             CCCCCEEECCCCcC--CcCChhHhhCCCCCCEEECCCCcCeecChhhhcCccCCEEECCCCCCCccC
Confidence            34556555554432  3355567888889999999887   7788777  88999999999888887

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=94.15  E-value=0.062  Score=47.87  Aligned_cols=61  Identities=10%  Similarity=0.053  Sum_probs=47.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+.....  ..+++..|.++.+|+.|+|+++   .+|... .  .+|++|+++++.++.+|.
T Consensus        99 l~~L~~L~l~~N~l--~~l~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~  165 (290)
T 1p9a_G           99 LPALTVLDVSFNRL--TSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPA  165 (290)
T ss_dssp             CTTCCEEECCSSCC--CCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCSCCCT
T ss_pred             CCCCCEEECCCCcC--cccCHHHHcCCCCCCEEECCCCCCCccChhhcccccCCCEEECCCCcCCccCH
Confidence            45677777766643  3566778999999999999988   555543 4  899999999999999983

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=94.14  E-value=0.028  Score=50.56  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.+++|+|+.|+|||||++.+..-+
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhhc
Confidence            3589999999999999999999866

>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=94.14  E-value=0.028  Score=44.93  Aligned_cols=21  Identities=29%  Similarity=0.618  Sum_probs=19.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+.+
T Consensus         5 ki~v~G~~~~GKssli~~l~~   25 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            578999999999999999986

>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=94.13  E-value=0.037  Score=45.39  Aligned_cols=24  Identities=17%  Similarity=0.136  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..--|+|+|.+|+|||||...+..
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~   29 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAK   29 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhc
Confidence            345688999999999999999986

>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=94.13  E-value=0.023  Score=49.89  Aligned_cols=23  Identities=30%  Similarity=0.260  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998764

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=94.13  E-value=0.023  Score=49.54  Aligned_cols=23  Identities=35%  Similarity=0.495  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||.+.++.-
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998763

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=94.13  E-value=0.041  Score=48.28  Aligned_cols=60  Identities=15%  Similarity=0.156  Sum_probs=32.2

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCCCCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENKCKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~~~LryL~l~~~~~~~lP~~  382 (385)
                      ..+++.+.+..+...  .+++  |.++++|+.|+|+++   .+|.....+|++|++++|.++.+|.|
T Consensus        62 l~~L~~L~L~~N~i~--~~~~--l~~l~~L~~L~L~~N~l~~l~~~~~~~L~~L~L~~N~l~~~~~l  124 (263)
T 1xeu_A           62 FTNLKELHLSHNQIS--DLSP--LKDLTKLEELSVNRNRLKNLNGIPSACLSRLFLDNNELRDTDSL  124 (263)
T ss_dssp             CTTCCEEECCSSCCC--CCGG--GTTCSSCCEEECCSSCCSCCTTCCCSSCCEEECCSSCCSBSGGG
T ss_pred             CCCCCEEECCCCccC--CChh--hccCCCCCEEECCCCccCCcCccccCcccEEEccCCccCCChhh
Confidence            445555555544321  1222  666667777777666   33321116677777777766666543

>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=94.12  E-value=0.028  Score=44.82  Aligned_cols=22  Identities=27%  Similarity=0.661  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~   25 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            3588999999999999999886

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=94.12  E-value=0.027  Score=51.13  Aligned_cols=25  Identities=32%  Similarity=0.424  Sum_probs=22.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +.++++|+|+.|+|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4789999999999999999999864

>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=94.11  E-value=0.023  Score=48.88  Aligned_cols=24  Identities=29%  Similarity=0.464  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|+|+.|+|||||.+.++..+
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            489999999999999999998743

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=94.11  E-value=0.065  Score=49.07  Aligned_cols=60  Identities=12%  Similarity=0.126  Sum_probs=48.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .+.++.+.+.....  ..++...|.++++|+.|+|+++   .+ |..+.  .+|++|++++|.++.+|
T Consensus        51 ~~~L~~L~l~~n~i--~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~  116 (353)
T 2z80_A           51 TEAVKSLDLSNNRI--TYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLS  116 (353)
T ss_dssp             CTTCCEEECTTSCC--CEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSSCC
T ss_pred             cccCcEEECCCCcC--cccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCcCC
Confidence            34678888776653  3467778999999999999998   33 45677  89999999999999988

>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=94.11  E-value=0.029  Score=46.36  Aligned_cols=25  Identities=16%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+...|+|+|.+|+|||||...+..
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~   45 (195)
T 1svi_A           21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3456789999999999999999875

>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=94.10  E-value=0.023  Score=50.02  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        51 ei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEEcCCCCcHHHHHHHHHcC
Confidence            48999999999999999998864

>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=94.10  E-value=0.028  Score=46.32  Aligned_cols=24  Identities=21%  Similarity=0.279  Sum_probs=20.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..--|+|+|.+|+|||||...+.+
T Consensus        19 ~~~ki~ivG~~~vGKSsL~~~~~~   42 (184)
T 3ihw_A           19 PELKVGIVGNLSSGKSALVHRYLT   42 (184)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhc
Confidence            345688999999999999998876

>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=94.10  E-value=0.038  Score=44.86  Aligned_cols=25  Identities=28%  Similarity=0.498  Sum_probs=21.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .....|+|+|.+|+|||||...+..
T Consensus         6 ~~~~~i~v~G~~~~GKSsli~~l~~   30 (182)
T 1ky3_A            6 KNILKVIILGDSGVGKTSLMHRYVN   30 (182)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHh
Confidence            3456789999999999999999886

>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=94.10  E-value=0.029  Score=45.12  Aligned_cols=23  Identities=22%  Similarity=0.450  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .-.|+|+|.+|+|||||...+..
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCE   28 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECcCCCCHHHHHHHHHc
Confidence            44688999999999999999886

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.09  E-value=0.026  Score=47.95  Aligned_cols=24  Identities=25%  Similarity=0.441  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+|+|+|+.|+||||+++.+.+.+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            378999999999999999998864

>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=94.08  E-value=0.016  Score=50.96  Aligned_cols=27  Identities=19%  Similarity=0.166  Sum_probs=23.4

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +...|+|.|..|+||||+|+.+++.+.
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            457899999999999999999887653

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=94.07  E-value=0.065  Score=52.17  Aligned_cols=59  Identities=17%  Similarity=0.246  Sum_probs=35.5

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKL  379 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~l  379 (385)
                      ..+++.+.+..+..  ..+++..|.++++|++|+|+++   .+|.. ++  .+|++|++++|.++.+
T Consensus        49 l~~L~~L~Ls~n~i--~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~  113 (549)
T 2z81_A           49 CANLQVLILKSSRI--NTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTL  113 (549)
T ss_dssp             CTTCCEEECTTSCC--CEECTTTTTTCTTCCEEECTTSCCCSCCHHHHTTCTTCCEEECTTCCCSSS
T ss_pred             CCcccEEECCCCCc--CccChhhccccccCCEEECCCCccCccCHHHhccCCCCcEEECCCCccccc
Confidence            34455555554432  2345566777777777777776   33332 44  6777777777777644

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=94.07  E-value=0.071  Score=51.01  Aligned_cols=85  Identities=18%  Similarity=0.097  Sum_probs=45.9

Q ss_pred             EEEEEEcCCCchHHHHHH-HHHHHhhC------CCCceEEEeeccccccCCCChHHHHHHHHHHHh--------CCCCCC
Q 044214           53 YALGIWGIGGIGKTTIAR-AIFDKISG------DFDGSCFLENVREESQIPGGLSCLRQKLLSNLL--------KDKNVM  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~-~~~~~~~~------~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~--------~~~~~~  117 (385)
                      +.++|.|.+|+|||+||. .++++...      +-+..+.+..+++.   +..+.++.+.+...-.        ...++.
T Consensus       163 QR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR---~~Ev~~~~~~~~~~g~m~~tvvV~atad~p  239 (510)
T 2ck3_A          163 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQK---RSTVAQLVKRLTDADAMKYTIVVSATASDA  239 (510)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCC---HHHHHHHHHHHHHTTCGGGEEEEEECTTSC
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCC---cHHHHHHHHHHHhcCCcccceEEEECCCCC
Confidence            468899999999999965 56665541      23432333323322   1345556665554210        111111


Q ss_pred             --------chHHHHHHHh--CCceEEEEEeCCC
Q 044214          118 --------PYIDLNFRRL--GHMKVLIVFDDVT  140 (385)
Q Consensus       118 --------~~~~~l~~~l--~~k~~LlVlDdv~  140 (385)
                              ...-.+.+++  .++.+|+++||+.
T Consensus       240 ~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dslt  272 (510)
T 2ck3_A          240 APLQYLAPYSGCSMGEYFRDNGKHALIIYDDLS  272 (510)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHH
Confidence                    1111222222  5799999999994

>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=94.06  E-value=0.03  Score=44.72  Aligned_cols=21  Identities=29%  Similarity=0.276  Sum_probs=19.1

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~   75 (385)
                      |+|+|.+|+|||||...+...
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999999864

>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=94.06  E-value=0.02  Score=48.75  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++.-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            37999999999999999998764

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.05  E-value=0.057  Score=49.65  Aligned_cols=27  Identities=22%  Similarity=0.343  Sum_probs=23.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..+|+|+|.+|+|||||...+.....
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            467999999999999999999997553

>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=94.04  E-value=0.03  Score=44.85  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=19.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999999886

>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=94.02  E-value=0.027  Score=45.85  Aligned_cols=23  Identities=22%  Similarity=0.304  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999863

>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=94.01  E-value=0.031  Score=44.87  Aligned_cols=23  Identities=22%  Similarity=0.452  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      --|+|+|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999999863

>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=93.99  E-value=0.094  Score=57.63  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=29.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -.+|.|.|.+|+||||||.+++......-..++|++
T Consensus       732 G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS  767 (1706)
T 3cmw_A          732 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  767 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEe
Confidence            358999999999999999999987654434566765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.99  E-value=0.025  Score=49.69  Aligned_cols=24  Identities=29%  Similarity=0.436  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|+|..|+|||||.+.++.-+
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhccC
Confidence            489999999999999999998643

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=93.99  E-value=0.033  Score=47.76  Aligned_cols=24  Identities=38%  Similarity=0.391  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..++|.|++|+||||+|+.+++++
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999876

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=93.99  E-value=0.1  Score=48.00  Aligned_cols=37  Identities=22%  Similarity=0.183  Sum_probs=28.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh--CCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS--GDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~--~~f~~~~w~~   87 (385)
                      ...++...|-||+||||+|..++..+.  ..-..+.-++
T Consensus        17 ~~~i~v~sgKGGvGKTTvaanLA~~lA~~~~G~rVLLvD   55 (354)
T 2woj_A           17 THKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLIS   55 (354)
T ss_dssp             SCCEEEEEESTTSSHHHHHHHHHHHHHHHCTTSCEEEEE
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            345777889999999999999998877  5544555554

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.98  E-value=0.028  Score=45.03  Aligned_cols=21  Identities=29%  Similarity=0.476  Sum_probs=18.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+..
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            478999999999999998864

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=93.98  E-value=0.06  Score=51.03  Aligned_cols=58  Identities=14%  Similarity=0.133  Sum_probs=32.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGVK  378 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~~  378 (385)
                      .+++.+.+..+.. ...+++..|.++++|++|+|+++    ..|..++  .+|++|++++|.++.
T Consensus        54 ~~L~~L~L~~n~~-~~~i~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~  117 (455)
T 3v47_A           54 QDLQFLKVEQQTP-GLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDG  117 (455)
T ss_dssp             TTCCEEECCCCST-TCEECTTTTTTCTTCCEEECTTCTTCEECTTTTTTCTTCCEEECTTSCCBT
T ss_pred             ccccEEECcCCcc-cceECcccccccccCCEEeCCCCccCccChhhccCcccCCEEeCCCCCCCc
Confidence            3444554444422 12345556666777777777666    2255565  677777777766653

>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=93.97  E-value=0.025  Score=49.53  Aligned_cols=23  Identities=39%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|.|+.|+|||||.+.++.-
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998763

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=93.97  E-value=0.063  Score=52.65  Aligned_cols=60  Identities=13%  Similarity=0.158  Sum_probs=42.4

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..++.+.+.....  ..+++..|.++++|++|+|+++   .+ |+.+.  .+|++|++++|.++.+|.
T Consensus        52 ~~L~~L~Ls~N~i--~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~  117 (562)
T 3a79_B           52 PRTKALSLSQNSI--SELRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHNRLQNISC  117 (562)
T ss_dssp             TTCCEEECCSSCC--CCCCGGGTTTCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECTTSCCCEECS
T ss_pred             CCcCEEECCCCCc--cccChhhhccCCCccEEECCCCCCCcCCHHHhCCCCCCCEEECCCCcCCccCc
Confidence            4566666665542  3455667888888888888877   33 55666  788888888888887774

>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=93.95  E-value=0.031  Score=46.09  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .--|+|+|.+|+|||||...+..
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~   43 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLT   43 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHh
Confidence            45688999999999999999886

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.94  E-value=0.026  Score=49.95  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||++.++.-
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998763

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=93.94  E-value=0.075  Score=47.67  Aligned_cols=52  Identities=19%  Similarity=0.201  Sum_probs=34.9

Q ss_pred             hhHHHHHHhhc--CCCCCeEEEEEEcC-CCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           36 STVEEIESLLG--VESKGVYALGIWGI-GGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        36 ~~l~~l~~~L~--~~~~~~~vv~I~G~-gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++.|...|.  ......++|+|+|. ||+||||+|..++..+...-..+..+.
T Consensus        86 Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID  140 (299)
T 3cio_A           86 EAVRALRTSLHFAMMETENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFID  140 (299)
T ss_dssp             HHHHHHHHHHHHHTSSCSCCEEEEEESSSSSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHhccCCCCeEEEEECCCCCCChHHHHHHHHHHHHhCCCcEEEEE
Confidence            34444544343  12345679999986 899999999999987755444555554

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=93.93  E-value=0.073  Score=44.15  Aligned_cols=57  Identities=16%  Similarity=0.252  Sum_probs=46.4

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGV  377 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~  377 (385)
                      ..+++.+.+.....  ..+++..|.++++|++|+|+++    ..|..+.  .+|++|+++++++.
T Consensus        77 l~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~  139 (192)
T 1w8a_A           77 ASHIQELQLGENKI--KEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             CTTCCEEECCSCCC--CEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cccCCEEECCCCcC--CccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCcc
Confidence            56788888877653  4567788999999999999998    3467777  89999999999875

>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=93.93  E-value=0.025  Score=53.18  Aligned_cols=24  Identities=21%  Similarity=0.371  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...+++|+|..|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            456899999999999999999987

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=93.92  E-value=0.043  Score=54.31  Aligned_cols=27  Identities=26%  Similarity=0.366  Sum_probs=24.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..+|.|.|++|+||||+|+.+.+.+.
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~   77 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLV   77 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            457899999999999999999999763

>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=93.92  E-value=0.032  Score=46.33  Aligned_cols=23  Identities=30%  Similarity=0.515  Sum_probs=20.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            34688999999999999999875

>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=93.92  E-value=0.042  Score=44.09  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=19.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            3588999999999999999863

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=93.91  E-value=0.042  Score=54.08  Aligned_cols=59  Identities=10%  Similarity=0.045  Sum_probs=47.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc--CCCCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF--NGENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l--p~~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+..+....  + + .|.++++|++|+|+++   .+  |..++  .+|++|++++|++..+|.
T Consensus       485 l~~L~~L~Ls~N~l~~--l-p-~l~~l~~L~~L~Ls~N~l~~~~~p~~l~~l~~L~~L~L~~N~l~~~~~  550 (567)
T 1dce_A          485 LRCLEVLQASDNALEN--V-D-GVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSLCQEEG  550 (567)
T ss_dssp             CTTCCEEECCSSCCCC--C-G-GGTTCSSCCEEECCSSCCCSSSTTGGGGGCTTCCEEECTTSGGGGSSS
T ss_pred             CCCCCEEECCCCCCCC--C-c-ccCCCCCCcEEECCCCCCCCCCCcHHHhcCCCCCEEEecCCcCCCCcc
Confidence            5677888887765432  3 3 7899999999999988   44  77787  899999999999988874

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=93.90  E-value=0.036  Score=45.15  Aligned_cols=23  Identities=30%  Similarity=0.486  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-|.|.|.+|+||||+|.++..+
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            46889999999999999999874

>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=93.89  E-value=0.06  Score=50.39  Aligned_cols=36  Identities=8%  Similarity=0.075  Sum_probs=26.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      -.++.|+|.+|+|||||+..++-....      .-..++|+.
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid  219 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID  219 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEe
Confidence            358999999999999999988743321      224577776

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=93.87  E-value=0.054  Score=47.54  Aligned_cols=35  Identities=20%  Similarity=0.370  Sum_probs=25.6

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++.+.+.....+...|+|+|.+|+|||||...+..
T Consensus        24 ~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~   58 (262)
T 3def_A           24 EFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIG   58 (262)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHT
T ss_pred             HHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhC
Confidence            33333433333556789999999999999999986

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=93.87  E-value=0.067  Score=45.18  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=25.3

Q ss_pred             EEEE-EcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           54 ALGI-WGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        54 vv~I-~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +|+| .+-||+||||+|..++..+...- .+..+.
T Consensus         2 vI~v~s~KGGvGKTT~a~~LA~~la~~g-~VlliD   35 (209)
T 3cwq_A            2 IITVASFKGGVGKTTTAVHLSAYLALQG-ETLLID   35 (209)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHTTS-CEEEEE
T ss_pred             EEEEEcCCCCCcHHHHHHHHHHHHHhcC-CEEEEE
Confidence            4555 57899999999999999876655 555554

>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=93.87  E-value=0.034  Score=44.53  Aligned_cols=22  Identities=18%  Similarity=0.454  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHc
Confidence            4688999999999999999986

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.86  E-value=0.14  Score=57.16  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=30.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -.++.|+|.+|+||||||.+++......-..++|++
T Consensus       383 G~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis  418 (2050)
T 3cmu_A          383 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            458999999999999999999987765545677776

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=93.85  E-value=0.072  Score=52.73  Aligned_cols=60  Identities=15%  Similarity=0.192  Sum_probs=40.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCC-C--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGEN-K--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i-~--~~LryL~l~~~~~~~lP  380 (385)
                      ...++.+.+..+.  ...+++..|.++++|++|+|+++   .+|..+ +  .+|++|++++|.+..+|
T Consensus        98 l~~L~~L~L~~n~--l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~  163 (597)
T 3oja_B           98 AHTIQKLYMGFNA--IRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIE  163 (597)
T ss_dssp             CTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCC
T ss_pred             CCCCCEEECCCCc--CCCCCHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCCEEEeeCCcCCCCC
Confidence            4556666665554  23456666777788888888777   566554 4  77888888888777765

>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=93.84  E-value=0.034  Score=46.05  Aligned_cols=22  Identities=27%  Similarity=0.344  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..|+|+|.+|+|||||...+.+
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3688999999999999999886

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.83  E-value=0.041  Score=44.13  Aligned_cols=22  Identities=27%  Similarity=0.800  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4578999999999999999986

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.83  E-value=0.033  Score=45.86  Aligned_cols=24  Identities=21%  Similarity=0.486  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ...|+|+|.+|+|||||...+...
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHcC
Confidence            457889999999999999999864

>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=93.83  E-value=0.047  Score=43.74  Aligned_cols=22  Identities=18%  Similarity=0.385  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~   25 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVE   25 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            4688999999999999999885

>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=93.82  E-value=0.027  Score=45.84  Aligned_cols=23  Identities=22%  Similarity=0.419  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .--|+|+|.+|+|||||...+..
T Consensus         7 ~~ki~~vG~~~vGKTsli~~l~~   29 (178)
T 2iwr_A            7 ELRLGVLGDARSGKSSLIHRFLT   29 (178)
T ss_dssp             EEEEEEECCGGGCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999999986

>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=93.82  E-value=0.13  Score=49.85  Aligned_cols=52  Identities=8%  Similarity=-0.099  Sum_probs=37.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQKLLSNL  110 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l  110 (385)
                      -.++.|.|.+|+||||||.+++...... -..++|++ .     . .+..++...++...
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s-~-----E-~s~~~l~~r~~~~~  294 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAM-L-----E-ESVEETAEDLIGLH  294 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEE-S-----S-SCHHHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEe-c-----c-CCHHHHHHHHHHHH
Confidence            3589999999999999999999877554 34566765 2     1 44556666665543

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.82  E-value=0.028  Score=49.55  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||.+.++.-
T Consensus        34 e~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            48999999999999999998763

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=93.81  E-value=0.095  Score=49.60  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=19.0

Q ss_pred             CccccCCCCCCcEEEecCc---ccCCCCC-CCeeEEEcCCCCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS---SFNGENK-CKISYLQDPGFAGVKL  379 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~---~lp~~i~-~~LryL~l~~~~~~~l  379 (385)
                      +...|.++++|+.|+|+++   .+|..-. .+|++|+|++|.++.+
T Consensus       177 ~~~~~~~l~~L~~L~L~~n~l~~~~~~~~l~~L~~L~Ls~N~l~~~  222 (440)
T 3zyj_A          177 SEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAI  222 (440)
T ss_dssp             CTTTTTTCSSCCEEECTTSCCSSCCCCTTCSSCCEEECTTSCCCEE
T ss_pred             CcchhhcccccCeecCCCCcCccccccCCCcccCEEECCCCccCcc
Confidence            3334444555555555544   3332111 4555555555554443

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=93.80  E-value=0.11  Score=45.49  Aligned_cols=57  Identities=12%  Similarity=0.082  Sum_probs=30.0

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVK  378 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~  378 (385)
                      .+++.+.+.....  ..+.+..|.++.+|+.|+++++   .++. .++  .+|++|+++++.++.
T Consensus        76 ~~L~~L~L~~n~l--~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~  138 (276)
T 2z62_A           76 SHLSTLILTGNPI--QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQS  138 (276)
T ss_dssp             TTCCEEECTTCCC--CEECTTTTTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCC
T ss_pred             cCCCEEECCCCcc--CccChhhhcCCccccEEECCCCCccccCchhcccCCCCCEEECcCCccce
Confidence            3444544444332  2334455666666666666655   2222 344  566666666666655

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=93.79  E-value=0.038  Score=52.86  Aligned_cols=83  Identities=18%  Similarity=0.111  Sum_probs=45.5

Q ss_pred             EEEEEEcCCCchHHHHHH-HHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh--------CCCCCC------
Q 044214           53 YALGIWGIGGIGKTTIAR-AIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL--------KDKNVM------  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~-~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~--------~~~~~~------  117 (385)
                      +.++|.|.+|+|||+||. .++++..  -+..+.+..+++.   ...+.++.+.+...-.        ...++.      
T Consensus       176 QR~~I~g~~g~GKT~Lal~~I~~~~~--~dv~~V~~~IGeR---~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~  250 (515)
T 2r9v_A          176 QRELIIGDRQTGKTAIAIDTIINQKG--QGVYCIYVAIGQK---KSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYI  250 (515)
T ss_dssp             CBEEEEEETTSSHHHHHHHHHHTTTT--TTEEEEEEEESCC---HHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHH
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHhhc--CCcEEEEEEcCCC---cHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHH
Confidence            468899999999999965 5666542  3433222223322   1445566666654211        111111      


Q ss_pred             --chHHHHHHHh--CCceEEEEEeCCC
Q 044214          118 --PYIDLNFRRL--GHMKVLIVFDDVT  140 (385)
Q Consensus       118 --~~~~~l~~~l--~~k~~LlVlDdv~  140 (385)
                        ...-.+.+++  .++.+|+++||+.
T Consensus       251 a~~~a~tiAEyfrd~G~dVLli~DslT  277 (515)
T 2r9v_A          251 APYAGCAMGEYFAYSGRDALVVYDDLS  277 (515)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEEETHH
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEeccHH
Confidence              1111222222  5799999999994

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.79  E-value=0.029  Score=49.90  Aligned_cols=24  Identities=25%  Similarity=0.343  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++|+|..|+|||||.+.++..+
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            489999999999999999988643

>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=93.78  E-value=0.046  Score=45.61  Aligned_cols=25  Identities=28%  Similarity=0.433  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....|+|+|.+|+|||||...+...
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            4567899999999999999998863

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=93.77  E-value=0.046  Score=44.22  Aligned_cols=25  Identities=24%  Similarity=0.375  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ....|+|+|.+|+|||||...+...
T Consensus        14 ~~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           14 YIFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECCCCCCHHHHHHHHHcC
Confidence            3567899999999999999999863

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=93.76  E-value=0.039  Score=44.76  Aligned_cols=25  Identities=28%  Similarity=0.472  Sum_probs=21.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +...-|+|+|.+|+|||||...+..
T Consensus         7 ~~~~~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B            7 DHLFKLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHHCS
T ss_pred             CcceEEEEECCCCCCHHHHHHHHhc
Confidence            3456789999999999999999875

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.76  E-value=0.029  Score=49.09  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|..|+|||||.+.++.-
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999999864

>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=93.74  E-value=0.041  Score=44.54  Aligned_cols=23  Identities=22%  Similarity=0.566  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||||...+..
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~   29 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVT   29 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHc
Confidence            45689999999999999999975

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=93.74  E-value=0.07  Score=50.75  Aligned_cols=60  Identities=12%  Similarity=0.128  Sum_probs=33.9

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCC-CC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGE-NK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~-i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+..+..  ..+.+..|.++.+|+.|+|+++   .+|.. +.  .+|++|++++|.++.+|
T Consensus        98 l~~L~~L~Ls~n~i--~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~  163 (452)
T 3zyi_A           98 LHHLEVLQLGRNSI--RQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELWLRNNPIESIP  163 (452)
T ss_dssp             CTTCCEEECCSSCC--CEECTTTTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCCEEECCSCCCCEEC
T ss_pred             CCCCCEEECCCCcc--CCcChhhccCcccCCEEECCCCcCCccChhhhcccCCCCEEECCCCCcceeC
Confidence            34455555554432  2344556666666666666665   34433 33  56666666666666555

>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=0.048  Score=43.80  Aligned_cols=23  Identities=35%  Similarity=0.390  Sum_probs=20.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...|+|+|.+|+|||||...+..
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            35688999999999999999975

>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=93.73  E-value=0.039  Score=44.93  Aligned_cols=24  Identities=17%  Similarity=0.392  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ....|+|+|.+|+|||||...+.+
T Consensus         5 ~~~ki~~~G~~~~GKSsli~~l~~   28 (181)
T 3t5g_A            5 KSRKIAILGYRSVGKSSLTIQFVE   28 (181)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHc
Confidence            345789999999999999999985

>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=93.73  E-value=0.048  Score=44.45  Aligned_cols=25  Identities=32%  Similarity=0.345  Sum_probs=20.8

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .....|+|+|.+|+|||||...+..
T Consensus        16 ~~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           16 NKELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            3456788999999999999988764

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=93.71  E-value=0.036  Score=46.12  Aligned_cols=23  Identities=30%  Similarity=0.599  Sum_probs=20.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~   73 (385)
                      ....|+|+|.+|+|||||...+.
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~   44 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFG   44 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHH
Confidence            45678999999999999999885

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.70  E-value=0.056  Score=43.76  Aligned_cols=24  Identities=21%  Similarity=0.338  Sum_probs=20.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..--|+|+|.+|+|||||...+..
T Consensus         5 ~~~ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            5 RQLKIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHG
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHh
Confidence            345688999999999999999875

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=93.69  E-value=0.039  Score=52.36  Aligned_cols=83  Identities=16%  Similarity=0.067  Sum_probs=48.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC----CceEEEeeccccccCCCChHHHHHHHHHHHhC--------CCCCC---
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF----DGSCFLENVREESQIPGGLSCLRQKLLSNLLK--------DKNVM---  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f----~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~--------~~~~~---  117 (385)
                      +.++|.|.+|+|||+|+..+++......    +..+++- +++..   ..+.++.+++...-..        ..++.   
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~-iGER~---~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~  228 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAA-MGITN---EEAQYFMSDFEKTGALERAVVFLNLADDPAVE  228 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEE-EEECH---HHHHHHHHHHHHHSGGGGEEEEEEETTSCHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEE-ccCCc---HHHHHHHHHHHhccCccceEEEEECCCCCHHH
Confidence            4678899999999999999998754321    2333433 33321   4456666666543111        11111   


Q ss_pred             -----chHHHHHHHh---CCceEEEEEeCC
Q 044214          118 -----PYIDLNFRRL---GHMKVLIVFDDV  139 (385)
Q Consensus       118 -----~~~~~l~~~l---~~k~~LlVlDdv  139 (385)
                           ...-.+.+++   .++.+|+++||+
T Consensus       229 r~~~~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          229 RIVTPRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence                 1112233333   369999999998

>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=93.69  E-value=0.049  Score=45.77  Aligned_cols=24  Identities=17%  Similarity=0.136  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...-|+|+|.+|+|||||...+..
T Consensus        27 ~~~ki~vvG~~~vGKSsLi~~l~~   50 (205)
T 1gwn_A           27 VKCKIVVVGDSQCGKTALLHVFAK   50 (205)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             eeeEEEEECCCCCCHHHHHHHHhc
Confidence            445788999999999999999986

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=93.69  E-value=0.061  Score=47.41  Aligned_cols=25  Identities=24%  Similarity=0.513  Sum_probs=21.8

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .....|+++|.+|+|||||...+..
T Consensus        37 ~~~~~I~vvG~~g~GKSSLin~l~~   61 (270)
T 1h65_A           37 VNSLTILVMGKGGVGKSSTVNSIIG   61 (270)
T ss_dssp             CCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHhC
Confidence            3456789999999999999999986

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=93.69  E-value=0.1  Score=46.10  Aligned_cols=60  Identities=10%  Similarity=0.023  Sum_probs=41.2

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..++...|.++++|+.|+|+++    ..|..+.  .+|++|++++|.+..+|
T Consensus       152 l~~L~~L~l~~n~l--~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~  217 (285)
T 1ozn_A          152 LGNLTHLFLHGNRI--SSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALP  217 (285)
T ss_dssp             CTTCCEEECCSSCC--CEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCC
T ss_pred             CCCccEEECCCCcc--cccCHHHhcCccccCEEECCCCcccccCHhHccCcccccEeeCCCCcCCcCC
Confidence            45566666665542  3455666778888888888877    2356666  78888888888877766

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.69  E-value=0.038  Score=48.84  Aligned_cols=23  Identities=26%  Similarity=0.582  Sum_probs=20.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++|+|..|+|||||.+.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998743

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=93.68  E-value=0.06  Score=43.90  Aligned_cols=25  Identities=36%  Similarity=0.679  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ..-.|+|+|.+|+|||||...+.+.
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            4557889999999999999999863

>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=93.68  E-value=0.31  Score=44.37  Aligned_cols=95  Identities=9%  Similarity=-0.057  Sum_probs=56.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGH  129 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~  129 (385)
                      -.++..++|..|.||++.+..+.+.+. ..|+....+. ..   .. .++.++...+...                -+-+
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~---~~-~~~~~l~~~~~~~----------------plf~   75 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFS-ID---PN-TDWNAIFSLCQAM----------------SLFA   75 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEE-CC---TT-CCHHHHHHHHHHH----------------HHCC
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEE-ec---CC-CCHHHHHHHhcCc----------------CCcc
Confidence            456899999999999999999998653 3454221121 11   12 4455444433111                1234


Q ss_pred             ceEEEEEeCCCC---hhhhhHhhccCCCCCCCcEEEEEec
Q 044214          130 MKVLIVFDDVTC---FSQLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus       130 k~~LlVlDdv~~---~~~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      ++-++|+|+++.   ....+.+...+....+++.+|+++.
T Consensus        76 ~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~  115 (343)
T 1jr3_D           76 SRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGN  115 (343)
T ss_dssp             SCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEES
T ss_pred             CCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcC
Confidence            566888899854   3455666655554445776766653

>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=93.68  E-value=0.051  Score=44.40  Aligned_cols=24  Identities=17%  Similarity=0.390  Sum_probs=21.1

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...-|+|+|.+|+|||||...+..
T Consensus         9 ~~~ki~v~G~~~~GKSsli~~l~~   32 (186)
T 2bme_A            9 FLFKFLVIGNAGTGKSCLLHQFIE   32 (186)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHc
Confidence            345788999999999999999986

>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=93.64  E-value=0.039  Score=45.21  Aligned_cols=22  Identities=27%  Similarity=0.631  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+.+
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~   26 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQ   26 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            4588999999999999999986

>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=93.64  E-value=0.031  Score=45.87  Aligned_cols=21  Identities=19%  Similarity=0.295  Sum_probs=19.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~   23 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTG   23 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999886

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=93.64  E-value=0.14  Score=45.49  Aligned_cols=52  Identities=15%  Similarity=0.194  Sum_probs=36.2

Q ss_pred             hhHHHHHHhhc--CCCCCeEEEEEEcC-CCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           36 STVEEIESLLG--VESKGVYALGIWGI-GGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        36 ~~l~~l~~~L~--~~~~~~~vv~I~G~-gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++.|...|.  ....+.++|+|+|. ||+||||+|..++..+...-..++.+.
T Consensus        74 Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID  128 (286)
T 3la6_A           74 EAIRSLRTSLHFAMMQAQNNVLMMTGVSPSIGMTFVCANLAAVISQTNKRVLLID  128 (286)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEEEESSSSSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHHHHHHHHhhhccCCCCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            45556655553  22345678888775 899999999999998776655566665

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=93.63  E-value=0.049  Score=45.36  Aligned_cols=59  Identities=10%  Similarity=0.058  Sum_probs=27.4

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCccc----CCCCC--CCeeEEEcCCCC-CCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSF----NGENK--CKISYLQDPGFA-GVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~l----p~~i~--~~LryL~l~~~~-~~~lP  380 (385)
                      .+++.+.+..+..  ....+..|.++++|++|+|+++.+    |..++  .+|++|++++|. ++.+|
T Consensus        88 ~~L~~L~l~~n~l--~~~~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~  153 (197)
T 4ezg_A           88 SNLERLRIMGKDV--TSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM  153 (197)
T ss_dssp             TTCCEEEEECTTC--BGGGSCCCTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG
T ss_pred             CCCCEEEeECCcc--CcccChhhcCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH
Confidence            4455555544432  111233445555555555555522    33333  555555555554 55444

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=93.63  E-value=0.091  Score=49.76  Aligned_cols=61  Identities=10%  Similarity=0.029  Sum_probs=43.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---c-cCCCCC--CCeeEEEcCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---S-FNGENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~-lp~~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..+++.+.+.....  ..+.+..|.++++|++|+|+++   . .|..++  .+|++|++++|.++.+|.
T Consensus       322 l~~L~~L~Ls~N~l--~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~  388 (455)
T 3v47_A          322 LTHLLKLNLSQNFL--GSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQLKSVPD  388 (455)
T ss_dssp             CTTCCEEECCSSCC--CEECGGGGTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCCT
T ss_pred             cccCCEEECCCCcc--CCcChhHhcCcccCCEEECCCCcccccChhhccccccccEEECCCCccccCCH
Confidence            34566666655432  3456677888888888888887   2 356666  788888888888888773

>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=93.61  E-value=0.052  Score=44.55  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...-|+|+|.+|+|||||...+..
T Consensus        10 ~~~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           10 YLIKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeEEEEEECCCCCCHHHHHHHHhc
Confidence            345788999999999999999986

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=93.61  E-value=0.066  Score=51.82  Aligned_cols=60  Identities=23%  Similarity=0.171  Sum_probs=36.1

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      ..++.+.+..+..  ..+.+..|.++++|++|+|+++   .+ |..++  .+|++|++++|.++.+|.
T Consensus        21 ~~L~~L~Ls~n~i--~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~   86 (520)
T 2z7x_B           21 QKTTILNISQNYI--SELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHNKLVKISC   86 (520)
T ss_dssp             TTCSEEECCSSCC--CCCCHHHHTTCTTCCEEECCSSCCCEEEGGGGTTCTTCCEEECCSSCCCEEEC
T ss_pred             ccccEEECCCCcc--cccChhhccccccccEEecCCCccCCcChHHhhcccCCCEEecCCCceeecCc
Confidence            3455555555432  2344456677777777777766   22 45555  677777777777766663

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=93.59  E-value=0.049  Score=48.69  Aligned_cols=48  Identities=19%  Similarity=0.207  Sum_probs=31.3

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEc---CCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           37 TVEEIESLLGVESKGVYALGIWG---IGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G---~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.++.+.+..   +.++|+|++   -||+||||+|..++..+...-..+.-+.
T Consensus        22 ~~~~~~r~~~~---~~~~i~v~~~s~KGGvGKTT~a~nLA~~la~~G~rVlliD   72 (298)
T 2oze_A           22 ILEELRRILSN---KNEAIVILNNYFKGGVGKSKLSTMFAYLTDKLNLKVLMID   72 (298)
T ss_dssp             HHHHHHHHHHH---HCSCEEEEECCSSSSSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHhcC---CCcEEEEEeccCCCCchHHHHHHHHHHHHHhCCCeEEEEe
Confidence            44555555542   234666765   8999999999999987654433444444

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=93.57  E-value=0.092  Score=48.75  Aligned_cols=60  Identities=15%  Similarity=0.189  Sum_probs=39.8

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+.....  ..++...|.++++|++|+|+++   .+ |..+.  .+|++|+++++.++.+|
T Consensus       116 l~~L~~L~L~~n~l--~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~  181 (390)
T 3o6n_A          116 VPLLTVLVLERNDL--SSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVD  181 (390)
T ss_dssp             CTTCCEEECCSSCC--CCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSSCCSBCC
T ss_pred             CCCCCEEECCCCcc--CcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCCcCCccc
Confidence            45566776666543  2456666777888888888876   33 33455  77888888887776654

>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=93.57  E-value=0.13  Score=48.52  Aligned_cols=87  Identities=13%  Similarity=0.089  Sum_probs=48.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCc
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHM  130 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k  130 (385)
                      .-.+++|+|+.|+||||+.+.+...+... .+.+++..-.-.... .....  .    .+. ..........++..++..
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l~~~-~g~I~~~ed~ie~~~-~~~~q--~----~v~-~~~g~~f~~~lr~~Lrq~  236 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQELNSS-ERNILTVEDPIEFDI-DGIGQ--T----QVN-PRVDMTFARGLRAILRQD  236 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCT-TSCEEEEESSCCSCC-SSSEE--E----ECB-GGGTBCHHHHHHHHGGGC
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhcCCC-CCEEEEecccchhcc-CCcce--E----EEc-cccCcCHHHHHHHHhccC
Confidence            34589999999999999999999877544 344444311100000 00000  0    000 000114455667777777


Q ss_pred             eEEEEEeCCCChhhhh
Q 044214          131 KVLIVFDDVTCFSQLE  146 (385)
Q Consensus       131 ~~LlVlDdv~~~~~~~  146 (385)
                      +-++++.++.+.....
T Consensus       237 pd~i~vgEiRd~et~~  252 (418)
T 1p9r_A          237 PDVVMVGEIRDLETAQ  252 (418)
T ss_dssp             CSEEEESCCCSHHHHH
T ss_pred             CCeEEEcCcCCHHHHH
Confidence            7788888887655433

>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=93.56  E-value=0.04  Score=46.90  Aligned_cols=21  Identities=24%  Similarity=0.347  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|||||+|...+.+
T Consensus        15 KivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCcCHHHHHHHHHh
Confidence            477999999999999999875

>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=93.55  E-value=0.041  Score=44.52  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -.|+|+|.+|+|||||...+..
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHc
Confidence            4588999999999999999885

>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=93.54  E-value=0.12  Score=56.70  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=29.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      -+++.|+|.+|+||||||.+++......-..++|++
T Consensus       383 G~lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis  418 (1706)
T 3cmw_A          383 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEE
Confidence            458999999999999999999987655555677876

>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=93.53  E-value=0.042  Score=44.72  Aligned_cols=22  Identities=23%  Similarity=0.208  Sum_probs=19.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|+|+|.+|+|||||...+..
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~   30 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTS   30 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999998875

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=93.53  E-value=0.065  Score=44.87  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+|+|+|++|+||+|+|..+.+.+
T Consensus         9 ~~~~II~itGk~~SGKd~va~~l~~~~   35 (202)
T 3ch4_B            9 APRLVLLFSGKRKSGKDFVTEALQSRL   35 (202)
T ss_dssp             CCSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCChHHHHHHHHHHc
Confidence            345799999999999999999887755

>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=93.52  E-value=0.041  Score=45.64  Aligned_cols=24  Identities=29%  Similarity=0.577  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ..-|+|+|.+|+|||||...+...
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            456889999999999999998863

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=93.52  E-value=0.031  Score=50.30  Aligned_cols=22  Identities=41%  Similarity=0.658  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|+|..|+|||||++.+..
T Consensus        81 e~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           81 QTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             CEEEEESSSCHHHHHHHHHHTT
T ss_pred             CEEEEECCCCchHHHHHHHHHc
Confidence            5899999999999999998875

>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=93.52  E-value=0.042  Score=44.83  Aligned_cols=23  Identities=22%  Similarity=0.439  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||||...+..
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~   40 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMY   40 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHhh
Confidence            45688999999999999999886

>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=93.51  E-value=0.07  Score=43.77  Aligned_cols=24  Identities=29%  Similarity=0.184  Sum_probs=21.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +...|+|+|.+|+|||||...+..
T Consensus        15 ~~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           15 QEHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            445788999999999999999885

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.51  E-value=0.046  Score=50.56  Aligned_cols=26  Identities=15%  Similarity=0.240  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...++|+|..|+|||||++.++..+.
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999988653

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=93.50  E-value=0.091  Score=49.95  Aligned_cols=59  Identities=12%  Similarity=0.106  Sum_probs=47.6

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+.....  ..+.+..|.++++|++|+|+++   .+ |..+.  .+|++|+|++|.++.+|
T Consensus        75 ~~l~~L~L~~n~i--~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~  139 (452)
T 3zyi_A           75 SNTRYLNLMENNI--QMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTVIP  139 (452)
T ss_dssp             TTCSEEECCSSCC--CEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSBCC
T ss_pred             CCccEEECcCCcC--ceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCcCCccC
Confidence            4677777766643  4567788999999999999998   33 35666  89999999999999988

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.50  E-value=0.049  Score=45.09  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=21.5

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .....|+|+|.+|+|||||...+..
T Consensus        15 ~~~~ki~v~G~~~~GKSsl~~~l~~   39 (199)
T 4bas_A           15 KTKLQVVMCGLDNSGKTTIINQVKP   39 (199)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhc
Confidence            4467899999999999999999875

>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=93.50  E-value=0.045  Score=45.20  Aligned_cols=24  Identities=29%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .--|+|+|.+|+|||||...+...
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            346889999999999999999874

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=93.48  E-value=0.054  Score=48.29  Aligned_cols=58  Identities=17%  Similarity=0.226  Sum_probs=31.8

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      .+++.+.+..+.....    ..|.++++|+.|+|+++   .+|. +.  .+|++|++++|.++.+|.|
T Consensus       134 ~~L~~L~l~~n~l~~~----~~l~~l~~L~~L~L~~N~l~~~~~-l~~l~~L~~L~L~~N~i~~l~~l  196 (291)
T 1h6t_A          134 PQLESLYLGNNKITDI----TVLSRLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYLSKNHISDLRAL  196 (291)
T ss_dssp             TTCCEEECCSSCCCCC----GGGGGCTTCSEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCBCGGG
T ss_pred             CCCCEEEccCCcCCcc----hhhccCCCCCEEEccCCccccchh-hcCCCccCEEECCCCcCCCChhh
Confidence            4455555554432221    34566666666666666   2322 33  6666666666666666543

---

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	385
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	3e-19

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 84.5 bits (208), Expect = 3e-19
 Identities = 38/252 (15%), Positives = 71/252 (28%), Gaps = 52/252 (20%)

Query: 31  LVGVESTVEEI-ESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK----ISGDFDGSCF 85
               E  V+ + + L  +     + L + G  G GK+ IA     K    I  ++D   +
Sbjct: 22  CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVW 81

Query: 86  LENVREES------QIPGGLSCLRQKLLSNLLKDKNVMPYIDLNF---RRLGHMKVLIVF 136
           L++                L    +  L N    ++V   +         +     L VF
Sbjct: 82  LKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVF 141

Query: 137 DDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRVN------------------- 177
           DDV                    R ++TTR+ ++                          
Sbjct: 142 DDV------VQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLE 195

Query: 178 --AFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL----------VWESAISKLQRILHPS 225
                    +   E + +  ++ + G P  L +                 +KL+      
Sbjct: 196 AYGMPMPVGE-KEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVG 254

Query: 226 ILEVLKISYDSL 237
           +  +   SY SL
Sbjct: 255 VECITPYSYKSL 266

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	385
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.18
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.86
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.81
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.68
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.68
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.66
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.65
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.63
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.54
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.5
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.46
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.46
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.38
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.32
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.23
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.11
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.08
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.01
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.97
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.93
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.92
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.9
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.84
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.58
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.53
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.53
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.51
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.5
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.49
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.48
d1okkd2	207	GTPase domain of the signal recognition particle r	97.46
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.44
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.43
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.38
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.37
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.35
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.31
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.28
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.28
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.27
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.24
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.23
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.23
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.2
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.16
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.15
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.12
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.1
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.1
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.09
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.02
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.99
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.99
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.99
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.97
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.96
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.93
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.87
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.81
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.79
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.79
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.75
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.73
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.71
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.71
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.7
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.69
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.66
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.63
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.59
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.59
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.56
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.56
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.55
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.54
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.5
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.5
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.47
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	96.45
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.45
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.44
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.43
d2ifga3	156	High affinity nerve growth factor receptor, N-term	96.41
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.39
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.38
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.37
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	96.3
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.3
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	96.27
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.22
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.17
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	96.15
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.11
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.1
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.07
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.04
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	96.03
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	96.03
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	96.02
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.98
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.96
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.93
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.93
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.86
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.8
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.78
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.74
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	95.69
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.67
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.64
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	95.58
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.51
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.51
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	95.46
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.45
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.38
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.38
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.25
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.25
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.24
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.23
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.21
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.17
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.16
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	95.15
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	95.13
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	95.12
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	95.1
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.09
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	95.09
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	95.06
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.03
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	95.0
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.99
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.87
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.85
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.84
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.78
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.78
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.78
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.76
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	94.76
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	94.74
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	94.73
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.73
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.72
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.72
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.71
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	94.71
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.69
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	94.69
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.67
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.66
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.66
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.65
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	94.64
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.62
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.6
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.58
d2ifga3	156	High affinity nerve growth factor receptor, N-term	94.58
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.57
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.56
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.56
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.55
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.55
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.54
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.52
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.51
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	94.51
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	94.5
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.5
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.46
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.45
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.45
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.43
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.43
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.43
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	94.42
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.38
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.37
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.36
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	94.36
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.35
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.35
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.32
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.32
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.32
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	94.32
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	94.31
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	94.31
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.29
d1nrjb_	209	Signal recognition particle receptor beta-subunit	94.28
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	94.22
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	94.19
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	94.14
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	94.11
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.11
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.04
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	94.03
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.02
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.02
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	94.01
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	94.0
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.99
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.98
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	93.98
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.97
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.91
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.9
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.89
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	93.84
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	93.81
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.81
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	93.77
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.7
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	93.67
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	93.66
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.59
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	93.59
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	93.48
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.47
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	93.45
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.36
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.36
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	93.34
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	93.28
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	93.26
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.26
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	93.18
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.97
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	92.86
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	92.77
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.77
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	92.74
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.71
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	92.62
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.51
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	92.37
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	92.15
d1tuea_	205	Replication protein E1 helicase domain {Human papi	91.94
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	91.6
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	91.49
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	91.48
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	91.37
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	91.24
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	90.62
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	90.61
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	90.57
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	90.36
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	90.28
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	90.12
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	89.75
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	89.3
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	89.13
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.13
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	88.85
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	88.47
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	88.25
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	88.21
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	88.19
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	87.97
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	87.92
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	87.84
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	87.72
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	87.17
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	86.64
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	86.18
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	85.39
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	85.25
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.11
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	85.11
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	84.68
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	84.23
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.26
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	83.01
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	82.88
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	82.71
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	82.15
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	82.12
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	82.1
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	80.46
d1p3da1	96	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	80.45

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=9.8e-37  Score=274.29  Aligned_cols=222  Identities=18%  Similarity=0.105  Sum_probs=167.3

Q ss_pred             HHHHhhccCCCCCCCCCCccccchhHHHHHHhhcC-CCCCeEEEEEEcCCCchHHHHHHHHHHH----hhCCCCceEEEe
Q 044214           13 HILKRLDEVFRPRDNKNQLVGVESTVEEIESLLGV-ESKGVYALGIWGIGGIGKTTIARAIFDK----ISGDFDGSCFLE   87 (385)
Q Consensus        13 ~v~~~l~~~~~~~~~~~~~vGR~~~l~~l~~~L~~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~----~~~~f~~~~w~~   87 (385)
                      .+.+++..  ...+..+.++||+.++++|.++|.. .+.+.++|+|+||||+||||||++++++    ....|++++|++
T Consensus         6 ~~~~~l~~--~~~p~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~   83 (277)
T d2a5yb3           6 MLDRKLLL--GNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK   83 (277)
T ss_dssp             HHHHHHHH--TTCBCCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE
T ss_pred             hhcccccc--cCCCCCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEE
Confidence            34455444  3444667788999999999999864 4456789999999999999999999986    466799999998


Q ss_pred             eccccccCCCChHHHHHHHHH---HHhCCCC-----CC------chHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCC
Q 044214           88 NVREESQIPGGLSCLRQKLLS---NLLKDKN-----VM------PYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLD  153 (385)
Q Consensus        88 ~~~~~~~~~~~~~~l~~~ll~---~l~~~~~-----~~------~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~  153 (385)
                          ++.. .+...+...+..   .+.....     ..      .....+.+.+.++++|+||||+|+..+++.+..   
T Consensus        84 ----vs~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~---  155 (277)
T d2a5yb3          84 ----DSGT-APKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE---  155 (277)
T ss_dssp             ----CCCC-STTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH---
T ss_pred             ----ecCC-CCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcc---
Confidence                3333 444555444433   3322211     01      233457778899999999999999999887643   


Q ss_pred             CCCCCcEEEEEeccHHHHhhccc---------------------eecccCCCCCCchHHHHHHHHHhCCCccchhHH---
Q 044214          154 WLTPVSRIILTTRNKQVLRNWRV---------------------NAFKRNHPDVGNEKLSSNVMKYAQGVPLALKVL---  209 (385)
Q Consensus       154 ~~~~gs~ilvTtR~~~~~~~~~~---------------------~~~~~~~~~~~~~~~~~~i~~~~~GlPLal~~~---  209 (385)
                         .||+||||||+..++..+..                     ++|.... .+..++++++|+++|+|+||||+++   
T Consensus       156 ---~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~-~~~~~~~~~~iv~~c~GlPLAl~~ig~~  231 (277)
T d2a5yb3         156 ---LRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV-GEKEEDVLNKTIELSSGNPATLMMFFKS  231 (277)
T ss_dssp             ---TTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC---CHHHHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             ---cCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccC-chhhHHHHHHHHHHhCCCHHHHHHHHHH
Confidence               48899999999998876532                     3332222 2345788899999999999999999   


Q ss_pred             -------hHHHHHHHhhhccCcccchhhhhccccCchhhhhhhhhc
Q 044214          210 -------VWESAISKLQRILHPSILEVLKISYDSLEDKEKNIFLDV  248 (385)
Q Consensus       210 -------~w~~~l~~l~~~~~~~~~~~l~~sy~~L~~~~k~~~~~l  248 (385)
                             .|......+......++..++.+||+.||++.|.||.++
T Consensus       232 l~~k~~~~~~~~~~~L~~~~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         232 CEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             CCSSSHHHHHHHHHHHHHHCSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             hccCCHHHHHHHHHHHhcCcHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence                   777777778777778899999999999999999999864

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.18  E-value=1.2e-11  Score=108.99  Aligned_cols=51  Identities=20%  Similarity=0.374  Sum_probs=42.2

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .|...++.||||++++++|.+..      .+.|.|+|++|+|||+|+++++++....
T Consensus         6 ~p~~~~~~f~GR~~el~~l~~~~------~~~i~i~G~~G~GKTsLl~~~~~~~~~~   56 (283)
T d2fnaa2           6 SPKDNRKDFFDREKEIEKLKGLR------APITLVLGLRRTGKSSIIKIGINELNLP   56 (283)
T ss_dssp             SCCCSGGGSCCCHHHHHHHHHTC------SSEEEEEESTTSSHHHHHHHHHHHHTCC
T ss_pred             CCCCChhhCCChHHHHHHHHhcc------CCEEEEEcCCCCcHHHHHHHHHHHCCCC
Confidence            44456789999999999998742      2478999999999999999999887543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.86  E-value=3.5e-08  Score=85.27  Aligned_cols=148  Identities=16%  Similarity=0.213  Sum_probs=89.2

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEeeccccccC---CCCh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLENVREESQI---PGGL   99 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~~~~~~~~~---~~~~   99 (385)
                      +..+||+++++++...|....  -.-+.++|.+|||||+++..+++++...      ....+|..+.......   ....
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~--k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~   95 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDF   95 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCH
T ss_pred             CcccChHHHHHHHHHHHhcCc--cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhH
Confidence            458999999999999998432  2356699999999999999999976331      2445666543322110   0222


Q ss_pred             HHHHHHHHHHHhCCCCCCchHHHHHHHh-CCceEEEEEeCCCCh----------hhhhHhh-ccCCCCCCCcEEEEEecc
Q 044214          100 SCLRQKLLSNLLKDKNVMPYIDLNFRRL-GHMKVLIVFDDVTCF----------SQLESLM-GSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       100 ~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~~k~~LlVlDdv~~~----------~~~~~l~-~~~~~~~~gs~ilvTtR~  167 (385)
                      ...+..+                 .+.+ +.+++++++|++...          .+...++ +.+.  ...-++|.||..
T Consensus        96 e~r~~~i-----------------~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~  156 (268)
T d1r6bx2          96 EKRFKAL-----------------LKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTY  156 (268)
T ss_dssp             HHHHHHH-----------------HHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECH
T ss_pred             HHHHHHH-----------------HHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCH
Confidence            3222222                 2333 356799999998532          2344444 4443  335678888888


Q ss_pred             HHHHhhccc-----eecccCCCCCCchHHHHHHHH
Q 044214          168 KQVLRNWRV-----NAFKRNHPDVGNEKLSSNVMK  197 (385)
Q Consensus       168 ~~~~~~~~~-----~~~~~~~~~~~~~~~~~~i~~  197 (385)
                      .+.......     ..|..-.-.+...+.+.+|++
T Consensus       157 eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~  191 (268)
T d1r6bx2         157 QEFSNIFEKDRALARRFQKIDITEPSIEETVQIIN  191 (268)
T ss_dssp             HHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHH
T ss_pred             HHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHH
Confidence            877655433     444444333344555666654

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.81  E-value=2.1e-08  Score=87.36  Aligned_cols=115  Identities=17%  Similarity=0.193  Sum_probs=77.1

Q ss_pred             CCCCCCCCccccchhHHHHHHhhcC----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCC
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLGV----ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGG   98 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~~----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~   98 (385)
                      .|...+..++||+.+++++.++|..    .....+.+.|+|++|+|||++|+.+++.+.+.........+....    ..
T Consensus        10 ~~~y~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~----~~   85 (276)
T d1fnna2          10 SPSYVPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIY----RN   85 (276)
T ss_dssp             STTCCCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTC----CS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhh----hh
Confidence            4445667799999999999988852    334567899999999999999999999987765544433322222    56


Q ss_pred             hHHHHHHHHHHHhCCCCCC-----chHHHHHHHh--CCceEEEEEeCCCC
Q 044214           99 LSCLRQKLLSNLLKDKNVM-----PYIDLNFRRL--GHMKVLIVFDDVTC  141 (385)
Q Consensus        99 ~~~l~~~ll~~l~~~~~~~-----~~~~~l~~~l--~~k~~LlVlDdv~~  141 (385)
                      .......+...........     .....+.+.+  .......++|++++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~  135 (276)
T d1fnna2          86 FTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFN  135 (276)
T ss_dssp             HHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGG
T ss_pred             hhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHH
Confidence            6677777777665544322     3333333333  23567777787754

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.68  E-value=3.3e-08  Score=80.81  Aligned_cols=127  Identities=12%  Similarity=0.104  Sum_probs=74.6

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEeeccccccCCCChHHH
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      +..+||+++++++...|....  -.-+.++|.+|||||+++..+++++...      -+..+|..+......-.....++
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~--k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~   99 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEF   99 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccC--CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHH
Confidence            458999999999999998432  2356799999999999999999976321      24556654333221110111111


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHh--CCceEEEEEeCCCCh----------hhhhHhhccCCCCCCCcEEEEEeccHHH
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRL--GHMKVLIVFDDVTCF----------SQLESLMGSLDWLTPVSRIILTTRNKQV  170 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l--~~k~~LlVlDdv~~~----------~~~~~l~~~~~~~~~gs~ilvTtR~~~~  170 (385)
                      .              +....+.+.+  ...+++|++|++...          +.-+-+.+.+.  ...-++|.||..+..
T Consensus       100 E--------------~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey  163 (195)
T d1jbka_         100 E--------------ERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEY  163 (195)
T ss_dssp             H--------------HHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHH
T ss_pred             H--------------HHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHH
Confidence            1              1112222222  245799999999432          11233334443  234578888877666


Q ss_pred             Hhh
Q 044214          171 LRN  173 (385)
Q Consensus       171 ~~~  173 (385)
                      ...
T Consensus       164 ~~~  166 (195)
T d1jbka_         164 RQY  166 (195)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.68  E-value=5.7e-08  Score=82.48  Aligned_cols=126  Identities=16%  Similarity=0.244  Sum_probs=74.6

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEeeccccccCCCChHHHHH
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLENVREESQIPGGLSCLRQ  104 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~~l~~  104 (385)
                      ..-.++||.++.++.|.+++..  +..+.+.++|++|+||||+|+.+++.+... +...+...+.   +.. .+......
T Consensus        11 ~~~~divg~~~~~~~L~~~i~~--~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~---~~~-~~~~~~~~   84 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKFVDE--GKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNA---SDD-RGIDVVRN   84 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHT--TCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECT---TSC-CSHHHHHT
T ss_pred             CCHHHccCcHHHHHHHHHHHHc--CCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecc---ccc-CCeeeeec
Confidence            3457799999999999999984  344457799999999999999999986543 2222222211   111 22222222


Q ss_pred             HHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          105 KLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       105 ~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..........           ...++.-++|+|+++.  ......++..+......+.++++|...
T Consensus        85 ~~~~~~~~~~-----------~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  139 (227)
T d1sxjc2          85 QIKDFASTRQ-----------IFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  139 (227)
T ss_dssp             HHHHHHHBCC-----------SSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             chhhcccccc-----------ccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcH
Confidence            2211111110           1123456888999963  344445554444445677777777653

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.66  E-value=1.2e-08  Score=86.61  Aligned_cols=128  Identities=15%  Similarity=0.273  Sum_probs=74.8

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCC-CceEEEeeccccccCCCChHHHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDF-DGSCFLENVREESQIPGGLSCLR  103 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~~l~  103 (385)
                      |..-.++||.++.++.|.+++..  +..+.+.++|++|+||||+|+.+++.+...+ ...++..+....    .+...+.
T Consensus        11 P~~~~d~ig~~~~~~~L~~~~~~--~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~----~~~~~i~   84 (224)
T d1sxjb2          11 PQVLSDIVGNKETIDRLQQIAKD--GNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDD----RGIDVVR   84 (224)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHS--CCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSC----CSHHHHH
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHc--CCCCeEEEECCCCCCchhhHHHHHHHHhcccccccccccccccc----CCceehh
Confidence            34457899999999999999984  3444577999999999999999998765432 222223222221    3333333


Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          104 QKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       104 ~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..+.........          ...++.-++|+|+++..  .....++..+......+++++++.+.
T Consensus        85 ~~~~~~~~~~~~----------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          85 NQIKHFAQKKLH----------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             THHHHHHHBCCC----------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             hHHHHHHHhhcc----------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            333222211111          01235568889999643  33333333333334566666666543

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.65  E-value=6.9e-08  Score=82.42  Aligned_cols=135  Identities=18%  Similarity=0.199  Sum_probs=75.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC---CCceEEEeeccccccCCCChHH
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD---FDGSCFLENVREESQIPGGLSC  101 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~---f~~~~w~~~~~~~~~~~~~~~~  101 (385)
                      |..-++++|.++.++.|..++..  +..+.+.++|++|+||||+|+.+++++...   ......+. .   +.. .....
T Consensus         8 P~~~~diig~~~~~~~l~~~i~~--~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~-~---~~~-~~~~~   80 (237)
T d1sxjd2           8 PKNLDEVTAQDHAVTVLKKTLKS--ANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN-A---SDE-RGISI   80 (237)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTC--TTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC-S---SSC-CCHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHc--CCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhee-c---ccc-ccchH
Confidence            34456799999999999999984  344458899999999999999999875321   12222222 1   111 33333


Q ss_pred             HHHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh--hhhhHhhccCCCCCCCcEEEEEecc
Q 044214          102 LRQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       102 l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      ....+ ...............+......+.-++|+|+++..  .....+..........+++++|+.+
T Consensus        81 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2          81 VREKV-KNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             HTTHH-HHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHH-HHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccc
Confidence            22222 22221111112222233344445557999999633  3333333333333456667666654

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.63  E-value=2.9e-08  Score=84.64  Aligned_cols=52  Identities=27%  Similarity=0.358  Sum_probs=43.7

Q ss_pred             CCCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      |..-++++|.++.+++|..++..  +..+.+.++|++|+||||+|+.+++.+..
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~--~~~~~lll~Gp~G~GKTtla~~iak~l~~   71 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKT--GSMPHLLFAGPPGVGKTTAALALARELFG   71 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHH--TCCCEEEEESCTTSSHHHHHHHHHHHHHG
T ss_pred             CCCHHHccCcHHHHHHHHHHHHc--CCCCeEEEECCCCCcHHHHHHHHHHHHHh
Confidence            34567899999999999999984  34556889999999999999999987643

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.54  E-value=3.2e-07  Score=78.41  Aligned_cols=52  Identities=25%  Similarity=0.305  Sum_probs=42.6

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .-.+++|.++.++.|.+++..+. -++.+.|+|++|+||||+|+.+++.+...
T Consensus        10 ~~~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~   61 (239)
T d1njfa_          10 TFADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCE   61 (239)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHHHHCT
T ss_pred             CHHHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCc
Confidence            44789999999999999998432 24567899999999999999999876443

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.50  E-value=3.9e-07  Score=82.99  Aligned_cols=123  Identities=15%  Similarity=0.179  Sum_probs=68.5

Q ss_pred             CCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC-C-----CCceEEEeeccccccC---CCCh
Q 044214           29 NQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG-D-----FDGSCFLENVREESQI---PGGL   99 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~-----f~~~~w~~~~~~~~~~---~~~~   99 (385)
                      +..|||+.+++++...|.....  .-+.++|.+|||||+++..+++++.. .     .+..+|..++......   ....
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k--~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~   99 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTK--NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEF   99 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSC--CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CH
T ss_pred             CCCcCcHHHHHHHHHHHhcCCC--CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhH
Confidence            4589999999999999984222  23467899999999999999987522 1     3456776644332110   0112


Q ss_pred             HHHHHHHHHHHhCCCCCCchHHHHHHHh-C-CceEEEEEeCCCCh----------hhhhHhhccCCCCCCCcEEEEEecc
Q 044214          100 SCLRQKLLSNLLKDKNVMPYIDLNFRRL-G-HMKVLIVFDDVTCF----------SQLESLMGSLDWLTPVSRIILTTRN  167 (385)
Q Consensus       100 ~~l~~~ll~~l~~~~~~~~~~~~l~~~l-~-~k~~LlVlDdv~~~----------~~~~~l~~~~~~~~~gs~ilvTtR~  167 (385)
                      ..                 ....+...+ . ..+++|++|++...          +.-.-|.+.+.  ...-++|.+|..
T Consensus       100 e~-----------------r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~  160 (387)
T d1qvra2         100 EE-----------------RLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTL  160 (387)
T ss_dssp             HH-----------------HHHHHHHHHHTTCSSEEEEECCC-------------------HHHHH--TTCCCEEEEECH
T ss_pred             HH-----------------HHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCH
Confidence            22                 222222222 2 34799999999543          11233334443  234567777776


Q ss_pred             HHHHh
Q 044214          168 KQVLR  172 (385)
Q Consensus       168 ~~~~~  172 (385)
                      .....
T Consensus       161 ~ey~~  165 (387)
T d1qvra2         161 DEYRE  165 (387)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.46  E-value=3.3e-07  Score=80.01  Aligned_cols=112  Identities=16%  Similarity=0.159  Sum_probs=69.9

Q ss_pred             CCCCCCCccccchhHHHHHHhhc----CC---CCCeEEEEEEcCCCchHHHHHHHHHHHhhCC-----C-CceEEEeecc
Q 044214           24 PRDNKNQLVGVESTVEEIESLLG----VE---SKGVYALGIWGIGGIGKTTIARAIFDKISGD-----F-DGSCFLENVR   90 (385)
Q Consensus        24 ~~~~~~~~vGR~~~l~~l~~~L~----~~---~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-----f-~~~~w~~~~~   90 (385)
                      +...|+.++||+.++++|.+.+.    .+   ++...++.|+|++|+|||++++.+++.+.+.     . ....++.   
T Consensus        11 ~~~~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~---   87 (287)
T d1w5sa2          11 ENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN---   87 (287)
T ss_dssp             TTCCCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE---
T ss_pred             CccCCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeec---
Confidence            34467889999999999988663    11   1223456778999999999999999876332     1 1223333   


Q ss_pred             ccccCCCChHHHHHHHHHHHhCCCCCC-----chHHHHHHHh--CCceEEEEEeCCC
Q 044214           91 EESQIPGGLSCLRQKLLSNLLKDKNVM-----PYIDLNFRRL--GHMKVLIVFDDVT  140 (385)
Q Consensus        91 ~~~~~~~~~~~l~~~ll~~l~~~~~~~-----~~~~~l~~~l--~~k~~LlVlDdv~  140 (385)
                       .... .....................     .....+....  .+...++++|.++
T Consensus        88 -~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          88 -AFNA-PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             -GGGC-CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             -cccc-cchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence             2222 556666667766665544321     3333444333  3467788888884

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.46  E-value=3.3e-07  Score=78.78  Aligned_cols=50  Identities=26%  Similarity=0.305  Sum_probs=41.0

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-++++|.++..+.|.+++.... ..+.+.|+|++|+||||+|+.+++.+
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            345679999999999999887433 34457799999999999999999875

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.38  E-value=6.4e-07  Score=76.73  Aligned_cols=51  Identities=16%  Similarity=0.079  Sum_probs=38.3

Q ss_pred             CCccccchhHHHHHHhhc-------C-CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           29 NQLVGVESTVEEIESLLG-------V-ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~-------~-~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.+||..+.++.+.+...       . .....+-|.++|++|+|||++|+.+++.....
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~   67 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFP   67 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCS
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhccccc
Confidence            558998887776655432       1 22346778999999999999999999976543

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.32  E-value=4.5e-07  Score=77.99  Aligned_cols=51  Identities=29%  Similarity=0.382  Sum_probs=42.3

Q ss_pred             CCCCccccchhHHHHHHhhcC---------------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           27 NKNQLVGVESTVEEIESLLGV---------------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~---------------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .-.+++|.+..+++|.+++..               +....+.+.++|++|+||||+|+.+++.+.
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~   77 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG   77 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            457899999999999998742               223456899999999999999999999764

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.23  E-value=1.9e-06  Score=71.96  Aligned_cols=124  Identities=19%  Similarity=0.179  Sum_probs=70.8

Q ss_pred             CCCccccchhH--HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHH
Q 044214           28 KNQLVGVESTV--EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQK  105 (385)
Q Consensus        28 ~~~~vGR~~~l--~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~  105 (385)
                      .+.++|-..++  +.+.++..........+.|+|.+|+|||.|++++++........+++++           ..++...
T Consensus        10 dnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~-----------~~~~~~~   78 (213)
T d1l8qa2          10 ENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQA   78 (213)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHHH
T ss_pred             hhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEec-----------hHHHHHH
Confidence            34456765544  3445555433333445789999999999999999998877766666665           1223333


Q ss_pred             HHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCCCh---hhhhH-hhccCCC-CCCCcEEEEEeccH
Q 044214          106 LLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVTCF---SQLES-LMGSLDW-LTPVSRIILTTRNK  168 (385)
Q Consensus       106 ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~---~~~~~-l~~~~~~-~~~gs~ilvTtR~~  168 (385)
                      +...+...     ....+.+.+++ -=+|++||++..   ..|+. +...+.. ...|.+||+||+..
T Consensus        79 ~~~~~~~~-----~~~~~~~~~~~-~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          79 MVEHLKKG-----TINEFRNMYKS-VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             HHHHHHHT-----CHHHHHHHHHT-CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             HHHHHHcc-----chhhHHHHHhh-ccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCc
Confidence            33333221     12223333332 348899999632   33333 2211110 13577899999864

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.11  E-value=1e-05  Score=67.17  Aligned_cols=124  Identities=15%  Similarity=0.106  Sum_probs=66.9

Q ss_pred             cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHhC-
Q 044214           34 VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLLK-  112 (385)
Q Consensus        34 R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~-  112 (385)
                      -+...+++.+.+..+. -.+.+.++|++|+||||+|+.+++.+...-...      ...    .....-...+...... 
T Consensus         7 ~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~------~~~----~~~~~~~~~i~~~~~~~   75 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQG------HKS----CGHCRGCQLMQAGTHPD   75 (207)
T ss_dssp             GHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT------TBC----CSCSHHHHHHHHTCCTT
T ss_pred             cHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccc------ccc----ccccchhhhhhhccccc
Confidence            3455777777777322 245688999999999999999998763221100      000    0000000011110000 


Q ss_pred             ------CCC-C---CchHHHHHHHh-----CCceEEEEEeCCCC--hhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          113 ------DKN-V---MPYIDLNFRRL-----GHMKVLIVFDDVTC--FSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       113 ------~~~-~---~~~~~~l~~~l-----~~k~~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                            ... .   .+.+..+.+.+     .+++-++|+||++.  .+....++..+.....+..+|+||++.
T Consensus        76 ~~~~~~~~~~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~  148 (207)
T d1a5ta2          76 YYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (207)
T ss_dssp             EEEECCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             cchhhhhhcccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecCh
Confidence                  000 0   02223333332     24667999999974  445666666665555778888877765

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.08  E-value=1.5e-05  Score=68.53  Aligned_cols=50  Identities=24%  Similarity=0.393  Sum_probs=38.3

Q ss_pred             CCccccchhHHHHHHhhc----C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           29 NQLVGVESTVEEIESLLG----V-------ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~----~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ++++|-++..++|.+.+.    .       +-...+-+.++|++|+|||++|+++++....
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~   64 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA   64 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCC
Confidence            457889988888877642    1       2233567899999999999999999997543

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.01  E-value=9.6e-06  Score=69.15  Aligned_cols=55  Identities=24%  Similarity=0.366  Sum_probs=40.5

Q ss_pred             CCCCCCCCccccchhHHHHHHhhc---C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           23 RPRDNKNQLVGVESTVEEIESLLG---V-------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        23 ~~~~~~~~~vGR~~~l~~l~~~L~---~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +|...-++++|-++..++|.+.+.   .       +...++-+.++|++|+|||+||+.+++...
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~   67 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR   67 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcC
Confidence            444455779999988777665431   1       223356789999999999999999998764

>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=97.97  E-value=1.2e-05  Score=68.78  Aligned_cols=51  Identities=25%  Similarity=0.300  Sum_probs=38.4

Q ss_pred             CCCCccccchhHHHHHHhh---cC-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           27 NKNQLVGVESTVEEIESLL---GV-------ESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L---~~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .=.+++|.++..++|.+.+   ..       +....+.+.++|++|+|||++|+.+++...
T Consensus        10 t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~   70 (256)
T d1lv7a_          10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK   70 (256)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcC
Confidence            3367899998888776543   21       123356788999999999999999998774

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.93  E-value=2.2e-06  Score=72.80  Aligned_cols=54  Identities=20%  Similarity=0.336  Sum_probs=43.0

Q ss_pred             CCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           26 DNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ..-+++||-+..+++|..++..   .....+.+.++|++|+|||++|+.+++.+...
T Consensus         6 ~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~   62 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN   62 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC
T ss_pred             CcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCC
Confidence            3457899999999999998852   12234567899999999999999999987544

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.92  E-value=3.4e-06  Score=71.73  Aligned_cols=55  Identities=22%  Similarity=0.372  Sum_probs=43.1

Q ss_pred             CCCCCCccccchhHHHHHHhhcC---CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           25 RDNKNQLVGVESTVEEIESLLGV---ESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        25 ~~~~~~~vGR~~~l~~l~~~L~~---~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      |..-+++||-++..++|..++..   ....++.+.++|++|+||||+|+.+++.....
T Consensus         5 P~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~   62 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN   62 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            34456799999999999888752   22345678899999999999999999876543

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.90  E-value=6.6e-05  Score=61.49  Aligned_cols=113  Identities=11%  Similarity=0.068  Sum_probs=69.3

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC---CCceEEEeeccccccCCCChHHHHHHHHHHHhCC
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD---FDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD  113 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~---f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~  113 (385)
                      +++.+.+++.  .+....+.++|.+|+|||++|..+.+.+...   .+...++...+   .. -++.++. .+...+...
T Consensus         2 ~~~~l~~~i~--~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~---~~-I~Id~IR-~i~~~~~~~   74 (198)
T d2gnoa2           2 QLETLKRIIE--KSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG---EN-IGIDDIR-TIKDFLNYS   74 (198)
T ss_dssp             HHHHHHHHHH--TCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS---SC-BCHHHHH-HHHHHHTSC
T ss_pred             HHHHHHHHHh--cCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCc---CC-CCHHHHH-HHHHHHhhC
Confidence            5677777777  3457789999999999999999999866433   23455554111   11 2333332 233333222


Q ss_pred             CCCCchHHHHHHHhCCceEEEEEeCCC--ChhhhhHhhccCCCCCCCcEEEEEeccH
Q 044214          114 KNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNK  168 (385)
Q Consensus       114 ~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~~~~~~~gs~ilvTtR~~  168 (385)
                      ..            .+++=++|+|+++  +.+....|+..+..-..++.+|++|.+.
T Consensus        75 ~~------------~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          75 PE------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             CS------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             cc------------cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCCh
Confidence            11            2455589999997  4455666666655445677776666554

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.84  E-value=1.1e-05  Score=69.56  Aligned_cols=51  Identities=24%  Similarity=0.330  Sum_probs=38.4

Q ss_pred             CCCccccchhHHHHHHhhc----C-------CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           28 KNQLVGVESTVEEIESLLG----V-------ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        28 ~~~~vGR~~~l~~l~~~L~----~-------~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -.+++|-++..++|.+.+.    .       +-...+-|.++|++|+|||+||+.+++....
T Consensus         6 f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~   67 (265)
T d1r7ra3           6 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQA   67 (265)
T ss_dssp             CSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTC
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCC
Confidence            3568888888777776542    1       2233567899999999999999999998753

>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=97.58  E-value=2.5e-05  Score=62.55  Aligned_cols=37  Identities=22%  Similarity=0.195  Sum_probs=29.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      +..+|.|+|++|+||||+|+.+++++... ++...++.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~~~~~~~~~~   42 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL   42 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhcCCCchhhhh
Confidence            44689999999999999999999988654 44444443

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.53  E-value=1.9e-05  Score=63.60  Aligned_cols=26  Identities=15%  Similarity=0.240  Sum_probs=23.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++.|+|.|++|+||||||+.++++..
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999998753

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.53  E-value=7.2e-05  Score=60.79  Aligned_cols=40  Identities=28%  Similarity=0.431  Sum_probs=31.3

Q ss_pred             CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           48 ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        48 ~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+.-+|+|.|.+|+||||||+.+.+.+..........+
T Consensus        18 ~~~~~~iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~   57 (198)
T d1rz3a_          18 KTAGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFH   57 (198)
T ss_dssp             CCSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cCCCCEEEEEECCCCCCHHHHHHHHHHHhccccccceecc
Confidence            3456678999999999999999999988766655444443

>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=97.51  E-value=0.00015  Score=63.74  Aligned_cols=117  Identities=14%  Similarity=0.168  Sum_probs=60.4

Q ss_pred             CccccchhHHHHHHhhc-------CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHH
Q 044214           30 QLVGVESTVEEIESLLG-------VESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCL  102 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~-------~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l  102 (385)
                      .++|-++.++.+...+.       ..+....++.++|+.|+|||.+|+.+++.+-..-...+-+. ..+.+.. .....+
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~-~~~~~~~-~~~~~L  101 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRID-MTEYMEK-HAVSRL  101 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEEC-TTTCCSS-GGGGGC
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEe-ccccccc-hhhhhh
Confidence            47898888887766543       11222347889999999999999999997643322222232 2222111 112222


Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHhCCceEEEEEeCCC--ChhhhhHhhccC
Q 044214          103 RQKLLSNLLKDKNVMPYIDLNFRRLGHMKVLIVFDDVT--CFSQLESLMGSL  152 (385)
Q Consensus       103 ~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~LlVlDdv~--~~~~~~~l~~~~  152 (385)
                      ...--...+... ...+.+.++   +....+++||+++  +.+.+..+...+
T Consensus       102 ~g~~~gyvG~~~-~~~l~~~~~---~~p~~Vvl~DEieK~~~~v~~~ll~~l  149 (315)
T d1qvra3         102 IGAPPGYVGYEE-GGQLTEAVR---RRPYSVILFDEIEKAHPDVFNILLQIL  149 (315)
T ss_dssp             ---------------CHHHHHH---HCSSEEEEESSGGGSCHHHHHHHHHHH
T ss_pred             cCCCCCCcCccc-CChHHHHHH---hCCCcEEEEehHhhcCHHHHHHHHHHh
Confidence            111111111100 012223332   2456899999997  445555555443

>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=97.50  E-value=0.0005  Score=56.30  Aligned_cols=38  Identities=18%  Similarity=0.309  Sum_probs=28.9

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      .+.+.+|.++|+.|+||||-+.+++.+++.+-..+..+
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~li   43 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLA   43 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            45578999999999999999988888776443333333

>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=97.49  E-value=3.3e-05  Score=62.82  Aligned_cols=36  Identities=22%  Similarity=0.209  Sum_probs=30.2

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ..+|.++|++|+||||+|+.++.++...+....++.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~~~~~~~~~~   54 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   54 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCccchh
Confidence            468889999999999999999998877766665554

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.48  E-value=1.6e-05  Score=62.64  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=22.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.|.|+|++|+||||+|+.+++++.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            3688899999999999999999863

>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=97.46  E-value=0.00046  Score=56.48  Aligned_cols=58  Identities=14%  Similarity=0.022  Sum_probs=38.1

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      ++.++|.++|+.|+||||.+.+++..++.+-..+..+.    .........+-++...+.++
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit----~Dt~R~gA~eQL~~~a~~l~   61 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCA----GDTFRAAGGTQLSEWGKRLS   61 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEC----CCCSSTTHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEE----eccccccchhhHhhcccccC
Confidence            35679999999999999998888887765545566665    22111444444555555444

>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=97.44  E-value=0.0003  Score=57.65  Aligned_cols=38  Identities=24%  Similarity=0.168  Sum_probs=29.4

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.+++.++|+.|+||||.+.+++.+++.+-..+..+.
T Consensus         8 ~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit   45 (207)
T d1ls1a2           8 KDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA   45 (207)
T ss_dssp             CSSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            34579999999999999999988887765544555554

>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=97.43  E-value=4.9e-05  Score=60.23  Aligned_cols=29  Identities=21%  Similarity=0.211  Sum_probs=25.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ++++|+|.+|+|||||+.++.+.+..+.-
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~~~g~   31 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALCARGI   31 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCC
Confidence            58999999999999999999998765543

>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=97.38  E-value=4.5e-05  Score=60.54  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=22.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++|.|+|++|+||||+|+++++.+
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            589999999999999999999864

>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=97.37  E-value=5e-05  Score=60.93  Aligned_cols=28  Identities=21%  Similarity=0.221  Sum_probs=24.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      +.|.|+|++|+|||||+++++..+....
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~~   29 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSSG   29 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHTT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHCC
Confidence            4689999999999999999999875543

>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=97.35  E-value=5.5e-05  Score=58.83  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ++|.|+|++|+||||+|+++..+
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            57889999999999999998764

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.31  E-value=0.00011  Score=62.99  Aligned_cols=30  Identities=33%  Similarity=0.513  Sum_probs=25.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.++.|.++|++|+|||+||+.+++.+...
T Consensus        30 ~~P~~ilL~GpPGtGKT~la~~la~~~~~~   59 (273)
T d1gvnb_          30 ESPTAFLLGGQPGSGKTSLRSAIFEETQGN   59 (273)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHTTTC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhcc
Confidence            457789999999999999999999977544

>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=97.28  E-value=7.4e-05  Score=59.27  Aligned_cols=28  Identities=18%  Similarity=0.377  Sum_probs=24.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+++.|.|++|+||||+|+.+++++.
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4578999999999999999999998763

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=97.28  E-value=6.4e-05  Score=59.65  Aligned_cols=23  Identities=30%  Similarity=0.504  Sum_probs=21.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|+|++|+||||+|+.+++++
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47799999999999999999876

>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=97.27  E-value=0.00012  Score=58.80  Aligned_cols=29  Identities=21%  Similarity=0.319  Sum_probs=25.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ++|+|.|++|+||||+++.+++++.....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~~~   30 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKEGV   30 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            58999999999999999999998866543

>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=97.24  E-value=6.7e-05  Score=59.74  Aligned_cols=25  Identities=20%  Similarity=0.252  Sum_probs=23.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++|.|.|.+|+||||+|+.+++++.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcC
Confidence            5899999999999999999999764

>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=97.23  E-value=0.00011  Score=59.76  Aligned_cols=28  Identities=21%  Similarity=0.175  Sum_probs=25.0

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+++.+|.|.|++|+||||+|+.+++++
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3567899999999999999999999865

>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=97.23  E-value=0.00017  Score=58.00  Aligned_cols=36  Identities=17%  Similarity=0.206  Sum_probs=28.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++|.|.|++|+||||+|+.+++.+..+.-....+.
T Consensus         1 mkiivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~~   36 (194)
T d1nksa_           1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            368999999999999999999998876544444443

>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=97.20  E-value=8.8e-05  Score=58.75  Aligned_cols=24  Identities=29%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhC
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      |.+.|++|+||||+|+.+++++.-
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~   27 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGV   27 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            456699999999999999998743

>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=97.16  E-value=0.00015  Score=57.29  Aligned_cols=28  Identities=18%  Similarity=0.101  Sum_probs=25.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ++++|+|..|+|||||+.++...++.+-
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~g   29 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVREG   29 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhCC
Confidence            6899999999999999999999886653

>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=97.15  E-value=0.00011  Score=58.26  Aligned_cols=26  Identities=31%  Similarity=0.357  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +...|.|.|++|+||||+|+.+++++
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            44568899999999999999999874

>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=97.12  E-value=0.00076  Score=55.33  Aligned_cols=40  Identities=15%  Similarity=0.242  Sum_probs=31.4

Q ss_pred             CCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           48 ESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        48 ~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.++.+|.++|+.|+||||-+.+++.++..+-..+..+.
T Consensus         7 ~~~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit   46 (213)
T d1vmaa2           7 PPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA   46 (213)
T ss_dssp             CSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEe
Confidence            3567789999999999999988888887655545566665

>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=97.10  E-value=0.00016  Score=58.95  Aligned_cols=28  Identities=21%  Similarity=0.249  Sum_probs=25.0

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+..++|.|.|++|+||||+|+.+++++
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568899999999999999999999865

>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=97.10  E-value=0.0001  Score=58.18  Aligned_cols=22  Identities=36%  Similarity=0.576  Sum_probs=20.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.+++++
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6788999999999999999987

>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=97.09  E-value=0.00023  Score=58.43  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      +.+|.++|.+|+||||+|+++++.+...
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~~   29 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3579999999999999999999876544

>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=97.02  E-value=0.00011  Score=58.47  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=21.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .|.++|++|+||||+|+.+++++.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            467889999999999999999874

>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=96.99  E-value=0.0012  Score=53.94  Aligned_cols=39  Identities=21%  Similarity=0.132  Sum_probs=25.9

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ...+.+|.++|+.|+||||.+.+++.+++.+-..+..+.
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit   47 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVG   47 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEE
Confidence            346789999999999999988888876654434455665

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.99  E-value=0.00012  Score=58.20  Aligned_cols=24  Identities=38%  Similarity=0.346  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -++|.|.|++|+||||+|+.++++
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999998764

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.99  E-value=0.00015  Score=57.84  Aligned_cols=26  Identities=19%  Similarity=0.192  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +++.+|.++|++|+||||+|++++..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            45779999999999999999988754

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.97  E-value=0.0005  Score=59.11  Aligned_cols=49  Identities=20%  Similarity=0.215  Sum_probs=37.0

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++..+.+.+.  .++.++|.++|-||+||||+|..++..+...-..+.-+.
T Consensus         7 ~~~~~~~~~~--~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD   55 (279)
T d1ihua2           7 SLSALVDDIA--RNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTT   55 (279)
T ss_dssp             CHHHHHHHHH--TTSCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cHHHHHHHhh--cCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4666777777  567899999999999999999998886655433454444

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.96  E-value=0.00017  Score=63.34  Aligned_cols=49  Identities=20%  Similarity=0.304  Sum_probs=36.0

Q ss_pred             CccccchhHHHHHHhhc-------C-----CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           30 QLVGVESTVEEIESLLG-------V-----ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~-------~-----~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..+|-++.++.+...+.       .     .....+.+.++|++|+|||.||+.+++....
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~   75 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA   75 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTC
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcccc
Confidence            47888888887765441       0     0113467789999999999999999997653

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=96.93  E-value=0.0012  Score=57.54  Aligned_cols=28  Identities=25%  Similarity=0.363  Sum_probs=23.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ++.++|++|+|||.||+.++..+..++.
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~~~~~~~  152 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEALGGKDK  152 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHHHHTTSC
T ss_pred             eEEEECCCCccHHHHHHHHHHHhcCCCC
Confidence            5666899999999999999998875543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.87  E-value=0.0015  Score=53.62  Aligned_cols=34  Identities=18%  Similarity=0.262  Sum_probs=27.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      ..|+|.|+.|+||||+++.+.+.+..+...++++
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            4789999999999999999999886654344444

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.81  E-value=0.00033  Score=55.72  Aligned_cols=24  Identities=33%  Similarity=0.590  Sum_probs=21.6

Q ss_pred             EEEEcCCCchHHHHHHHHHHHhhC
Q 044214           55 LGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      |+|+|++|+|||||++.++..+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCC
Confidence            789999999999999999987644

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.79  E-value=0.0031  Score=53.52  Aligned_cols=127  Identities=18%  Similarity=0.201  Sum_probs=69.6

Q ss_pred             hHHHHHHHHHHHHhhcc--CCCCCCCCCCcccc-chhHHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214            4 SELINEVVNHILKRLDE--VFRPRDNKNQLVGV-ESTVEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus         4 ~~~i~~i~~~v~~~l~~--~~~~~~~~~~~vGR-~~~l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .+.++....++.+++..  ++..-......+.+ ..-...|-..|. .+-+.-+++-|+|.+|+||||||.+++...+..
T Consensus         8 ~k~~~~~~~~i~k~~g~~~i~~~~~~~~~~~~~i~TG~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~   87 (269)
T d1mo6a1           8 EKALELAVAQIEKSYGKGSVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA   87 (269)
T ss_dssp             HHHHHHHHHHHHHHHCTTSSCCTTCCCCCCSCCBCCSCHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhCCcceEECCCccCCccceEccCCHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcC
Confidence            44566666777666653  10000111111111 111223444453 333456799999999999999999998876666


Q ss_pred             CCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC---------chHHHHHHHh-CCceEEEEEeCCC
Q 044214           80 FDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM---------PYIDLNFRRL-GHMKVLIVFDDVT  140 (385)
Q Consensus        80 f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~---------~~~~~l~~~l-~~k~~LlVlDdv~  140 (385)
                      -..++|+. ....    .+..     .++.++...++.         +..+.+.... .++.-|+|+|.+-
T Consensus        88 g~~~vyID-tE~~----~~~e-----~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1          88 GGVAAFID-AEHA----LDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             TCEEEEEE-SSCC----CCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTCEEEEEEECST
T ss_pred             CCEEEEEE-CCcc----CCHH-----HHHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCCEEEEeccc
Confidence            66788887 2222    3332     234444433322         2233333333 3467899999984

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=96.79  E-value=0.00069  Score=57.94  Aligned_cols=36  Identities=22%  Similarity=0.366  Sum_probs=28.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.|+|+|-||+||||+|..++..+...-..+.-+.
T Consensus         1 mr~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID   36 (269)
T d1cp2a_           1 MRQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVG   36 (269)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCEEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            368999999999999999999998766544455554

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.75  E-value=0.00035  Score=57.77  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=23.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++|+|.|++|+||||+|+.+++++
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3599999999999999999999976

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.73  E-value=0.00046  Score=55.85  Aligned_cols=25  Identities=28%  Similarity=0.288  Sum_probs=22.6

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.+|.|.|++|+||||.|+.+++++
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999999875

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.71  E-value=0.0011  Score=58.16  Aligned_cols=48  Identities=17%  Similarity=0.119  Sum_probs=35.5

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      .++.+.+....++..+|+|+|.+|+|||||..++..........+.-+
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavl   88 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVI   88 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeee
Confidence            345555555567789999999999999999999998766554444333

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.71  E-value=0.0012  Score=57.96  Aligned_cols=41  Identities=22%  Similarity=0.354  Sum_probs=32.3

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      ..++.+.+....++..+|+|+|.+|+|||||.-++...+..
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~   77 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTA   77 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhh
Confidence            44555555555667899999999999999999999986543

>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=96.70  E-value=0.00056  Score=56.19  Aligned_cols=39  Identities=15%  Similarity=0.175  Sum_probs=29.4

Q ss_pred             CCCeEEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEe
Q 044214           49 SKGVYALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLE   87 (385)
Q Consensus        49 ~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~   87 (385)
                      ..+..+|-++|++|+||||||+++.+++.. .....+++.
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   60 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEc
Confidence            345679999999999999999999987643 233444543

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.69  E-value=0.0005  Score=56.63  Aligned_cols=27  Identities=19%  Similarity=0.390  Sum_probs=23.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +-+|+|.|..|+||||+|+.+.+.+..
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            458999999999999999999987643

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.66  E-value=0.0011  Score=55.56  Aligned_cols=47  Identities=13%  Similarity=0.169  Sum_probs=36.6

Q ss_pred             HHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           41 IESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        41 l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      |-+.|..+=+.-.++.|+|.+|+|||+||.+++.........++|++
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            33344422234568999999999999999999998888888888887

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.63  E-value=0.004  Score=52.85  Aligned_cols=85  Identities=19%  Similarity=0.205  Sum_probs=51.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC-CCCceEEEeeccccccCCCChHHHHHHHHHHHhCC-C-------------CCC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG-DFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKD-K-------------NVM  117 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~-~-------------~~~  117 (385)
                      +.++|.|.+|+|||+|+..+++.... +=+..+++. +++..   ....++..++...-... .             ++.
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~-iGer~---~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~  144 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG-VGERT---REGNDLYHEMIESGVINLKDATSKVALVYGQMNEP  144 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEE-ESCCH---HHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSC
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEEE-eccCh---HHHHHHHHHHHhcCccccccccceEEEEEECCCCC
Confidence            46999999999999999999987543 334455554 33221   44556666665531110 0             111


Q ss_pred             --------chHHHHHHHh---CCceEEEEEeCCCC
Q 044214          118 --------PYIDLNFRRL---GHMKVLIVFDDVTC  141 (385)
Q Consensus       118 --------~~~~~l~~~l---~~k~~LlVlDdv~~  141 (385)
                              ...-.+.+++   +++.+|+++||+..
T Consensus       145 ~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr  179 (276)
T d2jdid3         145 PGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFR  179 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhH
Confidence                    1122233443   37899999999943

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=96.59  E-value=0.00049  Score=55.51  Aligned_cols=24  Identities=29%  Similarity=0.192  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..|.|.|++|+||||+|+.+++++
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            357799999999999999999876

>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=96.59  E-value=0.00045  Score=55.93  Aligned_cols=28  Identities=29%  Similarity=0.498  Sum_probs=23.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      .|+|+|++|+|||||+++++++....|.
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~~   29 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIFG   29 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCcee
Confidence            4779999999999999999987655543

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=96.56  E-value=0.00076  Score=54.34  Aligned_cols=25  Identities=36%  Similarity=0.480  Sum_probs=21.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ++++| |.|++|+||||+|+.+++++
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHHh
Confidence            45566 78999999999999999875

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.56  E-value=0.0031  Score=53.57  Aligned_cols=126  Identities=17%  Similarity=0.119  Sum_probs=68.7

Q ss_pred             hHHHHHHHHHHHHhhccCCCC--C-CCCCCcccc-chhHHHHHHhhc-CCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214            4 SELINEVVNHILKRLDEVFRP--R-DNKNQLVGV-ESTVEEIESLLG-VESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus         4 ~~~i~~i~~~v~~~l~~~~~~--~-~~~~~~vGR-~~~l~~l~~~L~-~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      .+.|+.+...+-+++..- +.  . .....-+-+ ..-...|-..|. .+=+.-+++-|+|.+|+|||+||..++...+.
T Consensus         5 ~~~~~~~~~~i~k~~g~~-~~~~~~~~~~~~~~~i~TGs~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk   83 (268)
T d1xp8a1           5 SKAIETAMSQIEKAFGKG-SIMKLGAESKLDVQVVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQK   83 (268)
T ss_dssp             HHHHHHHHHHHHHHHCTT-SSCCTTSCCCCCCCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCc-ceEECCCcCCCCCCeEcCCCHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHh
Confidence            356777787777777541 11  0 111111111 111223334443 22134569999999999999999999987655


Q ss_pred             CCCceEEEeeccccccCCCChHHHHHHHHHHHhCCCCCC---------chHHHHHHHhC-CceEEEEEeCCC
Q 044214           79 DFDGSCFLENVREESQIPGGLSCLRQKLLSNLLKDKNVM---------PYIDLNFRRLG-HMKVLIVFDDVT  140 (385)
Q Consensus        79 ~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~~~~~~~---------~~~~~l~~~l~-~k~~LlVlDdv~  140 (385)
                      .-..++|+. ....    ++.     .+++.++...++.         +..+.+....+ +..-|+|+|-+-
T Consensus        84 ~g~~v~yiD-tE~~----~~~-----~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1          84 AGGTCAFID-AEHA----LDP-----VYARALGVNTDELLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             TTCCEEEEE-SSCC----CCH-----HHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             CCCEEEEEE-CCcc----CCH-----HHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCcEEEEeccc
Confidence            545678887 2222    333     2445554433322         33334444443 345688999883

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.55  E-value=0.0022  Score=54.38  Aligned_cols=37  Identities=19%  Similarity=0.264  Sum_probs=31.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .-+++-|+|.+|+||||||.+++...+..-..++|++
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyid   89 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID   89 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEc
Confidence            3469999999999999999999987766666778887

>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=96.54  E-value=0.00045  Score=55.71  Aligned_cols=31  Identities=29%  Similarity=0.451  Sum_probs=25.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCce
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGS   83 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~   83 (385)
                      +.|+|+|++|+|||||++.++++....|...
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~~~~   32 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSFGFS   32 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEEEC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcceeEE
Confidence            3478999999999999999998765555433

>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=96.50  E-value=0.0014  Score=56.50  Aligned_cols=38  Identities=24%  Similarity=0.188  Sum_probs=29.6

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.+++|.+.|-||+||||+|..++..+.++-..+..++
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD   43 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS   43 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEe
Confidence            34678999999999999999999987765544455554

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.50  E-value=0.0007  Score=53.99  Aligned_cols=22  Identities=36%  Similarity=0.463  Sum_probs=20.4

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.+++++
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7799999999999999999876

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.47  E-value=0.00079  Score=55.63  Aligned_cols=23  Identities=30%  Similarity=0.435  Sum_probs=21.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +|+|-|++|+||||+|+.+++++
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999999976

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.45  E-value=0.00087  Score=50.04  Aligned_cols=60  Identities=10%  Similarity=0.048  Sum_probs=43.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      ...++.+.+.....  ..+ +..|..+++|++|+++++   .+|. ++  .+|++|+++++.+..+|.+
T Consensus        19 l~~L~~L~ls~N~l--~~l-p~~~~~l~~L~~L~l~~N~i~~l~~-~~~l~~L~~L~l~~N~i~~~~~~   83 (124)
T d1dcea3          19 LLLVTHLDLSHNRL--RAL-PPALAALRCLEVLQASDNALENVDG-VANLPRLQELLLCNNRLQQSAAI   83 (124)
T ss_dssp             GTTCCEEECCSSCC--CCC-CGGGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSSCCCSSSTT
T ss_pred             CCCCCEEECCCCcc--Ccc-hhhhhhhhcccccccccccccccCc-cccccccCeEECCCCccCCCCCc
Confidence            45567776666543  223 345788999999999988   5554 55  8999999999999888754

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=96.45  E-value=0.0017  Score=56.92  Aligned_cols=49  Identities=20%  Similarity=0.306  Sum_probs=38.2

Q ss_pred             CCccccchhHHHHHHhhc-------CCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           29 NQLVGVESTVEEIESLLG-------VESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        29 ~~~vGR~~~l~~l~~~L~-------~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ...+|-+..++.+...+.       ..+....++.++|++|+|||.||+.+++.+.
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~   77 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG   77 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc
Confidence            458999999998876552       1223355788999999999999999998763

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=96.44  E-value=0.00087  Score=54.09  Aligned_cols=26  Identities=27%  Similarity=0.386  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.-.|.|.|++|+||||+|+.+++++
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHH
Confidence            33456678999999999999999864

>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=96.43  E-value=0.00077  Score=54.56  Aligned_cols=26  Identities=27%  Similarity=0.203  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.++|.|.|++|+||||+|+.+++++
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999999864

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.0023  Score=49.78  Aligned_cols=61  Identities=15%  Similarity=0.097  Sum_probs=44.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+..... ...++...|..+.+|+.|+|+++   .+| ..+.  .+|++|+|+++.++.+|
T Consensus        30 l~~l~~L~l~~n~~-l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~   96 (156)
T d2ifga3          30 AENLTELYIENQQH-LQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLS   96 (156)
T ss_dssp             CSCCSEEECCSCSS-CCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCC
T ss_pred             ccccCeeecCCCcc-ccccCchhhccccccCcceeeccccCCcccccccccccccceeccCCCCcccC
Confidence            45566666653321 34567788889999999999987   554 3355  88999999999998888

>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=96.39  E-value=0.00064  Score=54.36  Aligned_cols=31  Identities=23%  Similarity=0.397  Sum_probs=25.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCce
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGS   83 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~   83 (385)
                      +.|+|+|++|+|||||++++.++..+.|...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~~~~~~~   34 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHPDRFAYP   34 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCTTTEECC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCCcCeeec
Confidence            4789999999999999999998766655433

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=96.38  E-value=0.00092  Score=53.43  Aligned_cols=23  Identities=35%  Similarity=0.504  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .|.|.|++|+||||+|+.+++++
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36789999999999999999876

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.37  E-value=0.00093  Score=53.34  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -|.|.|++|+||||+|+.+++++
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36788999999999999999876

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=96.30  E-value=0.0012  Score=58.91  Aligned_cols=31  Identities=26%  Similarity=0.163  Sum_probs=26.7

Q ss_pred             CCCCeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           48 ESKGVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        48 ~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +.++.+.+.++|++|+|||++|..+++.+..
T Consensus       150 ~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         150 NIPKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCCCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4456678999999999999999999998764

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.30  E-value=0.0029  Score=54.89  Aligned_cols=31  Identities=29%  Similarity=0.274  Sum_probs=26.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHhhCCC
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKISGDF   80 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f   80 (385)
                      ..+-+|+|.|.+|+||||+|+.+...+...+
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~  108 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLSRWP  108 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTST
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHhhhc
Confidence            4577999999999999999999999886554

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=96.27  E-value=0.0019  Score=55.77  Aligned_cols=36  Identities=22%  Similarity=0.372  Sum_probs=27.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .+.|+|+|-||+||||+|..++..+...-..+.-+.
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID   37 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVG   37 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            467889999999999999999887655533455555

>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=96.22  E-value=0.0012  Score=52.69  Aligned_cols=25  Identities=24%  Similarity=0.480  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ++|.|+|++|+|||||++.+.++..
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            4789999999999999999887653

>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=96.17  E-value=0.0014  Score=52.27  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=19.5

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.+++++
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4577999999999999999875

>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=96.15  E-value=0.0024  Score=52.82  Aligned_cols=36  Identities=25%  Similarity=0.293  Sum_probs=29.2

Q ss_pred             eEEEEEE-cCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           52 VYALGIW-GIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        52 ~~vv~I~-G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      .++|+|+ |-||+||||+|..++..+...-..+..+.
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~~la~~g~~VlliD   37 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGVALAQLGHDVTIVD   37 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CEEEEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEe
Confidence            3688887 88999999999999987766655677775

>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=96.11  E-value=0.0074  Score=50.33  Aligned_cols=45  Identities=18%  Similarity=0.158  Sum_probs=31.3

Q ss_pred             HhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhC------CCCceEEEe
Q 044214           43 SLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISG------DFDGSCFLE   87 (385)
Q Consensus        43 ~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~------~f~~~~w~~   87 (385)
                      ++|..+=..-+++.|+|.+|+|||++|.+++.....      .+..+.|+.
T Consensus        28 ~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~   78 (258)
T d1v5wa_          28 KLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID   78 (258)
T ss_dssp             HHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             HhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEec
Confidence            344433345679999999999999999999975432      234455555

>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=96.10  E-value=0.0016  Score=51.84  Aligned_cols=22  Identities=32%  Similarity=0.338  Sum_probs=20.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHHh
Q 044214           55 LGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      |.|.|++|+||||+|+.++++.
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6689999999999999999875

>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=96.07  E-value=0.0016  Score=54.85  Aligned_cols=46  Identities=26%  Similarity=0.237  Sum_probs=35.8

Q ss_pred             CccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           30 QLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +|||....++++.+.+..-...-..|.|.|..|+|||++|+.+.+.
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            4899998898888877642222234789999999999999999864

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=96.04  E-value=0.002  Score=51.79  Aligned_cols=22  Identities=36%  Similarity=0.422  Sum_probs=19.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~   73 (385)
                      +-+|+|+|..|+||||+|..+.
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            5689999999999999998774

>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=96.03  E-value=0.0011  Score=58.67  Aligned_cols=47  Identities=23%  Similarity=0.227  Sum_probs=33.9

Q ss_pred             CCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           27 NKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        27 ~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-...+|.+.....|.-....  .+..-|.|.|.+|+|||+||+.+..-
T Consensus         5 ~f~~I~Gq~~~kral~laa~~--~~~h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVD--PGIGGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHC--GGGCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhc--cCCCeEEEECCCCccHHHHHHHHHHh
Confidence            346789998777765543321  11235889999999999999999864

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.03  E-value=0.0034  Score=54.25  Aligned_cols=59  Identities=12%  Similarity=0.155  Sum_probs=46.2

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..++.+.+....  ...+.+..|.++++|++|+|+++   .+|.++.  .+|++|++++|.++.+|
T Consensus       195 ~~l~~L~~s~n~--l~~~~~~~~~~l~~L~~L~L~~N~L~~lp~~l~~l~~L~~L~Ls~N~i~~i~  258 (305)
T d1xkua_         195 NNLAKLGLSFNS--ISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIG  258 (305)
T ss_dssp             TTCCEEECCSSC--CCEECTTTGGGSTTCCEEECCSSCCSSCCTTTTTCSSCCEEECCSSCCCCCC
T ss_pred             cccccccccccc--ccccccccccccccceeeecccccccccccccccccCCCEEECCCCccCccC
Confidence            445555555443  34566788889999999999988   7888888  89999999999999987

>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=96.02  E-value=0.0091  Score=49.62  Aligned_cols=54  Identities=15%  Similarity=0.077  Sum_probs=33.8

Q ss_pred             HHHHHHhCCceEEEEEeCCC---Ch---hhhhHhhccCCCCCCCcEEEEEeccHHHHhhccc
Q 044214          121 DLNFRRLGHMKVLIVFDDVT---CF---SQLESLMGSLDWLTPVSRIILTTRNKQVLRNWRV  176 (385)
Q Consensus       121 ~~l~~~l~~k~~LlVlDdv~---~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~~~~~~~~  176 (385)
                      -.+...+...+=+|+||..-   +.   ..+..+...+.  ..|..||+||.+.+.+...+.
T Consensus       142 v~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~~~~--~~g~tii~~tH~l~~~~~~~d  201 (238)
T d1vpla_         142 LLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQAS--QEGLTILVSSHNMLEVEFLCD  201 (238)
T ss_dssp             HHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHHH--HTTCEEEEEECCHHHHTTTCS
T ss_pred             HHHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHHHHH--hcCCEEEEEeCCHHHHHHhCC
Confidence            34566677788899999984   22   22333333332  246679999998877766543

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.98  E-value=0.0013  Score=53.16  Aligned_cols=27  Identities=26%  Similarity=0.126  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++.+|+|-|..|+||||+++.+.+..
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            456689999999999999999887644

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=95.96  E-value=0.002  Score=55.11  Aligned_cols=50  Identities=16%  Similarity=0.003  Sum_probs=33.4

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeecc
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVR   90 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~   90 (385)
                      ++.+.|.+ -.+-+.++|.|..|+|||+|+..+++... ++-..++++..++
T Consensus        32 r~ID~l~P-igrGQr~~I~g~~g~GKT~l~~~i~~~~~~~~~~~v~~~~~ig   82 (289)
T d1xpua3          32 RVLDLASP-IGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLID   82 (289)
T ss_dssp             HHHHHHSC-CBTTCEEEEEECSSSSHHHHHHHHHHHHHHHCTTSEEEEEEEE
T ss_pred             eeeeeccc-ccCCCeeeEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEeec
Confidence            45555553 12335789999999999999999998653 3444555554333

>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=95.93  E-value=0.0043  Score=53.04  Aligned_cols=34  Identities=18%  Similarity=0.193  Sum_probs=27.2

Q ss_pred             cCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           46 GVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        46 ~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ......+-+|+|.|..|+||||||..+...+.+.
T Consensus        21 ~~~~~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~   54 (286)
T d1odfa_          21 ETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEK   54 (286)
T ss_dssp             TTTCCSCEEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             hcCCCCCEEEEeECCCCCCHHHHHHHHHHHHHHH
Confidence            3344556799999999999999999998876544

>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=95.93  E-value=0.003  Score=52.59  Aligned_cols=28  Identities=21%  Similarity=0.345  Sum_probs=23.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      ||+|.|+.|+|||||..++.+.......
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~~~~   29 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLEDNYK   29 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTTTSC
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhCCe
Confidence            7899999999999999999876654443

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.86  E-value=0.0039  Score=50.63  Aligned_cols=26  Identities=23%  Similarity=0.426  Sum_probs=23.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      .|+|-|+-|+||||+++.+.+.+..+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            58999999999999999999988654

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.80  E-value=0.0015  Score=55.98  Aligned_cols=28  Identities=14%  Similarity=0.198  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +..+|+|.|.+|+||||+|+.+.+.++.
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            4569999999999999999999887644

>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=95.78  E-value=0.012  Score=48.17  Aligned_cols=28  Identities=25%  Similarity=0.329  Sum_probs=24.7

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      -+.|+|-|+-|+||||+++.+.+.+..+
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~~   30 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQPN   30 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTTS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHhC
Confidence            3579999999999999999999987654

>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=95.74  E-value=0.0031  Score=52.55  Aligned_cols=28  Identities=25%  Similarity=0.310  Sum_probs=24.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      +++.|+|-|+-|+||||+++.+.+.+..
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            3679999999999999999999987543

>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=95.69  E-value=0.014  Score=47.42  Aligned_cols=35  Identities=23%  Similarity=0.312  Sum_probs=27.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCC-CCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGD-FDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~-f~~~~w~~   87 (385)
                      +.|+|-|+.|+||||++..+.+.+... +..+++..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~~~~~   38 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTR   38 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEec
Confidence            468999999999999999999987554 45555543

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.67  E-value=0.0054  Score=50.73  Aligned_cols=35  Identities=23%  Similarity=0.283  Sum_probs=28.2

Q ss_pred             EEEEEE-cCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIW-GIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~-G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      ++|+|+ +-||+||||+|..++..+...-..++.+.
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD   38 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVD   38 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            688888 66999999999999987766655566665

>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=95.64  E-value=0.025  Score=47.67  Aligned_cols=25  Identities=24%  Similarity=0.335  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .+..|+|.+|+||||||.+++..+.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3788999999999999999987653

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.58  E-value=0.0068  Score=44.87  Aligned_cols=60  Identities=10%  Similarity=0.075  Sum_probs=40.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC--CCC--CCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG--ENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~--~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      ..+++.+.+.......  +  +.|.++++|+.|+++++   .+|.  .+.  .+|++|+++++++...|.+
T Consensus        42 l~~L~~L~l~~N~i~~--l--~~~~~l~~L~~L~l~~N~i~~~~~~~~l~~~~~L~~L~l~~N~i~~~~~~  108 (124)
T d1dcea3          42 LRCLEVLQASDNALEN--V--DGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSLCQEEGI  108 (124)
T ss_dssp             CTTCCEEECCSSCCCC--C--GGGTTCSSCCEEECCSSCCCSSSTTGGGGGCTTCCEEECTTSGGGGSSSC
T ss_pred             hhcccccccccccccc--c--CccccccccCeEECCCCccCCCCCchhhcCCCCCCEEECCCCcCCcCccH
Confidence            5567777777665422  2  24788888888888887   3442  233  6888888888887766643

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.51  E-value=0.0088  Score=49.84  Aligned_cols=37  Identities=16%  Similarity=0.182  Sum_probs=28.2

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHhhCC------CCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKISGD------FDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~~~~------f~~~~w~~   87 (385)
                      .-+++.|+|.+|+|||++|.+++......      ....+|+.
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            45799999999999999999998765322      34455655

>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=95.51  E-value=0.0036  Score=50.97  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .++.|+|++|+|||||.+.+.++.
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            478899999999999999998864

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=95.46  E-value=0.0027  Score=55.20  Aligned_cols=60  Identities=13%  Similarity=0.097  Sum_probs=41.8

Q ss_pred             CeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc-----ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          321 KIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS-----SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       321 ~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~-----~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .|..+.+...........+..+.++++|++|+|+++     .+|.+|+  .+|+||++++|.+..+|
T Consensus        51 ~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~  117 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAI  117 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEEC
T ss_pred             EEEEEECCCCCCCCCCCCChHHhcCccccccccccccccccccccccccccccchhhhccccccccc
Confidence            355666655543222223456778899999999763     6888888  88999999888876655

>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=95.45  E-value=0.0041  Score=47.82  Aligned_cols=21  Identities=29%  Similarity=0.276  Sum_probs=18.9

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~   75 (385)
                      |.|+|.+|+|||||..++...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998763

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.0046  Score=50.24  Aligned_cols=26  Identities=19%  Similarity=0.129  Sum_probs=22.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      -.++.|.|.+|+|||+||.+++....
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            35899999999999999999987653

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.38  E-value=0.01  Score=52.57  Aligned_cols=35  Identities=23%  Similarity=0.133  Sum_probs=25.0

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ....+...+.     .+++.|+|.+|.||||++.++...+
T Consensus       153 Q~~A~~~al~-----~~~~vI~G~pGTGKTt~i~~~l~~l  187 (359)
T d1w36d1         153 QKVAAAVALT-----RRISVISGGPGTGKTTTVAKLLAAL  187 (359)
T ss_dssp             HHHHHHHHHT-----BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc-----CCeEEEEcCCCCCceehHHHHHHHH
Confidence            4444444443     2589999999999999988776544

>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=95.25  E-value=0.044  Score=46.23  Aligned_cols=52  Identities=12%  Similarity=-0.011  Sum_probs=34.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh-CCCCceEEEeeccccccCCCChHHHHHHHHHHHh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS-GDFDGSCFLENVREESQIPGGLSCLRQKLLSNLL  111 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~l~  111 (385)
                      .++.|.|.+|+|||+++.+++..+. ..=..+.+++ .     . .+...+...++....
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s-~-----E-~~~~~~~~r~~~~~~   88 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM-L-----E-ESVEETAEDLIGLHN   88 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE-S-----S-SCHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEee-e-----c-cchhhHHhHHHHHhh
Confidence            4788999999999999999987642 3222344443 1     1 445566666655444

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.25  E-value=0.0049  Score=52.40  Aligned_cols=35  Identities=20%  Similarity=0.100  Sum_probs=25.8

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.++|.|.+|+|||+|+.........+....++..
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~~~~~~~v~V~~~  102 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILNQQGQNVICVYVA  102 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCCTTTCEEEEEE
T ss_pred             ceEeeccCCCCChHHHHHHHHhhhcccCceeeeee
Confidence            45889999999999999987654444445555554

>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=95.24  E-value=0.0024  Score=53.19  Aligned_cols=25  Identities=20%  Similarity=0.190  Sum_probs=22.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+.|+|-|+-|+||||+|+.+.+.+
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999999988755

>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=95.23  E-value=0.008  Score=47.17  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=20.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++---|+|+|.+|+|||||..++..
T Consensus        14 ~~~~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          14 DQEVRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCC
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHhc
Confidence            3334577999999999999988754

>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=95.21  E-value=0.005  Score=47.69  Aligned_cols=21  Identities=38%  Similarity=0.460  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            377999999999999999876

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.17  E-value=0.0081  Score=47.23  Aligned_cols=32  Identities=31%  Similarity=0.392  Sum_probs=22.9

Q ss_pred             HHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           42 ESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        42 ~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+.+.-.... .-|+|+|.+|+|||||..++..
T Consensus         4 ~~~~~~~~k~-~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_           4 LQFLGLYKKT-GKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             HHHHTCTTCC-EEEEEEEETTSSHHHHHHHHSC
T ss_pred             HHhccccCCC-CEEEEECCCCCCHHHHHHHHhC
Confidence            3444433333 4577999999999999988764

>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=95.16  E-value=0.0058  Score=54.35  Aligned_cols=25  Identities=24%  Similarity=0.343  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-+...|+.|||||-||+.+++..
T Consensus        68 ~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcceeeeCCCCccHHHHHHHHHhhc
Confidence            4558889999999999999999865

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.15  E-value=0.008  Score=46.79  Aligned_cols=17  Identities=12%  Similarity=-0.050  Sum_probs=8.3

Q ss_pred             CCeeEEEcCCCCCCCCC
Q 044214          364 CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       364 ~~LryL~l~~~~~~~lP  380 (385)
                      .+|++|++++|++..+|
T Consensus       112 ~~L~~L~l~~N~i~~~~  128 (162)
T d1a9na_         112 KSLTYLCILRNPVTNKK  128 (162)
T ss_dssp             TTCCEEECCSSGGGGST
T ss_pred             cccchhhcCCCcccccc
Confidence            44555555555444444

>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=95.13  E-value=0.0095  Score=48.46  Aligned_cols=35  Identities=14%  Similarity=0.066  Sum_probs=27.7

Q ss_pred             EEEEEEcCC-CchHHHHHHHHHHHhhCCCCceEEEe
Q 044214           53 YALGIWGIG-GIGKTTIARAIFDKISGDFDGSCFLE   87 (385)
Q Consensus        53 ~vv~I~G~g-GiGKTtLA~~~~~~~~~~f~~~~w~~   87 (385)
                      +.+.|+|-| ||||||++..++.-+.++-..+..+.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEEC
Confidence            568899998 99999999999998766544455554

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=95.12  E-value=0.01  Score=48.70  Aligned_cols=60  Identities=8%  Similarity=0.066  Sum_probs=43.8

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcccCC--CCC--CCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNG--ENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~lp~--~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      ...++.+.+.....    .....|.++++|+.|+|+++.+.+  .+.  .+|++|++++|+++.+|.|
T Consensus       150 ~~~L~~L~l~~n~~----~~~~~l~~l~~L~~L~Ls~n~l~~l~~l~~l~~L~~L~Ls~N~lt~i~~l  213 (227)
T d1h6ua2         150 LTNLQYLSIGNAQV----SDLTPLANLSKLTTLKADDNKISDISPLASLPNLIEVHLKNNQISDVSPL  213 (227)
T ss_dssp             CTTCCEEECCSSCC----CCCGGGTTCTTCCEEECCSSCCCCCGGGGGCTTCCEEECTTSCCCBCGGG
T ss_pred             cccccccccccccc----ccchhhcccccceecccCCCccCCChhhcCCCCCCEEECcCCcCCCCccc
Confidence            45577777765542    123448899999999999984432  244  8999999999999988854

>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=95.10  E-value=0.013  Score=45.79  Aligned_cols=21  Identities=38%  Similarity=0.536  Sum_probs=17.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377889999999999988765

>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=95.09  E-value=0.0058  Score=49.05  Aligned_cols=25  Identities=16%  Similarity=0.470  Sum_probs=22.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++.+.|+|+|.+|+|||||...+.+
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcC
Confidence            4566799999999999999999974

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=95.09  E-value=0.0082  Score=51.97  Aligned_cols=46  Identities=9%  Similarity=-0.073  Sum_probs=38.3

Q ss_pred             CccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCC-CCCCCC
Q 044214          338 NTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGV-KLNNFG  383 (385)
Q Consensus       338 ~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~-~lP~~~  383 (385)
                      ....+..+++|++|+|+++    .+|.+|+  .+|++|+|++|.+. .+|+++
T Consensus       236 ~~~~~~~~~~L~~L~Ls~N~l~g~iP~~l~~L~~L~~L~Ls~N~l~g~iP~~~  288 (313)
T d1ogqa_         236 DLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQGG  288 (313)
T ss_dssp             BGGGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSSEEEEECCCST
T ss_pred             cccccccccccccccCccCeecccCChHHhCCCCCCEEECcCCcccccCCCcc
Confidence            3445788899999999987    6888888  89999999999887 788764

>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=95.06  E-value=0.0059  Score=47.48  Aligned_cols=20  Identities=20%  Similarity=0.474  Sum_probs=18.4

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+++|.+|+|||||+.++.+
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67999999999999998885

>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=95.03  E-value=0.006  Score=47.94  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=18.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+.++.+
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            377899999999999999875

>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=95.02  E-value=0.0062  Score=47.49  Aligned_cols=21  Identities=24%  Similarity=0.328  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+.++.+
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477999999999999999886

>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=95.00  E-value=0.0063  Score=47.30  Aligned_cols=21  Identities=19%  Similarity=0.297  Sum_probs=19.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|.++|.+|+|||+|+.++.+
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999986

>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=94.99  E-value=0.0099  Score=46.65  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=20.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..--|+|+|.+|+|||+|...+.+
T Consensus         5 ~~~Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           5 ETHKLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeEEEEEECCCCcCHHHHHHHHHh
Confidence            344577999999999999999876

>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=94.87  E-value=0.007  Score=47.20  Aligned_cols=21  Identities=24%  Similarity=0.428  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+.++.+
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999876

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.85  E-value=0.0052  Score=50.99  Aligned_cols=26  Identities=12%  Similarity=0.088  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .-+++.|+|.+|+||||||.+++...
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~   58 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTC   58 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34699999999999999999998643

>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=94.84  E-value=0.0073  Score=46.87  Aligned_cols=20  Identities=25%  Similarity=0.371  Sum_probs=18.5

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+|+|.+|+|||+|+.++.+
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            77899999999999999886

>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=94.78  E-value=0.008  Score=48.90  Aligned_cols=20  Identities=35%  Similarity=0.400  Sum_probs=18.1

Q ss_pred             EEEEEcCCCchHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~   73 (385)
                      +|+|+|..|+||||+|+.+.
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998664

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=94.78  E-value=0.0078  Score=50.00  Aligned_cols=22  Identities=36%  Similarity=0.367  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||++.++.
T Consensus        30 e~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4899999999999999999976

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.78  E-value=0.011  Score=48.97  Aligned_cols=25  Identities=24%  Similarity=0.207  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      -.++.|.|.+|+|||++|.+++...
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4699999999999999999998754

>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=94.76  E-value=0.0066  Score=50.12  Aligned_cols=22  Identities=32%  Similarity=0.299  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.++.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCcchhhHhccC
Confidence            4899999999999999997765

>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=94.76  E-value=0.0079  Score=46.85  Aligned_cols=21  Identities=24%  Similarity=0.569  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~   25 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVT   25 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477999999999999999986

>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=94.74  E-value=0.008  Score=47.07  Aligned_cols=21  Identities=29%  Similarity=0.518  Sum_probs=19.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999886

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.73  E-value=0.015  Score=46.42  Aligned_cols=41  Identities=12%  Similarity=0.153  Sum_probs=19.5

Q ss_pred             eCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCC
Q 044214          337 LNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGV  377 (385)
Q Consensus       337 ~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~  377 (385)
                      +++..|.++++|++|+|+++   .+|. .+.  .+|++|+|.++++.
T Consensus        93 l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          93 ISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             ECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cCHHHHhCCCcccccccCCccccccCHHHhcCCcccccccccccccc
Confidence            44445555555555555554   3332 233  45555555554443

>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=94.73  E-value=0.0078  Score=54.34  Aligned_cols=120  Identities=13%  Similarity=0.077  Sum_probs=69.5

Q ss_pred             ccccc-hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccCCCChHHHHHHHHHH
Q 044214           31 LVGVE-STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQIPGGLSCLRQKLLSN  109 (385)
Q Consensus        31 ~vGR~-~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~~l~~~ll~~  109 (385)
                      -.|.. ..++.+.+++..   ...+|.|.|+.|.||||....+.+.+...-..++-+.+--+. .. ....        +
T Consensus       139 ~LG~~~~~~~~l~~l~~~---~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~-~~-~~~~--------q  205 (401)
T d1p9ra_         139 SLGMTAHNHDNFRRLIKR---PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEF-DI-DGIG--------Q  205 (401)
T ss_dssp             GSCCCHHHHHHHHHHHTS---SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCS-CC-SSSE--------E
T ss_pred             hhcccHHHHHHHHHHHhh---hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCccc-cc-CCCC--------e
Confidence            34544 445566666653   346999999999999999999998764433333333211110 00 0000        0


Q ss_pred             HhC-CCCCCchHHHHHHHhCCceEEEEEeCCCChhhhhHhhccCCCCCCCcEEEEEec
Q 044214          110 LLK-DKNVMPYIDLNFRRLGHMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus       110 l~~-~~~~~~~~~~l~~~l~~k~~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      ... ..........++..|+..+=+|++.++.+.+........-.   .|..|+-|-.
T Consensus       206 ~~v~~~~~~~~~~~l~~~lR~dPDvi~igEiRd~~ta~~a~~aa~---tGhlV~tTlH  260 (401)
T d1p9ra_         206 TQVNPRVDMTFARGLRAILRQDPDVVMVGEIRDLETAQIAVQASL---TGHLVMSTLH  260 (401)
T ss_dssp             EECBGGGTBCHHHHHHHHGGGCCSEEEESCCCSHHHHHHHHHHHH---TTCEEEEEEC
T ss_pred             eeecCCcCCCHHHHHHHHHhhcCCEEEecCcCChHHHHHHHHHHh---cCCeEEEEec
Confidence            000 00112556778888888888999999988877666554422   3544444443

>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=94.72  E-value=0.0082  Score=46.93  Aligned_cols=21  Identities=19%  Similarity=0.395  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+.++.+
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999886

>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=94.72  E-value=0.0072  Score=47.26  Aligned_cols=20  Identities=25%  Similarity=0.760  Sum_probs=18.1

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+|+|.+|+|||||..++..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            67899999999999998876

>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=94.71  E-value=0.0083  Score=46.87  Aligned_cols=21  Identities=29%  Similarity=0.309  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|.+|+|||||...+.+
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            478999999999999999875

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.71  E-value=0.0086  Score=46.59  Aligned_cols=57  Identities=7%  Similarity=0.054  Sum_probs=43.3

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .++|.+.+.......  + +..+..+++|++|+|+++   .++ .+.  .+|++|++++|.++.+|
T Consensus        18 ~~lr~L~L~~n~I~~--i-~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~   79 (162)
T d1a9na_          18 VRDRELDLRGYKIPV--I-ENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNRICRIG   79 (162)
T ss_dssp             TSCEEEECTTSCCCS--C-CCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSCCCEEC
T ss_pred             CcCcEEECCCCCCCc--c-CccccccccCCEEECCCCCCCccC-CcccCcchhhhhcccccccCCC
Confidence            356777776664322  2 456788999999999998   554 355  89999999999999887

>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=94.69  E-value=0.0084  Score=46.71  Aligned_cols=20  Identities=25%  Similarity=0.518  Sum_probs=18.3

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+|+|.+|+|||+|..++.+
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67889999999999999876

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.69  E-value=0.02  Score=49.09  Aligned_cols=59  Identities=15%  Similarity=0.106  Sum_probs=47.7

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---cc-CCCCC--CCeeEEEcCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SF-NGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~l-p~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      .+++.+.+....  -..+++..|.++.+|+.|+++++   .+ |..|.  .+|++|++++|+++.+|
T Consensus        31 ~~l~~L~Ls~N~--i~~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n~l~~l~   95 (305)
T d1xkua_          31 PDTALLDLQNNK--ITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELP   95 (305)
T ss_dssp             TTCCEEECCSSC--CCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCC
T ss_pred             CCCCEEECcCCc--CCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccCCccCcCc
Confidence            457777776654  34566778999999999999988   54 56677  99999999999999998

>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=94.67  E-value=0.0086  Score=49.30  Aligned_cols=26  Identities=31%  Similarity=0.418  Sum_probs=23.0

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +.+++..|+|.-|+|||||.+++.+.
T Consensus         1 ~~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           1 NPIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CCEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            35789999999999999999998874

>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=94.66  E-value=0.0086  Score=49.44  Aligned_cols=22  Identities=32%  Similarity=0.350  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.++.
T Consensus        27 ei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4899999999999999998875

>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=94.66  E-value=0.0086  Score=46.74  Aligned_cols=20  Identities=30%  Similarity=0.695  Sum_probs=18.4

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+++|.+|+|||+|..++.+
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            57899999999999999987

>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=94.65  E-value=0.016  Score=45.30  Aligned_cols=34  Identities=26%  Similarity=0.227  Sum_probs=25.1

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...+.+++.  .... .|.|+|.+|+|||||..++..
T Consensus         4 ~~~~~~~~~--~k~~-kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1           4 FTRIWRLFN--HQEH-KVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             HHHHHHHHT--TSCE-EEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHhC--CCeE-EEEEECCCCCCHHHHHHHHhc
Confidence            345666665  3334 567999999999999998875

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.64  E-value=0.016  Score=46.20  Aligned_cols=60  Identities=7%  Similarity=-0.022  Sum_probs=43.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+....  ...+....|..+..|+.|+|+++   .+|. .|.  .+|++|+|+++.++.+|
T Consensus        53 l~~L~~L~L~~N~--i~~~~~~~~~~~~~L~~L~Ls~N~l~~l~~~~F~~l~~L~~L~L~~N~l~~i~  118 (192)
T d1w8aa_          53 LPHLVKLELKRNQ--LTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVM  118 (192)
T ss_dssp             CTTCCEEECCSSC--CCCBCTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEEC
T ss_pred             CceEeeeeccccc--cccccccccccccccceeeeccccccccCHHHHhCCCcccccccCCccccccC
Confidence            4456666665443  34566778888888888888887   5554 455  88999999999888887

>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=94.62  E-value=0.006  Score=49.37  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|+|+.|+|||||.+.++..
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcc
Confidence            48999999999999999999864

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=94.60  E-value=0.0075  Score=50.09  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|..|+|||||++.++.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHcC
Confidence            4899999999999999999865

>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=94.58  E-value=0.0082  Score=46.89  Aligned_cols=21  Identities=29%  Similarity=0.476  Sum_probs=18.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+..+.+
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhC
Confidence            477999999999999998865

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.58  E-value=0.023  Score=43.70  Aligned_cols=57  Identities=14%  Similarity=0.077  Sum_probs=46.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGV  377 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~  377 (385)
                      ..+++.+.+....  -..+.+..|..+++|++|+|+++   .+|.++-  ..|++|+|+++++.
T Consensus        55 l~~L~~L~Ls~N~--l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~~~l~~L~L~~Np~~  116 (156)
T d2ifga3          55 LGELRNLTIVKSG--LRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPLH  116 (156)
T ss_dssp             CCCCSEEECCSSC--CCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCCEEECCSSCCC
T ss_pred             ccccCcceeeccc--cCCcccccccccccccceeccCCCCcccChhhhccccccccccCCCccc
Confidence            4567777776665  35678899999999999999998   7777655  78999999998774

>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=94.57  E-value=0.0094  Score=46.42  Aligned_cols=21  Identities=29%  Similarity=0.618  Sum_probs=18.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|||||+|..++.+
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            367999999999999999876

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.56  E-value=0.0086  Score=50.31  Aligned_cols=22  Identities=36%  Similarity=0.466  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..++|+|..|+|||||++.+..
T Consensus        42 e~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            4899999999999999999865

>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=94.56  E-value=0.0093  Score=46.65  Aligned_cols=21  Identities=29%  Similarity=0.550  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            477899999999999999876

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=94.55  E-value=0.0089  Score=49.78  Aligned_cols=22  Identities=36%  Similarity=0.567  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..++|+|..|+|||||++.+..
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            4899999999999999999876

>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=94.55  E-value=0.012  Score=46.53  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .--|+|+|.+|||||+|..++.+
T Consensus         5 ~iKivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           5 AIKCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHHh
Confidence            33578999999999999999876

>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=94.54  E-value=0.0086  Score=46.47  Aligned_cols=21  Identities=33%  Similarity=0.442  Sum_probs=18.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~   24 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNG   24 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            367999999999999998865

>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=94.52  E-value=0.0096  Score=46.68  Aligned_cols=21  Identities=19%  Similarity=0.419  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|.+|+|||+|+.++..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999875

>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=94.51  E-value=0.0098  Score=49.30  Aligned_cols=22  Identities=41%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.+..
T Consensus        33 e~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCChHHHHHHHHHc
Confidence            4899999999999999999876

>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=94.51  E-value=0.0098  Score=46.63  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+.+
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            478999999999999999875

>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=94.50  E-value=0.0099  Score=46.19  Aligned_cols=21  Identities=19%  Similarity=0.406  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|.+|+|||||..++.+
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377999999999999999876

>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=94.50  E-value=0.012  Score=45.66  Aligned_cols=23  Identities=17%  Similarity=0.424  Sum_probs=19.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-|+|+|.+|+|||+|...+.+
T Consensus         4 ~~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           4 SRKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCcCHHHHHHHHHh
Confidence            34578899999999999999875

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.46  E-value=0.0097  Score=49.00  Aligned_cols=22  Identities=32%  Similarity=0.268  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.++.
T Consensus        27 e~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            4899999999999999999986

>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=94.45  E-value=0.0096  Score=48.26  Aligned_cols=21  Identities=48%  Similarity=0.575  Sum_probs=18.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIF   73 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~   73 (385)
                      -+|+|+|..|+||||+|+.+.
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            479999999999999988663

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.45  E-value=0.0091  Score=49.77  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -..++|+|..|+|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999875

>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=94.43  E-value=0.0084  Score=47.62  Aligned_cols=21  Identities=38%  Similarity=0.392  Sum_probs=18.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||+..+.+
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            477999999999999998875

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.43  E-value=0.0085  Score=50.46  Aligned_cols=22  Identities=36%  Similarity=0.424  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|+|+.|+|||||++.++.
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHc
Confidence            4899999999999999999976

>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=94.43  E-value=0.016  Score=45.76  Aligned_cols=34  Identities=29%  Similarity=0.268  Sum_probs=22.9

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+.+.|....... -|.++|.+|+|||||..++..
T Consensus         6 ~~~~~l~~~~k~~-KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_           6 SMFDKLWGSNKEL-RILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             HHHGGGTTCSSCE-EEEEEEETTSSHHHHHHHTCC
T ss_pred             HHHHHHhCCCceE-EEEEECCCCCCHHHHHHHHhc
Confidence            3444343323344 466999999999999988753

>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=94.42  E-value=0.011  Score=48.47  Aligned_cols=37  Identities=19%  Similarity=0.111  Sum_probs=25.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH-hhCCCCceEEEe
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK-ISGDFDGSCFLE   87 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~-~~~~f~~~~w~~   87 (385)
                      .-.++.|+|.+|+|||+||.+++.. ....-..+.|++
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            3458999999999999999987653 222223345554

>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=94.38  E-value=0.017  Score=52.64  Aligned_cols=76  Identities=17%  Similarity=0.253  Sum_probs=44.5

Q ss_pred             CccccchhHHHHHHhhc--------CCCC----CeEEEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccC--
Q 044214           30 QLVGVESTVEEIESLLG--------VESK----GVYALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQI--   95 (385)
Q Consensus        30 ~~vGR~~~l~~l~~~L~--------~~~~----~~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~--   95 (385)
                      +.||-++..+.+.-.+.        ....    ..+=|.++|+.|+|||-||+.+++.+.--|    ........++.  
T Consensus        15 yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPF----v~~daT~fTeaGY   90 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPF----IKVEATKFTEVGY   90 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE----EEEEGGGGC----
T ss_pred             cccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCE----EEeecceeeecce
Confidence            47777777766654431        1111    134588999999999999999998663222    11111111111  


Q ss_pred             -CCChHHHHHHHHHH
Q 044214           96 -PGGLSCLRQKLLSN  109 (385)
Q Consensus        96 -~~~~~~l~~~ll~~  109 (385)
                       ..++..+.+.++..
T Consensus        91 vG~DVesii~~L~~~  105 (443)
T d1g41a_          91 VGKEVDSIIRDLTDS  105 (443)
T ss_dssp             CCCCTHHHHHHHHHH
T ss_pred             eecchhHHHHHHHHH
Confidence             15677777776643

>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=94.37  E-value=0.013  Score=46.06  Aligned_cols=21  Identities=33%  Similarity=0.264  Sum_probs=18.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         4 KivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            467889999999999988876

>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=94.36  E-value=0.011  Score=45.23  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+..
T Consensus         2 KI~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999876

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.36  E-value=0.01  Score=49.73  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..++|+|..|+|||||++.+..
T Consensus        41 e~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            5899999999999999999865

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.35  E-value=0.011  Score=48.91  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=20.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +++|.|+.|+|||||.+.++.-
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl   47 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCChHHHHHHHHHcC
Confidence            7789999999999999999863

>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=94.35  E-value=0.011  Score=45.89  Aligned_cols=21  Identities=29%  Similarity=0.640  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         5 Ki~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            377899999999999999886

>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=94.32  E-value=0.012  Score=46.00  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=18.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|..++.+
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367899999999999999876

>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=94.32  E-value=0.012  Score=45.98  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=19.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .|+|.|.+|+|||||..++..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999874

>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=94.32  E-value=0.012  Score=46.02  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||+|+.++.+
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            488999999999999998876

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.32  E-value=0.011  Score=50.43  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -.+++|+|+.|+|||||++.++..
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            358999999999999999999864

>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=94.31  E-value=0.014  Score=48.49  Aligned_cols=24  Identities=25%  Similarity=0.274  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +++|+|+|..|+||||+|..+.+.
T Consensus         1 M~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           1 MKLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            368999999999999999998774

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=94.31  E-value=0.013  Score=51.78  Aligned_cols=58  Identities=9%  Similarity=0.102  Sum_probs=34.1

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      .+++.+.+..+....  +  +-+..+++|++|+|+++   .+|. ++  .+|+||++++|+++.+|.|
T Consensus        44 ~~l~~L~l~~~~I~~--l--~gl~~L~nL~~L~Ls~N~l~~l~~-l~~L~~L~~L~L~~n~i~~i~~l  106 (384)
T d2omza2          44 DQVTTLQADRLGIKS--I--DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITPL  106 (384)
T ss_dssp             TTCCEEECCSSCCCC--C--TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGGG
T ss_pred             CCCCEEECCCCCCCC--c--cccccCCCCCEEeCcCCcCCCCcc-ccCCccccccccccccccccccc
Confidence            456666665554321  1  23456677777777776   3432 44  6777777777777666543

>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=94.29  E-value=0.012  Score=46.26  Aligned_cols=21  Identities=19%  Similarity=0.368  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|..|+|||||+.++.+
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            478999999999999999876

>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=94.28  E-value=0.012  Score=47.53  Aligned_cols=22  Identities=23%  Similarity=0.197  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +.|+|+|.+|+|||||..++.+
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~   25 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTT   25 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3789999999999999999986

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.22  E-value=0.021  Score=48.09  Aligned_cols=39  Identities=10%  Similarity=0.047  Sum_probs=21.1

Q ss_pred             eCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCC
Q 044214          337 LNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFA  375 (385)
Q Consensus       337 ~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~  375 (385)
                      ++...|..+.+|+.|+|+++   .+|.++.  .+|++|+|++++
T Consensus       163 ~~~~~~~~l~~L~~L~Ls~N~L~~lp~~~~~~~~L~~L~L~~Np  206 (266)
T d1p9ag_         163 LPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNP  206 (266)
T ss_dssp             CCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCCCSEEECCSCC
T ss_pred             cCccccccccccceeecccCCCcccChhHCCCCCCCEEEecCCC
Confidence            44445555555555555555   4555444  555555555544

>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=94.19  E-value=0.011  Score=46.97  Aligned_cols=21  Identities=33%  Similarity=0.428  Sum_probs=18.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|.++|.+|+|||+|..++..
T Consensus         4 KivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            367999999999999998765

>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=94.14  E-value=0.013  Score=46.39  Aligned_cols=21  Identities=29%  Similarity=0.488  Sum_probs=18.9

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||+..+.+
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377999999999999999876

>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=94.11  E-value=0.015  Score=45.64  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...|+|+|.+|+|||||...+..
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~   27 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLG   27 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            45799999999999999999986

>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=94.11  E-value=0.013  Score=46.48  Aligned_cols=21  Identities=24%  Similarity=0.324  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|.|+|.+|+|||+|..++.+
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            478999999999999999876

>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=94.04  E-value=0.014  Score=46.74  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+.+
T Consensus         8 KivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhh
Confidence            478999999999999999886

>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=94.03  E-value=0.014  Score=46.04  Aligned_cols=21  Identities=19%  Similarity=0.242  Sum_probs=18.8

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|..|+|||+|+..+.+
T Consensus         4 KivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367899999999999999887

>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=94.02  E-value=0.016  Score=45.37  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +..|+|+|.+|+|||||..++.+
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhC
Confidence            56789999999999999999986

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.02  E-value=0.049  Score=46.18  Aligned_cols=23  Identities=30%  Similarity=0.115  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +.++|.|.+|+|||+|+..+...
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHh
Confidence            46889999999999999988764

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.034  Score=46.68  Aligned_cols=60  Identities=13%  Similarity=0.081  Sum_probs=46.7

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCC-CCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNG-ENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~-~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ...++.+.+....  ...+++..|..+..|++|+++++   .+|. .+.  .+|++|+|+++.++.||
T Consensus       123 l~~l~~L~l~~n~--l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~L~~lp  188 (266)
T d1p9ag_         123 LGELQELYLKGNE--LKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYTIP  188 (266)
T ss_dssp             CTTCCEEECTTSC--CCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             ccccccccccccc--cceeccccccccccchhcccccccccccCccccccccccceeecccCCCcccC
Confidence            3455566655543  34567888999999999999998   5554 455  89999999999999999

>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=94.00  E-value=0.015  Score=45.36  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .-|+|+|.+|+|||+|..++.+
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           5 HKVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4578999999999999999875

>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=93.99  E-value=0.014  Score=47.06  Aligned_cols=21  Identities=24%  Similarity=0.281  Sum_probs=19.4

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999876

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.98  E-value=0.011  Score=49.12  Aligned_cols=22  Identities=45%  Similarity=0.601  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.+..
T Consensus        32 e~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHHc
Confidence            4899999999999999999986

>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=93.98  E-value=0.014  Score=45.71  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=19.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      --|.++|.+|+|||+|+..+..
T Consensus         4 ~Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           4 YRVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3578999999999999998864

>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=93.97  E-value=0.031  Score=42.90  Aligned_cols=26  Identities=31%  Similarity=0.392  Sum_probs=23.0

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      ..-+|.+.|.=|+||||+++.+++.+
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhc
Confidence            34589999999999999999999864

>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=93.91  E-value=0.013  Score=46.76  Aligned_cols=19  Identities=26%  Similarity=0.501  Sum_probs=17.4

Q ss_pred             EEEEEcCCCchHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAI   72 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~   72 (385)
                      -|.|.|.+|+|||+|..++
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4679999999999999998

>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=93.90  E-value=0.015  Score=45.44  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||+..+.+
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            488999999999999998876

>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=93.89  E-value=0.016  Score=44.86  Aligned_cols=21  Identities=33%  Similarity=0.385  Sum_probs=18.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|++.|.+|+|||||..++..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            366889999999999998865

>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=93.84  E-value=0.016  Score=46.20  Aligned_cols=21  Identities=24%  Similarity=0.279  Sum_probs=18.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|.+|+|||+|..++.+
T Consensus         5 KvvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367899999999999998876

>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=93.81  E-value=0.018  Score=45.25  Aligned_cols=23  Identities=26%  Similarity=0.416  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-|.|.|.+|+||||+|.++..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            46889999999999999998864

>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=93.81  E-value=0.017  Score=45.43  Aligned_cols=20  Identities=30%  Similarity=0.496  Sum_probs=18.5

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+++|.+|+|||+|..++.+
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999875

>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=93.77  E-value=0.017  Score=45.03  Aligned_cols=21  Identities=33%  Similarity=0.659  Sum_probs=18.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|.++|.+|+|||+|..++.+
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            366889999999999999886

>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=93.70  E-value=0.017  Score=45.95  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -|.+.|.+|+|||+|..++...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999998654

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=93.67  E-value=0.022  Score=45.60  Aligned_cols=39  Identities=10%  Similarity=0.090  Sum_probs=16.6

Q ss_pred             cCCCCCCcEEEecCcccCC--CCC--CCeeEEEcCCCCCCCCC
Q 044214          342 FTKMPKLRFLKFYSSSFNG--ENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       342 ~~~~~~LrvL~l~~~~lp~--~i~--~~LryL~l~~~~~~~lP  380 (385)
                      +..+++|++|+|+++.+..  .++  .+|++|++++|.+..+|
T Consensus        58 l~~l~nL~~L~Ls~N~l~~~~~l~~l~~L~~L~l~~n~~~~~~  100 (199)
T d2omxa2          58 VEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADIT  100 (199)
T ss_dssp             GGGCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSSCCCCCG
T ss_pred             cccCCCcCcCccccccccCcccccCCccccccccccccccccc
Confidence            3444455555555442211  122  44455555444444444

>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=93.66  E-value=0.031  Score=45.64  Aligned_cols=33  Identities=27%  Similarity=0.431  Sum_probs=26.0

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -+++|.++|..     +..+++|.+|||||||..++..
T Consensus        85 g~~~L~~~l~~-----kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          85 GIEELKEYLKG-----KISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             THHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHST
T ss_pred             hHhhHHHHhcC-----CeEEEECCCCCCHHHHHHhhcc
Confidence            36777777752     3678899999999999998864

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.59  E-value=0.013  Score=46.20  Aligned_cols=20  Identities=25%  Similarity=0.479  Sum_probs=18.5

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999864

>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=93.59  E-value=0.02  Score=45.04  Aligned_cols=21  Identities=24%  Similarity=0.488  Sum_probs=19.0

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+++|.+|+|||+|..++.+
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            477999999999999998876

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=93.48  E-value=0.035  Score=46.53  Aligned_cols=38  Identities=24%  Similarity=0.387  Sum_probs=27.8

Q ss_pred             hHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           37 TVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        37 ~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+.++...+.......--|+|+|.+|+|||||...++.
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg   54 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIG   54 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhC
Confidence            34455555554444455788999999999999999986

>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=93.47  E-value=0.016  Score=45.56  Aligned_cols=21  Identities=19%  Similarity=0.295  Sum_probs=19.2

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||...+.+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            488999999999999999875

>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=93.45  E-value=0.019  Score=45.02  Aligned_cols=23  Identities=30%  Similarity=0.443  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .-|.|.|.+|+||||+|.++..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            46889999999999999998863

>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=93.36  E-value=0.021  Score=43.84  Aligned_cols=21  Identities=24%  Similarity=0.294  Sum_probs=18.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            367999999999999999875

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.36  E-value=0.018  Score=47.81  Aligned_cols=22  Identities=36%  Similarity=0.428  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|.|||||.+.+..
T Consensus        33 ei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999999975

>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=93.34  E-value=0.024  Score=44.16  Aligned_cols=23  Identities=30%  Similarity=0.420  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +-|.|.|.+|+||||+|.++.++
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            46889999999999999998875

>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=93.28  E-value=0.71  Score=36.54  Aligned_cols=47  Identities=21%  Similarity=0.076  Sum_probs=33.6

Q ss_pred             CCCCCccccchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           26 DNKNQLVGVESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        26 ~~~~~~vGR~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      ..+..+-=|+-..+.+..++..   + + ..|.+..|.|||.+|..++.+..
T Consensus        64 ~~~~~~~Lr~yQ~eav~~~~~~---~-~-~ll~~~tG~GKT~~a~~~~~~~~  110 (206)
T d2fz4a1          64 YFDAEISLRDYQEKALERWLVD---K-R-GCIVLPTGSGKTHVAMAAINELS  110 (206)
T ss_dssp             CCCCCCCCCHHHHHHHHHHTTT---S-E-EEEEESSSTTHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhC---C-C-cEEEeCCCCCceehHHhHHHHhc
Confidence            3344566788888888777652   2 2 34678999999999988887653

>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=93.26  E-value=0.016  Score=45.86  Aligned_cols=21  Identities=24%  Similarity=0.539  Sum_probs=18.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999998864

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.26  E-value=0.019  Score=48.14  Aligned_cols=23  Identities=30%  Similarity=0.260  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+++|.|+.|+|||||++.++..
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCC
Confidence            48999999999999999999764

>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=93.18  E-value=0.017  Score=45.46  Aligned_cols=25  Identities=12%  Similarity=0.186  Sum_probs=21.2

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++...|+|+|.+++|||||..++..
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhC
Confidence            4556799999999999999988753

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.97  E-value=0.019  Score=48.17  Aligned_cols=22  Identities=27%  Similarity=0.380  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..++|+|..|+|||||++.+..
T Consensus        45 e~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTT
T ss_pred             CEEEEECCCCCcHHHHHHHHHh
Confidence            4899999999999999998754

>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=92.86  E-value=0.025  Score=46.29  Aligned_cols=22  Identities=32%  Similarity=0.374  Sum_probs=19.0

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .-|.+.|.+|+|||||..++..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3578999999999999998864

>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=92.77  E-value=0.02  Score=47.23  Aligned_cols=22  Identities=27%  Similarity=0.365  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++|.|+.|+|||||.+.++.
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            4899999999999999998876

>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=92.77  E-value=0.017  Score=45.25  Aligned_cols=21  Identities=29%  Similarity=0.381  Sum_probs=8.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            477899999999999988875

>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=92.74  E-value=0.027  Score=44.37  Aligned_cols=21  Identities=33%  Similarity=0.550  Sum_probs=19.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+|+|||||..++..
T Consensus        10 kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            478999999999999999885

>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=92.71  E-value=0.066  Score=46.38  Aligned_cols=100  Identities=16%  Similarity=0.038  Sum_probs=58.6

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEEeeccccccC-CCChHHHHHHHHHHHhCCCCCCchHHHHHHHhCCceE
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFLENVREESQI-PGGLSCLRQKLLSNLLKDKNVMPYIDLNFRRLGHMKV  132 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~~~~~~~~~~-~~~~~~l~~~ll~~l~~~~~~~~~~~~l~~~l~~k~~  132 (385)
                      -|.|+|..|+||||+.+.++..+.... .++-+....+..-. +....        ++ ....+....+.++..|+..+=
T Consensus       168 nili~G~tgSGKTT~l~al~~~i~~~~-rivtiEd~~El~l~~~~~~~--------~~-~~~~~~~~~~ll~~~lR~~pd  237 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFIPKEE-RIISIEDTEEIVFKHHKNYT--------QL-FFGGNITSADCLKSCLRMRPD  237 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSCTTC-CEEEEESSCCCCCSSCSSEE--------EE-ECBTTBCHHHHHHHHTTSCCS
T ss_pred             CEEEEeeccccchHHHHHHhhhccccc-ceeeccchhhhhcccccccc--------ee-ccccchhHHHHHHHHhccCCC
Confidence            378999999999999999988664432 23333333222110 00000        00 001122566778888888888


Q ss_pred             EEEEeCCCChhhhhHhhccCCCCCCCcEEEEEec
Q 044214          133 LIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTR  166 (385)
Q Consensus       133 LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR  166 (385)
                      .+|+..+...+.+..+ .....++.|  ++.|..
T Consensus       238 ~iivgEiR~~ea~~~l-~a~~tGh~g--~~tT~H  268 (323)
T d1g6oa_         238 RIILGELRSSEAYDFY-NVLCSGHKG--TLTTLH  268 (323)
T ss_dssp             EEEESCCCSTHHHHHH-HHHHTTCSC--EEEEEC
T ss_pred             cccCCccCchhHHHHH-HHHHhcCCc--EEEEEC
Confidence            8999999888877644 444433334  344443

>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=92.62  E-value=0.046  Score=47.55  Aligned_cols=30  Identities=30%  Similarity=0.418  Sum_probs=25.4

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhhCCCC
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKISGDFD   81 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~~~f~   81 (385)
                      +-.|.|-|.-|+||||+++.+.+.+..+..
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l~~~~~   35 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAASGGSP   35 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGGGCSSC
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHhccCCC
Confidence            457899999999999999999998766543

>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=92.51  E-value=0.038  Score=42.97  Aligned_cols=24  Identities=29%  Similarity=0.314  Sum_probs=19.8

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ...+ |.++|.+|+|||||..++.+
T Consensus        11 k~~k-IvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          11 KEMR-ILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             CCEE-EEEEEETTSSHHHHHHHTTC
T ss_pred             CeEE-EEEECCCCCCHHHHHHHHhc
Confidence            3455 66899999999999998864

>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=92.37  E-value=0.18  Score=37.09  Aligned_cols=25  Identities=20%  Similarity=0.251  Sum_probs=20.3

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ++.++..|+++.|.|||+++..++.
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~   30 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYA   30 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHH
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHH
Confidence            3567889999999999998866654

>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=92.15  E-value=0.015  Score=44.74  Aligned_cols=22  Identities=23%  Similarity=0.456  Sum_probs=19.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      -|+++|.+|+|||||..++..+
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999864

>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=91.94  E-value=0.063  Score=42.75  Aligned_cols=41  Identities=17%  Similarity=0.216  Sum_probs=32.6

Q ss_pred             hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           36 STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        36 ~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      .-+..+..+|. +.++...+.++|+++.|||.+|..+.+-+.
T Consensus        38 ~Fl~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          38 TFLGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            44666777775 345667899999999999999999988764

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=91.60  E-value=0.12  Score=44.50  Aligned_cols=56  Identities=14%  Similarity=0.072  Sum_probs=38.0

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcc---cCCCCCCCeeEEEcCCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSS---FNGENKCKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~---lp~~i~~~LryL~l~~~~~~~lP~~  382 (385)
                      ++++.+.+..+...  .++    ..+.+|+.|+|+++.   +|..+ .+|++|++++|+++.+|++
T Consensus       284 ~~L~~L~Ls~N~l~--~lp----~~~~~L~~L~L~~N~L~~l~~~~-~~L~~L~L~~N~L~~lp~~  342 (353)
T d1jl5a_         284 PSLEELNVSNNKLI--ELP----ALPPRLERLIASFNHLAEVPELP-QNLKQLHVEYNPLREFPDI  342 (353)
T ss_dssp             TTCCEEECCSSCCS--CCC----CCCTTCCEEECCSSCCSCCCCCC-TTCCEEECCSSCCSSCCCC
T ss_pred             CCCCEEECCCCccC--ccc----cccCCCCEEECCCCcCCcccccc-CCCCEEECcCCcCCCCCcc
Confidence            45666666554321  122    346789999999884   44311 6899999999999999964

>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=91.49  E-value=0.4  Score=37.85  Aligned_cols=32  Identities=19%  Similarity=0.070  Sum_probs=21.0

Q ss_pred             EEEEcCCCchHHHHHHH-HHHHhhCCCCceEEEe
Q 044214           55 LGIWGIGGIGKTTIARA-IFDKISGDFDGSCFLE   87 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~-~~~~~~~~f~~~~w~~   87 (385)
                      +.|.++.|.|||+.|.. ++..... ...++++.
T Consensus        43 ~il~apTGsGKT~~a~l~i~~~~~~-~~~vl~l~   75 (202)
T d2p6ra3          43 LLLAMPTAAGKTLLAEMAMVREAIK-GGKSLYVV   75 (202)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             EEEEcCCCCchhHHHHHHHHHHhhc-cCcceeec
Confidence            56899999999998744 3334433 23455554

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=91.48  E-value=0.042  Score=44.35  Aligned_cols=59  Identities=14%  Similarity=0.197  Sum_probs=42.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      ..+++.+.+..+....  +  ..++.+++|++|+++++   .+|. ++  .+|++|++.+|.+..+|.|
T Consensus        67 l~~L~~L~L~~n~i~~--l--~~~~~l~~L~~L~l~~n~i~~l~~-l~~l~~L~~L~l~~~~~~~~~~l  130 (210)
T d1h6ta2          67 LPNVTKLFLNGNKLTD--I--KPLANLKNLGWLFLDENKVKDLSS-LKDLKKLKSLSLEHNGISDINGL  130 (210)
T ss_dssp             CTTCCEEECCSSCCCC--C--GGGTTCTTCCEEECCSSCCCCGGG-GTTCTTCCEEECTTSCCCCCGGG
T ss_pred             CCCCCEEeCCCccccC--c--cccccCcccccccccccccccccc-ccccccccccccccccccccccc
Confidence            5678888777765322  2  23678889999999887   4443 44  7899999999888777644

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=91.37  E-value=0.011  Score=47.58  Aligned_cols=39  Identities=15%  Similarity=0.082  Sum_probs=20.4

Q ss_pred             cCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          342 FTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       342 ~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      |.++++|++|+|+++   .+|..+.  .+|++|++++|.++.+|
T Consensus        66 l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N~i~~l~  109 (198)
T d1m9la_          66 LSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLS  109 (198)
T ss_dssp             HHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEEECCCHH
T ss_pred             ccCCccccChhhcccccccccccccccccccccccccccccccc
Confidence            455556666666655   3333222  35666666665555443

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=91.24  E-value=0.1  Score=41.43  Aligned_cols=61  Identities=11%  Similarity=0.160  Sum_probs=42.5

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcccCC--CCC--CCeeEEEcCCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNG--ENK--CKISYLQDPGFAGVKLNNFG  383 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~lp~--~i~--~~LryL~l~~~~~~~lP~~~  383 (385)
                      ..+++.+.+.....   . ....+..+.+|+.|++.++.+..  .++  .+|++|++++|+++.+|.|+
T Consensus       127 l~~L~~L~l~~n~l---~-~~~~l~~~~~L~~L~l~~n~l~~l~~l~~l~~L~~L~ls~N~i~~i~~l~  191 (199)
T d2omxa2         127 LTNLNRLELSSNTI---S-DISALSGLTSLQQLNFSSNQVTDLKPLANLTTLERLDISSNKVSDISVLA  191 (199)
T ss_dssp             CTTCSEEECCSSCC---C-CCGGGTTCTTCSEEECCSSCCCCCGGGTTCTTCCEEECCSSCCCCCGGGG
T ss_pred             hhhhHHhhhhhhhh---c-ccccccccccccccccccccccCCccccCCCCCCEEECCCCCCCCCcccc
Confidence            34566666665532   1 12357889999999999883332  244  89999999999998887553

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=90.62  E-value=0.053  Score=47.63  Aligned_cols=60  Identities=15%  Similarity=0.207  Sum_probs=41.2

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcccC--CCCC--CCeeEEEcCCCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFN--GENK--CKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~lp--~~i~--~~LryL~l~~~~~~~lP~~  382 (385)
                      ...++.+.+.......  +  ..|..+++|+.|+|++|.+.  ..+.  .+|++|++++|+++.+|.|
T Consensus       306 ~~~l~~L~ls~n~l~~--l--~~l~~l~~L~~L~L~~n~l~~l~~l~~l~~L~~L~l~~N~l~~l~~l  369 (384)
T d2omza2         306 LKNLTYLTLYFNNISD--I--SPVSSLTKLQRLFFANNKVSDVSSLANLTNINWLSAGHNQISDLTPL  369 (384)
T ss_dssp             CTTCSEEECCSSCCSC--C--GGGGGCTTCCEEECCSSCCCCCGGGGGCTTCCEEECCSSCCCBCGGG
T ss_pred             hcccCeEECCCCCCCC--C--cccccCCCCCEEECCCCCCCCChhHcCCCCCCEEECCCCcCCCChhh
Confidence            3445555555443221  2  23788999999999998432  2456  8999999999999888744

>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=90.61  E-value=0.057  Score=46.91  Aligned_cols=33  Identities=24%  Similarity=0.259  Sum_probs=25.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHhhCCCCceEEE
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKISGDFDGSCFL   86 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~~~~f~~~~w~   86 (385)
                      .|+|-|.-|+||||+++.+.+.+..+-..+.++
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~   39 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAITPNRILLI   39 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCceEEE
Confidence            589999999999999999998765543344444

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.57  E-value=0.18  Score=42.33  Aligned_cols=60  Identities=10%  Similarity=-0.009  Sum_probs=39.6

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc----ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS----SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~----~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ...++.+.+....  -..+++..|.++++|+.|++.++    -.|..|.  .+|++|+++++.+..+|
T Consensus       152 ~~~L~~L~l~~N~--l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~i~~~~  217 (284)
T d1ozna_         152 LGNLTHLFLHGNR--ISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSALP  217 (284)
T ss_dssp             CTTCCEEECCSSC--CCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCCC
T ss_pred             ccchhhcccccCc--ccccchhhhccccccchhhhhhccccccChhHhhhhhhccccccccccccccc
Confidence            3455666555443  23456677777777888777766    3356666  67778888777777766

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=90.36  E-value=0.14  Score=42.81  Aligned_cols=37  Identities=22%  Similarity=0.188  Sum_probs=28.7

Q ss_pred             HHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHh
Q 044214           40 EIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        40 ~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      .+..+|....++...+.++|+|+.|||+++..+.+-+
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3444565444566788999999999999999988865

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=90.28  E-value=0.15  Score=40.84  Aligned_cols=57  Identities=19%  Similarity=0.162  Sum_probs=30.1

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+..+....  +  ..+..++.|+.|+++++   .++ .+.  .+|+++++.++.+..++
T Consensus        89 l~~L~~L~l~~n~i~~--l--~~l~~l~~L~~L~l~~~~~~~~~-~l~~l~~l~~l~~~~n~l~~~~  150 (210)
T d1h6ta2          89 LKNLGWLFLDENKVKD--L--SSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKITDIT  150 (210)
T ss_dssp             CTTCCEEECCSSCCCC--G--GGGTTCTTCCEEECTTSCCCCCG-GGGGCTTCCEEECCSSCCCCCG
T ss_pred             Cccccccccccccccc--c--ccccccccccccccccccccccc-cccccccccccccccccccccc
Confidence            3445555555443211  1  23566666777776665   222 222  56666666666665544

>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=90.12  E-value=1.1  Score=36.20  Aligned_cols=23  Identities=30%  Similarity=0.030  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .+++.|+|+...||||+.+.++-
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHH
Confidence            46889999999999999999875

>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=89.75  E-value=0.043  Score=44.92  Aligned_cols=32  Identities=22%  Similarity=0.309  Sum_probs=22.9

Q ss_pred             HHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           38 VEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        38 l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +++|.++|.   +  +..++.|.+|||||||...+..
T Consensus        88 l~~L~~~l~---~--~~~vl~G~SGVGKSSLiN~L~~  119 (231)
T d1t9ha2          88 LADIIPHFQ---D--KTTVFAGQSGVGKSSLLNAISP  119 (231)
T ss_dssp             CTTTGGGGT---T--SEEEEEESHHHHHHHHHHHHCC
T ss_pred             HHHHHHhhc---c--ceEEEECCCCccHHHHHHhhcc
Confidence            344555554   2  2456889999999999988864

>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=89.30  E-value=0.12  Score=43.62  Aligned_cols=26  Identities=31%  Similarity=0.264  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           50 KGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        50 ~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .+.|-|+|+|-+|.|||||+-++...
T Consensus         4 ~~iRni~i~gh~~~GKTtL~e~ll~~   29 (276)
T d2bv3a2           4 KRLRNIGIAAHIDAGKTTTTERILYY   29 (276)
T ss_dssp             GGEEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             hhceEEEEEeCCCCCHHHHHHHHHHh
Confidence            35678999999999999999998764

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=89.13  E-value=0.15  Score=41.21  Aligned_cols=58  Identities=16%  Similarity=0.094  Sum_probs=28.2

Q ss_pred             CCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcccCC--CCC--CCeeEEEcCCCCCCCCCC
Q 044214          320 QKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSSFNG--ENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       320 ~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~lp~--~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      .+++.+.+..+....  +  ..+++|++|+.|+|+++.+-.  .+.  .+|++|++.+|.++.+|.
T Consensus        41 ~~L~~L~l~~~~i~~--l--~~l~~l~~L~~L~ls~n~i~~~~~l~~l~~l~~l~~~~n~~~~i~~  102 (227)
T d1h6ua2          41 DGITTLSAFGTGVTT--I--EGVQYLNNLIGLELKDNQITDLAPLKNLTKITELELSGNPLKNVSA  102 (227)
T ss_dssp             HTCCEEECTTSCCCC--C--TTGGGCTTCCEEECCSSCCCCCGGGTTCCSCCEEECCSCCCSCCGG
T ss_pred             CCcCEEECCCCCCCc--c--hhHhcCCCCcEeecCCceeecccccccccccccccccccccccccc
Confidence            345555555443211  1  224556666666666552221  122  556666666555555553

>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=88.85  E-value=0.076  Score=45.95  Aligned_cols=26  Identities=31%  Similarity=0.294  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +..|+|-|.=|+||||+++.+.+...
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC---
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHHhC
Confidence            44689999999999999999987553

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=88.47  E-value=0.37  Score=40.26  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      ..-.|+|+|++.||||||+..+..
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~  134 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAK  134 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CceEEEEEecCccchhhhhhhhhc
Confidence            345689999999999999998886

>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=88.25  E-value=2.3  Score=34.04  Aligned_cols=22  Identities=27%  Similarity=0.083  Sum_probs=19.7

Q ss_pred             EEEEEEcCCCchHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      +++.|+|+...||||+.+.+.-
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHH
Confidence            3788999999999999999875

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.21  E-value=0.18  Score=42.42  Aligned_cols=32  Identities=19%  Similarity=0.307  Sum_probs=25.8

Q ss_pred             hhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           44 LLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        44 ~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .|..-.+.+.||+|+|.-+.|||+|+..++..
T Consensus        24 ~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          24 ILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            33333456899999999999999999998863

>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=88.19  E-value=0.18  Score=42.21  Aligned_cols=24  Identities=33%  Similarity=0.560  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      .|-|+|.|-.|.|||||+-++...
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHHHH
Confidence            367899999999999999998653

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=87.97  E-value=0.012  Score=47.29  Aligned_cols=42  Identities=12%  Similarity=0.105  Sum_probs=26.6

Q ss_pred             ccccCCCCCCcEEEecCc---ccCCCCC--CCeeEEEcCCCCCCCCCC
Q 044214          339 TSTFTKMPKLRFLKFYSS---SFNGENK--CKISYLQDPGFAGVKLNN  381 (385)
Q Consensus       339 ~~~~~~~~~LrvL~l~~~---~lp~~i~--~~LryL~l~~~~~~~lP~  381 (385)
                      +..|..+.+|+.|+|+++   .++ .+.  .+|++|++++|.++.+|.
T Consensus        41 ~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~   87 (198)
T d1m9la_          41 DATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIEN   87 (198)
T ss_dssp             HHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSS
T ss_pred             hhHHhcccccceeECcccCCCCcc-cccCCccccChhhcccccccccc
Confidence            345666777777777766   333 244  677777777777776663

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=87.92  E-value=0.15  Score=41.59  Aligned_cols=23  Identities=26%  Similarity=0.234  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHH
Q 044214           53 YALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ++|+|.|-+++|||||+.++...
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhh
Confidence            46999999999999999988764

>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=87.84  E-value=0.13  Score=40.04  Aligned_cols=21  Identities=38%  Similarity=0.643  Sum_probs=19.1

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+++|||||..++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            489999999999999998874

>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=87.72  E-value=0.12  Score=46.24  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=20.0

Q ss_pred             eEEEEEEcCCCchHHHHHHHHHH
Q 044214           52 VYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        52 ~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .--|+|+|.+|+|||||...+..
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            34589999999999999999874

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.17  E-value=0.024  Score=43.92  Aligned_cols=60  Identities=17%  Similarity=0.127  Sum_probs=38.0

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCcc---cCC--CCC-CCeeEEEcCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSSS---FNG--ENK-CKISYLQDPGFAGVK  378 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~~---lp~--~i~-~~LryL~l~~~~~~~  378 (385)
                      ...++.+.+.......+......+.++++|+.|+|+++.   +++  .++ .+|+.|++.++++..
T Consensus        64 ~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~~  129 (162)
T d1koha1          64 IPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLSD  129 (162)
T ss_dssp             CTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTSS
T ss_pred             CCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCCcCc
Confidence            345666666666543333334556678888888888873   333  112 677888888887754

>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=86.64  E-value=0.92  Score=36.75  Aligned_cols=42  Identities=17%  Similarity=0.063  Sum_probs=30.0

Q ss_pred             hhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHHhhCC
Q 044214           36 STVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDKISGD   79 (385)
Q Consensus        36 ~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~~~~~   79 (385)
                      ...+++.+.+.  .+......|+|..|+|||-++...+...-+.
T Consensus        62 ~~~~~i~~~~~--~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~  103 (233)
T d2eyqa3          62 QAINAVLSDMC--QPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN  103 (233)
T ss_dssp             HHHHHHHHHHH--SSSCCEEEEECCCCTTTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHh--ccCccCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            44445555555  4455677899999999999999888765443

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=86.18  E-value=0.37  Score=41.13  Aligned_cols=40  Identities=10%  Similarity=0.006  Sum_probs=32.5

Q ss_pred             cCCCCCCcEEEecCc---ccCCCCCCCeeEEEcCCCCCCCCCCC
Q 044214          342 FTKMPKLRFLKFYSS---SFNGENKCKISYLQDPGFAGVKLNNF  382 (385)
Q Consensus       342 ~~~~~~LrvL~l~~~---~lp~~i~~~LryL~l~~~~~~~lP~~  382 (385)
                      +..+++|+.|+|++|   .+|..+ .+|++|++++|.++.+|+.
T Consensus       280 ~~~~~~L~~L~Ls~N~l~~lp~~~-~~L~~L~L~~N~L~~l~~~  322 (353)
T d1jl5a_         280 CDLPPSLEELNVSNNKLIELPALP-PRLERLIASFNHLAEVPEL  322 (353)
T ss_dssp             CCCCTTCCEEECCSSCCSCCCCCC-TTCCEEECCSSCCSCCCCC
T ss_pred             cccCCCCCEEECCCCccCcccccc-CCCCEEECCCCcCCccccc
Confidence            455789999999998   555432 6899999999999999954

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.39  E-value=0.3  Score=35.18  Aligned_cols=26  Identities=4%  Similarity=0.142  Sum_probs=22.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhhC
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKISG   78 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~~   78 (385)
                      -.|.+.|..|+||+|||.++..++.+
T Consensus         7 f~i~~tg~~~~gk~~ia~al~~~l~q   32 (122)
T d1g8fa3           7 FSIVLGNSLTVSREQLSIALLSTFLQ   32 (122)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            47889999999999999999887643

>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=85.25  E-value=0.21  Score=42.27  Aligned_cols=20  Identities=5%  Similarity=0.092  Sum_probs=15.3

Q ss_pred             CCcEEeCHHHHHHHHHHHhh
Q 044214          289 YKKIRMRDLLQELGGEIVRK  308 (385)
Q Consensus       289 ~~~~~mH~lv~~~a~~~~~~  308 (385)
                      ...|+.|.-|.++|-.+...
T Consensus       273 ~~nyRs~~~I~~~an~l~~~  292 (306)
T d1uaaa1         273 EQNYRSSGRILKAANILIAN  292 (306)
T ss_dssp             CCBSSSCHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHc
Confidence            44588899999998877554

>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=85.11  E-value=0.25  Score=42.07  Aligned_cols=22  Identities=9%  Similarity=0.208  Sum_probs=16.3

Q ss_pred             CCcEEeCHHHHHHHHHHHhhcc
Q 044214          289 YKKIRMRDLLQELGGEIVRKES  310 (385)
Q Consensus       289 ~~~~~mH~lv~~~a~~~~~~e~  310 (385)
                      +..|+.|.-|.++|..+.....
T Consensus       283 ~~nyRs~~~I~~~an~ll~~~~  304 (318)
T d1pjra1         283 EQNYRSTKRILQAANEVIEHNV  304 (318)
T ss_dssp             CBCSSSCHHHHHHHHHHHTTCS
T ss_pred             CCCCCCcHHHHHHHHHHHHcCc
Confidence            3457888999999988876543

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.68  E-value=0.48  Score=39.51  Aligned_cols=60  Identities=13%  Similarity=0.135  Sum_probs=40.3

Q ss_pred             cCCeeEEEeecCCceeeeeCccccCCCCCCcEEEecCc---ccC-CCCC--CCeeEEEcCCCCCCCCC
Q 044214          319 GQKIEDICLDMSKVIEICLNTSTFTKMPKLRFLKFYSS---SFN-GENK--CKISYLQDPGFAGVKLN  380 (385)
Q Consensus       319 ~~~~r~l~l~~~~~~~~~~~~~~~~~~~~LrvL~l~~~---~lp-~~i~--~~LryL~l~~~~~~~lP  380 (385)
                      ..+++.+.+....  ...+....+..+..|+.++++++   .+| ..+.  .+|+.|+++++.++.+|
T Consensus       104 l~~L~~L~l~~n~--~~~~~~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~l~~l~  169 (284)
T d1ozna_         104 LGRLHTLHLDRCG--LQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVP  169 (284)
T ss_dssp             CTTCCEEECTTSC--CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCEEC
T ss_pred             cccCCEEecCCcc--cccccccccchhcccchhhhccccccccChhHhccccchhhcccccCcccccc
Confidence            3556666666553  23445666777788888888876   444 3444  77888888888887776

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=84.23  E-value=0.28  Score=41.22  Aligned_cols=21  Identities=33%  Similarity=0.564  Sum_probs=19.3

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      .|+|+|++.+|||||-.++.+
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~   24 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTK   24 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHC
Confidence            589999999999999998886

>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=83.26  E-value=0.12  Score=40.61  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=19.7

Q ss_pred             EEEEEcCCCchHHHHHHHHHHHh
Q 044214           54 ALGIWGIGGIGKTTIARAIFDKI   76 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~~~   76 (385)
                      +.+|+|..|+||||+..++.--+
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            55688999999999999998654

>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=83.01  E-value=1.7  Score=33.71  Aligned_cols=35  Identities=23%  Similarity=0.003  Sum_probs=22.4

Q ss_pred             cchhHHHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHH
Q 044214           34 VESTVEEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        34 R~~~l~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+-..+.+..+..  . +   +.|+++.|.|||.+|..+..
T Consensus        11 r~~Q~~~~~~~~~--~-n---~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          11 RIYQEVIYAKCKE--T-N---CLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             CHHHHHHHHHGGG--S-C---EEEECCTTSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc--C-C---eEEEeCCCCcHHHHHHHHHH
Confidence            4445555555443  2 2   34779999999987776654

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.88  E-value=0.45  Score=41.16  Aligned_cols=36  Identities=17%  Similarity=0.348  Sum_probs=28.0

Q ss_pred             HHHHHhhcCCCCCeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           39 EEIESLLGVESKGVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        39 ~~l~~~L~~~~~~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      +.|.+++.. .+..|=|+|.|-.|.|||||+-.+...
T Consensus         5 ~~~~~lm~~-~~~IRNI~iiGhvd~GKTTL~d~Ll~~   40 (341)
T d1n0ua2           5 DQMRSLMDK-VTNVRNMSVIAHVDHGKSTLTDSLVQR   40 (341)
T ss_dssp             HHHHHHHHC-GGGEEEEEEECCGGGTHHHHHHHHHHH
T ss_pred             HHHHHHhcC-cccCcEEEEEeCCCCcHHHHHHHHHHH
Confidence            455555553 346888999999999999999998753

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=82.71  E-value=0.33  Score=41.11  Aligned_cols=21  Identities=43%  Similarity=0.623  Sum_probs=19.5

Q ss_pred             EEEEEcCCCchHHHHHHHHHH
Q 044214           54 ALGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        54 vv~I~G~gGiGKTtLA~~~~~   74 (385)
                      -|+|+|.+.+|||||-.++.+
T Consensus        12 kiGivG~Pn~GKSTlfnalT~   32 (296)
T d1ni3a1          12 KTGIVGMPNVGKSTFFRAITK   32 (296)
T ss_dssp             EEEEEECSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            499999999999999999986

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=82.12  E-value=0.43  Score=37.96  Aligned_cols=21  Identities=33%  Similarity=0.336  Sum_probs=19.0

Q ss_pred             EEEEcCCCchHHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~~   75 (385)
                      |+|.|-++.|||||+.++...
T Consensus         6 i~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHHHH
Confidence            889999999999999998754

>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=82.10  E-value=0.55  Score=41.83  Aligned_cols=25  Identities=24%  Similarity=0.215  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCchHHHHHHHHHHHhh
Q 044214           53 YALGIWGIGGIGKTTIARAIFDKIS   77 (385)
Q Consensus        53 ~vv~I~G~gGiGKTtLA~~~~~~~~   77 (385)
                      +.+.|+|..|+|||+++..+..+..
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~   75 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGL   75 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHH
Confidence            4589999999999999887776543

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {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 PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.46  E-value=0.4  Score=40.95  Aligned_cols=20  Identities=30%  Similarity=0.401  Sum_probs=18.6

Q ss_pred             EEEEcCCCchHHHHHHHHHH
Q 044214           55 LGIWGIGGIGKTTIARAIFD   74 (385)
Q Consensus        55 v~I~G~gGiGKTtLA~~~~~   74 (385)
                      |+|+|.+.+|||||-.++-.
T Consensus         3 v~lvG~pn~GKStlfn~lt~   22 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATL   22 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC
T ss_pred             EeEECCCCCCHHHHHHHHHC
Confidence            89999999999999999865

>d1p3da1 c.5.1.1 (A:11-106) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: MurCD N-terminal domain
superfamily: MurCD N-terminal domain
family: MurCD N-terminal domain
domain: UDP-N-acetylmuramate-alanine ligase MurC
species: Haemophilus influenzae [TaxId: 727]

Probab=80.45  E-value=0.73  Score=31.62  Aligned_cols=25  Identities=32%  Similarity=0.586  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCchHHHHHHHHHHH
Q 044214           51 GVYALGIWGIGGIGKTTIARAIFDK   75 (385)
Q Consensus        51 ~~~vv~I~G~gGiGKTtLA~~~~~~   75 (385)
                      ..+-|-+.|.||+|-+.||+.+.++
T Consensus         7 ~~~~ihfiGigG~GMs~LA~~L~~~   31 (96)
T d1p3da1           7 RVQQIHFIGIGGAGMSGIAEILLNE   31 (96)
T ss_dssp             TCCEEEEETTTSTTHHHHHHHHHHH
T ss_pred             hCCEEEEEEECHHHHHHHHHHHHhC
Confidence            4567889999999999999988874